pandoc-plot 1.7.0 → 1.8.0

raw patch · 47 files changed

+7336/−7228 lines, 47 filessetup-changedPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• CHANGELOG.md +350/−346
• LICENSE +339/−339
• MANUAL.md +663/−663
• README.md +170/−169
• Setup.hs +7/−7
• data/srctemplate.html +240/−240
• docs/MANUAL.html +569/−569
• example-config.yml +148/−148
• executable/ExampleConfig.hs +30/−30
• executable/Main.hs +326/−326
• executable/ManPage.hs +41/−41
• executable/OpenFile.hs +37/−37
• pandoc-plot.cabal +170/−168
• src/Text/Pandoc/Filter/Plot.hs +242/−242
• src/Text/Pandoc/Filter/Plot/Clean.hs +165/−165
• src/Text/Pandoc/Filter/Plot/Configuration.hs +414/−399
• src/Text/Pandoc/Filter/Plot/Embed.hs +190/−190
• src/Text/Pandoc/Filter/Plot/Internal.hs +28/−28
• src/Text/Pandoc/Filter/Plot/Monad.hs +424/−417
• src/Text/Pandoc/Filter/Plot/Monad/Logging.hs +161/−161
• src/Text/Pandoc/Filter/Plot/Monad/Types.hs +303/−300
• src/Text/Pandoc/Filter/Plot/Parse.hs +196/−196
• src/Text/Pandoc/Filter/Plot/Renderers.hs +212/−206
• src/Text/Pandoc/Filter/Plot/Renderers/Asymptote.hs +50/−0
• src/Text/Pandoc/Filter/Plot/Renderers/Bokeh.hs +80/−80
• src/Text/Pandoc/Filter/Plot/Renderers/D2.hs +48/−48
• src/Text/Pandoc/Filter/Plot/Renderers/GGPlot2.hs +59/−59
• src/Text/Pandoc/Filter/Plot/Renderers/GNUPlot.hs +71/−71
• src/Text/Pandoc/Filter/Plot/Renderers/Graphviz.hs +55/−55
• src/Text/Pandoc/Filter/Plot/Renderers/Mathematica.hs +53/−53
• src/Text/Pandoc/Filter/Plot/Renderers/Matlab.hs +71/−71
• src/Text/Pandoc/Filter/Plot/Renderers/Matplotlib.hs +88/−88
• src/Text/Pandoc/Filter/Plot/Renderers/Octave.hs +52/−52
• src/Text/Pandoc/Filter/Plot/Renderers/PlantUML.hs +62/−62
• src/Text/Pandoc/Filter/Plot/Renderers/PlotlyPython.hs +64/−64
• src/Text/Pandoc/Filter/Plot/Renderers/PlotlyR.hs +79/−79
• src/Text/Pandoc/Filter/Plot/Renderers/Plotsjl.hs +54/−54
• src/Text/Pandoc/Filter/Plot/Renderers/Prelude.hs +40/−40
• src/Text/Pandoc/Filter/Plot/Renderers/SageMath.hs +71/−71
• src/Text/Pandoc/Filter/Plot/Scripting.hs +218/−218
• src/Text/Pandoc/Filter/Plot/Scripting/Template.hs +23/−23
• tests/Common.hs +493/−473
• tests/Main.hs +161/−161
• tests/fixtures/.config-meta.yml +3/−3
• tests/fixtures/.verbose-config.yml +10/−10
• tests/fixtures/data.csv +4/−4
• tests/fixtures/plotfile.py +2/−2

@@ -1,346 +1,350 @@-# Change log--pandoc-plot uses [Semantic Versioning](http://semver.org/spec/v2.0.0.html)--## Release 1.7.0--* Added support for the declarative diagram language [D2](https://d2lang.com/), thanks to a contribution by Sanchayan Maity (#60).-* Added support for `optparse-applicative` v0.18.--## Release 1.6.2--* Fixed some imports which were removed in `mtl-2.3`.--## Release 1.6.1--* Fixed an issue where figure attributes were lost, which prevent other filters (e.g. pandoc-crossref) from working in conjunction with pandoc-plot.--## Release 1.6.0--* Support for pandoc 3. Support for older pandoc version has also been dropped (pandoc 2.19 and earlier).--## Release 1.5.5--* Fixed an issue where there was a race condition when rendering multiple identical figures (#53).--## Release 1.5.4--* Fixed an issue where graphviz plots in vector format were cropped when a DPI was specified (#40).--## Release 1.5.3--* Fixed an issue where the `tight_bbox` option for Matplotlib plots was ignored (#48).--## Release 1.5.2--* Overhauled the way executables are handled. This fixes an issue where executables specified in documents (rather than configuration) were ignored (#46).--## Release 1.5.1--* Figures with no captions (and no link to the source script), will now be shown as an image, without figure numbering (#37).--## Release 1.5.0--* Added support for [Sage](https://www.sagemath.org/) (#44).-* Fixed an issue where the parsing of default save format from configuration was overly restrictive (#42).-* Linux and Windows executables now built with GHC 9.2.--## Release 1.4.1--* Don't automatically defer javascript scripts when creating interactive figures (#39).--## Release 1.4.0--* The executable `pandoc-plot` now uses pandoc 2.17. Pandoc 2.11+ are still supported.-* Added support for `aeson` 2+.--## Release 1.3.0--* The executable `pandoc-plot` is now aware of final conversion format.-* Added a new function, `plotFilter`, which is aware of the pandoc's final conversion format. This allows for better defaults and error messages.-* Deprecated `plotTransform` in favour of `plotFilter`. `plotTransform` will be removed in the next major update (v2+).-* Save formats incompatible with toolkits will now show an appropriate error.-* The build system is now based on `cabal-install` rather than `stack`.-* Fixed an issue where some types of PlantUML diagrams (e.g. Gantt charts) would not be exported correctly (#30).--## Release 1.2.3--* Fixed an issue where MATLAB figures were not being saved in the right location (#27).-* Releases are now completely taken care of via Github actions.--## Release 1.2.2--* Executables are now built using GHC 9.0.1-* The executables are now built with Pandoc 2.14. Pandoc 2.11, 2.12, and 2.13 are still supported.--## Release 1.2.1--* Added the ability to save plots as LaTeX directly from the GNUplot toolkit. To do this, simply set the output format to `latex`. The figure content will be embedded in the output document, which only makes sense for final conversion to LaTeX. For example:--  ````markdown-    ```{.gnuplot format=latex caption="This is a test."}-    ...-    ```-  ````-  This patch was contributed by Saku Laesvuori.--## Release 1.2.0--* Fixed an issue where code blocks nested in other structures were detected properly. For example, in the following LaTeX snippet, plots would not be detected properly:-```latex-\begin{column}-  \begin{minted}[]{matplotlib}-  ...-  \end{minted}-\end{column}-```-Nested figures are not correctly identified.--* The executables are now built with Pandoc 2.13. Pandoc 2.11 and Pandoc 2.12 are still supported.--## Release 1.1.1--* Error messages now include the source script and line numbers.-* The executables are now built with Pandoc 2.12. Pandoc 2.11 is still supported.--## Release 1.1.0--* Added the [PlantUML](https://plantuml.com) toolkit (#18). Diagrams can be generated like so:--  ````markdown--  ```{.plantuml}-  @startuml-  Bob->Alice : hello-  @enduml-  ```--  ````-* Changed versioning scheme to match more common Major.Minor.Bugfix.--## Release 1.0.2.1--* `pandoc-plot` will now only render at most `N` figures in parallel, where `N` is the number of available CPU cores.-* Fixed an issue where error message would get mangled in strict-mode.--## Release 1.0.2.0--* Added the ability to run `pandoc-plot` in **strict mode**. By default, `pandoc-plot` leaves code blocks unchanged if a figure fails to be rendered.  In strict mode, `pandoc-plot` will immediately halt if it encounters a problem, such as a missing toolkit. You can activate strict mode via configuration:--```yaml-strict: true-```--* Added the ability to set command-line arguments for interpreters via configuration. For example, if you want to run the Matplotlib toolkit with all warnings shown:--```yaml-# Possible parameters for the Matplotlib toolkit-matplotlib:-  executable: python-  command_line_arguments: -Wa-```--Or if you want `julia` to use more than one thread:--```yaml-# Possible parameters for the Plotsjl toolkit-plotsjl:-  executable: julia-  command_line_arguments: --threads auto --optimize=0-```--* Fixed an issue where invoking the `plotsjl` toolkit on Windows would sometimes fail with the error: Unknown system error 50.-* Fixed an issue with R-based toolkits on Windows not being detected properly.--## Release 1.0.1.0--* Added the ability to change the "Source code" label to other languages via configuration.-* Added syntax highlighting to the linked source code.-* Fixed an issue where code blocks with unicode symbols (e.g. greek letters) would trip up pandoc-plot (#16).--## Release 1.0.0.0--* Added support for Pandoc 2.11. Unfortunately, there is no way to support prior versions of Pandoc at the same time.-* With release 1.0.0.0, `pandoc-plot` has stabilized. The Haskell library API will not change until version 2+. --## Release 0.9.4.0--* Fixed an issue where the current working directory was changed. This prevented users from referring to files in scripts with relative paths (#2).--## Release 0.9.3.0--* Added executable caching: repeated usage of a particular toolkit will be faster because executables are only looked-for once.-* Reverting the change from 0.8.1.0: internal machinery of `pandoc-plot` has been moved to the `Text.Pandoc.Filter.Plot.Internal` module, where there is no guarantee of backwards-compatibility after 1.0.0.-* Removed the `makePlot` function, which could not take advantage of multithreading and other key features of `pandoc-plot`.-* Fixed an issue where files required for tests were missing from source tarballs (#13).--## Release 0.9.2.0--* Fixed an issue where executables located on paths with spaces would not be invoked correctly (#12).-* Fixed an issue where R-paths were not normalized correctly.-* Fixed an issue where executables specified in configuration that did not exist would crash `pandoc-plot`.-* Fixed an issue where some R-based toolkits appeared to be available, but were not.--## Release 0.9.1.0--* Added the `file` parameter, which allows the user to read figure content from a file instead of using the code block content in documents. This is especially useful for complex figures, where you might want to have the help of your tooling in an IDE, for instance. Here's an example:--````markdown--```{.matplotlib file=myplot.py}-```--````-* Better error messages when specifying logger verbosity.-* Cleaning output directories with `pandoc-plot clean` now follows configuration values for logging. -* Fixed an issue where configuration in metadata did not get parsed properly.--## Release 0.9.0.0--* The `bokeh` toolkit now supports exporting plots as SVGs (#8).-* Interactive plots relying on javascript scripts will now defer loading the scripts (#9). -* Added the `dependencies` argument, which tells `pandoc-plot` what files are important to a particular figure (#10). If a file listed in `dependencies` changes (for example, a data file), `pandoc-plot` will re-render the associated figure.-* Better heuristic to determine what `bokeh` plot to save. This allows the user to export plots like the [`bokeh.layouts` module](https://docs.bokeh.org/en/latest/docs/user_guide/layout.html#creating-layouts).-* Added support for the `dpi` parameter in `graphviz` and `mathematica`.-* Added support for MATLAB's new `exportgraphics` function introduced in MATLAB 2020a. Older versions fallback to using `saveas`.--## Release 0.8.1.0--* The module `Text.Pandoc.Filter.Plot.Internal` is no longer exposed; instead, everything relevant is exposed by the `Text.Pandoc.Filter.Plot` module.-* Fixed an issue where script errors would be logged as debug messages.-* Interactive plots are now embedded directly in output (#7).--## Release 0.8.0.0--* Added a new output format, HTML, to produce interactive plots. Not all renderers support it. You can try with Plotly/Python and Plotly/R as follows:--````markdown--```{.plotly_python format=html}-import plotly.express as px-df = px.data.election()-fig = px.scatter_ternary(df, a="Joly", b="Coderre", c="Bergeron")-```--````--* Added a new toolkit, [`bokeh`](https://bokeh.org/). This toolkit can take advantage of the new HTML interactive output.-* Added a new toolkit, [`plotsjl`](http://docs.juliaplots.org/latest/).-* Separated the detailed information from `README.md` and into a proper `MANUAL.md`. This is now the information which will be shown with `pandoc-plot --manual`.-* Exposed the `pandoc-plot` version via `Text.Pandoc.Filter.Plot.pandocPlotVersion`.--## Release 0.7.2.1--* Fixed an issue where the `pandoc` version was not parsed properly, giving rise to errors when running `pandoc-plot`.-* Fixed an issue where logging errors were not always displayed.--## Release 0.7.2.0--* Removed dependency on `open-browser` package.-* Starting with this version, `pandoc` 2.8 and 2.9 are **no longer supported** due to a breaking API change in `pandoc` 2.10.-* Executables are now built with GHC 8.10.1.--## Release 0.7.1.0--* Better multi-threaded logging. Only one thread (the logging thread) performs IO on the log file. This prevents hang-ups when working on large documents. --## Release 0.7.0.0--* Added documentation on using `pandoc-plot` with LaTeX documents as well.-* Added preliminary support for logging to `pandoc-plot`. You can turn on this feature in the configuration as follows:--````yaml-logging:-    # Possible verbosity values: debug, error, warning, info, silent-    # debug level shows all messages-    # error level shows all but debug messages, etc.-    verbosity: info-    -    # OPTIONAL: log to file-    # Remove line below to log to stderr-    filepath: log.txt-````--* Removed dependencies `turtle`, `temporary`, `deepseq`, and `data-default-class`, resulting in improved build times by ~10%, and makes the executable smaller by 15-20%!--## Release 0.6.1.0--* Made the functions `availableToolkits` and `unavailableToolkits` public.-* Minor documentation fixes.-* Executables are now built with GHC 8.8.3.--## Release 0.6.0.0--New toolkits:-* Added support for the Plotly/R plotting library.-* Added support for Graphviz.--Other changes:-* The determination of which figures to re-render or not has been improved. For example, changing the caption will not trigger a re-render of a figure anymore.-* `pandoc-plot` will look for executables more thoroughly.-* `pandoc-plot toolkits` will now show the exact executable that is being used, if possible.-* Added a check when running the filter that the Pandoc version is at least 2.8. This is easier to understand that the default Pandoc warning on API incompatibility.-* Added the ability to write the example configuration to an arbitrary file using `pandoc-plot write-example-config`.-* Added the possibility to specify the configuration file via metadata. For example, in Markdown:--    ```markdown-    ----    title: My document-    author: John Doe-    plot-configuration: /path/to/file.yml-    ---     -    ```--or on the command line:--```bash-pandoc --filter pandoc-plot -M plot-configuration=/path/to/file.yml ...-```-* Added the ability to specify configuration file to the `pandoc-plot clean` and `pandoc-plot toolkits` commands.--## Release 0.5.0.0--* The `pandoc-plot` executable will now process documents in parallel. This should dramatically speed up processing of large documents with lots of figures. -This happens automatically through the function `plotTransform`.-* Added a benchmarking suite.-* Added `defaultConfiguration` so that people don't have to install the `data-default` package to get access to default configuration values. -* Added a check for the `matplotlib` toolkit, preventing users from using `matplotlib.pyplot.show` in figures. This would halt `pandoc-plot`.--## Release 0.4.0.1--* Fixed an issue where the `pandoc-plot` executable could not be built outside of its git repository.--## Release 0.4.0.0--* Updated documentation.-* Added a `--full-version` flag to the executable, which includes which version of pandoc/pandoc-types was used, as well as the git revision.-* Added the `clean` command to the executable. This can be used to clean-up output files produced by pandoc-plot.-* Changed the flag `--write-example-config` to the command `write-example-config`.-* Added the top-level function `cleanOutputDir` to clean output of pandoc-plot. This is only accessible if `pandoc-plot` is used as a library.-* Added a distinction between failure to render a figure because of a mistake, and failing to render a figure because the toolkit is not installed. `pandoc-plot` will give better error messages in the latter case.--## Release 0.3.0.0--* Added more examples.-* Added MacOS binaries built via Azure pipelines.-* BREAKING CHANGE: Parsing captions based on source file was not working. Captions format can be specified in the configuration file. This unfortunately changes the type signature of a few high-level functions.--## Release 0.2.2.0--* Fixed an issue where paths with spaces would not work (issue #2).-* Added Linux binaries built via Azure pipelines.--## Release 0.2.1.0--* Improved documentation.--## Release 0.2.0.0--* Added support for gnuplot.-* Added more tests for all toolkits.--* Fixed an issue where the package could not be installed because a source file was not included in the cabal file.--## Release 0.1.0.0--* Initial release+# Change log
+
+pandoc-plot uses [Semantic Versioning](http://semver.org/spec/v2.0.0.html)
+
+## Release 1.8.0
+
+* Added support for [Asymptote](https://asymptote.sourceforge.io/), thanks to a contribution by Michał J. Gajda (#61).
+
+## Release 1.7.0
+
+* Added support for the declarative diagram language [D2](https://d2lang.com/), thanks to a contribution by Sanchayan Maity (#60).
+* Added support for `optparse-applicative` v0.18.
+
+## Release 1.6.2
+
+* Fixed some imports which were removed in `mtl-2.3`.
+
+## Release 1.6.1
+
+* Fixed an issue where figure attributes were lost, which prevent other filters (e.g. pandoc-crossref) from working in conjunction with pandoc-plot.
+
+## Release 1.6.0
+
+* Support for pandoc 3. Support for older pandoc version has also been dropped (pandoc 2.19 and earlier).
+
+## Release 1.5.5
+
+* Fixed an issue where there was a race condition when rendering multiple identical figures (#53).
+
+## Release 1.5.4
+
+* Fixed an issue where graphviz plots in vector format were cropped when a DPI was specified (#40).
+
+## Release 1.5.3
+
+* Fixed an issue where the `tight_bbox` option for Matplotlib plots was ignored (#48).
+
+## Release 1.5.2
+
+* Overhauled the way executables are handled. This fixes an issue where executables specified in documents (rather than configuration) were ignored (#46).
+
+## Release 1.5.1
+
+* Figures with no captions (and no link to the source script), will now be shown as an image, without figure numbering (#37).
+
+## Release 1.5.0
+
+* Added support for [Sage](https://www.sagemath.org/) (#44).
+* Fixed an issue where the parsing of default save format from configuration was overly restrictive (#42).
+* Linux and Windows executables now built with GHC 9.2.
+
+## Release 1.4.1
+
+* Don't automatically defer javascript scripts when creating interactive figures (#39).
+
+## Release 1.4.0
+
+* The executable `pandoc-plot` now uses pandoc 2.17. Pandoc 2.11+ are still supported.
+* Added support for `aeson` 2+.
+
+## Release 1.3.0
+
+* The executable `pandoc-plot` is now aware of final conversion format.
+* Added a new function, `plotFilter`, which is aware of the pandoc's final conversion format. This allows for better defaults and error messages.
+* Deprecated `plotTransform` in favour of `plotFilter`. `plotTransform` will be removed in the next major update (v2+).
+* Save formats incompatible with toolkits will now show an appropriate error.
+* The build system is now based on `cabal-install` rather than `stack`.
+* Fixed an issue where some types of PlantUML diagrams (e.g. Gantt charts) would not be exported correctly (#30).
+
+## Release 1.2.3
+
+* Fixed an issue where MATLAB figures were not being saved in the right location (#27).
+* Releases are now completely taken care of via Github actions.
+
+## Release 1.2.2
+
+* Executables are now built using GHC 9.0.1
+* The executables are now built with Pandoc 2.14. Pandoc 2.11, 2.12, and 2.13 are still supported.
+
+## Release 1.2.1
+
+* Added the ability to save plots as LaTeX directly from the GNUplot toolkit. To do this, simply set the output format to `latex`. The figure content will be embedded in the output document, which only makes sense for final conversion to LaTeX. For example:
+
+  ````markdown
+    ```{.gnuplot format=latex caption="This is a test."}
+    ...
+    ```
+  ````
+  This patch was contributed by Saku Laesvuori.
+
+## Release 1.2.0
+
+* Fixed an issue where code blocks nested in other structures were detected properly. For example, in the following LaTeX snippet, plots would not be detected properly:
+```latex
+\begin{column}
+  \begin{minted}[]{matplotlib}
+  ...
+  \end{minted}
+\end{column}
+```
+Nested figures are not correctly identified.
+
+* The executables are now built with Pandoc 2.13. Pandoc 2.11 and Pandoc 2.12 are still supported.
+
+## Release 1.1.1
+
+* Error messages now include the source script and line numbers.
+* The executables are now built with Pandoc 2.12. Pandoc 2.11 is still supported.
+
+## Release 1.1.0
+
+* Added the [PlantUML](https://plantuml.com) toolkit (#18). Diagrams can be generated like so:
+
+  ````markdown
+
+  ```{.plantuml}
+  @startuml
+  Bob->Alice : hello
+  @enduml
+  ```
+
+  ````
+* Changed versioning scheme to match more common Major.Minor.Bugfix.
+
+## Release 1.0.2.1
+
+* `pandoc-plot` will now only render at most `N` figures in parallel, where `N` is the number of available CPU cores.
+* Fixed an issue where error message would get mangled in strict-mode.
+
+## Release 1.0.2.0
+
+* Added the ability to run `pandoc-plot` in **strict mode**. By default, `pandoc-plot` leaves code blocks unchanged if a figure fails to be rendered.  In strict mode, `pandoc-plot` will immediately halt if it encounters a problem, such as a missing toolkit. You can activate strict mode via configuration:
+
+```yaml
+strict: true
+```
+
+* Added the ability to set command-line arguments for interpreters via configuration. For example, if you want to run the Matplotlib toolkit with all warnings shown:
+
+```yaml
+# Possible parameters for the Matplotlib toolkit
+matplotlib:
+  executable: python
+  command_line_arguments: -Wa
+```
+
+Or if you want `julia` to use more than one thread:
+
+```yaml
+# Possible parameters for the Plotsjl toolkit
+plotsjl:
+  executable: julia
+  command_line_arguments: --threads auto --optimize=0
+```
+
+* Fixed an issue where invoking the `plotsjl` toolkit on Windows would sometimes fail with the error: Unknown system error 50.
+* Fixed an issue with R-based toolkits on Windows not being detected properly.
+
+## Release 1.0.1.0
+
+* Added the ability to change the "Source code" label to other languages via configuration.
+* Added syntax highlighting to the linked source code.
+* Fixed an issue where code blocks with unicode symbols (e.g. greek letters) would trip up pandoc-plot (#16).
+
+## Release 1.0.0.0
+
+* Added support for Pandoc 2.11. Unfortunately, there is no way to support prior versions of Pandoc at the same time.
+* With release 1.0.0.0, `pandoc-plot` has stabilized. The Haskell library API will not change until version 2+. 
+
+## Release 0.9.4.0
+
+* Fixed an issue where the current working directory was changed. This prevented users from referring to files in scripts with relative paths (#2).
+
+## Release 0.9.3.0
+
+* Added executable caching: repeated usage of a particular toolkit will be faster because executables are only looked-for once.
+* Reverting the change from 0.8.1.0: internal machinery of `pandoc-plot` has been moved to the `Text.Pandoc.Filter.Plot.Internal` module, where there is no guarantee of backwards-compatibility after 1.0.0.
+* Removed the `makePlot` function, which could not take advantage of multithreading and other key features of `pandoc-plot`.
+* Fixed an issue where files required for tests were missing from source tarballs (#13).
+
+## Release 0.9.2.0
+
+* Fixed an issue where executables located on paths with spaces would not be invoked correctly (#12).
+* Fixed an issue where R-paths were not normalized correctly.
+* Fixed an issue where executables specified in configuration that did not exist would crash `pandoc-plot`.
+* Fixed an issue where some R-based toolkits appeared to be available, but were not.
+
+## Release 0.9.1.0
+
+* Added the `file` parameter, which allows the user to read figure content from a file instead of using the code block content in documents. This is especially useful for complex figures, where you might want to have the help of your tooling in an IDE, for instance. Here's an example:
+
+````markdown
+
+```{.matplotlib file=myplot.py}
+```
+
+````
+* Better error messages when specifying logger verbosity.
+* Cleaning output directories with `pandoc-plot clean` now follows configuration values for logging. 
+* Fixed an issue where configuration in metadata did not get parsed properly.
+
+## Release 0.9.0.0
+
+* The `bokeh` toolkit now supports exporting plots as SVGs (#8).
+* Interactive plots relying on javascript scripts will now defer loading the scripts (#9). 
+* Added the `dependencies` argument, which tells `pandoc-plot` what files are important to a particular figure (#10). If a file listed in `dependencies` changes (for example, a data file), `pandoc-plot` will re-render the associated figure.
+* Better heuristic to determine what `bokeh` plot to save. This allows the user to export plots like the [`bokeh.layouts` module](https://docs.bokeh.org/en/latest/docs/user_guide/layout.html#creating-layouts).
+* Added support for the `dpi` parameter in `graphviz` and `mathematica`.
+* Added support for MATLAB's new `exportgraphics` function introduced in MATLAB 2020a. Older versions fallback to using `saveas`.
+
+## Release 0.8.1.0
+
+* The module `Text.Pandoc.Filter.Plot.Internal` is no longer exposed; instead, everything relevant is exposed by the `Text.Pandoc.Filter.Plot` module.
+* Fixed an issue where script errors would be logged as debug messages.
+* Interactive plots are now embedded directly in output (#7).
+
+## Release 0.8.0.0
+
+* Added a new output format, HTML, to produce interactive plots. Not all renderers support it. You can try with Plotly/Python and Plotly/R as follows:
+
+````markdown
+
+```{.plotly_python format=html}
+import plotly.express as px
+df = px.data.election()
+fig = px.scatter_ternary(df, a="Joly", b="Coderre", c="Bergeron")
+```
+
+````
+
+* Added a new toolkit, [`bokeh`](https://bokeh.org/). This toolkit can take advantage of the new HTML interactive output.
+* Added a new toolkit, [`plotsjl`](http://docs.juliaplots.org/latest/).
+* Separated the detailed information from `README.md` and into a proper `MANUAL.md`. This is now the information which will be shown with `pandoc-plot --manual`.
+* Exposed the `pandoc-plot` version via `Text.Pandoc.Filter.Plot.pandocPlotVersion`.
+
+## Release 0.7.2.1
+
+* Fixed an issue where the `pandoc` version was not parsed properly, giving rise to errors when running `pandoc-plot`.
+* Fixed an issue where logging errors were not always displayed.
+
+## Release 0.7.2.0
+
+* Removed dependency on `open-browser` package.
+* Starting with this version, `pandoc` 2.8 and 2.9 are **no longer supported** due to a breaking API change in `pandoc` 2.10.
+* Executables are now built with GHC 8.10.1.
+
+## Release 0.7.1.0
+
+* Better multi-threaded logging. Only one thread (the logging thread) performs IO on the log file. This prevents hang-ups when working on large documents. 
+
+## Release 0.7.0.0
+
+* Added documentation on using `pandoc-plot` with LaTeX documents as well.
+* Added preliminary support for logging to `pandoc-plot`. You can turn on this feature in the configuration as follows:
+
+````yaml
+logging:
+    # Possible verbosity values: debug, error, warning, info, silent
+    # debug level shows all messages
+    # error level shows all but debug messages, etc.
+    verbosity: info
+    
+    # OPTIONAL: log to file
+    # Remove line below to log to stderr
+    filepath: log.txt
+````
+
+* Removed dependencies `turtle`, `temporary`, `deepseq`, and `data-default-class`, resulting in improved build times by ~10%, and makes the executable smaller by 15-20%!
+
+## Release 0.6.1.0
+
+* Made the functions `availableToolkits` and `unavailableToolkits` public.
+* Minor documentation fixes.
+* Executables are now built with GHC 8.8.3.
+
+## Release 0.6.0.0
+
+New toolkits:
+* Added support for the Plotly/R plotting library.
+* Added support for Graphviz.
+
+Other changes:
+* The determination of which figures to re-render or not has been improved. For example, changing the caption will not trigger a re-render of a figure anymore.
+* `pandoc-plot` will look for executables more thoroughly.
+* `pandoc-plot toolkits` will now show the exact executable that is being used, if possible.
+* Added a check when running the filter that the Pandoc version is at least 2.8. This is easier to understand that the default Pandoc warning on API incompatibility.
+* Added the ability to write the example configuration to an arbitrary file using `pandoc-plot write-example-config`.
+* Added the possibility to specify the configuration file via metadata. For example, in Markdown:
+
+    ```markdown
+    ---
+    title: My document
+    author: John Doe
+    plot-configuration: /path/to/file.yml
+    ---     
+    ```
+
+or on the command line:
+
+```bash
+pandoc --filter pandoc-plot -M plot-configuration=/path/to/file.yml ...
+```
+* Added the ability to specify configuration file to the `pandoc-plot clean` and `pandoc-plot toolkits` commands.
+
+## Release 0.5.0.0
+
+* The `pandoc-plot` executable will now process documents in parallel. This should dramatically speed up processing of large documents with lots of figures. 
+This happens automatically through the function `plotTransform`.
+* Added a benchmarking suite.
+* Added `defaultConfiguration` so that people don't have to install the `data-default` package to get access to default configuration values. 
+* Added a check for the `matplotlib` toolkit, preventing users from using `matplotlib.pyplot.show` in figures. This would halt `pandoc-plot`.
+
+## Release 0.4.0.1
+
+* Fixed an issue where the `pandoc-plot` executable could not be built outside of its git repository.
+
+## Release 0.4.0.0
+
+* Updated documentation.
+* Added a `--full-version` flag to the executable, which includes which version of pandoc/pandoc-types was used, as well as the git revision.
+* Added the `clean` command to the executable. This can be used to clean-up output files produced by pandoc-plot.
+* Changed the flag `--write-example-config` to the command `write-example-config`.
+* Added the top-level function `cleanOutputDir` to clean output of pandoc-plot. This is only accessible if `pandoc-plot` is used as a library.
+* Added a distinction between failure to render a figure because of a mistake, and failing to render a figure because the toolkit is not installed. `pandoc-plot` will give better error messages in the latter case.
+
+## Release 0.3.0.0
+
+* Added more examples.
+* Added MacOS binaries built via Azure pipelines.
+* BREAKING CHANGE: Parsing captions based on source file was not working. Captions format can be specified in the configuration file. This unfortunately changes the type signature of a few high-level functions.
+
+## Release 0.2.2.0
+
+* Fixed an issue where paths with spaces would not work (issue #2).
+* Added Linux binaries built via Azure pipelines.
+
+## Release 0.2.1.0
+
+* Improved documentation.
+
+## Release 0.2.0.0
+
+* Added support for gnuplot.
+* Added more tests for all toolkits.
+
+* Fixed an issue where the package could not be installed because a source file was not included in the cabal file.
+
+## Release 0.1.0.0
+
+* Initial release

@@ -1,339 +1,339 @@-                    GNU GENERAL PUBLIC LICENSE-                       Version 2, June 1991-- Copyright (C) 1989, 1991 Free Software Foundation, Inc.,- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA- Everyone is permitted to copy and distribute verbatim copies- of this license document, but changing it is not allowed.--                            Preamble--  The licenses for most software are designed to take away your-freedom to share and change it.  By contrast, the GNU General Public-License is intended to guarantee your freedom to share and change free-software--to make sure the software is free for all its users.  This-General Public License applies to most of the Free Software-Foundation's software and to any other program whose authors commit to-using it.  (Some other Free Software Foundation software is covered by-the GNU Lesser General Public License instead.)  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See the-    GNU General Public License for more details.--    You should have received a copy of the GNU General Public License along-    with this program; if not, write to the Free Software Foundation, Inc.,-    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.--Also add information on how to contact you by electronic and paper mail.--If the program is interactive, make it output a short notice like this-when it starts in an interactive mode:--    Gnomovision version 69, Copyright (C) year name of author-    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.-    This is free software, and you are welcome to redistribute it-    under certain conditions; type `show c' for details.--The hypothetical commands `show w' and `show c' should show the appropriate-parts of the General Public License.  Of course, the commands you use may-be called something other than `show w' and `show c'; they could even be-mouse-clicks or menu items--whatever suits your program.--You should also get your employer (if you work as a programmer) or your-school, if any, to sign a "copyright disclaimer" for the program, if-necessary.  Here is a sample; alter the names:--  Yoyodyne, Inc., hereby disclaims all copyright interest in the program-  `Gnomovision' (which makes passes at compilers) written by James Hacker.--  <signature of Ty Coon>, 1 April 1989-  Ty Coon, President of Vice--This General Public License does not permit incorporating your program into-proprietary programs.  If your program is a subroutine library, you may-consider it more useful to permit linking proprietary applications with the-library.  If this is what you want to do, use the GNU Lesser General-Public License instead of this License.+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Lesser General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have.  You must make sure that they, too, receive or can get the
+source code.  And you must show them these terms so they know their
+rights.
+
+  We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software.  If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+  Finally, any free program is threatened constantly by software
+patents.  We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary.  To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
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+
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+source code as you receive it, in any medium, provided that you
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+copyright notice and disclaimer of warranty; keep intact all the
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+
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+
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+
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+with the Program (or with a work based on the Program) on a volume of
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+
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+
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+However, parties who have received copies, or rights, from you under
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+
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+signed it.  However, nothing else grants you permission to modify or
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+prohibited by law if you do not accept this License.  Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
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+
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+Program), the recipient automatically receives a license from the
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+
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+    <one line to give the program's name and a brief idea of what it does.>
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+Also add information on how to contact you by electronic and paper mail.
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+If the program is interactive, make it output a short notice like this
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+    Gnomovision version 69, Copyright (C) year name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
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+
+You should also get your employer (if you work as a programmer) or your
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+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.

@@ -1,663 +1,663 @@-<!---The file MANUAL.md is automatically generated by the tools/mkmanual.ps1 script. Do not edit manually.--->--## A Pandoc filter to generate figures from code blocks in documents--`pandoc-plot` turns code blocks present in your documents (Markdown, LaTeX, etc.) into embedded figures, using your plotting toolkit of choice, including Matplotlib, ggplot2, MATLAB, Mathematica, and more.---   [Features Overview](#features-overview)-    -   [Captions](#captions)-    -   [Link to source code](#link-to-source-code)-    -   [Preamble scripts](#preamble-scripts)-    -   [Support for interactive plots](#support-for-interactive-plots)-    -   [Performance](#performance)-    -   [Compatibility with pandoc-crossref](#compatibility-with-pandoc-crossref)--   [Detailed usage](#detailed-usage)-    -   [As a filter](#as-a-filter)-    -   [Syntax](#syntax)-        -   [Markdown](#markdown)-        -   [LaTeX](#latex)-    -   [Parameters and options](#parameters-and-options)-        -   [Code highlighting](#code-highlighting)-    -   [Interactive HTML figures](#interactive-html-figures)-    -   [Configuration](#configuration)-        -   [Executables](#executables)-        -   [Command-line arguments](#command-line-arguments)-        -   [Toolkit-specific options](#toolkit-specific-options)-        -   [Logging](#logging)-        -   [Strict mode](#strict-mode)-    -   [Other commands](#other-commands)-        -   [Finding installed toolkits](#finding-installed-toolkits)-        -   [Cleaning output](#cleaning-output)-        -   [Configuration template](#configuration-template)-    -   [As a Haskell library](#as-a-haskell-library)-        -   [Usage with Hakyll](#usage-with-hakyll)--   [Warning](#warning)--## Features Overview--### Captions--You can also specify a caption for your image. This is done using the optional `caption` parameter.--**Markdown**:--```` markdown-```{.matlabplot caption="This is a simple figure with a **Markdown** caption"}-x  = 0: .1 : 2*pi;-y1 = cos(x);-y2 = sin(x);--figure-plot(x, y1, 'b', x, y2, 'r-.', 'LineWidth', 2)-```-````--**LaTex**:--``` latex-\begin{minted}[caption=This is a simple figure with a caption]{matlabplot}-x  = 0: .1 : 2*pi;-y1 = cos(x);-y2 = sin(x);--figure-plot(x, y1, 'b', x, y2, 'r-.', 'LineWidth', 2)-\end{minted}-```--Caption formatting unfortunately cannot be determined automatically. To specify a caption format (e.g. “markdown”, “LaTeX”, etc.), see [Configuration](#configuration).--### Link to source code--In case of an output format that supports links (e.g. HTML), the embedded image generated by `pandoc-plot` can show a link to the source code which was used to generate the file. Therefore, other people can see what code was used to create your figures.--You can turn this on via the `source=true` key:--**Markdown**:--```` markdown-```{.mathplot source=true}-...-```-````--**LaTex**:--``` latex-\begin{minted}[source=true]{mathplot}-...-\end{minted}-```--or via a [configuration file](#Configuration).--### Preamble scripts--If you find yourself always repeating some steps, inclusion of scripts is possible using the `preamble` parameter. For example, if you want all Matplotlib plots to have the [`ggplot`](https://matplotlib.org/tutorials/introductory/customizing.html#sphx-glr-tutorials-introductory-customizing-py) style, you can write a very short preamble `style.py` like so:--``` python-import matplotlib.pyplot as plt-plt.style.use('ggplot')-```--and include it in your document as follows:--```` markdown-```{.matplotlib preamble=style.py}-plt.figure()-plt.plot([0,1,2,3,4], [1,2,3,4,5])-plt.title('This is an example figure')-```-````--Which is equivalent to writing the following markdown:--```` markdown-```{.matplotlib}-import matplotlib.pyplot as plt-plt.style.use('ggplot')--plt.figure()-plt.plot([0,1,2,3,4], [1,2,3,4,5])-plt.title('This is an example figure')-```-````--The equivalent LaTeX usage is as follows:--``` latex-\begin{minted}[include=style.py]{matplotlib}--\end{minted}-```--This `preamble` parameter is perfect for longer documents with many plots. Simply define the style you want in a separate script! You can also import packages this way, or define functions you often use.--### Support for interactive plots--Starting with version 0.8.0.0, `pandoc-plot` supports the creation of interactive plots (if a toolkit supports it). All you need to do is set the save format to `html`. The resulting plot is fully self-contained, so it can be displayed offline.--### Performance--`pandoc-plot` minimizes work, only generating figures if it absolutely must, i.e. if the content has changed. `pandoc-plot` will save the hash of the source code used to generate a figure in its filename. Before generating a figure, `pandoc-plot` will check it this figure already exists based on the hash of its source! This also means that there is no way to directly name figures.--Moreover, starting with version 0.5.0.0, `pandoc-plot` takes advantage of multicore CPUs, rendering figures **in parallel**.--Therefore, you can confidently run the filter on very large documents containing hundreds of figures, like a book or a thesis.--### Compatibility with pandoc-crossref--[`pandoc-crossref`](https://github.com/lierdakil/pandoc-crossref) is a pandoc filter that makes it effortless to cross-reference objects in Markdown documents.--You can use `pandoc-crossref` in conjunction with `pandoc-plot` for the ultimate figure-making pipeline. You can combine both in a figure like so:--```` markdown-```{#fig:myexample .plotly_python caption="This is a caption"}-# Insert figure script here-```--As you can see in @fig:myexample, ...-````--If the above source is located in file `myfile.md`, you can render the figure and references by applying `pandoc-plot` **first**, and then `pandoc-crossref`. For example:--``` bash-pandoc --filter pandoc-plot --filter pandoc-crossref -i myfile.md -o myfile.html-```--## Detailed usage--`pandoc-plot` is a command line executable with a few functions. You can take a look at the help using the `-h`/`--help` flag:--``` bash-pandoc-plot 1.3.0 - generate figures directly in documents--Usage: pandoc-plot.EXE [(-v|--version) | --full-version | (-m|--manual)] -                       [COMMAND] [AST]-  This pandoc filter generates plots from code blocks using a multitude of-  possible renderers. This allows to keep documentation and figures in perfect-  synchronicity.--Available options:-  -v,--version             Show version number and exit.-  --full-version           Show full version information and exit.-  -m,--manual              Open the manual page in the default web browser and-                           exit.-  -h,--help                Show this help text--Available commands:-  toolkits                 Show information on toolkits and exit.-  clean                    Clean output directories where figures from FILE and-                           log files might be stored. WARNING: All files in-                           those directories will be deleted.-  write-example-config     Write example configuration to a file and exit.--More information can be found via the manual (pandoc-plot --manual) or the-repository README, located at https://github.com/LaurentRDC/pandoc-plot-```--### As a filter--The most common use for `pandoc-plot` is as a pandoc filter, in which case it should be called without arguments. For example:--``` bash-pandoc --filter pandoc-plot -i input.md -o output.html-```--If `pandoc-plot` fails to render a code block into a figure, the filtering will not stop. Your code blocks will stay unchanged, unless you activate [strict mode](#strict-mode).--You can chain other filters with it (e.g., [`pandoc-crossref`](https://github.com/lierdakil/pandoc-crossref)) like so:--``` bash-pandoc --filter pandoc-plot --filter pandoc-crossref -i input.md -o output.html-```--### Syntax--The syntax for code blocks in documents is shown below. `pandoc-plot` looks for code blocks with a specific class, depending on the toolkit you want to use. `pandoc-plot` will run the code and capture the figure output. There can only be **one** figure per code block.--The possible parameters and options are described in [further below](#parameters-and-options).--#### Markdown--```` markdown-  ```{.cls param1=value1 param2=value2 ...}-  # script content-  ```-````--#### LaTeX--Note that the `minted` LaTeX package need not be installed.--``` latex-\begin{minted}[param1=value1, param2=value2, ...]{cls}-...-\end{minted}-```--### Parameters and options--There are parameters that affect the figure that will be included in your document. Here are all the possible general parameters, in Markdown syntax:--```` markdown-  ```{.cls -      .language-      directory=(path) -      caption=(text) -      format=(PNG|PDF|SVG|JPG|EPS|GIF|TIF|WEBP|HTML|LATEX) -      source=(true|True|false|False) -      source_label=(text)-      preamble=(path) -      dpi=(integer)-      dependencies=[...]-      file=(path)-      executable=(path) -      caption_format=(text)-      }-  # script content-  ```-````---   `cls` must be one of the following: `matplotlib`, `matlabplot`, `plotly_python`, `plotly_r`, `mathplot`, `octaveplot`, `ggplot2`, `gnuplot`, `graphviz`, `bokeh`, `plotsjl`, `plantuml` (*new in version 1.1.0*).--All following parameters are optional, with their default values controlled by the [configuration](#configuration).---   `language` specifies the programming language used in this block. This parameter is ignored by `pandoc-plot`, but your text editor may use it to highlight code. See [Code highlighting](#code-highlighting) below.--   `directory` is a path to the directory where the figure and source code will be saved. You cannot control the file name. This path is either absolute, or relative from the working directory where you call `pandoc-plot`.--   `caption` is the caption text. The format of the caption is specified in the `caption_format` parameter, described below.--   `format` is the desired filetype for the resulting figure. Possible values for `format` are \[`PNG`, `PDF`, `SVG`, `JPG`, `EPS`, `GIF`, `TIF`, `WEBP`, `HTML`, `LATEX`\]. Not all toolkits support all formats. See `pandoc-plot toolkits` for toolkit-specific information regarding save formats. The `HTML` format is special; it can produce standalone, offline, interactive plots. As such, it only makes sense to use this format when creating HTML documents. Similarly, the `LATEX` format is special; plots in the LaTeX format will be embedded in the document. Therefore, it only makes sense to use this format when creating LaTeX documents.--   `source` is a boolean toggle that determines whether the source code should be linked in the caption or not. Possible values are \[`true`, `True`, `false`, `False`\].--   `source_label` is the text that links to source code (if `source=true`). This is useful if you are writing text in a different language. The default is `source_label="Source Code"`. You might want to set this via the [configuration](#configuration) instead.--   `preamble` is a path to a script that will be included as a preamble to the content of the code block. This path is either absolute, or relative from the working directory where you call `pandoc-plot`.--   `dpi` is the pixel density of the figure in dots-per-inch. Possible values are positive integers. Not all toolkits respect this.--   `dependencies` is a list of files/directories that affect the figure, for example data files. If one of those files/directories changes, `pandoc-plot` will re-render the associated figure. Format is a comma-separated list, e.g. `dependencies=[data.txt, foo.bar, ~/wtv]`. Values for `dependencies` in the configuration file will be appended to the values in a code block.--   `file` is a path to a file from which to read the figure content. If this parameter is used, the content of the code block is ignored. By using this parameter, you can use all the standard tooling of your plotting toolkit of choice, which is especially useful for complex figures.--   `executable` is a path to the executable to use (e.g. `C:\\python3.exe`) or the name of the executable (e.g. `python3`).--   `caption_format` is the text format of the caption. Possible values are exactly the same as `pandoc`’s format specification, usually `FORMAT+EXTENSION-EXTENSION`. For example, captions in Markdown with raw LaTeX would be parsed correctly provided that `caption_format=markdown+raw_tex`. See Pandoc’s guide on [Specifying formats](https://pandoc.org/MANUAL.html#specifying-formats).--#### Code highlighting--If your editor supports code highlighting in code blocks, you can also include the programming language. In Markdown:--```` markdown-  ```{.language .cls (options)}-  # script content-  ```-````--or Latex:--``` latex-  \begin{minted}[(options)]{language, cls}-  # script content-  \end{minted}-```--For example, for GGPlot2 figures:--```` markdown-  ```{.r .ggplot2 caption=Highlighted code block}-  # script content-  ```-````--or (Latex):--``` latex-  \begin{minted}[caption=Highlighted code block]{r, ggplot2}-  # script content-  \end{minted}-```--This way, you benefit from code highlighting *and* `pandoc-plot`.--### Interactive HTML figures--Interactive HTML figures are available for a few toolkits, e.g. `bokeh`. To make a figure interactive, use the output format `format=html`. This only makes sense if your output file is also HTML.--You can take a look at the [demonstration page](https://laurentrdc.github.io/pandoc-plot/) for an example result.--Many interactive plots rely on javascript scripts stored on the internet. If you want to have a self-contained document that can be viewed offline – or you want your document to work for the next 10 years –, you can use pandoc’s `--self-contained` flag:--``` bash-pandoc --self-contained --filter pandoc-plot -i mydoc.md -o webpage.html -```--The resulting output `webpage.html` will contain everything, at the cost of size.--### Configuration--To avoid repetition, `pandoc-plot` can be configured using simple YAML-files. Here are **all** the possible parameters:--``` yaml-# This is an example configuration. Everything in this file is optional.-# Please refer to the documentation to know about the parameters herein.-#-# The `executable` parameter for all toolkits can be either the-# executable name (if it is present on the PATH), or-# the full path to the executable.-# E.g.:-#  executable: python3-#  executable: "C:\Python37\Scripts\python.exe"--# The following parameters affect all toolkits-# Directory where to save the plots. The path can be relative to pandoc-plot's-# current working directory, or absolute.-directory: plots/--# Whether or not to include a link to the source script in the caption. -# Particularly useful for HTML output.-source: false--# When `strict: false`, pandoc-plot will leave code blocks untouched if a plot-# could not be generated. This could happen if, for example, a toolkit is not-# installed. If you want pandoc-plot to fail instead, use `strict: true`.-strict: false--# Text label for links to source code.-# You can change this label if you are writing a document in a non-English language. -# This only matters if `source` is set to `true`.-source_label: Source code--# Default density of figures in dots per inches (DPI). -# This can be changed in the document specifically as well.-dpi: 80--# Default format in which to save the figures. This can be specified -# individually as well.-format: PNG--# Default files/directories on which all figures depend. If any of these files/directories-# changes, all figures will be re-rendered.-# Dependencies specified in code blocks will be appended to this list.-dependencies:-  - file1.txt-  - file2.txt--# Text format for the captions. Unfortunately, there is no way to detect-# this automatically. You can use the same notation as Pandoc's --from -# parameter, specified here: -#     https://pandoc.org/MANUAL.html#option--from-# Example: markdown, rst+raw_tex-caption_format: markdown+tex_math_dollars---# Logging configuration-logging:-  # Possible verbosity values: debug, error, warning, info, silent-  verbosity: warning-  # If the filepath below is not present, then pandoc-plot will log to stderr-  # Otherwise, log messages will be appended to the filepath.-  # filepath: path/to/file.txt--# The possible parameters for the Matplotlib toolkit-matplotlib:-  # preamble: matplotlib.py-  tight_bbox: false-  transparent: false-  executable: python-  command_line_arguments:--# The possible parameters for the MATLAB toolkit-matlabplot:-  # preamble: matlab.m-  executable: matlab-  command_line_arguments:--# The possible parameters for the Plotly/Python toolkit-plotly_python:-  # preamble: plotly-python.py-  executable: python-  command_line_arguments:--# The possible parameters for the Plotly/R toolkit-plotly_r:-  # preamble: plotly-r.r-  executable: Rscript-  command_line_arguments:--# The possible parameters for the Mathematica toolkit-mathplot:-  # preamble: mathematica.m-  executable: math-  command_line_arguments:--# The possible parameters for the GNU Octave toolkit-octaveplot:-  # preamble: octave.m-  executable: octave-  command_line_arguments:--# The possible parameters for the ggplot2 toolkit-ggplot2:-  # preamble: ggplot2.r-  executable: Rscript-  command_line_arguments:--# The possible parameters for the gnuplot toolkit-gnuplot:-  # preamble: gnuplot.gp-  executable: gnuplot-  command_line_arguments:--# The possible parameters for the graphviz toolkit-graphviz:-  # preamble: graphviz.dot-  executable: dot-  command_line_arguments:--bokeh:-  # preamble: bokeh.py-  executable: python-  command_line_arguments:--plotsjl:-  # preamble: plotsjl.jl-  executable: julia-  command_line_arguments:--plantuml:-  # preamble: plantuml.txt-  executable: java-  command_line_arguments: -jar plantuml.jar-  # On Linux, if you have `plantuml.jar` as an executable, you can also-  # use the following configuration instead:-  # plantuml:-  #   executable: plantuml-  #   command_line_arguments:-```--A file like the above sets the **default** values; you can still override them in documents directly.--The easiest way to specify configuration for `pandoc-plot` is to place a `.pandoc-plot.yml` file in the current working directory. You can also specify a configuration file in document metadata, under the `plot-configuration` key. For example, in Markdown:--``` markdown-----title: My document-author: John Doe-plot-configuration: /path/to/file.yml-----```--or on the command line, using the pandoc `-M/--metadata` flag:--``` bash-pandoc --filter pandoc-plot -M plot-configuration=/path/to/file.yml ...-```--The hierarchy of configuration files is as follows:--1.  A configuration file specified in the metadata under the `plot-configuration` key;-2.  Otherwise, a file in the current working directory named `.pandoc-plot.yml`;-3.  Finally, the default configuration is used.--#### Executables--The `executable` parameter for all toolkits can be either the executable name (if it is present on the PATH), or the full path to the executable.--Examples:--``` yaml-matplotlib:-  executable: python3-```--``` yaml-matlabplot:-  executable: "C:\Program Files\Matlab\R2019b\bin\matlab.exe"-```--#### Command-line arguments--*New in version 1.0.2.0*--The `command_line_arguments` parameter available for all toolkits provides a way to customize the way interpreters are run. For example, if you want to run the `matplotlib` toolkit with all warnings shown:--``` yaml-# The possible parameters for the Matplotlib toolkit-matplotlib:-  executable: python-  command_line_arguments: -Wa-```--Or if you want `julia` to use more than one thread:--``` yaml-# The possible parameters for the Matplotlib toolkit-plotsjl:-  executable: julia-  command_line_arguments: --threads auto-```--#### Toolkit-specific options--##### Matplotlib---   `tight_bbox` is a boolean that determines whether to use `bbox_inches="tight"` or not when saving Matplotlib figures. For example, `tight_bbox: true`. See [here](https://matplotlib.org/api/_as_gen/matplotlib.pyplot.savefig.html) for details.--   `transparent` is a boolean that determines whether to make Matplotlib figure background transparent or not. This is useful, for example, for displaying a plot on top of a colored background on a web page. High-resolution figures are not affected. For example, `transparent: true`.--#### Logging--If you are running `pandoc-plot` on a large document, you might want to turn on logging. You can do so via the configuration file as follows:--``` yaml-logging:-    # Possible verbosity values: debug, error, warning, info, silent-    # debug level shows all messages-    # error level shows all but debug messages, etc.-    verbosity: info-    -    # OPTIONAL: log to file-    # Remove line below to log to stderr-    filepath: log.txt-```--By default, `pandoc-plot` logs warnings and errors to the standard error stream only.--#### Strict mode--*New in version 1.0.2.0*--By default, `pandoc-plot` leaves code blocks unchanged if a figure fails to be rendered. This might be the case if a plotting toolkit is not installed, or if running the code to render a figure returns an error. In **strict mode**, `pandoc-plot` will immediately halt if it encounters a problem. You can activate strict mode via configuration:--``` yaml-strict: true-```--Strict mode is ideal if you want to ensure that the figures are correctly rendered in the document.--### Other commands--#### Finding installed toolkits--You can determine which toolkits are available on your current machine using the `pandoc-plot toolkits` command. Here is the full help text:--``` bash-Usage: pandoc-plot.EXE toolkits [--config PATH]-  Show information on toolkits and exit.--Available options:-  --config PATH            Path to optional configuration file.-  -h,--help                Show this help text-```--#### Cleaning output--Figures produced by `pandoc-plot` can be placed in a few different locations. You can set a default location in the [Configuration](#configuration), but you can also re-direct specific figures in other directories if you use the `directory=...` argument in code blocks. These figures will build up over time. You can use the `clean` command to scan documents and delete the associated `pandoc-plot` output files. For example, to delete the figures generated from the `input.md` file:--``` bash-pandoc-plot clean input.md-```--This sill remove all directories where a figure *could* have been placed. **WARNING**: all files will be removed.--Here is the full help text for the `clean` command:--``` bash-Usage: pandoc-plot.EXE clean [--config PATH] FILE-  Clean output directories where figures from FILE and log files might be-  stored. WARNING: All files in those directories will be deleted.--Available options:-  --config PATH            Path to optional configuration file.-  -h,--help                Show this help text-```--#### Configuration template--Because `pandoc-plot` supports a few toolkits, there are a lot of configuration options. Don’t start from scratch! The `write-example-config` command will create a file for you, which you can then modify:--``` bash-pandoc-plot write-example-config-```--You will need to re-name the file to `.pandoc-ploy.yml` to be able to use it, so don’t worry about overwriting your own configuration.--Here is the full help text for the `write-example-config` command:--``` bash-Usage: pandoc-plot.EXE write-example-config [--path FILE]-  Write example configuration to a file and exit.--Available options:-  --path FILE              Target location of the configuration file. Default is-                           ".example-pandoc-plot.yml"-  -h,--help                Show this help text-```--### As a Haskell library--To include the functionality of `pandoc-plot` in a Haskell package, you can use the `make` function (for single blocks) or `plotFilter` function (for entire documents). [Take a look at the documentation on Hackage](https://hackage.haskell.org/package/pandoc-plot).--#### Usage with Hakyll--In case you want to use the filter with your own Hakyll setup, you can use a transform function that works on entire documents:--``` haskell-import Text.Pandoc.Filter.Plot (plotFilter, defaultConfiguration)-import Text.Pandoc.Definition (Pandoc, Format(..)) -- from pandoc-types-import Hakyll--plotFilter' :: Pandoc -> IO Pandoc-plotFilter' = -  -- Notify pandoc-plot that the final conversion will be to HTML-  -- This helps give better error messages and adjust default values-  plotFilter defaultConfiguration (Just $ Format "html5") ---- Unsafe compiler is required because of the interaction--- in IO (i.e. running an external script).-makePlotPandocCompiler :: Compiler (Item String)-makePlotPandocCompiler = -  pandocCompilerWithTransformM-    defaultHakyllReaderOptions-    defaultHakyllWriterOptions-    (unsafeCompiler . plotFilter')-```--## Warning--Do not run this filter on unknown documents. There is nothing in `pandoc-plot` that can stop a script from performing **evil actions**.+<!--
+The file MANUAL.md is automatically generated by the tools/mkmanual.ps1 script. Do not edit manually.
+-->
+
+## A Pandoc filter to generate figures from code blocks in documents
+
+`pandoc-plot` turns code blocks present in your documents (Markdown, LaTeX, etc.) into embedded figures, using your plotting toolkit of choice, including Matplotlib, ggplot2, MATLAB, Mathematica, and more.
+
+-   [Features Overview](#features-overview)
+    -   [Captions](#captions)
+    -   [Link to source code](#link-to-source-code)
+    -   [Preamble scripts](#preamble-scripts)
+    -   [Support for interactive plots](#support-for-interactive-plots)
+    -   [Performance](#performance)
+    -   [Compatibility with pandoc-crossref](#compatibility-with-pandoc-crossref)
+-   [Detailed usage](#detailed-usage)
+    -   [As a filter](#as-a-filter)
+    -   [Syntax](#syntax)
+        -   [Markdown](#markdown)
+        -   [LaTeX](#latex)
+    -   [Parameters and options](#parameters-and-options)
+        -   [Code highlighting](#code-highlighting)
+    -   [Interactive HTML figures](#interactive-html-figures)
+    -   [Configuration](#configuration)
+        -   [Executables](#executables)
+        -   [Command-line arguments](#command-line-arguments)
+        -   [Toolkit-specific options](#toolkit-specific-options)
+        -   [Logging](#logging)
+        -   [Strict mode](#strict-mode)
+    -   [Other commands](#other-commands)
+        -   [Finding installed toolkits](#finding-installed-toolkits)
+        -   [Cleaning output](#cleaning-output)
+        -   [Configuration template](#configuration-template)
+    -   [As a Haskell library](#as-a-haskell-library)
+        -   [Usage with Hakyll](#usage-with-hakyll)
+-   [Warning](#warning)
+
+## Features Overview
+
+### Captions
+
+You can also specify a caption for your image. This is done using the optional `caption` parameter.
+
+**Markdown**:
+
+```` markdown
+```{.matlabplot caption="This is a simple figure with a **Markdown** caption"}
+x  = 0: .1 : 2*pi;
+y1 = cos(x);
+y2 = sin(x);
+
+figure
+plot(x, y1, 'b', x, y2, 'r-.', 'LineWidth', 2)
+```
+````
+
+**LaTex**:
+
+``` latex
+\begin{minted}[caption=This is a simple figure with a caption]{matlabplot}
+x  = 0: .1 : 2*pi;
+y1 = cos(x);
+y2 = sin(x);
+
+figure
+plot(x, y1, 'b', x, y2, 'r-.', 'LineWidth', 2)
+\end{minted}
+```
+
+Caption formatting unfortunately cannot be determined automatically. To specify a caption format (e.g. “markdown”, “LaTeX”, etc.), see [Configuration](#configuration).
+
+### Link to source code
+
+In case of an output format that supports links (e.g. HTML), the embedded image generated by `pandoc-plot` can show a link to the source code which was used to generate the file. Therefore, other people can see what code was used to create your figures.
+
+You can turn this on via the `source=true` key:
+
+**Markdown**:
+
+```` markdown
+```{.mathplot source=true}
+...
+```
+````
+
+**LaTex**:
+
+``` latex
+\begin{minted}[source=true]{mathplot}
+...
+\end{minted}
+```
+
+or via a [configuration file](#Configuration).
+
+### Preamble scripts
+
+If you find yourself always repeating some steps, inclusion of scripts is possible using the `preamble` parameter. For example, if you want all Matplotlib plots to have the [`ggplot`](https://matplotlib.org/tutorials/introductory/customizing.html#sphx-glr-tutorials-introductory-customizing-py) style, you can write a very short preamble `style.py` like so:
+
+``` python
+import matplotlib.pyplot as plt
+plt.style.use('ggplot')
+```
+
+and include it in your document as follows:
+
+```` markdown
+```{.matplotlib preamble=style.py}
+plt.figure()
+plt.plot([0,1,2,3,4], [1,2,3,4,5])
+plt.title('This is an example figure')
+```
+````
+
+Which is equivalent to writing the following markdown:
+
+```` markdown
+```{.matplotlib}
+import matplotlib.pyplot as plt
+plt.style.use('ggplot')
+
+plt.figure()
+plt.plot([0,1,2,3,4], [1,2,3,4,5])
+plt.title('This is an example figure')
+```
+````
+
+The equivalent LaTeX usage is as follows:
+
+``` latex
+\begin{minted}[include=style.py]{matplotlib}
+
+\end{minted}
+```
+
+This `preamble` parameter is perfect for longer documents with many plots. Simply define the style you want in a separate script! You can also import packages this way, or define functions you often use.
+
+### Support for interactive plots
+
+Starting with version 0.8.0.0, `pandoc-plot` supports the creation of interactive plots (if a toolkit supports it). All you need to do is set the save format to `html`. The resulting plot is fully self-contained, so it can be displayed offline.
+
+### Performance
+
+`pandoc-plot` minimizes work, only generating figures if it absolutely must, i.e. if the content has changed. `pandoc-plot` will save the hash of the source code used to generate a figure in its filename. Before generating a figure, `pandoc-plot` will check it this figure already exists based on the hash of its source! This also means that there is no way to directly name figures.
+
+Moreover, starting with version 0.5.0.0, `pandoc-plot` takes advantage of multicore CPUs, rendering figures **in parallel**.
+
+Therefore, you can confidently run the filter on very large documents containing hundreds of figures, like a book or a thesis.
+
+### Compatibility with pandoc-crossref
+
+[`pandoc-crossref`](https://github.com/lierdakil/pandoc-crossref) is a pandoc filter that makes it effortless to cross-reference objects in Markdown documents.
+
+You can use `pandoc-crossref` in conjunction with `pandoc-plot` for the ultimate figure-making pipeline. You can combine both in a figure like so:
+
+```` markdown
+```{#fig:myexample .plotly_python caption="This is a caption"}
+# Insert figure script here
+```
+
+As you can see in @fig:myexample, ...
+````
+
+If the above source is located in file `myfile.md`, you can render the figure and references by applying `pandoc-plot` **first**, and then `pandoc-crossref`. For example:
+
+``` bash
+pandoc --filter pandoc-plot --filter pandoc-crossref -i myfile.md -o myfile.html
+```
+
+## Detailed usage
+
+`pandoc-plot` is a command line executable with a few functions. You can take a look at the help using the `-h`/`--help` flag:
+
+``` bash
+pandoc-plot 1.3.0 - generate figures directly in documents
+
+Usage: pandoc-plot.EXE [(-v|--version) | --full-version | (-m|--manual)] 
+                       [COMMAND] [AST]
+  This pandoc filter generates plots from code blocks using a multitude of
+  possible renderers. This allows to keep documentation and figures in perfect
+  synchronicity.
+
+Available options:
+  -v,--version             Show version number and exit.
+  --full-version           Show full version information and exit.
+  -m,--manual              Open the manual page in the default web browser and
+                           exit.
+  -h,--help                Show this help text
+
+Available commands:
+  toolkits                 Show information on toolkits and exit.
+  clean                    Clean output directories where figures from FILE and
+                           log files might be stored. WARNING: All files in
+                           those directories will be deleted.
+  write-example-config     Write example configuration to a file and exit.
+
+More information can be found via the manual (pandoc-plot --manual) or the
+repository README, located at https://github.com/LaurentRDC/pandoc-plot
+```
+
+### As a filter
+
+The most common use for `pandoc-plot` is as a pandoc filter, in which case it should be called without arguments. For example:
+
+``` bash
+pandoc --filter pandoc-plot -i input.md -o output.html
+```
+
+If `pandoc-plot` fails to render a code block into a figure, the filtering will not stop. Your code blocks will stay unchanged, unless you activate [strict mode](#strict-mode).
+
+You can chain other filters with it (e.g., [`pandoc-crossref`](https://github.com/lierdakil/pandoc-crossref)) like so:
+
+``` bash
+pandoc --filter pandoc-plot --filter pandoc-crossref -i input.md -o output.html
+```
+
+### Syntax
+
+The syntax for code blocks in documents is shown below. `pandoc-plot` looks for code blocks with a specific class, depending on the toolkit you want to use. `pandoc-plot` will run the code and capture the figure output. There can only be **one** figure per code block.
+
+The possible parameters and options are described in [further below](#parameters-and-options).
+
+#### Markdown
+
+```` markdown
+  ```{.cls param1=value1 param2=value2 ...}
+  # script content
+  ```
+````
+
+#### LaTeX
+
+Note that the `minted` LaTeX package need not be installed.
+
+``` latex
+\begin{minted}[param1=value1, param2=value2, ...]{cls}
+...
+\end{minted}
+```
+
+### Parameters and options
+
+There are parameters that affect the figure that will be included in your document. Here are all the possible general parameters, in Markdown syntax:
+
+```` markdown
+  ```{.cls 
+      .language
+      directory=(path) 
+      caption=(text) 
+      format=(PNG|PDF|SVG|JPG|EPS|GIF|TIF|WEBP|HTML|LATEX) 
+      source=(true|True|false|False) 
+      source_label=(text)
+      preamble=(path) 
+      dpi=(integer)
+      dependencies=[...]
+      file=(path)
+      executable=(path) 
+      caption_format=(text)
+      }
+  # script content
+  ```
+````
+
+-   `cls` must be one of the following: `matplotlib`, `matlabplot`, `plotly_python`, `plotly_r`, `mathplot`, `octaveplot`, `ggplot2`, `gnuplot`, `graphviz`, `bokeh`, `plotsjl`, `plantuml` (*new in version 1.1.0*).
+
+All following parameters are optional, with their default values controlled by the [configuration](#configuration).
+
+-   `language` specifies the programming language used in this block. This parameter is ignored by `pandoc-plot`, but your text editor may use it to highlight code. See [Code highlighting](#code-highlighting) below.
+-   `directory` is a path to the directory where the figure and source code will be saved. You cannot control the file name. This path is either absolute, or relative from the working directory where you call `pandoc-plot`.
+-   `caption` is the caption text. The format of the caption is specified in the `caption_format` parameter, described below.
+-   `format` is the desired filetype for the resulting figure. Possible values for `format` are \[`PNG`, `PDF`, `SVG`, `JPG`, `EPS`, `GIF`, `TIF`, `WEBP`, `HTML`, `LATEX`\]. Not all toolkits support all formats. See `pandoc-plot toolkits` for toolkit-specific information regarding save formats. The `HTML` format is special; it can produce standalone, offline, interactive plots. As such, it only makes sense to use this format when creating HTML documents. Similarly, the `LATEX` format is special; plots in the LaTeX format will be embedded in the document. Therefore, it only makes sense to use this format when creating LaTeX documents.
+-   `source` is a boolean toggle that determines whether the source code should be linked in the caption or not. Possible values are \[`true`, `True`, `false`, `False`\].
+-   `source_label` is the text that links to source code (if `source=true`). This is useful if you are writing text in a different language. The default is `source_label="Source Code"`. You might want to set this via the [configuration](#configuration) instead.
+-   `preamble` is a path to a script that will be included as a preamble to the content of the code block. This path is either absolute, or relative from the working directory where you call `pandoc-plot`.
+-   `dpi` is the pixel density of the figure in dots-per-inch. Possible values are positive integers. Not all toolkits respect this.
+-   `dependencies` is a list of files/directories that affect the figure, for example data files. If one of those files/directories changes, `pandoc-plot` will re-render the associated figure. Format is a comma-separated list, e.g. `dependencies=[data.txt, foo.bar, ~/wtv]`. Values for `dependencies` in the configuration file will be appended to the values in a code block.
+-   `file` is a path to a file from which to read the figure content. If this parameter is used, the content of the code block is ignored. By using this parameter, you can use all the standard tooling of your plotting toolkit of choice, which is especially useful for complex figures.
+-   `executable` is a path to the executable to use (e.g. `C:\\python3.exe`) or the name of the executable (e.g. `python3`).
+-   `caption_format` is the text format of the caption. Possible values are exactly the same as `pandoc`’s format specification, usually `FORMAT+EXTENSION-EXTENSION`. For example, captions in Markdown with raw LaTeX would be parsed correctly provided that `caption_format=markdown+raw_tex`. See Pandoc’s guide on [Specifying formats](https://pandoc.org/MANUAL.html#specifying-formats).
+
+#### Code highlighting
+
+If your editor supports code highlighting in code blocks, you can also include the programming language. In Markdown:
+
+```` markdown
+  ```{.language .cls (options)}
+  # script content
+  ```
+````
+
+or Latex:
+
+``` latex
+  \begin{minted}[(options)]{language, cls}
+  # script content
+  \end{minted}
+```
+
+For example, for GGPlot2 figures:
+
+```` markdown
+  ```{.r .ggplot2 caption=Highlighted code block}
+  # script content
+  ```
+````
+
+or (Latex):
+
+``` latex
+  \begin{minted}[caption=Highlighted code block]{r, ggplot2}
+  # script content
+  \end{minted}
+```
+
+This way, you benefit from code highlighting *and* `pandoc-plot`.
+
+### Interactive HTML figures
+
+Interactive HTML figures are available for a few toolkits, e.g. `bokeh`. To make a figure interactive, use the output format `format=html`. This only makes sense if your output file is also HTML.
+
+You can take a look at the [demonstration page](https://laurentrdc.github.io/pandoc-plot/) for an example result.
+
+Many interactive plots rely on javascript scripts stored on the internet. If you want to have a self-contained document that can be viewed offline – or you want your document to work for the next 10 years –, you can use pandoc’s `--self-contained` flag:
+
+``` bash
+pandoc --self-contained --filter pandoc-plot -i mydoc.md -o webpage.html 
+```
+
+The resulting output `webpage.html` will contain everything, at the cost of size.
+
+### Configuration
+
+To avoid repetition, `pandoc-plot` can be configured using simple YAML
+files. Here are **all** the possible parameters:
+
+``` yaml
+# This is an example configuration. Everything in this file is optional.
+# Please refer to the documentation to know about the parameters herein.
+#
+# The `executable` parameter for all toolkits can be either the
+# executable name (if it is present on the PATH), or
+# the full path to the executable.
+# E.g.:
+#  executable: python3
+#  executable: "C:\Python37\Scripts\python.exe"
+
+# The following parameters affect all toolkits
+# Directory where to save the plots. The path can be relative to pandoc-plot's
+# current working directory, or absolute.
+directory: plots/
+
+# Whether or not to include a link to the source script in the caption. 
+# Particularly useful for HTML output.
+source: false
+
+# When `strict: false`, pandoc-plot will leave code blocks untouched if a plot
+# could not be generated. This could happen if, for example, a toolkit is not
+# installed. If you want pandoc-plot to fail instead, use `strict: true`.
+strict: false
+
+# Text label for links to source code.
+# You can change this label if you are writing a document in a non-English language. 
+# This only matters if `source` is set to `true`.
+source_label: Source code
+
+# Default density of figures in dots per inches (DPI). 
+# This can be changed in the document specifically as well.
+dpi: 80
+
+# Default format in which to save the figures. This can be specified 
+# individually as well.
+format: PNG
+
+# Default files/directories on which all figures depend. If any of these files/directories
+# changes, all figures will be re-rendered.
+# Dependencies specified in code blocks will be appended to this list.
+dependencies:
+  - file1.txt
+  - file2.txt
+
+# Text format for the captions. Unfortunately, there is no way to detect
+# this automatically. You can use the same notation as Pandoc's --from 
+# parameter, specified here: 
+#     https://pandoc.org/MANUAL.html#option--from
+# Example: markdown, rst+raw_tex
+caption_format: markdown+tex_math_dollars
+
+
+# Logging configuration
+logging:
+  # Possible verbosity values: debug, error, warning, info, silent
+  verbosity: warning
+  # If the filepath below is not present, then pandoc-plot will log to stderr
+  # Otherwise, log messages will be appended to the filepath.
+  # filepath: path/to/file.txt
+
+# The possible parameters for the Matplotlib toolkit
+matplotlib:
+  # preamble: matplotlib.py
+  tight_bbox: false
+  transparent: false
+  executable: python
+  command_line_arguments:
+
+# The possible parameters for the MATLAB toolkit
+matlabplot:
+  # preamble: matlab.m
+  executable: matlab
+  command_line_arguments:
+
+# The possible parameters for the Plotly/Python toolkit
+plotly_python:
+  # preamble: plotly-python.py
+  executable: python
+  command_line_arguments:
+
+# The possible parameters for the Plotly/R toolkit
+plotly_r:
+  # preamble: plotly-r.r
+  executable: Rscript
+  command_line_arguments:
+
+# The possible parameters for the Mathematica toolkit
+mathplot:
+  # preamble: mathematica.m
+  executable: math
+  command_line_arguments:
+
+# The possible parameters for the GNU Octave toolkit
+octaveplot:
+  # preamble: octave.m
+  executable: octave
+  command_line_arguments:
+
+# The possible parameters for the ggplot2 toolkit
+ggplot2:
+  # preamble: ggplot2.r
+  executable: Rscript
+  command_line_arguments:
+
+# The possible parameters for the gnuplot toolkit
+gnuplot:
+  # preamble: gnuplot.gp
+  executable: gnuplot
+  command_line_arguments:
+
+# The possible parameters for the graphviz toolkit
+graphviz:
+  # preamble: graphviz.dot
+  executable: dot
+  command_line_arguments:
+
+bokeh:
+  # preamble: bokeh.py
+  executable: python
+  command_line_arguments:
+
+plotsjl:
+  # preamble: plotsjl.jl
+  executable: julia
+  command_line_arguments:
+
+plantuml:
+  # preamble: plantuml.txt
+  executable: java
+  command_line_arguments: -jar plantuml.jar
+  # On Linux, if you have `plantuml.jar` as an executable, you can also
+  # use the following configuration instead:
+  # plantuml:
+  #   executable: plantuml
+  #   command_line_arguments:
+```
+
+A file like the above sets the **default** values; you can still override them in documents directly.
+
+The easiest way to specify configuration for `pandoc-plot` is to place a `.pandoc-plot.yml` file in the current working directory. You can also specify a configuration file in document metadata, under the `plot-configuration` key. For example, in Markdown:
+
+``` markdown
+---
+title: My document
+author: John Doe
+plot-configuration: /path/to/file.yml
+---
+```
+
+or on the command line, using the pandoc `-M/--metadata` flag:
+
+``` bash
+pandoc --filter pandoc-plot -M plot-configuration=/path/to/file.yml ...
+```
+
+The hierarchy of configuration files is as follows:
+
+1.  A configuration file specified in the metadata under the `plot-configuration` key;
+2.  Otherwise, a file in the current working directory named `.pandoc-plot.yml`;
+3.  Finally, the default configuration is used.
+
+#### Executables
+
+The `executable` parameter for all toolkits can be either the executable name (if it is present on the PATH), or the full path to the executable.
+
+Examples:
+
+``` yaml
+matplotlib:
+  executable: python3
+```
+
+``` yaml
+matlabplot:
+  executable: "C:\Program Files\Matlab\R2019b\bin\matlab.exe"
+```
+
+#### Command-line arguments
+
+*New in version 1.0.2.0*
+
+The `command_line_arguments` parameter available for all toolkits provides a way to customize the way interpreters are run. For example, if you want to run the `matplotlib` toolkit with all warnings shown:
+
+``` yaml
+# The possible parameters for the Matplotlib toolkit
+matplotlib:
+  executable: python
+  command_line_arguments: -Wa
+```
+
+Or if you want `julia` to use more than one thread:
+
+``` yaml
+# The possible parameters for the Matplotlib toolkit
+plotsjl:
+  executable: julia
+  command_line_arguments: --threads auto
+```
+
+#### Toolkit-specific options
+
+##### Matplotlib
+
+-   `tight_bbox` is a boolean that determines whether to use `bbox_inches="tight"` or not when saving Matplotlib figures. For example, `tight_bbox: true`. See [here](https://matplotlib.org/api/_as_gen/matplotlib.pyplot.savefig.html) for details.
+-   `transparent` is a boolean that determines whether to make Matplotlib figure background transparent or not. This is useful, for example, for displaying a plot on top of a colored background on a web page. High-resolution figures are not affected. For example, `transparent: true`.
+
+#### Logging
+
+If you are running `pandoc-plot` on a large document, you might want to turn on logging. You can do so via the configuration file as follows:
+
+``` yaml
+logging:
+    # Possible verbosity values: debug, error, warning, info, silent
+    # debug level shows all messages
+    # error level shows all but debug messages, etc.
+    verbosity: info
+    
+    # OPTIONAL: log to file
+    # Remove line below to log to stderr
+    filepath: log.txt
+```
+
+By default, `pandoc-plot` logs warnings and errors to the standard error stream only.
+
+#### Strict mode
+
+*New in version 1.0.2.0*
+
+By default, `pandoc-plot` leaves code blocks unchanged if a figure fails to be rendered. This might be the case if a plotting toolkit is not installed, or if running the code to render a figure returns an error. In **strict mode**, `pandoc-plot` will immediately halt if it encounters a problem. You can activate strict mode via configuration:
+
+``` yaml
+strict: true
+```
+
+Strict mode is ideal if you want to ensure that the figures are correctly rendered in the document.
+
+### Other commands
+
+#### Finding installed toolkits
+
+You can determine which toolkits are available on your current machine using the `pandoc-plot toolkits` command. Here is the full help text:
+
+``` bash
+Usage: pandoc-plot.EXE toolkits [--config PATH]
+  Show information on toolkits and exit.
+
+Available options:
+  --config PATH            Path to optional configuration file.
+  -h,--help                Show this help text
+```
+
+#### Cleaning output
+
+Figures produced by `pandoc-plot` can be placed in a few different locations. You can set a default location in the [Configuration](#configuration), but you can also re-direct specific figures in other directories if you use the `directory=...` argument in code blocks. These figures will build up over time. You can use the `clean` command to scan documents and delete the associated `pandoc-plot` output files. For example, to delete the figures generated from the `input.md` file:
+
+``` bash
+pandoc-plot clean input.md
+```
+
+This sill remove all directories where a figure *could* have been placed. **WARNING**: all files will be removed.
+
+Here is the full help text for the `clean` command:
+
+``` bash
+Usage: pandoc-plot.EXE clean [--config PATH] FILE
+  Clean output directories where figures from FILE and log files might be
+  stored. WARNING: All files in those directories will be deleted.
+
+Available options:
+  --config PATH            Path to optional configuration file.
+  -h,--help                Show this help text
+```
+
+#### Configuration template
+
+Because `pandoc-plot` supports a few toolkits, there are a lot of configuration options. Don’t start from scratch! The `write-example-config` command will create a file for you, which you can then modify:
+
+``` bash
+pandoc-plot write-example-config
+```
+
+You will need to re-name the file to `.pandoc-ploy.yml` to be able to use it, so don’t worry about overwriting your own configuration.
+
+Here is the full help text for the `write-example-config` command:
+
+``` bash
+Usage: pandoc-plot.EXE write-example-config [--path FILE]
+  Write example configuration to a file and exit.
+
+Available options:
+  --path FILE              Target location of the configuration file. Default is
+                           ".example-pandoc-plot.yml"
+  -h,--help                Show this help text
+```
+
+### As a Haskell library
+
+To include the functionality of `pandoc-plot` in a Haskell package, you can use the `make` function (for single blocks) or `plotFilter` function (for entire documents). [Take a look at the documentation on Hackage](https://hackage.haskell.org/package/pandoc-plot).
+
+#### Usage with Hakyll
+
+In case you want to use the filter with your own Hakyll setup, you can use a transform function that works on entire documents:
+
+``` haskell
+import Text.Pandoc.Filter.Plot (plotFilter, defaultConfiguration)
+import Text.Pandoc.Definition (Pandoc, Format(..)) -- from pandoc-types
+import Hakyll
+
+plotFilter' :: Pandoc -> IO Pandoc
+plotFilter' = 
+  -- Notify pandoc-plot that the final conversion will be to HTML
+  -- This helps give better error messages and adjust default values
+  plotFilter defaultConfiguration (Just $ Format "html5") 
+
+-- Unsafe compiler is required because of the interaction
+-- in IO (i.e. running an external script).
+makePlotPandocCompiler :: Compiler (Item String)
+makePlotPandocCompiler = 
+  pandocCompilerWithTransformM
+    defaultHakyllReaderOptions
+    defaultHakyllWriterOptions
+    (unsafeCompiler . plotFilter')
+```
+
+## Warning
+
+Do not run this filter on unknown documents. There is nothing in `pandoc-plot` that can stop a script from performing **evil actions**.

@@ -1,169 +1,170 @@-# pandoc-plot --## A Pandoc filter to generate figures from code blocks in documents--[![license](https://img.shields.io/badge/license-GPLv2+-lightgray.svg)](https://www.gnu.org/licenses/gpl.html) --`pandoc-plot` turns code blocks present in your documents (Markdown, LaTeX, etc.) into embedded figures, using your plotting toolkit of choice, including Matplotlib, ggplot2, MATLAB, Mathematica, and more.--## Overview--This program is a [Pandoc](https://pandoc.org/) filter. It can therefore-be used in the middle of conversion from input format to output format,-replacing code blocks with figures.--The filter recognizes code blocks with classes that match plotting-toolkits. For example, using the `matplotlib` toolkit:--```` markdown-# My document--This is a paragraph.--```{.matplotlib}-import matplotlib.pyplot as plt--plt.figure()-plt.plot([0,1,2,3,4], [1,2,3,4,5])-plt.title('This is an example figure')-```-````--Putting the above in `input.md`, we can then generate the plot and embed-it in an HTML page:--``` bash-pandoc --filter pandoc-plot input.md --output output.html-```--The resulting `output.html` looks like this:--```html-<h1 id="my-document">My document</h1>--<p>This is a paragraph.</p>--<figure>-<img src="plots\9671478262050082276.png" />-</figure>-```--## Supported toolkits--`pandoc-plot` currently supports the following plotting toolkits-(**installed separately**):--  - `matplotlib`: plots using the [matplotlib](https://matplotlib.org/)-    Python library;-  - `plotly_python` : plots using the-    [plotly](https://plotly.com/python/) Python library;-  - `plotly_r`: plots using the [plotly](https://plotly.com/r/) R-    library-  - `matlabplot`: plots using [MATLAB](https://www.mathworks.com/);-  - `mathplot` : plots using-    [Mathematica](https://www.wolfram.com/mathematica/);-  - `octaveplot`: plots using [GNU-    Octave](https://www.gnu.org/software/octave/);-  - `ggplot2`: plots using [ggplot2](https://ggplot2.tidyverse.org/);-  - `gnuplot`: plots using [gnuplot](http://www.gnuplot.info/);-  - `graphviz`: graphs using [Graphviz](http://graphviz.org/);-  - `bokeh`: plots using the [Bokeh](https://bokeh.org/) visualization library;-  - `plotsjl`: plots using the [Julia `Plots.jl`](https://docs.juliaplots.org/latest/) package;-  - `plantuml`: diagrams using the [PlantUML](https://plantuml.com/) software suite;-  - `sageplot`: plots using the [Sage](https://www.sagemath.org/) software system.-  - `d2`: plots using [D2](https://d2lang.com/). --To know which toolkits are useable on *your machine* (and which ones are-not available), you can check with the `toolkits` command:--``` bash-pandoc-plot toolkits-```--**Wish your plotting toolkit of choice was available? Please [raise an-issue](https://github.com/LaurentRDC/pandoc-plot/issues)\!**--## Documentation--You can find more information in the documentation, available either in the-source repository file `MANUAL.md`, on the [webpage](https://laurentrdc.github.io/pandoc-plot/MANUAL.html), or via the command `pandoc-plot --manual`.--## Installation--### Binaries and Installers--[![Latest release](https://img.shields.io/github/v/release/LaurentRDC/pandoc-plot)](https://github.com/LaurentRDC/pandoc-plot/releases)--Windows, Linux, and Mac OS binaries are available on the [GitHub release-page](https://github.com/LaurentRDC/pandoc-plot/releases). There are-also Windows installers.--### conda--[![Conda Version](https://anaconda.org/conda-forge/pandoc-plot/badges/version.svg)](https://anaconda.org/conda-forge/pandoc-plot)--Like `pandoc`, `pandoc-plot` is available as a package installable with-[`conda`](https://docs.conda.io/en/latest/). [Click here to see the-package page](https://anaconda.org/conda-forge/pandoc-plot).--To install in the current environment:--``` sh-conda install -c conda-forge pandoc-plot-```--### Homebrew --[![homebrew version](https://img.shields.io/homebrew/v/pandoc-plot)](https://formulae.brew.sh/formula/pandoc-plot)--`pandoc-plot` is available as a package via [`Homebrew`](https://brew.sh/). [Click here to see the package page](https://formulae.brew.sh/formula/pandoc-plot#default). --To install:--```sh-brew install pandoc-plot-```--### winget--You can install `pandoc-plot` from the [Windows Package-Manager](https://github.com/microsoft/winget-cli) `winget` (just like-`pandoc`). To install:--``` sh-winget install pandoc-plot-```--### Arch Linux--[![AUR version](https://img.shields.io/aur/version/pandoc-plot-bin)](https://aur.archlinux.org/packages/pandoc-plot-bin/)--You can install `pandoc-plot` from the [archlinux user repository](https://aur.archlinux.org/packages/pandoc-plot-bin/) as `pandoc-plot-bin`. You can install using e.g. `yay`:--```sh-yay -S pandoc-plot-bin-```--### From Hackage/Stackage--[![Hackage version](https://img.shields.io/hackage/v/pandoc-plot.svg)](http://hackage.haskell.org/package/pandoc-plot)--`pandoc-plot` is available on-[Hackage](http://hackage.haskell.org/package/pandoc-plot) and-[Stackage](https://www.stackage.org/nightly/package/pandoc-plot). Using-the [`cabal-install`](https://www.haskell.org/cabal/) tool:--``` bash-cabal update-cabal install-```--### From source--Building from source can be done using [`cabal`](https://www.haskell.org/cabal/):--``` bash-git clone https://github.com/LaurentRDC/pandoc-plot-cd pandoc-plot-cabal install # Alternatively, `stack install`-```+# pandoc-plot 
+
+## A Pandoc filter to generate figures from code blocks in documents
+
+[![license](https://img.shields.io/badge/license-GPLv2+-lightgray.svg)](https://www.gnu.org/licenses/gpl.html) 
+
+`pandoc-plot` turns code blocks present in your documents (Markdown, LaTeX, etc.) into embedded figures, using your plotting toolkit of choice, including Matplotlib, ggplot2, MATLAB, Mathematica, and more.
+
+## Overview
+
+This program is a [Pandoc](https://pandoc.org/) filter. It can therefore
+be used in the middle of conversion from input format to output format,
+replacing code blocks with figures.
+
+The filter recognizes code blocks with classes that match plotting
+toolkits. For example, using the `matplotlib` toolkit:
+
+```` markdown
+# My document
+
+This is a paragraph.
+
+```{.matplotlib}
+import matplotlib.pyplot as plt
+
+plt.figure()
+plt.plot([0,1,2,3,4], [1,2,3,4,5])
+plt.title('This is an example figure')
+```
+````
+
+Putting the above in `input.md`, we can then generate the plot and embed
+it in an HTML page:
+
+``` bash
+pandoc --filter pandoc-plot input.md --output output.html
+```
+
+The resulting `output.html` looks like this:
+
+```html
+<h1 id="my-document">My document</h1>
+
+<p>This is a paragraph.</p>
+
+<figure>
+<img src="plots\9671478262050082276.png" />
+</figure>
+```
+
+## Supported toolkits
+
+`pandoc-plot` currently supports the following plotting toolkits
+(**installed separately**):
+
+  - `matplotlib`: plots using the [matplotlib](https://matplotlib.org/)
+    Python library;
+  - `plotly_python` : plots using the
+    [plotly](https://plotly.com/python/) Python library;
+  - `plotly_r`: plots using the [plotly](https://plotly.com/r/) R
+    library
+  - `matlabplot`: plots using [MATLAB](https://www.mathworks.com/);
+  - `mathplot` : plots using
+    [Mathematica](https://www.wolfram.com/mathematica/);
+  - `octaveplot`: plots using [GNU
+    Octave](https://www.gnu.org/software/octave/);
+  - `ggplot2`: plots using [ggplot2](https://ggplot2.tidyverse.org/);
+  - `gnuplot`: plots using [gnuplot](http://www.gnuplot.info/);
+  - `graphviz`: graphs using [Graphviz](http://graphviz.org/);
+  - `bokeh`: plots using the [Bokeh](https://bokeh.org/) visualization library;
+  - `plotsjl`: plots using the [Julia `Plots.jl`](https://docs.juliaplots.org/latest/) package;
+  - `plantuml`: diagrams using the [PlantUML](https://plantuml.com/) software suite;
+  - `sageplot`: plots using the [Sage](https://www.sagemath.org/) software system;
+  - `d2`: plots using [D2](https://d2lang.com/);
+  - `asymptote`: plots using [Asymptote](https://asymptote.sourceforge.io/).
+
+To know which toolkits are useable on *your machine* (and which ones are
+not available), you can check with the `toolkits` command:
+
+``` bash
+pandoc-plot toolkits
+```
+
+**Wish your plotting toolkit of choice was available? Please [raise an
+issue](https://github.com/LaurentRDC/pandoc-plot/issues)\!**
+
+## Documentation
+
+You can find more information in the documentation, available either in the
+source repository file `MANUAL.md`, on the [webpage](https://laurentrdc.github.io/pandoc-plot/MANUAL.html), or via the command `pandoc-plot --manual`.
+
+## Installation
+
+### Binaries and Installers
+
+[![Latest release](https://img.shields.io/github/v/release/LaurentRDC/pandoc-plot)](https://github.com/LaurentRDC/pandoc-plot/releases)
+
+Windows, Linux, and Mac OS binaries are available on the [GitHub release
+page](https://github.com/LaurentRDC/pandoc-plot/releases). There are
+also Windows installers.
+
+### conda
+
+[![Conda Version](https://anaconda.org/conda-forge/pandoc-plot/badges/version.svg)](https://anaconda.org/conda-forge/pandoc-plot)
+
+Like `pandoc`, `pandoc-plot` is available as a package installable with
+[`conda`](https://docs.conda.io/en/latest/). [Click here to see the
+package page](https://anaconda.org/conda-forge/pandoc-plot).
+
+To install in the current environment:
+
+``` sh
+conda install -c conda-forge pandoc-plot
+```
+
+### Homebrew 
+
+[![homebrew version](https://img.shields.io/homebrew/v/pandoc-plot)](https://formulae.brew.sh/formula/pandoc-plot)
+
+`pandoc-plot` is available as a package via [`Homebrew`](https://brew.sh/). [Click here to see the package page](https://formulae.brew.sh/formula/pandoc-plot#default). 
+
+To install:
+
+```sh
+brew install pandoc-plot
+```
+
+### winget
+
+You can install `pandoc-plot` from the [Windows Package
+Manager](https://github.com/microsoft/winget-cli) `winget` (just like
+`pandoc`). To install:
+
+``` sh
+winget install pandoc-plot
+```
+
+### Arch Linux
+
+[![AUR version](https://img.shields.io/aur/version/pandoc-plot-bin)](https://aur.archlinux.org/packages/pandoc-plot-bin/)
+
+You can install `pandoc-plot` from the [archlinux user repository](https://aur.archlinux.org/packages/pandoc-plot-bin/) as `pandoc-plot-bin`. You can install using e.g. `yay`:
+
+```sh
+yay -S pandoc-plot-bin
+```
+
+### From Hackage/Stackage
+
+[![Hackage version](https://img.shields.io/hackage/v/pandoc-plot.svg)](http://hackage.haskell.org/package/pandoc-plot)
+
+`pandoc-plot` is available on
+[Hackage](http://hackage.haskell.org/package/pandoc-plot) and
+[Stackage](https://www.stackage.org/nightly/package/pandoc-plot). Using
+the [`cabal-install`](https://www.haskell.org/cabal/) tool:
+
+``` bash
+cabal update
+cabal install
+```
+
+### From source
+
+Building from source can be done using [`cabal`](https://www.haskell.org/cabal/):
+
+``` bash
+git clone https://github.com/LaurentRDC/pandoc-plot
+cd pandoc-plot
+cabal install # Alternatively, `stack install`
+```

@@ -1,7 +1,7 @@--- This script is used to build and install your package. Typically you don't--- need to change it. The Cabal documentation has more information about this--- file: <https://www.haskell.org/cabal/users-guide/installing-packages.html>.-import qualified Distribution.Simple--main :: IO ()-main = Distribution.Simple.defaultMain+-- This script is used to build and install your package. Typically you don't
+-- need to change it. The Cabal documentation has more information about this
+-- file: <https://www.haskell.org/cabal/users-guide/installing-packages.html>.
+import qualified Distribution.Simple
+
+main :: IO ()
+main = Distribution.Simple.defaultMain

@@ -1,241 +1,241 @@-<!DOCTYPE html>-<html xmlns="http://www.w3.org/1999/xhtml" lang="$lang$" xml:lang="$lang$"$if(dir)$ dir="$dir$"$endif$>-<head>-  <meta charset="utf-8" />-  <meta name="generator" content="pandoc-plot" />-  <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />-$for(author-meta)$-  <meta name="author" content="$author-meta$" />-$endfor$-$if(date-meta)$-  <meta name="dcterms.date" content="$date-meta$" />-$endif$-$if(keywords)$-  <meta name="keywords" content="$for(keywords)$$keywords$$sep$, $endfor$" />-$endif$-  <title>Generated figure</title>-  <style>-$if(document-css)$-html {-  line-height: $if(linestretch)$$linestretch$$else$1.5$endif$;-  font-family: $if(mainfont)$$mainfont$$else$Georgia, serif$endif$;-  font-size: $if(fontsize)$$fontsize$$else$20px$endif$;-  color: $if(fontcolor)$$fontcolor$$else$#1a1a1a$endif$;-  background-color: $if(backgroundcolor)$$backgroundcolor$$else$#fdfdfd$endif$;-}-body {-  margin: 0 auto;-  max-width: 36em;-  padding-left: $if(margin-left)$$margin-left$$else$50px$endif$;-  padding-right: $if(margin-right)$$margin-right$$else$50px$endif$;-  padding-top: $if(margin-top)$$margin-top$$else$50px$endif$;-  padding-bottom: $if(margin-bottom)$$margin-bottom$$else$50px$endif$;-  hyphens: auto;-  word-wrap: break-word;-  text-rendering: optimizeLegibility;-  font-kerning: normal;-}-@media (max-width: 600px) {-  body {-    font-size: 0.9em;-    padding: 1em;-  }-}-@media print {-  body {-    background-color: transparent;-    color: black;-    font-size: 12pt;-  }-  p, h2, h3 {-    orphans: 3;-    widows: 3;-  }-  h2, h3, h4 {-    page-break-after: avoid;-  }-}-p {-  margin: 1em 0;-}-a {-  color: $if(linkcolor)$$linkcolor$$else$#1a1a1a$endif$;-}-a:visited {-  color: $if(linkcolor)$$linkcolor$$else$#1a1a1a$endif$;-}-img {-  max-width: 100%;-}-h1, h2, h3, h4, h5, h6 {-  margin-top: 1.4em;-}-h5, h6 {-  font-size: 1em;-  font-style: italic;-}-h6 {-  font-weight: normal;-}-ol, ul {-  padding-left: 1.7em;-  margin-top: 1em;-}-li > ol, li > ul {-  margin-top: 0;-}-blockquote {-  margin: 1em 0 1em 1.7em;-  padding-left: 1em;-  border-left: 2px solid #e6e6e6;-  color: #606060;-}-code {-  font-family: $if(monofont)$$monofont$$else$Menlo, Monaco, 'Lucida Console', Consolas, monospace$endif$;-$if(monobackgroundcolor)$-  background-color: $monobackgroundcolor$;-  padding: .2em .4em;-$endif$-  font-size: 85%;-  margin: 0;-}-pre {-  margin: 1em 0;-$if(monobackgroundcolor)$-  background-color: $monobackgroundcolor$;-  padding: 1em;-$endif$-  overflow: auto;-}-pre code {-  padding: 0;-  overflow: visible;-}-.sourceCode {- background-color: transparent;- overflow: visible;-}-hr {-  background-color: #1a1a1a;-  border: none;-  height: 1px;-  margin: 1em 0;-}-table {-  margin: 1em 0;-  border-collapse: collapse;-  width: 100%;-  overflow-x: auto;-  display: block;-  font-variant-numeric: lining-nums tabular-nums;-}-table caption {-  margin-bottom: 0.75em;-}-tbody {-  margin-top: 0.5em;-  border-top: 1px solid $if(fontcolor)$$fontcolor$$else$#1a1a1a$endif$;-  border-bottom: 1px solid $if(fontcolor)$$fontcolor$$else$#1a1a1a$endif$;-}-th {-  border-top: 1px solid $if(fontcolor)$$fontcolor$$else$#1a1a1a$endif$;-  padding: 0.25em 0.5em 0.25em 0.5em;-}-td {-  padding: 0.125em 0.5em 0.25em 0.5em;-}-header {-  margin-bottom: 4em;-  text-align: center;-}-#TOC li {-  list-style: none;-}-#TOC a:not(:hover) {-  text-decoration: none;-}-$endif$-code{white-space: pre-wrap;}-span.smallcaps{font-variant: small-caps;}-span.underline{text-decoration: underline;}-div.column{display: inline-block; vertical-align: top; width: 50%;}-div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}-ul.task-list{list-style: none;}-$if(quotes)$-q { quotes: "“" "”" "‘" "’"; }-$endif$-$if(highlighting-css)$-$highlighting-css$-$endif$-$if(displaymath-css)$-.display.math{display: block; text-align: center; margin: 0.5rem auto;}-$endif$-$if(csl-css)$-div.csl-bib-body { }-div.csl-entry {-  clear: both;-$if(csl-entry-spacing)$-  margin-bottom: $csl-entry-spacing$;-$endif$-}-.hanging div.csl-entry {-  margin-left:2em;-  text-indent:-2em;-}-div.csl-left-margin {-  min-width:2em;-  float:left;-}-div.csl-right-inline {-  margin-left:2em;-  padding-left:1em;-}-div.csl-indent {-  margin-left: 2em;-}-$endif$-  </style>-$for(css)$-  <link rel="stylesheet" href="$css$" />-$endfor$-$if(math)$-  $math$-$endif$--$for(header-includes)$-  $header-includes$-$endfor$-</head>-<body>-$for(include-before)$-$include-before$-$endfor$-$if(title)$-<header id="title-block-header">-<h1 class="title">$title$</h1>-$if(subtitle)$-<p class="subtitle">$subtitle$</p>-$endif$-$for(author)$-<p class="author">$author$</p>-$endfor$-$if(date)$-<p class="date">$date$</p>-$endif$-</header>-$endif$-$if(toc)$-<nav id="$idprefix$TOC" role="doc-toc">-$if(toc-title)$-<h2 id="$idprefix$toc-title">$toc-title$</h2>-$endif$-$table-of-contents$-</nav>-$endif$-$body$-$for(include-after)$-$include-after$-$endfor$-<a href="https://github.com/LaurentRDC/pandoc-plot">Click here to see how this plot was generated.</a>-</body>+<!DOCTYPE html>
+<html xmlns="http://www.w3.org/1999/xhtml" lang="$lang$" xml:lang="$lang$"$if(dir)$ dir="$dir$"$endif$>
+<head>
+  <meta charset="utf-8" />
+  <meta name="generator" content="pandoc-plot" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
+$for(author-meta)$
+  <meta name="author" content="$author-meta$" />
+$endfor$
+$if(date-meta)$
+  <meta name="dcterms.date" content="$date-meta$" />
+$endif$
+$if(keywords)$
+  <meta name="keywords" content="$for(keywords)$$keywords$$sep$, $endfor$" />
+$endif$
+  <title>Generated figure</title>
+  <style>
+$if(document-css)$
+html {
+  line-height: $if(linestretch)$$linestretch$$else$1.5$endif$;
+  font-family: $if(mainfont)$$mainfont$$else$Georgia, serif$endif$;
+  font-size: $if(fontsize)$$fontsize$$else$20px$endif$;
+  color: $if(fontcolor)$$fontcolor$$else$#1a1a1a$endif$;
+  background-color: $if(backgroundcolor)$$backgroundcolor$$else$#fdfdfd$endif$;
+}
+body {
+  margin: 0 auto;
+  max-width: 36em;
+  padding-left: $if(margin-left)$$margin-left$$else$50px$endif$;
+  padding-right: $if(margin-right)$$margin-right$$else$50px$endif$;
+  padding-top: $if(margin-top)$$margin-top$$else$50px$endif$;
+  padding-bottom: $if(margin-bottom)$$margin-bottom$$else$50px$endif$;
+  hyphens: auto;
+  word-wrap: break-word;
+  text-rendering: optimizeLegibility;
+  font-kerning: normal;
+}
+@media (max-width: 600px) {
+  body {
+    font-size: 0.9em;
+    padding: 1em;
+  }
+}
+@media print {
+  body {
+    background-color: transparent;
+    color: black;
+    font-size: 12pt;
+  }
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/>-  <!--[if lt IE 9]>-    <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>-  <![endif]-->-</head>-<body>-<header id="title-block-header">-<h1 class="title">pandoc-plot 1.3.0 manual</h1>-</header>-<!---The file MANUAL.md is automatically generated by the tools/mkmanual.ps1 script. Do not edit manually.--->-<h2 id="a-pandoc-filter-to-generate-figures-from-code-blocks-in-documents">A Pandoc filter to generate figures from code blocks in documents</h2>-<p><code>pandoc-plot</code> turns code blocks present in your documents (Markdown, LaTeX, etc.) into embedded figures, using your plotting toolkit of choice, including Matplotlib, ggplot2, MATLAB, Mathematica, and more.</p>-<ul>-<li><a href="#features-overview">Features Overview</a>-<ul>-<li><a href="#captions">Captions</a></li>-<li><a href="#link-to-source-code">Link to source code</a></li>-<li><a href="#preamble-scripts">Preamble scripts</a></li>-<li><a href="#support-for-interactive-plots">Support for interactive plots</a></li>-<li><a href="#performance">Performance</a></li>-<li><a href="#compatibility-with-pandoc-crossref">Compatibility with pandoc-crossref</a></li>-</ul></li>-<li><a href="#detailed-usage">Detailed usage</a>-<ul>-<li><a href="#as-a-filter">As a filter</a></li>-<li><a href="#syntax">Syntax</a>-<ul>-<li><a href="#markdown">Markdown</a></li>-<li><a href="#latex">LaTeX</a></li>-</ul></li>-<li><a href="#parameters-and-options">Parameters and options</a>-<ul>-<li><a href="#code-highlighting">Code highlighting</a></li>-</ul></li>-<li><a href="#interactive-html-figures">Interactive HTML figures</a></li>-<li><a href="#configuration">Configuration</a>-<ul>-<li><a href="#executables">Executables</a></li>-<li><a href="#command-line-arguments">Command-line arguments</a></li>-<li><a href="#toolkit-specific-options">Toolkit-specific options</a></li>-<li><a href="#logging">Logging</a></li>-<li><a href="#strict-mode">Strict mode</a></li>-</ul></li>-<li><a href="#other-commands">Other commands</a>-<ul>-<li><a href="#finding-installed-toolkits">Finding installed toolkits</a></li>-<li><a href="#cleaning-output">Cleaning output</a></li>-<li><a href="#configuration-template">Configuration template</a></li>-</ul></li>-<li><a href="#as-a-haskell-library">As a Haskell library</a>-<ul>-<li><a href="#usage-with-hakyll">Usage with Hakyll</a></li>-</ul></li>-</ul></li>-<li><a href="#warning">Warning</a></li>-</ul>-<h2 id="features-overview">Features Overview</h2>-<h3 id="captions">Captions</h3>-<p>You can also specify a caption for your image. This is done using the optional <code>caption</code> parameter.</p>-<p><strong>Markdown</strong>:</p>-<div class="sourceCode" id="cb1"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="in">```{.matlabplot caption=&quot;This is a simple figure with a **Markdown** caption&quot;}</span></span>-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="in">x  = 0: .1 : 2*pi;</span></span>-<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="in">y1 = cos(x);</span></span>-<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="in">y2 = sin(x);</span></span>-<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="in">figure</span></span>-<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="in">plot(x, y1, &#39;b&#39;, x, y2, &#39;r-.&#39;, &#39;LineWidth&#39;, 2)</span></span>-<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span></code></pre></div>-<p><strong>LaTex</strong>:</p>-<div class="sourceCode" id="cb2"><pre class="sourceCode latex"><code class="sourceCode latex"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="kw">\begin</span>{<span class="ex">minted</span>}[caption=This is a simple figure with a caption]{matlabplot}</span>-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="vs">x  = 0: .1 : 2*pi;</span></span>-<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="vs">y1 = cos(x);</span></span>-<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="vs">y2 = sin(x);</span></span>-<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a><span class="vs">figure</span></span>-<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a><span class="vs">plot(x, y1, &#39;b&#39;, x, y2, &#39;r-.&#39;, &#39;LineWidth&#39;, 2)</span></span>-<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a><span class="kw">\end</span>{<span class="ex">minted</span>}</span></code></pre></div>-<p>Caption formatting unfortunately cannot be determined automatically. To specify a caption format (e.g. “markdown”, “LaTeX”, etc.), see <a href="#configuration">Configuration</a>.</p>-<h3 id="link-to-source-code">Link to source code</h3>-<p>In case of an output format that supports links (e.g. HTML), the embedded image generated by <code>pandoc-plot</code> can show a link to the source code which was used to generate the file. Therefore, other people can see what code was used to create your figures.</p>-<p>You can turn this on via the <code>source=true</code> key:</p>-<p><strong>Markdown</strong>:</p>-<div class="sourceCode" id="cb3"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="in">```{.mathplot source=true}</span></span>-<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="in">...</span></span>-<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span></code></pre></div>-<p><strong>LaTex</strong>:</p>-<div class="sourceCode" id="cb4"><pre class="sourceCode latex"><code class="sourceCode latex"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="kw">\begin</span>{<span class="ex">minted</span>}[source=true]{mathplot}</span>-<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="vs">...</span></span>-<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="kw">\end</span>{<span class="ex">minted</span>}</span></code></pre></div>-<p>or via a <a href="#Configuration">configuration file</a>.</p>-<h3 id="preamble-scripts">Preamble scripts</h3>-<p>If you find yourself always repeating some steps, inclusion of scripts is possible using the <code>preamble</code> parameter. For example, if you want all Matplotlib plots to have the <a href="https://matplotlib.org/tutorials/introductory/customizing.html#sphx-glr-tutorials-introductory-customizing-py"><code>ggplot</code></a> style, you can write a very short preamble <code>style.py</code> like so:</p>-<div class="sourceCode" id="cb5"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> matplotlib.pyplot <span class="im">as</span> plt</span>-<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>plt.style.use(<span class="st">&#39;ggplot&#39;</span>)</span></code></pre></div>-<p>and include it in your document as follows:</p>-<div class="sourceCode" id="cb6"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="in">```{.matplotlib preamble=style.py}</span></span>-<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a><span class="in">plt.figure()</span></span>-<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a><span class="in">plt.plot([0,1,2,3,4], [1,2,3,4,5])</span></span>-<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a><span class="in">plt.title(&#39;This is an example figure&#39;)</span></span>-<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span></code></pre></div>-<p>Which is equivalent to writing the following markdown:</p>-<div class="sourceCode" id="cb7"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="in">```{.matplotlib}</span></span>-<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a><span class="in">import matplotlib.pyplot as plt</span></span>-<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a><span class="in">plt.style.use(&#39;ggplot&#39;)</span></span>-<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a><span class="in">plt.figure()</span></span>-<span id="cb7-6"><a href="#cb7-6" aria-hidden="true" tabindex="-1"></a><span class="in">plt.plot([0,1,2,3,4], [1,2,3,4,5])</span></span>-<span id="cb7-7"><a href="#cb7-7" aria-hidden="true" tabindex="-1"></a><span class="in">plt.title(&#39;This is an example figure&#39;)</span></span>-<span id="cb7-8"><a href="#cb7-8" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span></code></pre></div>-<p>The equivalent LaTeX usage is as follows:</p>-<div class="sourceCode" id="cb8"><pre class="sourceCode latex"><code class="sourceCode latex"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="kw">\begin</span>{<span class="ex">minted</span>}[include=style.py]{matplotlib}</span>-<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a><span class="kw">\end</span>{<span class="ex">minted</span>}</span></code></pre></div>-<p>This <code>preamble</code> parameter is perfect for longer documents with many plots. Simply define the style you want in a separate script! You can also import packages this way, or define functions you often use.</p>-<h3 id="support-for-interactive-plots">Support for interactive plots</h3>-<p>Starting with version 0.8.0.0, <code>pandoc-plot</code> supports the creation of interactive plots (if a toolkit supports it). All you need to do is set the save format to <code>html</code>. The resulting plot is fully self-contained, so it can be displayed offline.</p>-<h3 id="performance">Performance</h3>-<p><code>pandoc-plot</code> minimizes work, only generating figures if it absolutely must, i.e. if the content has changed. <code>pandoc-plot</code> will save the hash of the source code used to generate a figure in its filename. Before generating a figure, <code>pandoc-plot</code> will check it this figure already exists based on the hash of its source! This also means that there is no way to directly name figures.</p>-<p>Moreover, starting with version 0.5.0.0, <code>pandoc-plot</code> takes advantage of multicore CPUs, rendering figures <strong>in parallel</strong>.</p>-<p>Therefore, you can confidently run the filter on very large documents containing hundreds of figures, like a book or a thesis.</p>-<h3 id="compatibility-with-pandoc-crossref">Compatibility with pandoc-crossref</h3>-<p><a href="https://github.com/lierdakil/pandoc-crossref"><code>pandoc-crossref</code></a> is a pandoc filter that makes it effortless to cross-reference objects in Markdown documents.</p>-<p>You can use <code>pandoc-crossref</code> in conjunction with <code>pandoc-plot</code> for the ultimate figure-making pipeline. You can combine both in a figure like so:</p>-<div class="sourceCode" id="cb9"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="in">```{#fig:myexample .plotly_python caption=&quot;This is a caption&quot;}</span></span>-<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="in"># Insert figure script here</span></span>-<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>-<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a>As you can see in @fig:myexample, ...</span></code></pre></div>-<p>If the above source is located in file <code>myfile.md</code>, you can render the figure and references by applying <code>pandoc-plot</code> <strong>first</strong>, and then <code>pandoc-crossref</code>. For example:</p>-<div class="sourceCode" id="cb10"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc</span> <span class="at">--filter</span> pandoc-plot <span class="at">--filter</span> pandoc-crossref <span class="at">-i</span> myfile.md <span class="at">-o</span> myfile.html</span></code></pre></div>-<h2 id="detailed-usage">Detailed usage</h2>-<p><code>pandoc-plot</code> is a command line executable with a few functions. You can take a look at the help using the <code>-h</code>/<code>--help</code> flag:</p>-<div class="sourceCode" id="cb11"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc-plot</span> 1.3.0 <span class="at">-</span> generate figures directly in documents</span>-<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb11-3"><a href="#cb11-3" aria-hidden="true" tabindex="-1"></a><span class="ex">Usage:</span> pandoc-plot.EXE [<span class="er">(</span><span class="ex">-v</span><span class="kw">|</span><span class="ex">--version</span><span class="kw">)</span> <span class="kw">|</span> <span class="ex">--full-version</span> <span class="kw">|</span> <span class="kw">(</span><span class="ex">-m</span><span class="kw">|</span><span class="ex">--manual</span><span class="kw">)</span><span class="ex">]</span> </span>-<span id="cb11-4"><a href="#cb11-4" aria-hidden="true" tabindex="-1"></a>                       <span class="ex">[COMMAND]</span> [AST]</span>-<span id="cb11-5"><a href="#cb11-5" aria-hidden="true" tabindex="-1"></a>  <span class="ex">This</span> pandoc filter generates plots from code blocks using a multitude of</span>-<span id="cb11-6"><a href="#cb11-6" aria-hidden="true" tabindex="-1"></a>  <span class="ex">possible</span> renderers. This allows to keep documentation and figures in perfect</span>-<span id="cb11-7"><a href="#cb11-7" aria-hidden="true" tabindex="-1"></a>  <span class="ex">synchronicity.</span></span>-<span id="cb11-8"><a href="#cb11-8" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb11-9"><a href="#cb11-9" aria-hidden="true" tabindex="-1"></a><span class="ex">Available</span> options:</span>-<span id="cb11-10"><a href="#cb11-10" aria-hidden="true" tabindex="-1"></a>  <span class="ex">-v,--version</span>             Show version number and exit.</span>-<span id="cb11-11"><a href="#cb11-11" aria-hidden="true" tabindex="-1"></a>  <span class="ex">--full-version</span>           Show full version information and exit.</span>-<span id="cb11-12"><a href="#cb11-12" aria-hidden="true" tabindex="-1"></a>  <span class="ex">-m,--manual</span>              Open the manual page in the default web browser and</span>-<span id="cb11-13"><a href="#cb11-13" aria-hidden="true" tabindex="-1"></a>                           <span class="ex">exit.</span></span>-<span id="cb11-14"><a href="#cb11-14" aria-hidden="true" tabindex="-1"></a>  <span class="ex">-h,--help</span>                Show this help text</span>-<span id="cb11-15"><a href="#cb11-15" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb11-16"><a href="#cb11-16" aria-hidden="true" tabindex="-1"></a><span class="ex">Available</span> commands:</span>-<span id="cb11-17"><a href="#cb11-17" aria-hidden="true" tabindex="-1"></a>  <span class="ex">toolkits</span>                 Show information on toolkits and exit.</span>-<span id="cb11-18"><a href="#cb11-18" aria-hidden="true" tabindex="-1"></a>  <span class="ex">clean</span>                    Clean output directories where figures from FILE and</span>-<span id="cb11-19"><a href="#cb11-19" aria-hidden="true" tabindex="-1"></a>                           <span class="ex">log</span> files might be stored. WARNING: All files in</span>-<span id="cb11-20"><a href="#cb11-20" aria-hidden="true" tabindex="-1"></a>                           <span class="ex">those</span> directories will be deleted.</span>-<span id="cb11-21"><a href="#cb11-21" aria-hidden="true" tabindex="-1"></a>  <span class="ex">write-example-config</span>     Write example configuration to a file and exit.</span>-<span id="cb11-22"><a href="#cb11-22" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb11-23"><a href="#cb11-23" aria-hidden="true" tabindex="-1"></a><span class="ex">More</span> information can be found via the manual <span class="er">(</span><span class="ex">pandoc-plot</span> <span class="at">--manual</span><span class="kw">)</span> <span class="ex">or</span> the</span>-<span id="cb11-24"><a href="#cb11-24" aria-hidden="true" tabindex="-1"></a><span class="ex">repository</span> README, located at https://github.com/LaurentRDC/pandoc-plot</span></code></pre></div>-<h3 id="as-a-filter">As a filter</h3>-<p>The most common use for <code>pandoc-plot</code> is as a pandoc filter, in which case it should be called without arguments. For example:</p>-<div class="sourceCode" id="cb12"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc</span> <span class="at">--filter</span> pandoc-plot <span class="at">-i</span> input.md <span class="at">-o</span> output.html</span></code></pre></div>-<p>If <code>pandoc-plot</code> fails to render a code block into a figure, the filtering will not stop. Your code blocks will stay unchanged, unless you activate <a href="#strict-mode">strict mode</a>.</p>-<p>You can chain other filters with it (e.g., <a href="https://github.com/lierdakil/pandoc-crossref"><code>pandoc-crossref</code></a>) like so:</p>-<div class="sourceCode" id="cb13"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc</span> <span class="at">--filter</span> pandoc-plot <span class="at">--filter</span> pandoc-crossref <span class="at">-i</span> input.md <span class="at">-o</span> output.html</span></code></pre></div>-<h3 id="syntax">Syntax</h3>-<p>The syntax for code blocks in documents is shown below. <code>pandoc-plot</code> looks for code blocks with a specific class, depending on the toolkit you want to use. <code>pandoc-plot</code> will run the code and capture the figure output. There can only be <strong>one</strong> figure per code block.</p>-<p>The possible parameters and options are described in <a href="#parameters-and-options">further below</a>.</p>-<h4 id="markdown">Markdown</h4>-<div class="sourceCode" id="cb14"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a>  <span class="in">```{.cls param1=value1 param2=value2 ...}</span></span>-<span id="cb14-2"><a href="#cb14-2" aria-hidden="true" tabindex="-1"></a><span class="in">  # script content</span></span>-<span id="cb14-3"><a href="#cb14-3" aria-hidden="true" tabindex="-1"></a><span class="in">  ```</span></span></code></pre></div>-<h4 id="latex">LaTeX</h4>-<p>Note that the <code>minted</code> LaTeX package need not be installed.</p>-<div class="sourceCode" id="cb15"><pre class="sourceCode latex"><code class="sourceCode latex"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a><span class="kw">\begin</span>{<span class="ex">minted</span>}[param1=value1, param2=value2, ...]{cls}</span>-<span id="cb15-2"><a href="#cb15-2" aria-hidden="true" tabindex="-1"></a><span class="vs">...</span></span>-<span id="cb15-3"><a href="#cb15-3" aria-hidden="true" tabindex="-1"></a><span class="kw">\end</span>{<span class="ex">minted</span>}</span></code></pre></div>-<h3 id="parameters-and-options">Parameters and options</h3>-<p>There are parameters that affect the figure that will be included in your document. Here are all the possible general parameters, in Markdown syntax:</p>-<div class="sourceCode" id="cb16"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a>  <span class="in">```{.cls </span></span>-<span id="cb16-2"><a href="#cb16-2" aria-hidden="true" tabindex="-1"></a><span class="in">      .language</span></span>-<span id="cb16-3"><a href="#cb16-3" aria-hidden="true" tabindex="-1"></a><span class="in">      directory=(path) </span></span>-<span id="cb16-4"><a href="#cb16-4" aria-hidden="true" tabindex="-1"></a><span class="in">      caption=(text) </span></span>-<span id="cb16-5"><a href="#cb16-5" aria-hidden="true" tabindex="-1"></a><span class="in">      format=(PNG|PDF|SVG|JPG|EPS|GIF|TIF|WEBP|HTML|LATEX) </span></span>-<span id="cb16-6"><a href="#cb16-6" aria-hidden="true" tabindex="-1"></a><span class="in">      source=(true|True|false|False) </span></span>-<span id="cb16-7"><a href="#cb16-7" aria-hidden="true" tabindex="-1"></a><span class="in">      source_label=(text)</span></span>-<span id="cb16-8"><a href="#cb16-8" aria-hidden="true" tabindex="-1"></a><span class="in">      preamble=(path) </span></span>-<span id="cb16-9"><a href="#cb16-9" aria-hidden="true" tabindex="-1"></a><span class="in">      dpi=(integer)</span></span>-<span id="cb16-10"><a href="#cb16-10" aria-hidden="true" tabindex="-1"></a><span class="in">      dependencies=[...]</span></span>-<span id="cb16-11"><a href="#cb16-11" aria-hidden="true" tabindex="-1"></a><span class="in">      file=(path)</span></span>-<span id="cb16-12"><a href="#cb16-12" aria-hidden="true" tabindex="-1"></a><span class="in">      executable=(path) </span></span>-<span id="cb16-13"><a href="#cb16-13" aria-hidden="true" tabindex="-1"></a><span class="in">      caption_format=(text)</span></span>-<span id="cb16-14"><a href="#cb16-14" aria-hidden="true" tabindex="-1"></a><span class="in">      }</span></span>-<span id="cb16-15"><a href="#cb16-15" aria-hidden="true" tabindex="-1"></a><span class="in">  # script content</span></span>-<span id="cb16-16"><a href="#cb16-16" aria-hidden="true" tabindex="-1"></a><span class="in">  ```</span></span></code></pre></div>-<ul>-<li><code>cls</code> must be one of the following: <code>matplotlib</code>, <code>matlabplot</code>, <code>plotly_python</code>, <code>plotly_r</code>, <code>mathplot</code>, <code>octaveplot</code>, <code>ggplot2</code>, <code>gnuplot</code>, <code>graphviz</code>, <code>bokeh</code>, <code>plotsjl</code>, <code>plantuml</code> (<em>new in version 1.1.0</em>).</li>-</ul>-<p>All following parameters are optional, with their default values controlled by the <a href="#configuration">configuration</a>.</p>-<ul>-<li><code>language</code> specifies the programming language used in this block. This parameter is ignored by <code>pandoc-plot</code>, but your text editor may use it to highlight code. See <a href="#code-highlighting">Code highlighting</a> below.</li>-<li><code>directory</code> is a path to the directory where the figure and source code will be saved. You cannot control the file name. This path is either absolute, or relative from the working directory where you call <code>pandoc-plot</code>.</li>-<li><code>caption</code> is the caption text. The format of the caption is specified in the <code>caption_format</code> parameter, described below.</li>-<li><code>format</code> is the desired filetype for the resulting figure. Possible values for <code>format</code> are [<code>PNG</code>, <code>PDF</code>, <code>SVG</code>, <code>JPG</code>, <code>EPS</code>, <code>GIF</code>, <code>TIF</code>, <code>WEBP</code>, <code>HTML</code>, <code>LATEX</code>]. Not all toolkits support all formats. See <code>pandoc-plot toolkits</code> for toolkit-specific information regarding save formats. The <code>HTML</code> format is special; it can produce standalone, offline, interactive plots. As such, it only makes sense to use this format when creating HTML documents. Similarly, the <code>LATEX</code> format is special; plots in the LaTeX format will be embedded in the document. Therefore, it only makes sense to use this format when creating LaTeX documents.</li>-<li><code>source</code> is a boolean toggle that determines whether the source code should be linked in the caption or not. Possible values are [<code>true</code>, <code>True</code>, <code>false</code>, <code>False</code>].</li>-<li><code>source_label</code> is the text that links to source code (if <code>source=true</code>). This is useful if you are writing text in a different language. The default is <code>source_label=&quot;Source Code&quot;</code>. You might want to set this via the <a href="#configuration">configuration</a> instead.</li>-<li><code>preamble</code> is a path to a script that will be included as a preamble to the content of the code block. This path is either absolute, or relative from the working directory where you call <code>pandoc-plot</code>.</li>-<li><code>dpi</code> is the pixel density of the figure in dots-per-inch. Possible values are positive integers. Not all toolkits respect this.</li>-<li><code>dependencies</code> is a list of files/directories that affect the figure, for example data files. If one of those files/directories changes, <code>pandoc-plot</code> will re-render the associated figure. Format is a comma-separated list, e.g. <code>dependencies=[data.txt, foo.bar, ~/wtv]</code>. Values for <code>dependencies</code> in the configuration file will be appended to the values in a code block.</li>-<li><code>file</code> is a path to a file from which to read the figure content. If this parameter is used, the content of the code block is ignored. By using this parameter, you can use all the standard tooling of your plotting toolkit of choice, which is especially useful for complex figures.</li>-<li><code>executable</code> is a path to the executable to use (e.g. <code>C:\\python3.exe</code>) or the name of the executable (e.g. <code>python3</code>).</li>-<li><code>caption_format</code> is the text format of the caption. Possible values are exactly the same as <code>pandoc</code>’s format specification, usually <code>FORMAT+EXTENSION-EXTENSION</code>. For example, captions in Markdown with raw LaTeX would be parsed correctly provided that <code>caption_format=markdown+raw_tex</code>. See Pandoc’s guide on <a href="https://pandoc.org/MANUAL.html#specifying-formats">Specifying formats</a>.</li>-</ul>-<h4 id="code-highlighting">Code highlighting</h4>-<p>If your editor supports code highlighting in code blocks, you can also include the programming language. In Markdown:</p>-<div class="sourceCode" id="cb17"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a>  <span class="in">```{.language .cls (options)}</span></span>-<span id="cb17-2"><a href="#cb17-2" aria-hidden="true" tabindex="-1"></a><span class="in">  # script content</span></span>-<span id="cb17-3"><a href="#cb17-3" aria-hidden="true" tabindex="-1"></a><span class="in">  ```</span></span></code></pre></div>-<p>or Latex:</p>-<div class="sourceCode" id="cb18"><pre class="sourceCode latex"><code class="sourceCode latex"><span id="cb18-1"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a>  <span class="kw">\begin</span>{<span class="ex">minted</span>}[(options)]{language, cls}</span>-<span id="cb18-2"><a href="#cb18-2" aria-hidden="true" tabindex="-1"></a><span class="vs">  # script content</span></span>-<span id="cb18-3"><a href="#cb18-3" aria-hidden="true" tabindex="-1"></a><span class="vs">  </span><span class="kw">\end</span>{<span class="ex">minted</span>}</span></code></pre></div>-<p>For example, for GGPlot2 figures:</p>-<div class="sourceCode" id="cb19"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a>  <span class="in">```{.r .ggplot2 caption=Highlighted code block}</span></span>-<span id="cb19-2"><a href="#cb19-2" aria-hidden="true" tabindex="-1"></a><span class="in">  # script content</span></span>-<span id="cb19-3"><a href="#cb19-3" aria-hidden="true" tabindex="-1"></a><span class="in">  ```</span></span></code></pre></div>-<p>or (Latex):</p>-<div class="sourceCode" id="cb20"><pre class="sourceCode latex"><code class="sourceCode latex"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a>  <span class="kw">\begin</span>{<span class="ex">minted</span>}[caption=Highlighted code block]{r, ggplot2}</span>-<span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a><span class="vs">  # script content</span></span>-<span id="cb20-3"><a href="#cb20-3" aria-hidden="true" tabindex="-1"></a><span class="vs">  </span><span class="kw">\end</span>{<span class="ex">minted</span>}</span></code></pre></div>-<p>This way, you benefit from code highlighting <em>and</em> <code>pandoc-plot</code>.</p>-<h3 id="interactive-html-figures">Interactive HTML figures</h3>-<p>Interactive HTML figures are available for a few toolkits, e.g. <code>bokeh</code>. To make a figure interactive, use the output format <code>format=html</code>. This only makes sense if your output file is also HTML.</p>-<p>You can take a look at the <a href="https://laurentrdc.github.io/pandoc-plot/">demonstration page</a> for an example result.</p>-<p>Many interactive plots rely on javascript scripts stored on the internet. If you want to have a self-contained document that can be viewed offline – or you want your document to work for the next 10 years –, you can use pandoc’s <code>--self-contained</code> flag:</p>-<div class="sourceCode" id="cb21"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc</span> <span class="at">--self-contained</span> <span class="at">--filter</span> pandoc-plot <span class="at">-i</span> mydoc.md <span class="at">-o</span> webpage.html </span></code></pre></div>-<p>The resulting output <code>webpage.html</code> will contain everything, at the cost of size.</p>-<h3 id="configuration">Configuration</h3>-<p>To avoid repetition, <code>pandoc-plot</code> can be configured using simple YAML-files. Here are <strong>all</strong> the possible parameters:</p>-<div class="sourceCode" id="cb22"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a><span class="co"># This is an example configuration. Everything in this file is optional.</span></span>-<span id="cb22-2"><a href="#cb22-2" aria-hidden="true" tabindex="-1"></a><span class="co"># Please refer to the documentation to know about the parameters herein.</span></span>-<span id="cb22-3"><a href="#cb22-3" aria-hidden="true" tabindex="-1"></a><span class="co">#</span></span>-<span id="cb22-4"><a href="#cb22-4" aria-hidden="true" tabindex="-1"></a><span class="co"># The `executable` parameter for all toolkits can be either the</span></span>-<span id="cb22-5"><a href="#cb22-5" aria-hidden="true" tabindex="-1"></a><span class="co"># executable name (if it is present on the PATH), or</span></span>-<span id="cb22-6"><a href="#cb22-6" aria-hidden="true" tabindex="-1"></a><span class="co"># the full path to the executable.</span></span>-<span id="cb22-7"><a href="#cb22-7" aria-hidden="true" tabindex="-1"></a><span class="co"># E.g.:</span></span>-<span id="cb22-8"><a href="#cb22-8" aria-hidden="true" tabindex="-1"></a><span class="co">#  executable: python3</span></span>-<span id="cb22-9"><a href="#cb22-9" aria-hidden="true" tabindex="-1"></a><span class="co">#  executable: &quot;C:\Python37\Scripts\python.exe&quot;</span></span>-<span id="cb22-10"><a href="#cb22-10" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-11"><a href="#cb22-11" aria-hidden="true" tabindex="-1"></a><span class="co"># The following parameters affect all toolkits</span></span>-<span id="cb22-12"><a href="#cb22-12" aria-hidden="true" tabindex="-1"></a><span class="co"># Directory where to save the plots. The path can be relative to pandoc-plot&#39;s</span></span>-<span id="cb22-13"><a href="#cb22-13" aria-hidden="true" tabindex="-1"></a><span class="co"># current working directory, or absolute.</span></span>-<span id="cb22-14"><a href="#cb22-14" aria-hidden="true" tabindex="-1"></a><span class="fu">directory</span><span class="kw">:</span><span class="at"> plots/</span></span>-<span id="cb22-15"><a href="#cb22-15" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-16"><a href="#cb22-16" aria-hidden="true" tabindex="-1"></a><span class="co"># Whether or not to include a link to the source script in the caption. </span></span>-<span id="cb22-17"><a href="#cb22-17" aria-hidden="true" tabindex="-1"></a><span class="co"># Particularly useful for HTML output.</span></span>-<span id="cb22-18"><a href="#cb22-18" aria-hidden="true" tabindex="-1"></a><span class="fu">source</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>-<span id="cb22-19"><a href="#cb22-19" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-20"><a href="#cb22-20" aria-hidden="true" tabindex="-1"></a><span class="co"># When `strict: false`, pandoc-plot will leave code blocks untouched if a plot</span></span>-<span id="cb22-21"><a href="#cb22-21" aria-hidden="true" tabindex="-1"></a><span class="co"># could not be generated. This could happen if, for example, a toolkit is not</span></span>-<span id="cb22-22"><a href="#cb22-22" aria-hidden="true" tabindex="-1"></a><span class="co"># installed. If you want pandoc-plot to fail instead, use `strict: true`.</span></span>-<span id="cb22-23"><a href="#cb22-23" aria-hidden="true" tabindex="-1"></a><span class="fu">strict</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>-<span id="cb22-24"><a href="#cb22-24" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-25"><a href="#cb22-25" aria-hidden="true" tabindex="-1"></a><span class="co"># Text label for links to source code.</span></span>-<span id="cb22-26"><a href="#cb22-26" aria-hidden="true" tabindex="-1"></a><span class="co"># You can change this label if you are writing a document in a non-English language. </span></span>-<span id="cb22-27"><a href="#cb22-27" aria-hidden="true" tabindex="-1"></a><span class="co"># This only matters if `source` is set to `true`.</span></span>-<span id="cb22-28"><a href="#cb22-28" aria-hidden="true" tabindex="-1"></a><span class="fu">source_label</span><span class="kw">:</span><span class="at"> Source code</span></span>-<span id="cb22-29"><a href="#cb22-29" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-30"><a href="#cb22-30" aria-hidden="true" tabindex="-1"></a><span class="co"># Default density of figures in dots per inches (DPI). </span></span>-<span id="cb22-31"><a href="#cb22-31" aria-hidden="true" tabindex="-1"></a><span class="co"># This can be changed in the document specifically as well.</span></span>-<span id="cb22-32"><a href="#cb22-32" aria-hidden="true" tabindex="-1"></a><span class="fu">dpi</span><span class="kw">:</span><span class="at"> </span><span class="dv">80</span></span>-<span id="cb22-33"><a href="#cb22-33" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-34"><a href="#cb22-34" aria-hidden="true" tabindex="-1"></a><span class="co"># Default format in which to save the figures. This can be specified </span></span>-<span id="cb22-35"><a href="#cb22-35" aria-hidden="true" tabindex="-1"></a><span class="co"># individually as well.</span></span>-<span id="cb22-36"><a href="#cb22-36" aria-hidden="true" tabindex="-1"></a><span class="fu">format</span><span class="kw">:</span><span class="at"> PNG</span></span>-<span id="cb22-37"><a href="#cb22-37" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-38"><a href="#cb22-38" aria-hidden="true" tabindex="-1"></a><span class="co"># Default files/directories on which all figures depend. If any of these files/directories</span></span>-<span id="cb22-39"><a href="#cb22-39" aria-hidden="true" tabindex="-1"></a><span class="co"># changes, all figures will be re-rendered.</span></span>-<span id="cb22-40"><a href="#cb22-40" aria-hidden="true" tabindex="-1"></a><span class="co"># Dependencies specified in code blocks will be appended to this list.</span></span>-<span id="cb22-41"><a href="#cb22-41" aria-hidden="true" tabindex="-1"></a><span class="fu">dependencies</span><span class="kw">:</span></span>-<span id="cb22-42"><a href="#cb22-42" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="kw">-</span><span class="at"> file1.txt</span></span>-<span id="cb22-43"><a href="#cb22-43" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="kw">-</span><span class="at"> file2.txt</span></span>-<span id="cb22-44"><a href="#cb22-44" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-45"><a href="#cb22-45" aria-hidden="true" tabindex="-1"></a><span class="co"># Text format for the captions. Unfortunately, there is no way to detect</span></span>-<span id="cb22-46"><a href="#cb22-46" aria-hidden="true" tabindex="-1"></a><span class="co"># this automatically. You can use the same notation as Pandoc&#39;s --from </span></span>-<span id="cb22-47"><a href="#cb22-47" aria-hidden="true" tabindex="-1"></a><span class="co"># parameter, specified here: </span></span>-<span id="cb22-48"><a href="#cb22-48" aria-hidden="true" tabindex="-1"></a><span class="co">#     https://pandoc.org/MANUAL.html#option--from</span></span>-<span id="cb22-49"><a href="#cb22-49" aria-hidden="true" tabindex="-1"></a><span class="co"># Example: markdown, rst+raw_tex</span></span>-<span id="cb22-50"><a href="#cb22-50" aria-hidden="true" tabindex="-1"></a><span class="fu">caption_format</span><span class="kw">:</span><span class="at"> markdown+tex_math_dollars</span></span>-<span id="cb22-51"><a href="#cb22-51" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-52"><a href="#cb22-52" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-53"><a href="#cb22-53" aria-hidden="true" tabindex="-1"></a><span class="co"># Logging configuration</span></span>-<span id="cb22-54"><a href="#cb22-54" aria-hidden="true" tabindex="-1"></a><span class="fu">logging</span><span class="kw">:</span></span>-<span id="cb22-55"><a href="#cb22-55" aria-hidden="true" tabindex="-1"></a><span class="co">  # Possible verbosity values: debug, error, warning, info, silent</span></span>-<span id="cb22-56"><a href="#cb22-56" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">verbosity</span><span class="kw">:</span><span class="at"> warning</span></span>-<span id="cb22-57"><a href="#cb22-57" aria-hidden="true" tabindex="-1"></a><span class="co">  # If the filepath below is not present, then pandoc-plot will log to stderr</span></span>-<span id="cb22-58"><a href="#cb22-58" aria-hidden="true" tabindex="-1"></a><span class="co">  # Otherwise, log messages will be appended to the filepath.</span></span>-<span id="cb22-59"><a href="#cb22-59" aria-hidden="true" tabindex="-1"></a><span class="co">  # filepath: path/to/file.txt</span></span>-<span id="cb22-60"><a href="#cb22-60" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-61"><a href="#cb22-61" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the Matplotlib toolkit</span></span>-<span id="cb22-62"><a href="#cb22-62" aria-hidden="true" tabindex="-1"></a><span class="fu">matplotlib</span><span class="kw">:</span></span>-<span id="cb22-63"><a href="#cb22-63" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: matplotlib.py</span></span>-<span id="cb22-64"><a href="#cb22-64" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">tight_bbox</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>-<span id="cb22-65"><a href="#cb22-65" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">transparent</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>-<span id="cb22-66"><a href="#cb22-66" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> python</span></span>-<span id="cb22-67"><a href="#cb22-67" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>-<span id="cb22-68"><a href="#cb22-68" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-69"><a href="#cb22-69" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the MATLAB toolkit</span></span>-<span id="cb22-70"><a href="#cb22-70" aria-hidden="true" tabindex="-1"></a><span class="fu">matlabplot</span><span class="kw">:</span></span>-<span id="cb22-71"><a href="#cb22-71" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: matlab.m</span></span>-<span id="cb22-72"><a href="#cb22-72" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> matlab</span></span>-<span id="cb22-73"><a href="#cb22-73" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>-<span id="cb22-74"><a href="#cb22-74" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-75"><a href="#cb22-75" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the Plotly/Python toolkit</span></span>-<span id="cb22-76"><a href="#cb22-76" aria-hidden="true" tabindex="-1"></a><span class="fu">plotly_python</span><span class="kw">:</span></span>-<span id="cb22-77"><a href="#cb22-77" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: plotly-python.py</span></span>-<span id="cb22-78"><a href="#cb22-78" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> python</span></span>-<span id="cb22-79"><a href="#cb22-79" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>-<span id="cb22-80"><a href="#cb22-80" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-81"><a href="#cb22-81" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the Plotly/R toolkit</span></span>-<span id="cb22-82"><a href="#cb22-82" aria-hidden="true" tabindex="-1"></a><span class="fu">plotly_r</span><span class="kw">:</span></span>-<span id="cb22-83"><a href="#cb22-83" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: plotly-r.r</span></span>-<span id="cb22-84"><a href="#cb22-84" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> Rscript</span></span>-<span id="cb22-85"><a href="#cb22-85" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>-<span id="cb22-86"><a href="#cb22-86" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-87"><a href="#cb22-87" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the Mathematica toolkit</span></span>-<span id="cb22-88"><a href="#cb22-88" aria-hidden="true" tabindex="-1"></a><span class="fu">mathplot</span><span class="kw">:</span></span>-<span id="cb22-89"><a href="#cb22-89" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: mathematica.m</span></span>-<span id="cb22-90"><a href="#cb22-90" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> math</span></span>-<span id="cb22-91"><a href="#cb22-91" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>-<span id="cb22-92"><a href="#cb22-92" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-93"><a href="#cb22-93" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the GNU Octave toolkit</span></span>-<span id="cb22-94"><a href="#cb22-94" aria-hidden="true" tabindex="-1"></a><span class="fu">octaveplot</span><span class="kw">:</span></span>-<span id="cb22-95"><a href="#cb22-95" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: octave.m</span></span>-<span id="cb22-96"><a href="#cb22-96" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> octave</span></span>-<span id="cb22-97"><a href="#cb22-97" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>-<span id="cb22-98"><a href="#cb22-98" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-99"><a href="#cb22-99" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the ggplot2 toolkit</span></span>-<span id="cb22-100"><a href="#cb22-100" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot2</span><span class="kw">:</span></span>-<span id="cb22-101"><a href="#cb22-101" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: ggplot2.r</span></span>-<span id="cb22-102"><a href="#cb22-102" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> Rscript</span></span>-<span id="cb22-103"><a href="#cb22-103" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>-<span id="cb22-104"><a href="#cb22-104" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-105"><a href="#cb22-105" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the gnuplot toolkit</span></span>-<span id="cb22-106"><a href="#cb22-106" aria-hidden="true" tabindex="-1"></a><span class="fu">gnuplot</span><span class="kw">:</span></span>-<span id="cb22-107"><a href="#cb22-107" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: gnuplot.gp</span></span>-<span id="cb22-108"><a href="#cb22-108" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> gnuplot</span></span>-<span id="cb22-109"><a href="#cb22-109" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>-<span id="cb22-110"><a href="#cb22-110" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-111"><a href="#cb22-111" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the graphviz toolkit</span></span>-<span id="cb22-112"><a href="#cb22-112" aria-hidden="true" tabindex="-1"></a><span class="fu">graphviz</span><span class="kw">:</span></span>-<span id="cb22-113"><a href="#cb22-113" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: graphviz.dot</span></span>-<span id="cb22-114"><a href="#cb22-114" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> dot</span></span>-<span id="cb22-115"><a href="#cb22-115" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>-<span id="cb22-116"><a href="#cb22-116" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-117"><a href="#cb22-117" aria-hidden="true" tabindex="-1"></a><span class="fu">bokeh</span><span class="kw">:</span></span>-<span id="cb22-118"><a href="#cb22-118" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: bokeh.py</span></span>-<span id="cb22-119"><a href="#cb22-119" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> python</span></span>-<span id="cb22-120"><a href="#cb22-120" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>-<span id="cb22-121"><a href="#cb22-121" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-122"><a href="#cb22-122" aria-hidden="true" tabindex="-1"></a><span class="fu">plotsjl</span><span class="kw">:</span></span>-<span id="cb22-123"><a href="#cb22-123" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: plotsjl.jl</span></span>-<span id="cb22-124"><a href="#cb22-124" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> julia</span></span>-<span id="cb22-125"><a href="#cb22-125" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>-<span id="cb22-126"><a href="#cb22-126" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb22-127"><a href="#cb22-127" aria-hidden="true" tabindex="-1"></a><span class="fu">plantuml</span><span class="kw">:</span></span>-<span id="cb22-128"><a href="#cb22-128" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: plantuml.txt</span></span>-<span id="cb22-129"><a href="#cb22-129" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> java</span></span>-<span id="cb22-130"><a href="#cb22-130" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span><span class="at"> -jar plantuml.jar</span></span>-<span id="cb22-131"><a href="#cb22-131" aria-hidden="true" tabindex="-1"></a><span class="co">  # On Linux, if you have `plantuml.jar` as an executable, you can also</span></span>-<span id="cb22-132"><a href="#cb22-132" aria-hidden="true" tabindex="-1"></a><span class="co">  # use the following configuration instead:</span></span>-<span id="cb22-133"><a href="#cb22-133" aria-hidden="true" tabindex="-1"></a><span class="co">  # plantuml:</span></span>-<span id="cb22-134"><a href="#cb22-134" aria-hidden="true" tabindex="-1"></a><span class="co">  #   executable: plantuml</span></span>-<span id="cb22-135"><a href="#cb22-135" aria-hidden="true" tabindex="-1"></a><span class="co">  #   command_line_arguments:</span></span></code></pre></div>-<p>A file like the above sets the <strong>default</strong> values; you can still override them in documents directly.</p>-<p>The easiest way to specify configuration for <code>pandoc-plot</code> is to place a <code>.pandoc-plot.yml</code> file in the current working directory. You can also specify a configuration file in document metadata, under the <code>plot-configuration</code> key. For example, in Markdown:</p>-<div class="sourceCode" id="cb23"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb23-1"><a href="#cb23-1" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>-<span id="cb23-2"><a href="#cb23-2" aria-hidden="true" tabindex="-1"></a><span class="an">title:</span><span class="co"> My document</span></span>-<span id="cb23-3"><a href="#cb23-3" aria-hidden="true" tabindex="-1"></a><span class="an">author:</span><span class="co"> John Doe</span></span>-<span id="cb23-4"><a href="#cb23-4" aria-hidden="true" tabindex="-1"></a><span class="an">plot-configuration:</span><span class="co"> /path/to/file.yml</span></span>-<span id="cb23-5"><a href="#cb23-5" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span></code></pre></div>-<p>or on the command line, using the pandoc <code>-M/--metadata</code> flag:</p>-<div class="sourceCode" id="cb24"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc</span> <span class="at">--filter</span> pandoc-plot <span class="at">-M</span> plot-configuration=/path/to/file.yml ...</span></code></pre></div>-<p>The hierarchy of configuration files is as follows:</p>-<ol type="1">-<li>A configuration file specified in the metadata under the <code>plot-configuration</code> key;</li>-<li>Otherwise, a file in the current working directory named <code>.pandoc-plot.yml</code>;</li>-<li>Finally, the default configuration is used.</li>-</ol>-<h4 id="executables">Executables</h4>-<p>The <code>executable</code> parameter for all toolkits can be either the executable name (if it is present on the PATH), or the full path to the executable.</p>-<p>Examples:</p>-<div class="sourceCode" id="cb25"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a><span class="fu">matplotlib</span><span class="kw">:</span></span>-<span id="cb25-2"><a href="#cb25-2" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> python3</span></span></code></pre></div>-<div class="sourceCode" id="cb26"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb26-1"><a href="#cb26-1" aria-hidden="true" tabindex="-1"></a><span class="fu">matlabplot</span><span class="kw">:</span></span>-<span id="cb26-2"><a href="#cb26-2" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> </span><span class="st">&quot;C:\Program Files\Matlab\R2019b</span><span class="sc">\b</span><span class="st">in\matlab.exe&quot;</span></span></code></pre></div>-<h4 id="command-line-arguments">Command-line arguments</h4>-<p><em>New in version 1.0.2.0</em></p>-<p>The <code>command_line_arguments</code> parameter available for all toolkits provides a way to customize the way interpreters are run. For example, if you want to run the <code>matplotlib</code> toolkit with all warnings shown:</p>-<div class="sourceCode" id="cb27"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the Matplotlib toolkit</span></span>-<span id="cb27-2"><a href="#cb27-2" aria-hidden="true" tabindex="-1"></a><span class="fu">matplotlib</span><span class="kw">:</span></span>-<span id="cb27-3"><a href="#cb27-3" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> python</span></span>-<span id="cb27-4"><a href="#cb27-4" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span><span class="at"> -Wa</span></span></code></pre></div>-<p>Or if you want <code>julia</code> to use more than one thread:</p>-<div class="sourceCode" id="cb28"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb28-1"><a href="#cb28-1" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the Matplotlib toolkit</span></span>-<span id="cb28-2"><a href="#cb28-2" aria-hidden="true" tabindex="-1"></a><span class="fu">plotsjl</span><span class="kw">:</span></span>-<span id="cb28-3"><a href="#cb28-3" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> julia</span></span>-<span id="cb28-4"><a href="#cb28-4" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span><span class="at"> --threads auto</span></span></code></pre></div>-<h4 id="toolkit-specific-options">Toolkit-specific options</h4>-<h5 id="matplotlib">Matplotlib</h5>-<ul>-<li><code>tight_bbox</code> is a boolean that determines whether to use <code>bbox_inches=&quot;tight&quot;</code> or not when saving Matplotlib figures. For example, <code>tight_bbox: true</code>. See <a href="https://matplotlib.org/api/_as_gen/matplotlib.pyplot.savefig.html">here</a> for details.</li>-<li><code>transparent</code> is a boolean that determines whether to make Matplotlib figure background transparent or not. This is useful, for example, for displaying a plot on top of a colored background on a web page. High-resolution figures are not affected. For example, <code>transparent: true</code>.</li>-</ul>-<h4 id="logging">Logging</h4>-<p>If you are running <code>pandoc-plot</code> on a large document, you might want to turn on logging. You can do so via the configuration file as follows:</p>-<div class="sourceCode" id="cb29"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb29-1"><a href="#cb29-1" aria-hidden="true" tabindex="-1"></a><span class="fu">logging</span><span class="kw">:</span></span>-<span id="cb29-2"><a href="#cb29-2" aria-hidden="true" tabindex="-1"></a><span class="co">    # Possible verbosity values: debug, error, warning, info, silent</span></span>-<span id="cb29-3"><a href="#cb29-3" aria-hidden="true" tabindex="-1"></a><span class="co">    # debug level shows all messages</span></span>-<span id="cb29-4"><a href="#cb29-4" aria-hidden="true" tabindex="-1"></a><span class="co">    # error level shows all but debug messages, etc.</span></span>-<span id="cb29-5"><a href="#cb29-5" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">verbosity</span><span class="kw">:</span><span class="at"> info</span></span>-<span id="cb29-6"><a href="#cb29-6" aria-hidden="true" tabindex="-1"></a><span class="at">    </span></span>-<span id="cb29-7"><a href="#cb29-7" aria-hidden="true" tabindex="-1"></a><span class="co">    # OPTIONAL: log to file</span></span>-<span id="cb29-8"><a href="#cb29-8" aria-hidden="true" tabindex="-1"></a><span class="co">    # Remove line below to log to stderr</span></span>-<span id="cb29-9"><a href="#cb29-9" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">filepath</span><span class="kw">:</span><span class="at"> log.txt</span></span></code></pre></div>-<p>By default, <code>pandoc-plot</code> logs warnings and errors to the standard error stream only.</p>-<h4 id="strict-mode">Strict mode</h4>-<p><em>New in version 1.0.2.0</em></p>-<p>By default, <code>pandoc-plot</code> leaves code blocks unchanged if a figure fails to be rendered. This might be the case if a plotting toolkit is not installed, or if running the code to render a figure returns an error. In <strong>strict mode</strong>, <code>pandoc-plot</code> will immediately halt if it encounters a problem. You can activate strict mode via configuration:</p>-<div class="sourceCode" id="cb30"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb30-1"><a href="#cb30-1" aria-hidden="true" tabindex="-1"></a><span class="fu">strict</span><span class="kw">:</span><span class="at"> </span><span class="ch">true</span></span></code></pre></div>-<p>Strict mode is ideal if you want to ensure that the figures are correctly rendered in the document.</p>-<h3 id="other-commands">Other commands</h3>-<h4 id="finding-installed-toolkits">Finding installed toolkits</h4>-<p>You can determine which toolkits are available on your current machine using the <code>pandoc-plot toolkits</code> command. Here is the full help text:</p>-<div class="sourceCode" id="cb31"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb31-1"><a href="#cb31-1" aria-hidden="true" tabindex="-1"></a><span class="ex">Usage:</span> pandoc-plot.EXE toolkits [--config PATH]</span>-<span id="cb31-2"><a href="#cb31-2" aria-hidden="true" tabindex="-1"></a>  <span class="ex">Show</span> information on toolkits and exit.</span>-<span id="cb31-3"><a href="#cb31-3" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb31-4"><a href="#cb31-4" aria-hidden="true" tabindex="-1"></a><span class="ex">Available</span> options:</span>-<span id="cb31-5"><a href="#cb31-5" aria-hidden="true" tabindex="-1"></a>  <span class="ex">--config</span> PATH            Path to optional configuration file.</span>-<span id="cb31-6"><a href="#cb31-6" aria-hidden="true" tabindex="-1"></a>  <span class="ex">-h,--help</span>                Show this help text</span></code></pre></div>-<h4 id="cleaning-output">Cleaning output</h4>-<p>Figures produced by <code>pandoc-plot</code> can be placed in a few different locations. You can set a default location in the <a href="#configuration">Configuration</a>, but you can also re-direct specific figures in other directories if you use the <code>directory=...</code> argument in code blocks. These figures will build up over time. You can use the <code>clean</code> command to scan documents and delete the associated <code>pandoc-plot</code> output files. For example, to delete the figures generated from the <code>input.md</code> file:</p>-<div class="sourceCode" id="cb32"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb32-1"><a href="#cb32-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc-plot</span> clean input.md</span></code></pre></div>-<p>This sill remove all directories where a figure <em>could</em> have been placed. <strong>WARNING</strong>: all files will be removed.</p>-<p>Here is the full help text for the <code>clean</code> command:</p>-<div class="sourceCode" id="cb33"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb33-1"><a href="#cb33-1" aria-hidden="true" tabindex="-1"></a><span class="ex">Usage:</span> pandoc-plot.EXE clean [--config PATH] FILE</span>-<span id="cb33-2"><a href="#cb33-2" aria-hidden="true" tabindex="-1"></a>  <span class="ex">Clean</span> output directories where figures from FILE and log files might be</span>-<span id="cb33-3"><a href="#cb33-3" aria-hidden="true" tabindex="-1"></a>  <span class="ex">stored.</span> WARNING: All files in those directories will be deleted.</span>-<span id="cb33-4"><a href="#cb33-4" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb33-5"><a href="#cb33-5" aria-hidden="true" tabindex="-1"></a><span class="ex">Available</span> options:</span>-<span id="cb33-6"><a href="#cb33-6" aria-hidden="true" tabindex="-1"></a>  <span class="ex">--config</span> PATH            Path to optional configuration file.</span>-<span id="cb33-7"><a href="#cb33-7" aria-hidden="true" tabindex="-1"></a>  <span class="ex">-h,--help</span>                Show this help text</span></code></pre></div>-<h4 id="configuration-template">Configuration template</h4>-<p>Because <code>pandoc-plot</code> supports a few toolkits, there are a lot of configuration options. Don’t start from scratch! The <code>write-example-config</code> command will create a file for you, which you can then modify:</p>-<div class="sourceCode" id="cb34"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb34-1"><a href="#cb34-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc-plot</span> write-example-config</span></code></pre></div>-<p>You will need to re-name the file to <code>.pandoc-ploy.yml</code> to be able to use it, so don’t worry about overwriting your own configuration.</p>-<p>Here is the full help text for the <code>write-example-config</code> command:</p>-<div class="sourceCode" id="cb35"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb35-1"><a href="#cb35-1" aria-hidden="true" tabindex="-1"></a><span class="ex">Usage:</span> pandoc-plot.EXE write-example-config [--path FILE]</span>-<span id="cb35-2"><a href="#cb35-2" aria-hidden="true" tabindex="-1"></a>  <span class="ex">Write</span> example configuration to a file and exit.</span>-<span id="cb35-3"><a href="#cb35-3" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb35-4"><a href="#cb35-4" aria-hidden="true" tabindex="-1"></a><span class="ex">Available</span> options:</span>-<span id="cb35-5"><a href="#cb35-5" aria-hidden="true" tabindex="-1"></a>  <span class="ex">--path</span> FILE              Target location of the configuration file. Default is</span>-<span id="cb35-6"><a href="#cb35-6" aria-hidden="true" tabindex="-1"></a>                           <span class="st">&quot;.example-pandoc-plot.yml&quot;</span></span>-<span id="cb35-7"><a href="#cb35-7" aria-hidden="true" tabindex="-1"></a>  <span class="ex">-h,--help</span>                Show this help text</span></code></pre></div>-<h3 id="as-a-haskell-library">As a Haskell library</h3>-<p>To include the functionality of <code>pandoc-plot</code> in a Haskell package, you can use the <code>make</code> function (for single blocks) or <code>plotFilter</code> function (for entire documents). <a href="https://hackage.haskell.org/package/pandoc-plot">Take a look at the documentation on Hackage</a>.</p>-<h4 id="usage-with-hakyll">Usage with Hakyll</h4>-<p>In case you want to use the filter with your own Hakyll setup, you can use a transform function that works on entire documents:</p>-<div class="sourceCode" id="cb36"><pre class="sourceCode haskell"><code class="sourceCode haskell"><span id="cb36-1"><a href="#cb36-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="dt">Text.Pandoc.Filter.Plot</span> (plotFilter, defaultConfiguration)</span>-<span id="cb36-2"><a href="#cb36-2" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="dt">Text.Pandoc.Definition</span> (<span class="dt">Pandoc</span>, <span class="dt">Format</span>(..)) <span class="co">-- from pandoc-types</span></span>-<span id="cb36-3"><a href="#cb36-3" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="dt">Hakyll</span></span>-<span id="cb36-4"><a href="#cb36-4" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb36-5"><a href="#cb36-5" aria-hidden="true" tabindex="-1"></a><span class="ot">plotFilter&#39; ::</span> <span class="dt">Pandoc</span> <span class="ot">-&gt;</span> <span class="dt">IO</span> <span class="dt">Pandoc</span></span>-<span id="cb36-6"><a href="#cb36-6" aria-hidden="true" tabindex="-1"></a>plotFilter&#39; <span class="ot">=</span> </span>-<span id="cb36-7"><a href="#cb36-7" aria-hidden="true" tabindex="-1"></a>  <span class="co">-- Notify pandoc-plot that the final conversion will be to HTML</span></span>-<span id="cb36-8"><a href="#cb36-8" aria-hidden="true" tabindex="-1"></a>  <span class="co">-- This helps give better error messages and adjust default values</span></span>-<span id="cb36-9"><a href="#cb36-9" aria-hidden="true" tabindex="-1"></a>  plotFilter defaultConfiguration (<span class="dt">Just</span> <span class="op">$</span> <span class="dt">Format</span> <span class="st">&quot;html5&quot;</span>) </span>-<span id="cb36-10"><a href="#cb36-10" aria-hidden="true" tabindex="-1"></a></span>-<span id="cb36-11"><a href="#cb36-11" aria-hidden="true" tabindex="-1"></a><span class="co">-- Unsafe compiler is required because of the interaction</span></span>-<span id="cb36-12"><a href="#cb36-12" aria-hidden="true" tabindex="-1"></a><span class="co">-- in IO (i.e. running an external script).</span></span>-<span id="cb36-13"><a href="#cb36-13" aria-hidden="true" tabindex="-1"></a><span class="ot">makePlotPandocCompiler ::</span> <span class="dt">Compiler</span> (<span class="dt">Item</span> <span class="dt">String</span>)</span>-<span id="cb36-14"><a href="#cb36-14" aria-hidden="true" tabindex="-1"></a>makePlotPandocCompiler <span class="ot">=</span> </span>-<span id="cb36-15"><a href="#cb36-15" aria-hidden="true" tabindex="-1"></a>  pandocCompilerWithTransformM</span>-<span id="cb36-16"><a href="#cb36-16" aria-hidden="true" tabindex="-1"></a>    defaultHakyllReaderOptions</span>-<span id="cb36-17"><a href="#cb36-17" aria-hidden="true" tabindex="-1"></a>    defaultHakyllWriterOptions</span>-<span id="cb36-18"><a href="#cb36-18" aria-hidden="true" tabindex="-1"></a>    (unsafeCompiler <span class="op">.</span> plotFilter&#39;)</span></code></pre></div>-<h2 id="warning">Warning</h2>-<p>Do not run this filter on unknown documents. There is nothing in <code>pandoc-plot</code> that can stop a script from performing <strong>evil actions</strong>.</p>-</body>-</html>+<!DOCTYPE html>
+<html xmlns="http://www.w3.org/1999/xhtml" lang xml:lang>
+<head>
+  <meta charset="utf-8" />
+  <meta name="generator" content="pandoc" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
+  <title>pandoc-plot 1.3.0 manual</title>
+  <style>
+    code{white-space: pre-wrap;}
+    span.smallcaps{font-variant: small-caps;}
+    span.underline{text-decoration: underline;}
+    div.column{display: inline-block; vertical-align: top; width: 50%;}
+    div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+    ul.task-list{list-style: none;}
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+  <!--[if lt IE 9]>
+    <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>
+  <![endif]-->
+</head>
+<body>
+<header id="title-block-header">
+<h1 class="title">pandoc-plot 1.3.0 manual</h1>
+</header>
+<!--
+The file MANUAL.md is automatically generated by the tools/mkmanual.ps1 script. Do not edit manually.
+-->
+<h2 id="a-pandoc-filter-to-generate-figures-from-code-blocks-in-documents">A Pandoc filter to generate figures from code blocks in documents</h2>
+<p><code>pandoc-plot</code> turns code blocks present in your documents (Markdown, LaTeX, etc.) into embedded figures, using your plotting toolkit of choice, including Matplotlib, ggplot2, MATLAB, Mathematica, and more.</p>
+<ul>
+<li><a href="#features-overview">Features Overview</a>
+<ul>
+<li><a href="#captions">Captions</a></li>
+<li><a href="#link-to-source-code">Link to source code</a></li>
+<li><a href="#preamble-scripts">Preamble scripts</a></li>
+<li><a href="#support-for-interactive-plots">Support for interactive plots</a></li>
+<li><a href="#performance">Performance</a></li>
+<li><a href="#compatibility-with-pandoc-crossref">Compatibility with pandoc-crossref</a></li>
+</ul></li>
+<li><a href="#detailed-usage">Detailed usage</a>
+<ul>
+<li><a href="#as-a-filter">As a filter</a></li>
+<li><a href="#syntax">Syntax</a>
+<ul>
+<li><a href="#markdown">Markdown</a></li>
+<li><a href="#latex">LaTeX</a></li>
+</ul></li>
+<li><a href="#parameters-and-options">Parameters and options</a>
+<ul>
+<li><a href="#code-highlighting">Code highlighting</a></li>
+</ul></li>
+<li><a href="#interactive-html-figures">Interactive HTML figures</a></li>
+<li><a href="#configuration">Configuration</a>
+<ul>
+<li><a href="#executables">Executables</a></li>
+<li><a href="#command-line-arguments">Command-line arguments</a></li>
+<li><a href="#toolkit-specific-options">Toolkit-specific options</a></li>
+<li><a href="#logging">Logging</a></li>
+<li><a href="#strict-mode">Strict mode</a></li>
+</ul></li>
+<li><a href="#other-commands">Other commands</a>
+<ul>
+<li><a href="#finding-installed-toolkits">Finding installed toolkits</a></li>
+<li><a href="#cleaning-output">Cleaning output</a></li>
+<li><a href="#configuration-template">Configuration template</a></li>
+</ul></li>
+<li><a href="#as-a-haskell-library">As a Haskell library</a>
+<ul>
+<li><a href="#usage-with-hakyll">Usage with Hakyll</a></li>
+</ul></li>
+</ul></li>
+<li><a href="#warning">Warning</a></li>
+</ul>
+<h2 id="features-overview">Features Overview</h2>
+<h3 id="captions">Captions</h3>
+<p>You can also specify a caption for your image. This is done using the optional <code>caption</code> parameter.</p>
+<p><strong>Markdown</strong>:</p>
+<div class="sourceCode" id="cb1"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="in">```{.matlabplot caption=&quot;This is a simple figure with a **Markdown** caption&quot;}</span></span>
+<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="in">x  = 0: .1 : 2*pi;</span></span>
+<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="in">y1 = cos(x);</span></span>
+<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="in">y2 = sin(x);</span></span>
+<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="in">figure</span></span>
+<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="in">plot(x, y1, &#39;b&#39;, x, y2, &#39;r-.&#39;, &#39;LineWidth&#39;, 2)</span></span>
+<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span></code></pre></div>
+<p><strong>LaTex</strong>:</p>
+<div class="sourceCode" id="cb2"><pre class="sourceCode latex"><code class="sourceCode latex"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="kw">\begin</span>{<span class="ex">minted</span>}[caption=This is a simple figure with a caption]{matlabplot}</span>
+<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="vs">x  = 0: .1 : 2*pi;</span></span>
+<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="vs">y1 = cos(x);</span></span>
+<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="vs">y2 = sin(x);</span></span>
+<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a><span class="vs">figure</span></span>
+<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a><span class="vs">plot(x, y1, &#39;b&#39;, x, y2, &#39;r-.&#39;, &#39;LineWidth&#39;, 2)</span></span>
+<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a><span class="kw">\end</span>{<span class="ex">minted</span>}</span></code></pre></div>
+<p>Caption formatting unfortunately cannot be determined automatically. To specify a caption format (e.g. “markdown”, “LaTeX”, etc.), see <a href="#configuration">Configuration</a>.</p>
+<h3 id="link-to-source-code">Link to source code</h3>
+<p>In case of an output format that supports links (e.g. HTML), the embedded image generated by <code>pandoc-plot</code> can show a link to the source code which was used to generate the file. Therefore, other people can see what code was used to create your figures.</p>
+<p>You can turn this on via the <code>source=true</code> key:</p>
+<p><strong>Markdown</strong>:</p>
+<div class="sourceCode" id="cb3"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="in">```{.mathplot source=true}</span></span>
+<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="in">...</span></span>
+<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span></code></pre></div>
+<p><strong>LaTex</strong>:</p>
+<div class="sourceCode" id="cb4"><pre class="sourceCode latex"><code class="sourceCode latex"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="kw">\begin</span>{<span class="ex">minted</span>}[source=true]{mathplot}</span>
+<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="vs">...</span></span>
+<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="kw">\end</span>{<span class="ex">minted</span>}</span></code></pre></div>
+<p>or via a <a href="#Configuration">configuration file</a>.</p>
+<h3 id="preamble-scripts">Preamble scripts</h3>
+<p>If you find yourself always repeating some steps, inclusion of scripts is possible using the <code>preamble</code> parameter. For example, if you want all Matplotlib plots to have the <a href="https://matplotlib.org/tutorials/introductory/customizing.html#sphx-glr-tutorials-introductory-customizing-py"><code>ggplot</code></a> style, you can write a very short preamble <code>style.py</code> like so:</p>
+<div class="sourceCode" id="cb5"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> matplotlib.pyplot <span class="im">as</span> plt</span>
+<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>plt.style.use(<span class="st">&#39;ggplot&#39;</span>)</span></code></pre></div>
+<p>and include it in your document as follows:</p>
+<div class="sourceCode" id="cb6"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="in">```{.matplotlib preamble=style.py}</span></span>
+<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a><span class="in">plt.figure()</span></span>
+<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a><span class="in">plt.plot([0,1,2,3,4], [1,2,3,4,5])</span></span>
+<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a><span class="in">plt.title(&#39;This is an example figure&#39;)</span></span>
+<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span></code></pre></div>
+<p>Which is equivalent to writing the following markdown:</p>
+<div class="sourceCode" id="cb7"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="in">```{.matplotlib}</span></span>
+<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a><span class="in">import matplotlib.pyplot as plt</span></span>
+<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a><span class="in">plt.style.use(&#39;ggplot&#39;)</span></span>
+<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a><span class="in">plt.figure()</span></span>
+<span id="cb7-6"><a href="#cb7-6" aria-hidden="true" tabindex="-1"></a><span class="in">plt.plot([0,1,2,3,4], [1,2,3,4,5])</span></span>
+<span id="cb7-7"><a href="#cb7-7" aria-hidden="true" tabindex="-1"></a><span class="in">plt.title(&#39;This is an example figure&#39;)</span></span>
+<span id="cb7-8"><a href="#cb7-8" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span></code></pre></div>
+<p>The equivalent LaTeX usage is as follows:</p>
+<div class="sourceCode" id="cb8"><pre class="sourceCode latex"><code class="sourceCode latex"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="kw">\begin</span>{<span class="ex">minted</span>}[include=style.py]{matplotlib}</span>
+<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a><span class="kw">\end</span>{<span class="ex">minted</span>}</span></code></pre></div>
+<p>This <code>preamble</code> parameter is perfect for longer documents with many plots. Simply define the style you want in a separate script! You can also import packages this way, or define functions you often use.</p>
+<h3 id="support-for-interactive-plots">Support for interactive plots</h3>
+<p>Starting with version 0.8.0.0, <code>pandoc-plot</code> supports the creation of interactive plots (if a toolkit supports it). All you need to do is set the save format to <code>html</code>. The resulting plot is fully self-contained, so it can be displayed offline.</p>
+<h3 id="performance">Performance</h3>
+<p><code>pandoc-plot</code> minimizes work, only generating figures if it absolutely must, i.e. if the content has changed. <code>pandoc-plot</code> will save the hash of the source code used to generate a figure in its filename. Before generating a figure, <code>pandoc-plot</code> will check it this figure already exists based on the hash of its source! This also means that there is no way to directly name figures.</p>
+<p>Moreover, starting with version 0.5.0.0, <code>pandoc-plot</code> takes advantage of multicore CPUs, rendering figures <strong>in parallel</strong>.</p>
+<p>Therefore, you can confidently run the filter on very large documents containing hundreds of figures, like a book or a thesis.</p>
+<h3 id="compatibility-with-pandoc-crossref">Compatibility with pandoc-crossref</h3>
+<p><a href="https://github.com/lierdakil/pandoc-crossref"><code>pandoc-crossref</code></a> is a pandoc filter that makes it effortless to cross-reference objects in Markdown documents.</p>
+<p>You can use <code>pandoc-crossref</code> in conjunction with <code>pandoc-plot</code> for the ultimate figure-making pipeline. You can combine both in a figure like so:</p>
+<div class="sourceCode" id="cb9"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="in">```{#fig:myexample .plotly_python caption=&quot;This is a caption&quot;}</span></span>
+<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="in"># Insert figure script here</span></span>
+<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
+<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a>As you can see in @fig:myexample, ...</span></code></pre></div>
+<p>If the above source is located in file <code>myfile.md</code>, you can render the figure and references by applying <code>pandoc-plot</code> <strong>first</strong>, and then <code>pandoc-crossref</code>. For example:</p>
+<div class="sourceCode" id="cb10"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc</span> <span class="at">--filter</span> pandoc-plot <span class="at">--filter</span> pandoc-crossref <span class="at">-i</span> myfile.md <span class="at">-o</span> myfile.html</span></code></pre></div>
+<h2 id="detailed-usage">Detailed usage</h2>
+<p><code>pandoc-plot</code> is a command line executable with a few functions. You can take a look at the help using the <code>-h</code>/<code>--help</code> flag:</p>
+<div class="sourceCode" id="cb11"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc-plot</span> 1.3.0 <span class="at">-</span> generate figures directly in documents</span>
+<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb11-3"><a href="#cb11-3" aria-hidden="true" tabindex="-1"></a><span class="ex">Usage:</span> pandoc-plot.EXE [<span class="er">(</span><span class="ex">-v</span><span class="kw">|</span><span class="ex">--version</span><span class="kw">)</span> <span class="kw">|</span> <span class="ex">--full-version</span> <span class="kw">|</span> <span class="kw">(</span><span class="ex">-m</span><span class="kw">|</span><span class="ex">--manual</span><span class="kw">)</span><span class="ex">]</span> </span>
+<span id="cb11-4"><a href="#cb11-4" aria-hidden="true" tabindex="-1"></a>                       <span class="ex">[COMMAND]</span> [AST]</span>
+<span id="cb11-5"><a href="#cb11-5" aria-hidden="true" tabindex="-1"></a>  <span class="ex">This</span> pandoc filter generates plots from code blocks using a multitude of</span>
+<span id="cb11-6"><a href="#cb11-6" aria-hidden="true" tabindex="-1"></a>  <span class="ex">possible</span> renderers. This allows to keep documentation and figures in perfect</span>
+<span id="cb11-7"><a href="#cb11-7" aria-hidden="true" tabindex="-1"></a>  <span class="ex">synchronicity.</span></span>
+<span id="cb11-8"><a href="#cb11-8" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb11-9"><a href="#cb11-9" aria-hidden="true" tabindex="-1"></a><span class="ex">Available</span> options:</span>
+<span id="cb11-10"><a href="#cb11-10" aria-hidden="true" tabindex="-1"></a>  <span class="ex">-v,--version</span>             Show version number and exit.</span>
+<span id="cb11-11"><a href="#cb11-11" aria-hidden="true" tabindex="-1"></a>  <span class="ex">--full-version</span>           Show full version information and exit.</span>
+<span id="cb11-12"><a href="#cb11-12" aria-hidden="true" tabindex="-1"></a>  <span class="ex">-m,--manual</span>              Open the manual page in the default web browser and</span>
+<span id="cb11-13"><a href="#cb11-13" aria-hidden="true" tabindex="-1"></a>                           <span class="ex">exit.</span></span>
+<span id="cb11-14"><a href="#cb11-14" aria-hidden="true" tabindex="-1"></a>  <span class="ex">-h,--help</span>                Show this help text</span>
+<span id="cb11-15"><a href="#cb11-15" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb11-16"><a href="#cb11-16" aria-hidden="true" tabindex="-1"></a><span class="ex">Available</span> commands:</span>
+<span id="cb11-17"><a href="#cb11-17" aria-hidden="true" tabindex="-1"></a>  <span class="ex">toolkits</span>                 Show information on toolkits and exit.</span>
+<span id="cb11-18"><a href="#cb11-18" aria-hidden="true" tabindex="-1"></a>  <span class="ex">clean</span>                    Clean output directories where figures from FILE and</span>
+<span id="cb11-19"><a href="#cb11-19" aria-hidden="true" tabindex="-1"></a>                           <span class="ex">log</span> files might be stored. WARNING: All files in</span>
+<span id="cb11-20"><a href="#cb11-20" aria-hidden="true" tabindex="-1"></a>                           <span class="ex">those</span> directories will be deleted.</span>
+<span id="cb11-21"><a href="#cb11-21" aria-hidden="true" tabindex="-1"></a>  <span class="ex">write-example-config</span>     Write example configuration to a file and exit.</span>
+<span id="cb11-22"><a href="#cb11-22" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb11-23"><a href="#cb11-23" aria-hidden="true" tabindex="-1"></a><span class="ex">More</span> information can be found via the manual <span class="er">(</span><span class="ex">pandoc-plot</span> <span class="at">--manual</span><span class="kw">)</span> <span class="ex">or</span> the</span>
+<span id="cb11-24"><a href="#cb11-24" aria-hidden="true" tabindex="-1"></a><span class="ex">repository</span> README, located at https://github.com/LaurentRDC/pandoc-plot</span></code></pre></div>
+<h3 id="as-a-filter">As a filter</h3>
+<p>The most common use for <code>pandoc-plot</code> is as a pandoc filter, in which case it should be called without arguments. For example:</p>
+<div class="sourceCode" id="cb12"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc</span> <span class="at">--filter</span> pandoc-plot <span class="at">-i</span> input.md <span class="at">-o</span> output.html</span></code></pre></div>
+<p>If <code>pandoc-plot</code> fails to render a code block into a figure, the filtering will not stop. Your code blocks will stay unchanged, unless you activate <a href="#strict-mode">strict mode</a>.</p>
+<p>You can chain other filters with it (e.g., <a href="https://github.com/lierdakil/pandoc-crossref"><code>pandoc-crossref</code></a>) like so:</p>
+<div class="sourceCode" id="cb13"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc</span> <span class="at">--filter</span> pandoc-plot <span class="at">--filter</span> pandoc-crossref <span class="at">-i</span> input.md <span class="at">-o</span> output.html</span></code></pre></div>
+<h3 id="syntax">Syntax</h3>
+<p>The syntax for code blocks in documents is shown below. <code>pandoc-plot</code> looks for code blocks with a specific class, depending on the toolkit you want to use. <code>pandoc-plot</code> will run the code and capture the figure output. There can only be <strong>one</strong> figure per code block.</p>
+<p>The possible parameters and options are described in <a href="#parameters-and-options">further below</a>.</p>
+<h4 id="markdown">Markdown</h4>
+<div class="sourceCode" id="cb14"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a>  <span class="in">```{.cls param1=value1 param2=value2 ...}</span></span>
+<span id="cb14-2"><a href="#cb14-2" aria-hidden="true" tabindex="-1"></a><span class="in">  # script content</span></span>
+<span id="cb14-3"><a href="#cb14-3" aria-hidden="true" tabindex="-1"></a><span class="in">  ```</span></span></code></pre></div>
+<h4 id="latex">LaTeX</h4>
+<p>Note that the <code>minted</code> LaTeX package need not be installed.</p>
+<div class="sourceCode" id="cb15"><pre class="sourceCode latex"><code class="sourceCode latex"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a><span class="kw">\begin</span>{<span class="ex">minted</span>}[param1=value1, param2=value2, ...]{cls}</span>
+<span id="cb15-2"><a href="#cb15-2" aria-hidden="true" tabindex="-1"></a><span class="vs">...</span></span>
+<span id="cb15-3"><a href="#cb15-3" aria-hidden="true" tabindex="-1"></a><span class="kw">\end</span>{<span class="ex">minted</span>}</span></code></pre></div>
+<h3 id="parameters-and-options">Parameters and options</h3>
+<p>There are parameters that affect the figure that will be included in your document. Here are all the possible general parameters, in Markdown syntax:</p>
+<div class="sourceCode" id="cb16"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a>  <span class="in">```{.cls </span></span>
+<span id="cb16-2"><a href="#cb16-2" aria-hidden="true" tabindex="-1"></a><span class="in">      .language</span></span>
+<span id="cb16-3"><a href="#cb16-3" aria-hidden="true" tabindex="-1"></a><span class="in">      directory=(path) </span></span>
+<span id="cb16-4"><a href="#cb16-4" aria-hidden="true" tabindex="-1"></a><span class="in">      caption=(text) </span></span>
+<span id="cb16-5"><a href="#cb16-5" aria-hidden="true" tabindex="-1"></a><span class="in">      format=(PNG|PDF|SVG|JPG|EPS|GIF|TIF|WEBP|HTML|LATEX) </span></span>
+<span id="cb16-6"><a href="#cb16-6" aria-hidden="true" tabindex="-1"></a><span class="in">      source=(true|True|false|False) </span></span>
+<span id="cb16-7"><a href="#cb16-7" aria-hidden="true" tabindex="-1"></a><span class="in">      source_label=(text)</span></span>
+<span id="cb16-8"><a href="#cb16-8" aria-hidden="true" tabindex="-1"></a><span class="in">      preamble=(path) </span></span>
+<span id="cb16-9"><a href="#cb16-9" aria-hidden="true" tabindex="-1"></a><span class="in">      dpi=(integer)</span></span>
+<span id="cb16-10"><a href="#cb16-10" aria-hidden="true" tabindex="-1"></a><span class="in">      dependencies=[...]</span></span>
+<span id="cb16-11"><a href="#cb16-11" aria-hidden="true" tabindex="-1"></a><span class="in">      file=(path)</span></span>
+<span id="cb16-12"><a href="#cb16-12" aria-hidden="true" tabindex="-1"></a><span class="in">      executable=(path) </span></span>
+<span id="cb16-13"><a href="#cb16-13" aria-hidden="true" tabindex="-1"></a><span class="in">      caption_format=(text)</span></span>
+<span id="cb16-14"><a href="#cb16-14" aria-hidden="true" tabindex="-1"></a><span class="in">      }</span></span>
+<span id="cb16-15"><a href="#cb16-15" aria-hidden="true" tabindex="-1"></a><span class="in">  # script content</span></span>
+<span id="cb16-16"><a href="#cb16-16" aria-hidden="true" tabindex="-1"></a><span class="in">  ```</span></span></code></pre></div>
+<ul>
+<li><code>cls</code> must be one of the following: <code>matplotlib</code>, <code>matlabplot</code>, <code>plotly_python</code>, <code>plotly_r</code>, <code>mathplot</code>, <code>octaveplot</code>, <code>ggplot2</code>, <code>gnuplot</code>, <code>graphviz</code>, <code>bokeh</code>, <code>plotsjl</code>, <code>plantuml</code> (<em>new in version 1.1.0</em>).</li>
+</ul>
+<p>All following parameters are optional, with their default values controlled by the <a href="#configuration">configuration</a>.</p>
+<ul>
+<li><code>language</code> specifies the programming language used in this block. This parameter is ignored by <code>pandoc-plot</code>, but your text editor may use it to highlight code. See <a href="#code-highlighting">Code highlighting</a> below.</li>
+<li><code>directory</code> is a path to the directory where the figure and source code will be saved. You cannot control the file name. This path is either absolute, or relative from the working directory where you call <code>pandoc-plot</code>.</li>
+<li><code>caption</code> is the caption text. The format of the caption is specified in the <code>caption_format</code> parameter, described below.</li>
+<li><code>format</code> is the desired filetype for the resulting figure. Possible values for <code>format</code> are [<code>PNG</code>, <code>PDF</code>, <code>SVG</code>, <code>JPG</code>, <code>EPS</code>, <code>GIF</code>, <code>TIF</code>, <code>WEBP</code>, <code>HTML</code>, <code>LATEX</code>]. Not all toolkits support all formats. See <code>pandoc-plot toolkits</code> for toolkit-specific information regarding save formats. The <code>HTML</code> format is special; it can produce standalone, offline, interactive plots. As such, it only makes sense to use this format when creating HTML documents. Similarly, the <code>LATEX</code> format is special; plots in the LaTeX format will be embedded in the document. Therefore, it only makes sense to use this format when creating LaTeX documents.</li>
+<li><code>source</code> is a boolean toggle that determines whether the source code should be linked in the caption or not. Possible values are [<code>true</code>, <code>True</code>, <code>false</code>, <code>False</code>].</li>
+<li><code>source_label</code> is the text that links to source code (if <code>source=true</code>). This is useful if you are writing text in a different language. The default is <code>source_label=&quot;Source Code&quot;</code>. You might want to set this via the <a href="#configuration">configuration</a> instead.</li>
+<li><code>preamble</code> is a path to a script that will be included as a preamble to the content of the code block. This path is either absolute, or relative from the working directory where you call <code>pandoc-plot</code>.</li>
+<li><code>dpi</code> is the pixel density of the figure in dots-per-inch. Possible values are positive integers. Not all toolkits respect this.</li>
+<li><code>dependencies</code> is a list of files/directories that affect the figure, for example data files. If one of those files/directories changes, <code>pandoc-plot</code> will re-render the associated figure. Format is a comma-separated list, e.g. <code>dependencies=[data.txt, foo.bar, ~/wtv]</code>. Values for <code>dependencies</code> in the configuration file will be appended to the values in a code block.</li>
+<li><code>file</code> is a path to a file from which to read the figure content. If this parameter is used, the content of the code block is ignored. By using this parameter, you can use all the standard tooling of your plotting toolkit of choice, which is especially useful for complex figures.</li>
+<li><code>executable</code> is a path to the executable to use (e.g. <code>C:\\python3.exe</code>) or the name of the executable (e.g. <code>python3</code>).</li>
+<li><code>caption_format</code> is the text format of the caption. Possible values are exactly the same as <code>pandoc</code>’s format specification, usually <code>FORMAT+EXTENSION-EXTENSION</code>. For example, captions in Markdown with raw LaTeX would be parsed correctly provided that <code>caption_format=markdown+raw_tex</code>. See Pandoc’s guide on <a href="https://pandoc.org/MANUAL.html#specifying-formats">Specifying formats</a>.</li>
+</ul>
+<h4 id="code-highlighting">Code highlighting</h4>
+<p>If your editor supports code highlighting in code blocks, you can also include the programming language. In Markdown:</p>
+<div class="sourceCode" id="cb17"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a>  <span class="in">```{.language .cls (options)}</span></span>
+<span id="cb17-2"><a href="#cb17-2" aria-hidden="true" tabindex="-1"></a><span class="in">  # script content</span></span>
+<span id="cb17-3"><a href="#cb17-3" aria-hidden="true" tabindex="-1"></a><span class="in">  ```</span></span></code></pre></div>
+<p>or Latex:</p>
+<div class="sourceCode" id="cb18"><pre class="sourceCode latex"><code class="sourceCode latex"><span id="cb18-1"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a>  <span class="kw">\begin</span>{<span class="ex">minted</span>}[(options)]{language, cls}</span>
+<span id="cb18-2"><a href="#cb18-2" aria-hidden="true" tabindex="-1"></a><span class="vs">  # script content</span></span>
+<span id="cb18-3"><a href="#cb18-3" aria-hidden="true" tabindex="-1"></a><span class="vs">  </span><span class="kw">\end</span>{<span class="ex">minted</span>}</span></code></pre></div>
+<p>For example, for GGPlot2 figures:</p>
+<div class="sourceCode" id="cb19"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a>  <span class="in">```{.r .ggplot2 caption=Highlighted code block}</span></span>
+<span id="cb19-2"><a href="#cb19-2" aria-hidden="true" tabindex="-1"></a><span class="in">  # script content</span></span>
+<span id="cb19-3"><a href="#cb19-3" aria-hidden="true" tabindex="-1"></a><span class="in">  ```</span></span></code></pre></div>
+<p>or (Latex):</p>
+<div class="sourceCode" id="cb20"><pre class="sourceCode latex"><code class="sourceCode latex"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a>  <span class="kw">\begin</span>{<span class="ex">minted</span>}[caption=Highlighted code block]{r, ggplot2}</span>
+<span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a><span class="vs">  # script content</span></span>
+<span id="cb20-3"><a href="#cb20-3" aria-hidden="true" tabindex="-1"></a><span class="vs">  </span><span class="kw">\end</span>{<span class="ex">minted</span>}</span></code></pre></div>
+<p>This way, you benefit from code highlighting <em>and</em> <code>pandoc-plot</code>.</p>
+<h3 id="interactive-html-figures">Interactive HTML figures</h3>
+<p>Interactive HTML figures are available for a few toolkits, e.g. <code>bokeh</code>. To make a figure interactive, use the output format <code>format=html</code>. This only makes sense if your output file is also HTML.</p>
+<p>You can take a look at the <a href="https://laurentrdc.github.io/pandoc-plot/">demonstration page</a> for an example result.</p>
+<p>Many interactive plots rely on javascript scripts stored on the internet. If you want to have a self-contained document that can be viewed offline – or you want your document to work for the next 10 years –, you can use pandoc’s <code>--self-contained</code> flag:</p>
+<div class="sourceCode" id="cb21"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc</span> <span class="at">--self-contained</span> <span class="at">--filter</span> pandoc-plot <span class="at">-i</span> mydoc.md <span class="at">-o</span> webpage.html </span></code></pre></div>
+<p>The resulting output <code>webpage.html</code> will contain everything, at the cost of size.</p>
+<h3 id="configuration">Configuration</h3>
+<p>To avoid repetition, <code>pandoc-plot</code> can be configured using simple YAML
+files. Here are <strong>all</strong> the possible parameters:</p>
+<div class="sourceCode" id="cb22"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a><span class="co"># This is an example configuration. Everything in this file is optional.</span></span>
+<span id="cb22-2"><a href="#cb22-2" aria-hidden="true" tabindex="-1"></a><span class="co"># Please refer to the documentation to know about the parameters herein.</span></span>
+<span id="cb22-3"><a href="#cb22-3" aria-hidden="true" tabindex="-1"></a><span class="co">#</span></span>
+<span id="cb22-4"><a href="#cb22-4" aria-hidden="true" tabindex="-1"></a><span class="co"># The `executable` parameter for all toolkits can be either the</span></span>
+<span id="cb22-5"><a href="#cb22-5" aria-hidden="true" tabindex="-1"></a><span class="co"># executable name (if it is present on the PATH), or</span></span>
+<span id="cb22-6"><a href="#cb22-6" aria-hidden="true" tabindex="-1"></a><span class="co"># the full path to the executable.</span></span>
+<span id="cb22-7"><a href="#cb22-7" aria-hidden="true" tabindex="-1"></a><span class="co"># E.g.:</span></span>
+<span id="cb22-8"><a href="#cb22-8" aria-hidden="true" tabindex="-1"></a><span class="co">#  executable: python3</span></span>
+<span id="cb22-9"><a href="#cb22-9" aria-hidden="true" tabindex="-1"></a><span class="co">#  executable: &quot;C:\Python37\Scripts\python.exe&quot;</span></span>
+<span id="cb22-10"><a href="#cb22-10" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-11"><a href="#cb22-11" aria-hidden="true" tabindex="-1"></a><span class="co"># The following parameters affect all toolkits</span></span>
+<span id="cb22-12"><a href="#cb22-12" aria-hidden="true" tabindex="-1"></a><span class="co"># Directory where to save the plots. The path can be relative to pandoc-plot&#39;s</span></span>
+<span id="cb22-13"><a href="#cb22-13" aria-hidden="true" tabindex="-1"></a><span class="co"># current working directory, or absolute.</span></span>
+<span id="cb22-14"><a href="#cb22-14" aria-hidden="true" tabindex="-1"></a><span class="fu">directory</span><span class="kw">:</span><span class="at"> plots/</span></span>
+<span id="cb22-15"><a href="#cb22-15" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-16"><a href="#cb22-16" aria-hidden="true" tabindex="-1"></a><span class="co"># Whether or not to include a link to the source script in the caption. </span></span>
+<span id="cb22-17"><a href="#cb22-17" aria-hidden="true" tabindex="-1"></a><span class="co"># Particularly useful for HTML output.</span></span>
+<span id="cb22-18"><a href="#cb22-18" aria-hidden="true" tabindex="-1"></a><span class="fu">source</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>
+<span id="cb22-19"><a href="#cb22-19" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-20"><a href="#cb22-20" aria-hidden="true" tabindex="-1"></a><span class="co"># When `strict: false`, pandoc-plot will leave code blocks untouched if a plot</span></span>
+<span id="cb22-21"><a href="#cb22-21" aria-hidden="true" tabindex="-1"></a><span class="co"># could not be generated. This could happen if, for example, a toolkit is not</span></span>
+<span id="cb22-22"><a href="#cb22-22" aria-hidden="true" tabindex="-1"></a><span class="co"># installed. If you want pandoc-plot to fail instead, use `strict: true`.</span></span>
+<span id="cb22-23"><a href="#cb22-23" aria-hidden="true" tabindex="-1"></a><span class="fu">strict</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>
+<span id="cb22-24"><a href="#cb22-24" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-25"><a href="#cb22-25" aria-hidden="true" tabindex="-1"></a><span class="co"># Text label for links to source code.</span></span>
+<span id="cb22-26"><a href="#cb22-26" aria-hidden="true" tabindex="-1"></a><span class="co"># You can change this label if you are writing a document in a non-English language. </span></span>
+<span id="cb22-27"><a href="#cb22-27" aria-hidden="true" tabindex="-1"></a><span class="co"># This only matters if `source` is set to `true`.</span></span>
+<span id="cb22-28"><a href="#cb22-28" aria-hidden="true" tabindex="-1"></a><span class="fu">source_label</span><span class="kw">:</span><span class="at"> Source code</span></span>
+<span id="cb22-29"><a href="#cb22-29" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-30"><a href="#cb22-30" aria-hidden="true" tabindex="-1"></a><span class="co"># Default density of figures in dots per inches (DPI). </span></span>
+<span id="cb22-31"><a href="#cb22-31" aria-hidden="true" tabindex="-1"></a><span class="co"># This can be changed in the document specifically as well.</span></span>
+<span id="cb22-32"><a href="#cb22-32" aria-hidden="true" tabindex="-1"></a><span class="fu">dpi</span><span class="kw">:</span><span class="at"> </span><span class="dv">80</span></span>
+<span id="cb22-33"><a href="#cb22-33" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-34"><a href="#cb22-34" aria-hidden="true" tabindex="-1"></a><span class="co"># Default format in which to save the figures. This can be specified </span></span>
+<span id="cb22-35"><a href="#cb22-35" aria-hidden="true" tabindex="-1"></a><span class="co"># individually as well.</span></span>
+<span id="cb22-36"><a href="#cb22-36" aria-hidden="true" tabindex="-1"></a><span class="fu">format</span><span class="kw">:</span><span class="at"> PNG</span></span>
+<span id="cb22-37"><a href="#cb22-37" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-38"><a href="#cb22-38" aria-hidden="true" tabindex="-1"></a><span class="co"># Default files/directories on which all figures depend. If any of these files/directories</span></span>
+<span id="cb22-39"><a href="#cb22-39" aria-hidden="true" tabindex="-1"></a><span class="co"># changes, all figures will be re-rendered.</span></span>
+<span id="cb22-40"><a href="#cb22-40" aria-hidden="true" tabindex="-1"></a><span class="co"># Dependencies specified in code blocks will be appended to this list.</span></span>
+<span id="cb22-41"><a href="#cb22-41" aria-hidden="true" tabindex="-1"></a><span class="fu">dependencies</span><span class="kw">:</span></span>
+<span id="cb22-42"><a href="#cb22-42" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="kw">-</span><span class="at"> file1.txt</span></span>
+<span id="cb22-43"><a href="#cb22-43" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="kw">-</span><span class="at"> file2.txt</span></span>
+<span id="cb22-44"><a href="#cb22-44" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-45"><a href="#cb22-45" aria-hidden="true" tabindex="-1"></a><span class="co"># Text format for the captions. Unfortunately, there is no way to detect</span></span>
+<span id="cb22-46"><a href="#cb22-46" aria-hidden="true" tabindex="-1"></a><span class="co"># this automatically. You can use the same notation as Pandoc&#39;s --from </span></span>
+<span id="cb22-47"><a href="#cb22-47" aria-hidden="true" tabindex="-1"></a><span class="co"># parameter, specified here: </span></span>
+<span id="cb22-48"><a href="#cb22-48" aria-hidden="true" tabindex="-1"></a><span class="co">#     https://pandoc.org/MANUAL.html#option--from</span></span>
+<span id="cb22-49"><a href="#cb22-49" aria-hidden="true" tabindex="-1"></a><span class="co"># Example: markdown, rst+raw_tex</span></span>
+<span id="cb22-50"><a href="#cb22-50" aria-hidden="true" tabindex="-1"></a><span class="fu">caption_format</span><span class="kw">:</span><span class="at"> markdown+tex_math_dollars</span></span>
+<span id="cb22-51"><a href="#cb22-51" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-52"><a href="#cb22-52" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-53"><a href="#cb22-53" aria-hidden="true" tabindex="-1"></a><span class="co"># Logging configuration</span></span>
+<span id="cb22-54"><a href="#cb22-54" aria-hidden="true" tabindex="-1"></a><span class="fu">logging</span><span class="kw">:</span></span>
+<span id="cb22-55"><a href="#cb22-55" aria-hidden="true" tabindex="-1"></a><span class="co">  # Possible verbosity values: debug, error, warning, info, silent</span></span>
+<span id="cb22-56"><a href="#cb22-56" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">verbosity</span><span class="kw">:</span><span class="at"> warning</span></span>
+<span id="cb22-57"><a href="#cb22-57" aria-hidden="true" tabindex="-1"></a><span class="co">  # If the filepath below is not present, then pandoc-plot will log to stderr</span></span>
+<span id="cb22-58"><a href="#cb22-58" aria-hidden="true" tabindex="-1"></a><span class="co">  # Otherwise, log messages will be appended to the filepath.</span></span>
+<span id="cb22-59"><a href="#cb22-59" aria-hidden="true" tabindex="-1"></a><span class="co">  # filepath: path/to/file.txt</span></span>
+<span id="cb22-60"><a href="#cb22-60" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-61"><a href="#cb22-61" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the Matplotlib toolkit</span></span>
+<span id="cb22-62"><a href="#cb22-62" aria-hidden="true" tabindex="-1"></a><span class="fu">matplotlib</span><span class="kw">:</span></span>
+<span id="cb22-63"><a href="#cb22-63" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: matplotlib.py</span></span>
+<span id="cb22-64"><a href="#cb22-64" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">tight_bbox</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>
+<span id="cb22-65"><a href="#cb22-65" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">transparent</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>
+<span id="cb22-66"><a href="#cb22-66" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> python</span></span>
+<span id="cb22-67"><a href="#cb22-67" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>
+<span id="cb22-68"><a href="#cb22-68" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-69"><a href="#cb22-69" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the MATLAB toolkit</span></span>
+<span id="cb22-70"><a href="#cb22-70" aria-hidden="true" tabindex="-1"></a><span class="fu">matlabplot</span><span class="kw">:</span></span>
+<span id="cb22-71"><a href="#cb22-71" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: matlab.m</span></span>
+<span id="cb22-72"><a href="#cb22-72" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> matlab</span></span>
+<span id="cb22-73"><a href="#cb22-73" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>
+<span id="cb22-74"><a href="#cb22-74" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-75"><a href="#cb22-75" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the Plotly/Python toolkit</span></span>
+<span id="cb22-76"><a href="#cb22-76" aria-hidden="true" tabindex="-1"></a><span class="fu">plotly_python</span><span class="kw">:</span></span>
+<span id="cb22-77"><a href="#cb22-77" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: plotly-python.py</span></span>
+<span id="cb22-78"><a href="#cb22-78" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> python</span></span>
+<span id="cb22-79"><a href="#cb22-79" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>
+<span id="cb22-80"><a href="#cb22-80" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-81"><a href="#cb22-81" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the Plotly/R toolkit</span></span>
+<span id="cb22-82"><a href="#cb22-82" aria-hidden="true" tabindex="-1"></a><span class="fu">plotly_r</span><span class="kw">:</span></span>
+<span id="cb22-83"><a href="#cb22-83" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: plotly-r.r</span></span>
+<span id="cb22-84"><a href="#cb22-84" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> Rscript</span></span>
+<span id="cb22-85"><a href="#cb22-85" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>
+<span id="cb22-86"><a href="#cb22-86" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-87"><a href="#cb22-87" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the Mathematica toolkit</span></span>
+<span id="cb22-88"><a href="#cb22-88" aria-hidden="true" tabindex="-1"></a><span class="fu">mathplot</span><span class="kw">:</span></span>
+<span id="cb22-89"><a href="#cb22-89" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: mathematica.m</span></span>
+<span id="cb22-90"><a href="#cb22-90" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> math</span></span>
+<span id="cb22-91"><a href="#cb22-91" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>
+<span id="cb22-92"><a href="#cb22-92" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-93"><a href="#cb22-93" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the GNU Octave toolkit</span></span>
+<span id="cb22-94"><a href="#cb22-94" aria-hidden="true" tabindex="-1"></a><span class="fu">octaveplot</span><span class="kw">:</span></span>
+<span id="cb22-95"><a href="#cb22-95" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: octave.m</span></span>
+<span id="cb22-96"><a href="#cb22-96" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> octave</span></span>
+<span id="cb22-97"><a href="#cb22-97" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>
+<span id="cb22-98"><a href="#cb22-98" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-99"><a href="#cb22-99" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the ggplot2 toolkit</span></span>
+<span id="cb22-100"><a href="#cb22-100" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot2</span><span class="kw">:</span></span>
+<span id="cb22-101"><a href="#cb22-101" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: ggplot2.r</span></span>
+<span id="cb22-102"><a href="#cb22-102" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> Rscript</span></span>
+<span id="cb22-103"><a href="#cb22-103" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>
+<span id="cb22-104"><a href="#cb22-104" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-105"><a href="#cb22-105" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the gnuplot toolkit</span></span>
+<span id="cb22-106"><a href="#cb22-106" aria-hidden="true" tabindex="-1"></a><span class="fu">gnuplot</span><span class="kw">:</span></span>
+<span id="cb22-107"><a href="#cb22-107" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: gnuplot.gp</span></span>
+<span id="cb22-108"><a href="#cb22-108" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> gnuplot</span></span>
+<span id="cb22-109"><a href="#cb22-109" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>
+<span id="cb22-110"><a href="#cb22-110" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-111"><a href="#cb22-111" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the graphviz toolkit</span></span>
+<span id="cb22-112"><a href="#cb22-112" aria-hidden="true" tabindex="-1"></a><span class="fu">graphviz</span><span class="kw">:</span></span>
+<span id="cb22-113"><a href="#cb22-113" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: graphviz.dot</span></span>
+<span id="cb22-114"><a href="#cb22-114" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> dot</span></span>
+<span id="cb22-115"><a href="#cb22-115" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>
+<span id="cb22-116"><a href="#cb22-116" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-117"><a href="#cb22-117" aria-hidden="true" tabindex="-1"></a><span class="fu">bokeh</span><span class="kw">:</span></span>
+<span id="cb22-118"><a href="#cb22-118" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: bokeh.py</span></span>
+<span id="cb22-119"><a href="#cb22-119" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> python</span></span>
+<span id="cb22-120"><a href="#cb22-120" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>
+<span id="cb22-121"><a href="#cb22-121" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-122"><a href="#cb22-122" aria-hidden="true" tabindex="-1"></a><span class="fu">plotsjl</span><span class="kw">:</span></span>
+<span id="cb22-123"><a href="#cb22-123" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: plotsjl.jl</span></span>
+<span id="cb22-124"><a href="#cb22-124" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> julia</span></span>
+<span id="cb22-125"><a href="#cb22-125" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span></span>
+<span id="cb22-126"><a href="#cb22-126" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb22-127"><a href="#cb22-127" aria-hidden="true" tabindex="-1"></a><span class="fu">plantuml</span><span class="kw">:</span></span>
+<span id="cb22-128"><a href="#cb22-128" aria-hidden="true" tabindex="-1"></a><span class="co">  # preamble: plantuml.txt</span></span>
+<span id="cb22-129"><a href="#cb22-129" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> java</span></span>
+<span id="cb22-130"><a href="#cb22-130" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span><span class="at"> -jar plantuml.jar</span></span>
+<span id="cb22-131"><a href="#cb22-131" aria-hidden="true" tabindex="-1"></a><span class="co">  # On Linux, if you have `plantuml.jar` as an executable, you can also</span></span>
+<span id="cb22-132"><a href="#cb22-132" aria-hidden="true" tabindex="-1"></a><span class="co">  # use the following configuration instead:</span></span>
+<span id="cb22-133"><a href="#cb22-133" aria-hidden="true" tabindex="-1"></a><span class="co">  # plantuml:</span></span>
+<span id="cb22-134"><a href="#cb22-134" aria-hidden="true" tabindex="-1"></a><span class="co">  #   executable: plantuml</span></span>
+<span id="cb22-135"><a href="#cb22-135" aria-hidden="true" tabindex="-1"></a><span class="co">  #   command_line_arguments:</span></span></code></pre></div>
+<p>A file like the above sets the <strong>default</strong> values; you can still override them in documents directly.</p>
+<p>The easiest way to specify configuration for <code>pandoc-plot</code> is to place a <code>.pandoc-plot.yml</code> file in the current working directory. You can also specify a configuration file in document metadata, under the <code>plot-configuration</code> key. For example, in Markdown:</p>
+<div class="sourceCode" id="cb23"><pre class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb23-1"><a href="#cb23-1" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>
+<span id="cb23-2"><a href="#cb23-2" aria-hidden="true" tabindex="-1"></a><span class="an">title:</span><span class="co"> My document</span></span>
+<span id="cb23-3"><a href="#cb23-3" aria-hidden="true" tabindex="-1"></a><span class="an">author:</span><span class="co"> John Doe</span></span>
+<span id="cb23-4"><a href="#cb23-4" aria-hidden="true" tabindex="-1"></a><span class="an">plot-configuration:</span><span class="co"> /path/to/file.yml</span></span>
+<span id="cb23-5"><a href="#cb23-5" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span></code></pre></div>
+<p>or on the command line, using the pandoc <code>-M/--metadata</code> flag:</p>
+<div class="sourceCode" id="cb24"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc</span> <span class="at">--filter</span> pandoc-plot <span class="at">-M</span> plot-configuration=/path/to/file.yml ...</span></code></pre></div>
+<p>The hierarchy of configuration files is as follows:</p>
+<ol type="1">
+<li>A configuration file specified in the metadata under the <code>plot-configuration</code> key;</li>
+<li>Otherwise, a file in the current working directory named <code>.pandoc-plot.yml</code>;</li>
+<li>Finally, the default configuration is used.</li>
+</ol>
+<h4 id="executables">Executables</h4>
+<p>The <code>executable</code> parameter for all toolkits can be either the executable name (if it is present on the PATH), or the full path to the executable.</p>
+<p>Examples:</p>
+<div class="sourceCode" id="cb25"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a><span class="fu">matplotlib</span><span class="kw">:</span></span>
+<span id="cb25-2"><a href="#cb25-2" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> python3</span></span></code></pre></div>
+<div class="sourceCode" id="cb26"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb26-1"><a href="#cb26-1" aria-hidden="true" tabindex="-1"></a><span class="fu">matlabplot</span><span class="kw">:</span></span>
+<span id="cb26-2"><a href="#cb26-2" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> </span><span class="st">&quot;C:\Program Files\Matlab\R2019b</span><span class="sc">\b</span><span class="st">in\matlab.exe&quot;</span></span></code></pre></div>
+<h4 id="command-line-arguments">Command-line arguments</h4>
+<p><em>New in version 1.0.2.0</em></p>
+<p>The <code>command_line_arguments</code> parameter available for all toolkits provides a way to customize the way interpreters are run. For example, if you want to run the <code>matplotlib</code> toolkit with all warnings shown:</p>
+<div class="sourceCode" id="cb27"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the Matplotlib toolkit</span></span>
+<span id="cb27-2"><a href="#cb27-2" aria-hidden="true" tabindex="-1"></a><span class="fu">matplotlib</span><span class="kw">:</span></span>
+<span id="cb27-3"><a href="#cb27-3" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> python</span></span>
+<span id="cb27-4"><a href="#cb27-4" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span><span class="at"> -Wa</span></span></code></pre></div>
+<p>Or if you want <code>julia</code> to use more than one thread:</p>
+<div class="sourceCode" id="cb28"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb28-1"><a href="#cb28-1" aria-hidden="true" tabindex="-1"></a><span class="co"># The possible parameters for the Matplotlib toolkit</span></span>
+<span id="cb28-2"><a href="#cb28-2" aria-hidden="true" tabindex="-1"></a><span class="fu">plotsjl</span><span class="kw">:</span></span>
+<span id="cb28-3"><a href="#cb28-3" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">executable</span><span class="kw">:</span><span class="at"> julia</span></span>
+<span id="cb28-4"><a href="#cb28-4" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">command_line_arguments</span><span class="kw">:</span><span class="at"> --threads auto</span></span></code></pre></div>
+<h4 id="toolkit-specific-options">Toolkit-specific options</h4>
+<h5 id="matplotlib">Matplotlib</h5>
+<ul>
+<li><code>tight_bbox</code> is a boolean that determines whether to use <code>bbox_inches=&quot;tight&quot;</code> or not when saving Matplotlib figures. For example, <code>tight_bbox: true</code>. See <a href="https://matplotlib.org/api/_as_gen/matplotlib.pyplot.savefig.html">here</a> for details.</li>
+<li><code>transparent</code> is a boolean that determines whether to make Matplotlib figure background transparent or not. This is useful, for example, for displaying a plot on top of a colored background on a web page. High-resolution figures are not affected. For example, <code>transparent: true</code>.</li>
+</ul>
+<h4 id="logging">Logging</h4>
+<p>If you are running <code>pandoc-plot</code> on a large document, you might want to turn on logging. You can do so via the configuration file as follows:</p>
+<div class="sourceCode" id="cb29"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb29-1"><a href="#cb29-1" aria-hidden="true" tabindex="-1"></a><span class="fu">logging</span><span class="kw">:</span></span>
+<span id="cb29-2"><a href="#cb29-2" aria-hidden="true" tabindex="-1"></a><span class="co">    # Possible verbosity values: debug, error, warning, info, silent</span></span>
+<span id="cb29-3"><a href="#cb29-3" aria-hidden="true" tabindex="-1"></a><span class="co">    # debug level shows all messages</span></span>
+<span id="cb29-4"><a href="#cb29-4" aria-hidden="true" tabindex="-1"></a><span class="co">    # error level shows all but debug messages, etc.</span></span>
+<span id="cb29-5"><a href="#cb29-5" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">verbosity</span><span class="kw">:</span><span class="at"> info</span></span>
+<span id="cb29-6"><a href="#cb29-6" aria-hidden="true" tabindex="-1"></a><span class="at">    </span></span>
+<span id="cb29-7"><a href="#cb29-7" aria-hidden="true" tabindex="-1"></a><span class="co">    # OPTIONAL: log to file</span></span>
+<span id="cb29-8"><a href="#cb29-8" aria-hidden="true" tabindex="-1"></a><span class="co">    # Remove line below to log to stderr</span></span>
+<span id="cb29-9"><a href="#cb29-9" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">filepath</span><span class="kw">:</span><span class="at"> log.txt</span></span></code></pre></div>
+<p>By default, <code>pandoc-plot</code> logs warnings and errors to the standard error stream only.</p>
+<h4 id="strict-mode">Strict mode</h4>
+<p><em>New in version 1.0.2.0</em></p>
+<p>By default, <code>pandoc-plot</code> leaves code blocks unchanged if a figure fails to be rendered. This might be the case if a plotting toolkit is not installed, or if running the code to render a figure returns an error. In <strong>strict mode</strong>, <code>pandoc-plot</code> will immediately halt if it encounters a problem. You can activate strict mode via configuration:</p>
+<div class="sourceCode" id="cb30"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb30-1"><a href="#cb30-1" aria-hidden="true" tabindex="-1"></a><span class="fu">strict</span><span class="kw">:</span><span class="at"> </span><span class="ch">true</span></span></code></pre></div>
+<p>Strict mode is ideal if you want to ensure that the figures are correctly rendered in the document.</p>
+<h3 id="other-commands">Other commands</h3>
+<h4 id="finding-installed-toolkits">Finding installed toolkits</h4>
+<p>You can determine which toolkits are available on your current machine using the <code>pandoc-plot toolkits</code> command. Here is the full help text:</p>
+<div class="sourceCode" id="cb31"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb31-1"><a href="#cb31-1" aria-hidden="true" tabindex="-1"></a><span class="ex">Usage:</span> pandoc-plot.EXE toolkits [--config PATH]</span>
+<span id="cb31-2"><a href="#cb31-2" aria-hidden="true" tabindex="-1"></a>  <span class="ex">Show</span> information on toolkits and exit.</span>
+<span id="cb31-3"><a href="#cb31-3" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb31-4"><a href="#cb31-4" aria-hidden="true" tabindex="-1"></a><span class="ex">Available</span> options:</span>
+<span id="cb31-5"><a href="#cb31-5" aria-hidden="true" tabindex="-1"></a>  <span class="ex">--config</span> PATH            Path to optional configuration file.</span>
+<span id="cb31-6"><a href="#cb31-6" aria-hidden="true" tabindex="-1"></a>  <span class="ex">-h,--help</span>                Show this help text</span></code></pre></div>
+<h4 id="cleaning-output">Cleaning output</h4>
+<p>Figures produced by <code>pandoc-plot</code> can be placed in a few different locations. You can set a default location in the <a href="#configuration">Configuration</a>, but you can also re-direct specific figures in other directories if you use the <code>directory=...</code> argument in code blocks. These figures will build up over time. You can use the <code>clean</code> command to scan documents and delete the associated <code>pandoc-plot</code> output files. For example, to delete the figures generated from the <code>input.md</code> file:</p>
+<div class="sourceCode" id="cb32"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb32-1"><a href="#cb32-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc-plot</span> clean input.md</span></code></pre></div>
+<p>This sill remove all directories where a figure <em>could</em> have been placed. <strong>WARNING</strong>: all files will be removed.</p>
+<p>Here is the full help text for the <code>clean</code> command:</p>
+<div class="sourceCode" id="cb33"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb33-1"><a href="#cb33-1" aria-hidden="true" tabindex="-1"></a><span class="ex">Usage:</span> pandoc-plot.EXE clean [--config PATH] FILE</span>
+<span id="cb33-2"><a href="#cb33-2" aria-hidden="true" tabindex="-1"></a>  <span class="ex">Clean</span> output directories where figures from FILE and log files might be</span>
+<span id="cb33-3"><a href="#cb33-3" aria-hidden="true" tabindex="-1"></a>  <span class="ex">stored.</span> WARNING: All files in those directories will be deleted.</span>
+<span id="cb33-4"><a href="#cb33-4" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb33-5"><a href="#cb33-5" aria-hidden="true" tabindex="-1"></a><span class="ex">Available</span> options:</span>
+<span id="cb33-6"><a href="#cb33-6" aria-hidden="true" tabindex="-1"></a>  <span class="ex">--config</span> PATH            Path to optional configuration file.</span>
+<span id="cb33-7"><a href="#cb33-7" aria-hidden="true" tabindex="-1"></a>  <span class="ex">-h,--help</span>                Show this help text</span></code></pre></div>
+<h4 id="configuration-template">Configuration template</h4>
+<p>Because <code>pandoc-plot</code> supports a few toolkits, there are a lot of configuration options. Don’t start from scratch! The <code>write-example-config</code> command will create a file for you, which you can then modify:</p>
+<div class="sourceCode" id="cb34"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb34-1"><a href="#cb34-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc-plot</span> write-example-config</span></code></pre></div>
+<p>You will need to re-name the file to <code>.pandoc-ploy.yml</code> to be able to use it, so don’t worry about overwriting your own configuration.</p>
+<p>Here is the full help text for the <code>write-example-config</code> command:</p>
+<div class="sourceCode" id="cb35"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb35-1"><a href="#cb35-1" aria-hidden="true" tabindex="-1"></a><span class="ex">Usage:</span> pandoc-plot.EXE write-example-config [--path FILE]</span>
+<span id="cb35-2"><a href="#cb35-2" aria-hidden="true" tabindex="-1"></a>  <span class="ex">Write</span> example configuration to a file and exit.</span>
+<span id="cb35-3"><a href="#cb35-3" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb35-4"><a href="#cb35-4" aria-hidden="true" tabindex="-1"></a><span class="ex">Available</span> options:</span>
+<span id="cb35-5"><a href="#cb35-5" aria-hidden="true" tabindex="-1"></a>  <span class="ex">--path</span> FILE              Target location of the configuration file. Default is</span>
+<span id="cb35-6"><a href="#cb35-6" aria-hidden="true" tabindex="-1"></a>                           <span class="st">&quot;.example-pandoc-plot.yml&quot;</span></span>
+<span id="cb35-7"><a href="#cb35-7" aria-hidden="true" tabindex="-1"></a>  <span class="ex">-h,--help</span>                Show this help text</span></code></pre></div>
+<h3 id="as-a-haskell-library">As a Haskell library</h3>
+<p>To include the functionality of <code>pandoc-plot</code> in a Haskell package, you can use the <code>make</code> function (for single blocks) or <code>plotFilter</code> function (for entire documents). <a href="https://hackage.haskell.org/package/pandoc-plot">Take a look at the documentation on Hackage</a>.</p>
+<h4 id="usage-with-hakyll">Usage with Hakyll</h4>
+<p>In case you want to use the filter with your own Hakyll setup, you can use a transform function that works on entire documents:</p>
+<div class="sourceCode" id="cb36"><pre class="sourceCode haskell"><code class="sourceCode haskell"><span id="cb36-1"><a href="#cb36-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="dt">Text.Pandoc.Filter.Plot</span> (plotFilter, defaultConfiguration)</span>
+<span id="cb36-2"><a href="#cb36-2" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="dt">Text.Pandoc.Definition</span> (<span class="dt">Pandoc</span>, <span class="dt">Format</span>(..)) <span class="co">-- from pandoc-types</span></span>
+<span id="cb36-3"><a href="#cb36-3" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="dt">Hakyll</span></span>
+<span id="cb36-4"><a href="#cb36-4" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb36-5"><a href="#cb36-5" aria-hidden="true" tabindex="-1"></a><span class="ot">plotFilter&#39; ::</span> <span class="dt">Pandoc</span> <span class="ot">-&gt;</span> <span class="dt">IO</span> <span class="dt">Pandoc</span></span>
+<span id="cb36-6"><a href="#cb36-6" aria-hidden="true" tabindex="-1"></a>plotFilter&#39; <span class="ot">=</span> </span>
+<span id="cb36-7"><a href="#cb36-7" aria-hidden="true" tabindex="-1"></a>  <span class="co">-- Notify pandoc-plot that the final conversion will be to HTML</span></span>
+<span id="cb36-8"><a href="#cb36-8" aria-hidden="true" tabindex="-1"></a>  <span class="co">-- This helps give better error messages and adjust default values</span></span>
+<span id="cb36-9"><a href="#cb36-9" aria-hidden="true" tabindex="-1"></a>  plotFilter defaultConfiguration (<span class="dt">Just</span> <span class="op">$</span> <span class="dt">Format</span> <span class="st">&quot;html5&quot;</span>) </span>
+<span id="cb36-10"><a href="#cb36-10" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb36-11"><a href="#cb36-11" aria-hidden="true" tabindex="-1"></a><span class="co">-- Unsafe compiler is required because of the interaction</span></span>
+<span id="cb36-12"><a href="#cb36-12" aria-hidden="true" tabindex="-1"></a><span class="co">-- in IO (i.e. running an external script).</span></span>
+<span id="cb36-13"><a href="#cb36-13" aria-hidden="true" tabindex="-1"></a><span class="ot">makePlotPandocCompiler ::</span> <span class="dt">Compiler</span> (<span class="dt">Item</span> <span class="dt">String</span>)</span>
+<span id="cb36-14"><a href="#cb36-14" aria-hidden="true" tabindex="-1"></a>makePlotPandocCompiler <span class="ot">=</span> </span>
+<span id="cb36-15"><a href="#cb36-15" aria-hidden="true" tabindex="-1"></a>  pandocCompilerWithTransformM</span>
+<span id="cb36-16"><a href="#cb36-16" aria-hidden="true" tabindex="-1"></a>    defaultHakyllReaderOptions</span>
+<span id="cb36-17"><a href="#cb36-17" aria-hidden="true" tabindex="-1"></a>    defaultHakyllWriterOptions</span>
+<span id="cb36-18"><a href="#cb36-18" aria-hidden="true" tabindex="-1"></a>    (unsafeCompiler <span class="op">.</span> plotFilter&#39;)</span></code></pre></div>
+<h2 id="warning">Warning</h2>
+<p>Do not run this filter on unknown documents. There is nothing in <code>pandoc-plot</code> that can stop a script from performing <strong>evil actions</strong>.</p>
+</body>
+</html>

@@ -1,148 +1,148 @@--# This is an example configuration. Everything in this file is optional.-# Please refer to the documentation to know about the parameters herein.-#-# The `executable` parameter for all toolkits can be either the-# executable name (if it is present on the PATH), or-# the full path to the executable.-# E.g.:-#  executable: python3-#  executable: "C:\Python37\Scripts\python.exe"--# The following parameters affect all toolkits-# Directory where to save the plots. The path can be relative to pandoc-plot's-# current working directory, or absolute.-directory: plots/--# Whether or not to include a link to the source script in the caption. -# Particularly useful for HTML output.-source: false--# When `strict: false`, pandoc-plot will leave code blocks untouched if a plot-# could not be generated. This could happen if, for example, a toolkit is not-# installed. If you want pandoc-plot to fail instead, use `strict: true`.-strict: false--# Text label for links to source code.-# You can change this label if you are writing a document in a non-English language. -# This only matters if `source` is set to `true`.-source_label: Source code--# Default density of figures in dots per inches (DPI). -# This can be changed in the document specifically as well.-dpi: 80--# Default format in which to save the figures. This can be specified -# individually as well.-format: PNG--# Default files/directories on which all figures depend. If any of these files/directories-# changes, all figures will be re-rendered.-# Dependencies specified in code blocks will be appended to this list.-dependencies:-  - file1.txt-  - file2.txt--# Text format for the captions. Unfortunately, there is no way to detect-# this automatically. You can use the same notation as Pandoc's --from -# parameter, specified here: -#     https://pandoc.org/MANUAL.html#option--from-# Example: markdown, rst+raw_tex-caption_format: markdown+tex_math_dollars---# Logging configuration-logging:-  # Possible verbosity values: debug, error, warning, info, silent-  verbosity: warning-  # If the filepath below is not present, then pandoc-plot will log to stderr-  # Otherwise, log messages will be appended to the filepath.-  # filepath: path/to/file.txt--# The possible parameters for the Matplotlib toolkit-matplotlib:-  # preamble: matplotlib.py-  tight_bbox: false-  transparent: false-  executable: python-  command_line_arguments:--# The possible parameters for the MATLAB toolkit-matlabplot:-  # preamble: matlab.m-  executable: matlab-  command_line_arguments:--# The possible parameters for the Plotly/Python toolkit-plotly_python:-  # preamble: plotly-python.py-  executable: python-  command_line_arguments:--# The possible parameters for the Plotly/R toolkit-plotly_r:-  # preamble: plotly-r.r-  executable: Rscript-  command_line_arguments:--# The possible parameters for the Mathematica toolkit-mathplot:-  # preamble: mathematica.m-  executable: math-  command_line_arguments:--# The possible parameters for the GNU Octave toolkit-octaveplot:-  # preamble: octave.m-  executable: octave-  command_line_arguments:--# The possible parameters for the ggplot2 toolkit-ggplot2:-  # preamble: ggplot2.r-  executable: Rscript-  command_line_arguments:--# The possible parameters for the gnuplot toolkit-gnuplot:-  # preamble: gnuplot.gp-  executable: gnuplot-  command_line_arguments:--# The possible parameters for the graphviz toolkit-graphviz:-  # preamble: graphviz.dot-  executable: dot-  command_line_arguments:--# The possible parameters for the Bokeh toolkit using Python-bokeh:-  # preamble: bokeh.py-  executable: python-  command_line_arguments:--# The possible parameters for the Plots.jl toolkit using Julia-plotsjl:-  # preamble: plotsjl.jl-  executable: julia-  command_line_arguments:--# The possible parameters for the PlantUML toolkit-plantuml:-  # preamble: plantuml.txt-  executable: java-  command_line_arguments: -jar plantuml.jar-  # On Linux, if you have `plantuml.jar` as an executable, you can also-  # use the following configuration instead:-  # plantuml:-  #   executable: plantuml-  #   command_line_arguments:--sageplot:-  # preamble: sageplot.sage-  executable: sage-  command_line_arguments:--d2:-  executable: d2-  command_line_arguments:+
+# This is an example configuration. Everything in this file is optional.
+# Please refer to the documentation to know about the parameters herein.
+#
+# The `executable` parameter for all toolkits can be either the
+# executable name (if it is present on the PATH), or
+# the full path to the executable.
+# E.g.:
+#  executable: python3
+#  executable: "C:\Python37\Scripts\python.exe"
+
+# The following parameters affect all toolkits
+# Directory where to save the plots. The path can be relative to pandoc-plot's
+# current working directory, or absolute.
+directory: plots/
+
+# Whether or not to include a link to the source script in the caption. 
+# Particularly useful for HTML output.
+source: false
+
+# When `strict: false`, pandoc-plot will leave code blocks untouched if a plot
+# could not be generated. This could happen if, for example, a toolkit is not
+# installed. If you want pandoc-plot to fail instead, use `strict: true`.
+strict: false
+
+# Text label for links to source code.
+# You can change this label if you are writing a document in a non-English language. 
+# This only matters if `source` is set to `true`.
+source_label: Source code
+
+# Default density of figures in dots per inches (DPI). 
+# This can be changed in the document specifically as well.
+dpi: 80
+
+# Default format in which to save the figures. This can be specified 
+# individually as well.
+format: PNG
+
+# Default files/directories on which all figures depend. If any of these files/directories
+# changes, all figures will be re-rendered.
+# Dependencies specified in code blocks will be appended to this list.
+dependencies:
+  - file1.txt
+  - file2.txt
+
+# Text format for the captions. Unfortunately, there is no way to detect
+# this automatically. You can use the same notation as Pandoc's --from 
+# parameter, specified here: 
+#     https://pandoc.org/MANUAL.html#option--from
+# Example: markdown, rst+raw_tex
+caption_format: markdown+tex_math_dollars
+
+
+# Logging configuration
+logging:
+  # Possible verbosity values: debug, error, warning, info, silent
+  verbosity: warning
+  # If the filepath below is not present, then pandoc-plot will log to stderr
+  # Otherwise, log messages will be appended to the filepath.
+  # filepath: path/to/file.txt
+
+# The possible parameters for the Matplotlib toolkit
+matplotlib:
+  # preamble: matplotlib.py
+  tight_bbox: false
+  transparent: false
+  executable: python
+  command_line_arguments:
+
+# The possible parameters for the MATLAB toolkit
+matlabplot:
+  # preamble: matlab.m
+  executable: matlab
+  command_line_arguments:
+
+# The possible parameters for the Plotly/Python toolkit
+plotly_python:
+  # preamble: plotly-python.py
+  executable: python
+  command_line_arguments:
+
+# The possible parameters for the Plotly/R toolkit
+plotly_r:
+  # preamble: plotly-r.r
+  executable: Rscript
+  command_line_arguments:
+
+# The possible parameters for the Mathematica toolkit
+mathplot:
+  # preamble: mathematica.m
+  executable: math
+  command_line_arguments:
+
+# The possible parameters for the GNU Octave toolkit
+octaveplot:
+  # preamble: octave.m
+  executable: octave
+  command_line_arguments:
+
+# The possible parameters for the ggplot2 toolkit
+ggplot2:
+  # preamble: ggplot2.r
+  executable: Rscript
+  command_line_arguments:
+
+# The possible parameters for the gnuplot toolkit
+gnuplot:
+  # preamble: gnuplot.gp
+  executable: gnuplot
+  command_line_arguments:
+
+# The possible parameters for the graphviz toolkit
+graphviz:
+  # preamble: graphviz.dot
+  executable: dot
+  command_line_arguments:
+
+# The possible parameters for the Bokeh toolkit using Python
+bokeh:
+  # preamble: bokeh.py
+  executable: python
+  command_line_arguments:
+
+# The possible parameters for the Plots.jl toolkit using Julia
+plotsjl:
+  # preamble: plotsjl.jl
+  executable: julia
+  command_line_arguments:
+
+# The possible parameters for the PlantUML toolkit
+plantuml:
+  # preamble: plantuml.txt
+  executable: java
+  command_line_arguments: -jar plantuml.jar
+  # On Linux, if you have `plantuml.jar` as an executable, you can also
+  # use the following configuration instead:
+  # plantuml:
+  #   executable: plantuml
+  #   command_line_arguments:
+
+sageplot:
+  # preamble: sageplot.sage
+  executable: sage
+  command_line_arguments:
+
+d2:
+  executable: d2
+  command_line_arguments:

@@ -1,30 +1,30 @@-{-# LANGUAGE TemplateHaskellQuotes #-}--module ExampleConfig (embedExampleConfig) where--import Data.Functor ((<&>))-import Data.String (IsString (fromString))-import Data.Text (unpack)-import qualified Data.Text.IO as TIO-import Language.Haskell.TH.Syntax-  ( Exp (AppE, LitE, VarE),-    Lit (StringL),-    Q,-    Quasi (qAddDependentFile),-    runIO,-  )--docFile :: FilePath-docFile = "example-config.yml"--readDocFile :: IO String-readDocFile = TIO.readFile docFile <&> unpack--embedExampleConfig :: Q Exp-embedExampleConfig = do-  qAddDependentFile docFile-  s <- runIO readDocFile-  strToExp s-  where-    strToExp :: String -> Q Exp-    strToExp s = return $ VarE 'fromString `AppE` LitE (StringL s)+{-# LANGUAGE TemplateHaskellQuotes #-}
+
+module ExampleConfig (embedExampleConfig) where
+
+import Data.Functor ((<&>))
+import Data.String (IsString (fromString))
+import Data.Text (unpack)
+import qualified Data.Text.IO as TIO
+import Language.Haskell.TH.Syntax
+  ( Exp (AppE, LitE, VarE),
+    Lit (StringL),
+    Q,
+    Quasi (qAddDependentFile),
+    runIO,
+  )
+
+docFile :: FilePath
+docFile = "example-config.yml"
+
+readDocFile :: IO String
+readDocFile = TIO.readFile docFile <&> unpack
+
+embedExampleConfig :: Q Exp
+embedExampleConfig = do
+  qAddDependentFile docFile
+  s <- runIO readDocFile
+  strToExp s
+  where
+    strToExp :: String -> Q Exp
+    strToExp s = return $ VarE 'fromString `AppE` LitE (StringL s)

@@ -1,326 +1,326 @@-{-# LANGUAGE ApplicativeDo #-}-{-# LANGUAGE CPP #-}-{-# LANGUAGE LambdaCase #-}-{-# LANGUAGE OverloadedStrings #-}-{-# LANGUAGE RecordWildCards #-}-{-# LANGUAGE TemplateHaskell #-}--module Main where--import Control.Monad (join, msum, void, when)-import Data.List (intersperse, (\\))-import Data.Text (unpack)-import qualified Data.Text.IO as TIO-import Data.Version (parseVersion, showVersion)-import qualified Data.Version as V-import Development.GitRev (gitHash)-import ExampleConfig (embedExampleConfig)-import GHC.IO.Encoding (setLocaleEncoding, utf8)-import ManPage (embedManualHtml)-import OpenFile (openFile)-import Options.Applicative-  ( Alternative ((<|>)),-    Parser,-    command,-    execParser,-    flag,-    footerDoc,-    fullDesc,-    header,-    help,-    helper,-    info,-    long,-    metavar,-    optional,-    progDesc,-    short,-    strArgument,-    strOption,-    subparser,-    value,-    (<**>),-  )-import qualified Options.Applicative.Help.Pretty as P-import System.Directory (doesFileExist, getTemporaryDirectory)-import System.Environment (lookupEnv)-import System.FilePath ((</>))-import System.IO (hPutStrLn, stderr)-import Text.Pandoc (pandocVersion)-import Text.Pandoc.Definition (pandocTypesVersion)-import Text.Pandoc.Filter.Plot-  ( Configuration (..),-    availableToolkits,-    configuration,-    defaultConfiguration,-    pandocPlotVersion,-    plotFilter,-  )-import Text.Pandoc.Filter.Plot.Internal-  ( cleanOutputDirs,-    cls,-    configurationPathMeta,-    executable,-    pathToExe,-    readDoc,-    runPlotM,-    supportedSaveFormats,-    toolkits,-  )-import Text.Pandoc.JSON (toJSONFilter)-import Text.ParserCombinators.ReadP (readP_to_S)---- The difference between commands and flags is that commands require knowledge of--- the configuration, while flags only display static information.---- Please note that for some reason, makeVersion [2, 11, 0, 0] > makeVersion [2, 11]-minimumPandocVersion :: V.Version-minimumPandocVersion = V.makeVersion [2, 11]--data Command-  = Clean (Maybe FilePath) FilePath-  | WriteConfig FilePath-  | Toolkits (Maybe FilePath)--data Flag-  = Version-  | FullVersion-  | Manual-  deriving (Eq)--main :: IO ()-main = do-  setLocaleEncoding utf8-  join $ execParser opts-  where-    opts =-      info-        (optparse <**> helper)-        ( fullDesc-            <> progDesc-              ( unlines-                  [ "This pandoc filter generates plots from code blocks using a multitude of ",-                    "possible renderers. This allows to keep documentation and figures in",-                    "perfect synchronicity."-                  ]-              )-            <> header (mconcat ["pandoc-plot ", V.showVersion pandocPlotVersion, " - generate figures directly in documents"])-            <> footerDoc-              ( Just $-                  P.vsep-                    [ "More information can be found via the manual (pandoc-plot --manual) or the",-                      "repository README, located at https://github.com/LaurentRDC/pandoc-plot"-                    ]-              )-        )--    optparse = do-      flag_ <- flagParser-      command_ <- commandParser-      -- The extra optional input below only serves to show-      -- to the user that the last argument is the AST from pandoc-      -- The parsed input is never used-      input <- optional $ strArgument (metavar "AST")-      return $ go flag_ command_ input--    go :: Maybe Flag -> Maybe Command -> Maybe String -> IO ()-    go (Just Version) _ _ = putStrLn (V.showVersion pandocPlotVersion)-    go (Just FullVersion) _ _ = showFullVersion-    go (Just Manual) _ _ = showManPage-    go _ (Just (Toolkits mfp)) _ = showAvailableToolkits mfp-    go _ (Just (Clean mfp fp)) _ = clean mfp fp-    go _ (Just (WriteConfig fp)) _ = writeFile fp $(embedExampleConfig)-    go Nothing Nothing _ = toJSONFilterWithConfig--flagParser :: Parser (Maybe Flag)-flagParser = versionP <|> fullVersionP <|> manualP-  where-    versionP =-      flag-        Nothing-        (Just Version)-        ( mconcat-            [ long "version",-              short 'v',-              help "Show version number and exit."-            ]-        )--    fullVersionP =-      flag-        Nothing-        (Just FullVersion)-        ( mconcat-            [ long "full-version",-              help "Show full version information and exit."-            ]-        )--    manualP =-      flag-        Nothing-        (Just Manual)-        ( mconcat-            [ long "manual",-              short 'm',-              help "Open the manual page in the default web browser and exit."-            ]-        )--commandParser :: Parser (Maybe Command)-commandParser =-  optional $-    subparser $-      mconcat-        [ command-            "toolkits"-            ( info (toolkitsP <**> helper) (progDesc "Show information on toolkits and exit.")-            ),-          command-            "clean"-            ( info-                (cleanP <**> helper)-                ( progDesc-                    ( unlines-                        [ "Clean output directories where figures from FILE and log files might be stored.",-                          "WARNING: All files in those directories will be deleted."-                        ]-                    )-                )-            ),-          command-            "write-example-config"-            ( info (writeConfigP <**> helper) (progDesc "Write example configuration to a file and exit.")-            )-        ]-  where-    configP = optional $ strOption (mconcat [long "config", metavar "PATH", help "Path to optional configuration file."])-    toolkitsP = Toolkits <$> configP-    cleanP = Clean <$> configP <*> strArgument (metavar "FILE")-    writeConfigP =-      WriteConfig-        <$> strOption-          ( mconcat-              [ long "path",-                metavar "FILE",-                value ".example-pandoc-plot.yml",-                help "Target location of the configuration file. Default is \".example-pandoc-plot.yml\""-              ]-          )---- | Determine configuration and run filter.------ Priority for configuration:------     (1) Loaded from filepath stored in document metadata, under the key @plot-configuration@;------     (2) Loaded from file @.pandoc-plot.yml@ in current work directory;------     (3) Default configuration-toJSONFilterWithConfig :: IO ()-toJSONFilterWithConfig = do-  upToDatePandoc <- checkRuntimePandocVersion-  when upToDatePandoc $-    toJSONFilter $ \mfmt doc -> do-      c <- maybe localConfig configuration (configurationPathMeta doc)-      plotFilter c mfmt doc---- | Check that the runtime version of Pandoc is at least 2.11. The return value--- indicates whether the Pandoc version is new enough or not.-checkRuntimePandocVersion :: IO Bool-checkRuntimePandocVersion = do-  -- Pandoc runs filters in an environment with two variables:-  -- PANDOV_VERSION and PANDOC_READER_OPTS-  -- We can use the former to ensure that people are not-  -- using an old version of pandoc-  pandocV <- lookupEnv "PANDOC_VERSION"-  case pandocV >>= readVersion of-    Nothing -> return True-    Just v ->-      if v < minimumPandocVersion-        then do-          hPutStrLn stderr $-            mconcat-              [ "ERROR (pandoc-plot) The pandoc-plot filter only ",-                "supports Pandoc 2.11 and newer. ",-                "but you are using Pandoc ",-                showVersion v-              ]-          return False-        else return True-  where-    readVersion = fmap fst . lastMaybe . readP_to_S parseVersion-    lastMaybe xs = if length xs > 1 then Just (last xs) else Nothing---- | Load configuration from local file @.pandoc-plot.yml@.--- If the file does not exist, the default configuration will be used.-localConfig :: IO Configuration-localConfig = do-  configExists <- doesFileExist ".pandoc-plot.yml"-  if configExists-    then configuration ".pandoc-plot.yml"-    else return defaultConfiguration--showFullVersion :: IO ()-showFullVersion = do-  putStrLn $ "pandoc-plot " <> V.showVersion pandocPlotVersion-  putStrLn $ "Git revision " <> $gitHash-  putStrLn $-    mconcat-      [ "Compiled with pandoc ",-        V.showVersion pandocVersion,-        " and pandoc-types ",-        V.showVersion pandocTypesVersion,-        " using GHC ",-        TOOL_VERSION_ghc -- Constant defined by CPP-      ]--showAvailableToolkits :: Maybe FilePath -> IO ()-showAvailableToolkits mfp = do-  c <- maybe localConfig configuration mfp--  putStrLn "\nAVAILABLE TOOLKITS\n"-  available <- availableToolkits c-  mapM_ (availToolkitInfo c) available-  putStrLn "\nUNAVAILABLE TOOLKITS\n"-  -- We don't use unavailableToolkits because this would force-  -- more IO actions-  let unavailable = toolkits \\ available-  mapM_ (unavailToolkitInfo c) unavailable-  where-    toolkitInfo avail conf tk = do-      putStrLn $ "Toolkit: " <> show tk-      when avail $ do-        exe <- runPlotM Nothing conf $ executable tk-        putStrLn $ "    Executable: " <> pathToExe exe-      putStrLn $ "    Code block trigger: " <> (unpack . cls $ tk)-      putStrLn $ "    Supported save formats: " <> (mconcat . intersperse ", " . fmap show $ supportedSaveFormats tk)-      putStrLn mempty-    availToolkitInfo = toolkitInfo True-    unavailToolkitInfo = toolkitInfo False---- | Clean output directories associated with a file------ Priority for configuration are the same as @toJSONFilterWithConfig@.-clean ::-  Maybe FilePath -> -- Use configuration file?-  FilePath -> -- Document to clean-  IO ()-clean mfp fp = do-  doc <- readDoc fp-  -- Note the priority for configuration:-  --   (1) path of argument --config-  --   (2) document metadata-  --   (3) local .pandoc-plot.yml-  --   (4) default config-  conf <- maybe localConfig configuration $ firstJusts [configurationPathMeta doc, mfp]-  void (cleanOutputDirs conf doc)-  where-    firstJusts :: [Maybe a] -> Maybe a-    firstJusts = msum--showManPage :: IO ()-showManPage = do-  manualPath <- (</> "pandoc-plot-manual.html") <$> getTemporaryDirectory-  TIO.writeFile manualPath $(embedManualHtml)-  openFile ("file:///" <> manualPath)+{-# LANGUAGE ApplicativeDo #-}
+{-# LANGUAGE CPP #-}
+{-# LANGUAGE LambdaCase #-}
+{-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE RecordWildCards #-}
+{-# LANGUAGE TemplateHaskell #-}
+
+module Main where
+
+import Control.Monad (join, msum, void, when)
+import Data.List (intersperse, (\\))
+import Data.Text (unpack)
+import qualified Data.Text.IO as TIO
+import Data.Version (parseVersion, showVersion)
+import qualified Data.Version as V
+import Development.GitRev (gitHash)
+import ExampleConfig (embedExampleConfig)
+import GHC.IO.Encoding (setLocaleEncoding, utf8)
+import ManPage (embedManualHtml)
+import OpenFile (openFile)
+import Options.Applicative
+  ( Alternative ((<|>)),
+    Parser,
+    command,
+    execParser,
+    flag,
+    footerDoc,
+    fullDesc,
+    header,
+    help,
+    helper,
+    info,
+    long,
+    metavar,
+    optional,
+    progDesc,
+    short,
+    strArgument,
+    strOption,
+    subparser,
+    value,
+    (<**>),
+  )
+import qualified Options.Applicative.Help.Pretty as P
+import System.Directory (doesFileExist, getTemporaryDirectory)
+import System.Environment (lookupEnv)
+import System.FilePath ((</>))
+import System.IO (hPutStrLn, stderr)
+import Text.Pandoc (pandocVersion)
+import Text.Pandoc.Definition (pandocTypesVersion)
+import Text.Pandoc.Filter.Plot
+  ( Configuration (..),
+    availableToolkits,
+    configuration,
+    defaultConfiguration,
+    pandocPlotVersion,
+    plotFilter,
+  )
+import Text.Pandoc.Filter.Plot.Internal
+  ( cleanOutputDirs,
+    cls,
+    configurationPathMeta,
+    executable,
+    pathToExe,
+    readDoc,
+    runPlotM,
+    supportedSaveFormats,
+    toolkits,
+  )
+import Text.Pandoc.JSON (toJSONFilter)
+import Text.ParserCombinators.ReadP (readP_to_S)
+
+-- The difference between commands and flags is that commands require knowledge of
+-- the configuration, while flags only display static information.
+
+-- Please note that for some reason, makeVersion [2, 11, 0, 0] > makeVersion [2, 11]
+minimumPandocVersion :: V.Version
+minimumPandocVersion = V.makeVersion [2, 11]
+
+data Command
+  = Clean (Maybe FilePath) FilePath
+  | WriteConfig FilePath
+  | Toolkits (Maybe FilePath)
+
+data Flag
+  = Version
+  | FullVersion
+  | Manual
+  deriving (Eq)
+
+main :: IO ()
+main = do
+  setLocaleEncoding utf8
+  join $ execParser opts
+  where
+    opts =
+      info
+        (optparse <**> helper)
+        ( fullDesc
+            <> progDesc
+              ( unlines
+                  [ "This pandoc filter generates plots from code blocks using a multitude of ",
+                    "possible renderers. This allows to keep documentation and figures in",
+                    "perfect synchronicity."
+                  ]
+              )
+            <> header (mconcat ["pandoc-plot ", V.showVersion pandocPlotVersion, " - generate figures directly in documents"])
+            <> footerDoc
+              ( Just $
+                  P.vsep
+                    [ "More information can be found via the manual (pandoc-plot --manual) or the",
+                      "repository README, located at https://github.com/LaurentRDC/pandoc-plot"
+                    ]
+              )
+        )
+
+    optparse = do
+      flag_ <- flagParser
+      command_ <- commandParser
+      -- The extra optional input below only serves to show
+      -- to the user that the last argument is the AST from pandoc
+      -- The parsed input is never used
+      input <- optional $ strArgument (metavar "AST")
+      return $ go flag_ command_ input
+
+    go :: Maybe Flag -> Maybe Command -> Maybe String -> IO ()
+    go (Just Version) _ _ = putStrLn (V.showVersion pandocPlotVersion)
+    go (Just FullVersion) _ _ = showFullVersion
+    go (Just Manual) _ _ = showManPage
+    go _ (Just (Toolkits mfp)) _ = showAvailableToolkits mfp
+    go _ (Just (Clean mfp fp)) _ = clean mfp fp
+    go _ (Just (WriteConfig fp)) _ = writeFile fp $(embedExampleConfig)
+    go Nothing Nothing _ = toJSONFilterWithConfig
+
+flagParser :: Parser (Maybe Flag)
+flagParser = versionP <|> fullVersionP <|> manualP
+  where
+    versionP =
+      flag
+        Nothing
+        (Just Version)
+        ( mconcat
+            [ long "version",
+              short 'v',
+              help "Show version number and exit."
+            ]
+        )
+
+    fullVersionP =
+      flag
+        Nothing
+        (Just FullVersion)
+        ( mconcat
+            [ long "full-version",
+              help "Show full version information and exit."
+            ]
+        )
+
+    manualP =
+      flag
+        Nothing
+        (Just Manual)
+        ( mconcat
+            [ long "manual",
+              short 'm',
+              help "Open the manual page in the default web browser and exit."
+            ]
+        )
+
+commandParser :: Parser (Maybe Command)
+commandParser =
+  optional $
+    subparser $
+      mconcat
+        [ command
+            "toolkits"
+            ( info (toolkitsP <**> helper) (progDesc "Show information on toolkits and exit.")
+            ),
+          command
+            "clean"
+            ( info
+                (cleanP <**> helper)
+                ( progDesc
+                    ( unlines
+                        [ "Clean output directories where figures from FILE and log files might be stored.",
+                          "WARNING: All files in those directories will be deleted."
+                        ]
+                    )
+                )
+            ),
+          command
+            "write-example-config"
+            ( info (writeConfigP <**> helper) (progDesc "Write example configuration to a file and exit.")
+            )
+        ]
+  where
+    configP = optional $ strOption (mconcat [long "config", metavar "PATH", help "Path to optional configuration file."])
+    toolkitsP = Toolkits <$> configP
+    cleanP = Clean <$> configP <*> strArgument (metavar "FILE")
+    writeConfigP =
+      WriteConfig
+        <$> strOption
+          ( mconcat
+              [ long "path",
+                metavar "FILE",
+                value ".example-pandoc-plot.yml",
+                help "Target location of the configuration file. Default is \".example-pandoc-plot.yml\""
+              ]
+          )
+
+-- | Determine configuration and run filter.
+--
+-- Priority for configuration:
+--
+--     (1) Loaded from filepath stored in document metadata, under the key @plot-configuration@;
+--
+--     (2) Loaded from file @.pandoc-plot.yml@ in current work directory;
+--
+--     (3) Default configuration
+toJSONFilterWithConfig :: IO ()
+toJSONFilterWithConfig = do
+  upToDatePandoc <- checkRuntimePandocVersion
+  when upToDatePandoc $
+    toJSONFilter $ \mfmt doc -> do
+      c <- maybe localConfig configuration (configurationPathMeta doc)
+      plotFilter c mfmt doc
+
+-- | Check that the runtime version of Pandoc is at least 2.11. The return value
+-- indicates whether the Pandoc version is new enough or not.
+checkRuntimePandocVersion :: IO Bool
+checkRuntimePandocVersion = do
+  -- Pandoc runs filters in an environment with two variables:
+  -- PANDOV_VERSION and PANDOC_READER_OPTS
+  -- We can use the former to ensure that people are not
+  -- using an old version of pandoc
+  pandocV <- lookupEnv "PANDOC_VERSION"
+  case pandocV >>= readVersion of
+    Nothing -> return True
+    Just v ->
+      if v < minimumPandocVersion
+        then do
+          hPutStrLn stderr $
+            mconcat
+              [ "ERROR (pandoc-plot) The pandoc-plot filter only ",
+                "supports Pandoc 2.11 and newer. ",
+                "but you are using Pandoc ",
+                showVersion v
+              ]
+          return False
+        else return True
+  where
+    readVersion = fmap fst . lastMaybe . readP_to_S parseVersion
+    lastMaybe xs = if length xs > 1 then Just (last xs) else Nothing
+
+-- | Load configuration from local file @.pandoc-plot.yml@.
+-- If the file does not exist, the default configuration will be used.
+localConfig :: IO Configuration
+localConfig = do
+  configExists <- doesFileExist ".pandoc-plot.yml"
+  if configExists
+    then configuration ".pandoc-plot.yml"
+    else return defaultConfiguration
+
+showFullVersion :: IO ()
+showFullVersion = do
+  putStrLn $ "pandoc-plot " <> V.showVersion pandocPlotVersion
+  putStrLn $ "Git revision " <> $gitHash
+  putStrLn $
+    mconcat
+      [ "Compiled with pandoc ",
+        V.showVersion pandocVersion,
+        " and pandoc-types ",
+        V.showVersion pandocTypesVersion,
+        " using GHC ",
+        TOOL_VERSION_ghc -- Constant defined by CPP
+      ]
+
+showAvailableToolkits :: Maybe FilePath -> IO ()
+showAvailableToolkits mfp = do
+  c <- maybe localConfig configuration mfp
+
+  putStrLn "\nAVAILABLE TOOLKITS\n"
+  available <- availableToolkits c
+  mapM_ (availToolkitInfo c) available
+  putStrLn "\nUNAVAILABLE TOOLKITS\n"
+  -- We don't use unavailableToolkits because this would force
+  -- more IO actions
+  let unavailable = toolkits \\ available
+  mapM_ (unavailToolkitInfo c) unavailable
+  where
+    toolkitInfo avail conf tk = do
+      putStrLn $ "Toolkit: " <> show tk
+      when avail $ do
+        exe <- runPlotM Nothing conf $ executable tk
+        putStrLn $ "    Executable: " <> pathToExe exe
+      putStrLn $ "    Code block trigger: " <> (unpack . cls $ tk)
+      putStrLn $ "    Supported save formats: " <> (mconcat . intersperse ", " . fmap show $ supportedSaveFormats tk)
+      putStrLn mempty
+    availToolkitInfo = toolkitInfo True
+    unavailToolkitInfo = toolkitInfo False
+
+-- | Clean output directories associated with a file
+--
+-- Priority for configuration are the same as @toJSONFilterWithConfig@.
+clean ::
+  Maybe FilePath -> -- Use configuration file?
+  FilePath -> -- Document to clean
+  IO ()
+clean mfp fp = do
+  doc <- readDoc fp
+  -- Note the priority for configuration:
+  --   (1) path of argument --config
+  --   (2) document metadata
+  --   (3) local .pandoc-plot.yml
+  --   (4) default config
+  conf <- maybe localConfig configuration $ firstJusts [configurationPathMeta doc, mfp]
+  void (cleanOutputDirs conf doc)
+  where
+    firstJusts :: [Maybe a] -> Maybe a
+    firstJusts = msum
+
+showManPage :: IO ()
+showManPage = do
+  manualPath <- (</> "pandoc-plot-manual.html") <$> getTemporaryDirectory
+  TIO.writeFile manualPath $(embedManualHtml)
+  openFile ("file:///" <> manualPath)

@@ -1,41 +1,41 @@-{-# LANGUAGE OverloadedStrings #-}-{-# LANGUAGE TemplateHaskell #-}---- |--- This module was inspired by pandoc-crossref--- |-module ManPage (embedManualHtml) where--import Control.Monad (unless)-import Data.String (fromString)-import Data.Text (unpack)-import qualified Data.Text.IO as TIO-import Language.Haskell.TH.Syntax-  ( Exp (AppE, LitE, VarE),-    Lit (StringL),-    Q,-    Quasi (qAddDependentFile),-    runIO,-  )-import System.Directory (doesFileExist)-import System.FilePath ((</>))--docFile :: FilePath-docFile = "docs" </> "MANUAL.html"--readDocFile :: IO String-readDocFile = TIO.readFile docFile >>= return . unpack--embedManualHtml :: Q Exp-embedManualHtml = do-  -- Ensure that the manual file exists-  -- even if it is empty-  manualExists <- runIO $ doesFileExist docFile-  unless manualExists (runIO $ TIO.writeFile docFile mempty)--  qAddDependentFile docFile-  d <- runIO readDocFile-  strToExp d-  where-    strToExp :: String -> Q Exp-    strToExp s = return $ VarE 'fromString `AppE` LitE (StringL s)+{-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE TemplateHaskell #-}
+
+-- |
+-- This module was inspired by pandoc-crossref
+-- |
+module ManPage (embedManualHtml) where
+
+import Control.Monad (unless)
+import Data.String (fromString)
+import Data.Text (unpack)
+import qualified Data.Text.IO as TIO
+import Language.Haskell.TH.Syntax
+  ( Exp (AppE, LitE, VarE),
+    Lit (StringL),
+    Q,
+    Quasi (qAddDependentFile),
+    runIO,
+  )
+import System.Directory (doesFileExist)
+import System.FilePath ((</>))
+
+docFile :: FilePath
+docFile = "docs" </> "MANUAL.html"
+
+readDocFile :: IO String
+readDocFile = TIO.readFile docFile >>= return . unpack
+
+embedManualHtml :: Q Exp
+embedManualHtml = do
+  -- Ensure that the manual file exists
+  -- even if it is empty
+  manualExists <- runIO $ doesFileExist docFile
+  unless manualExists (runIO $ TIO.writeFile docFile mempty)
+
+  qAddDependentFile docFile
+  d <- runIO readDocFile
+  strToExp d
+  where
+    strToExp :: String -> Q Exp
+    strToExp s = return $ VarE 'fromString `AppE` LitE (StringL s)

@@ -1,37 +1,37 @@--- |--- Module      : $header$--- Copyright   : (c) Laurent P René de Cotret, 2019 - present--- License     : GNU GPL, version 2 or above--- Maintainer  : laurent.decotret@outlook.com--- Stability   : internal--- Portability : portable------ Open a file in its default program.-module OpenFile (openFile) where--import Data.List (isInfixOf)-import System.Info (os)-import System.Process.Typed (proc, runProcess_, shell)--openFile :: FilePath -> IO ()-openFile-  -- Aliases taken from cabal's Distribution.System module-  | os `elem` ["mingw32", "win32", "cygwin32"] = openFileWindows-  | any (`isInfixOf` os) ["linux", "bsd"] = openFileLinux-  | os `elem` ["darwin"] = openFileMacOS-  | otherwise = error $ "Unsupported OS: " <> os--openFileWindows :: FilePath -> IO ()-openFileWindows fp =-  -- Call looks like: cmd /c 'start "" "my_filepath.html"'-  runProcess_ $ shell $ mconcat ["cmd /c start ", quoted mempty, " ", quoted fp]-  where-    quoted f = mconcat ["\"", f, "\""]--openFileLinux :: FilePath -> IO ()-openFileLinux fp =-  runProcess_ (proc "sh" ["-c", "xdg-open \"$0\" 2>&1 > /dev/null", fp])--openFileMacOS :: FilePath -> IO ()-openFileMacOS fp =-  runProcess_ (proc "open" [fp])+-- |
+-- Module      : $header$
+-- Copyright   : (c) Laurent P René de Cotret, 2019 - present
+-- License     : GNU GPL, version 2 or above
+-- Maintainer  : laurent.decotret@outlook.com
+-- Stability   : internal
+-- Portability : portable
+--
+-- Open a file in its default program.
+module OpenFile (openFile) where
+
+import Data.List (isInfixOf)
+import System.Info (os)
+import System.Process.Typed (proc, runProcess_, shell)
+
+openFile :: FilePath -> IO ()
+openFile
+  -- Aliases taken from cabal's Distribution.System module
+  | os `elem` ["mingw32", "win32", "cygwin32"] = openFileWindows
+  | any (`isInfixOf` os) ["linux", "bsd"] = openFileLinux
+  | os `elem` ["darwin"] = openFileMacOS
+  | otherwise = error $ "Unsupported OS: " <> os
+
+openFileWindows :: FilePath -> IO ()
+openFileWindows fp =
+  -- Call looks like: cmd /c 'start "" "my_filepath.html"'
+  runProcess_ $ shell $ mconcat ["cmd /c start ", quoted mempty, " ", quoted fp]
+  where
+    quoted f = mconcat ["\"", f, "\""]
+
+openFileLinux :: FilePath -> IO ()
+openFileLinux fp =
+  runProcess_ (proc "sh" ["-c", "xdg-open \"$0\" 2>&1 > /dev/null", fp])
+
+openFileMacOS :: FilePath -> IO ()
+openFileMacOS fp =
+  runProcess_ (proc "open" [fp])

@@ -1,168 +1,170 @@-cabal-version:  2.2-name:           pandoc-plot-version:        1.7.0-synopsis:       A Pandoc filter to include figures generated from code blocks using your plotting toolkit of choice.-description:    A Pandoc filter to include figures generated from code blocks. -                Keep the document and code in the same location. Output is -                captured and included as a figure.-category:       Text-copyright:      (c) 2019-present Laurent P. René de Cotret-homepage:       https://github.com/LaurentRDC/pandoc-plot#readme-bug-reports:    https://github.com/LaurentRDC/pandoc-plot/issues-author:         Laurent P. René de Cotret-maintainer:     Laurent P. René de Cotret-license:        GPL-2.0-or-later-license-file:   LICENSE-build-type:     Simple-tested-with:    GHC == 8.10.4, -                GHC == 9.0.1, -                GHC == 9.2.1, -                GHC == 9.2.2,-                GHC == 9.4.4,-                GHC == 9.6.1-extra-source-files:-    CHANGELOG.md-    LICENSE-    README.md-    MANUAL.md-    docs/MANUAL.html-    example-config.yml--    data/srctemplate.html--    tests/fixtures/.config-meta.yml-    tests/fixtures/.empty-config.yml-    tests/fixtures/.verbose-config.yml-    tests/fixtures/plotfile.py-    tests/fixtures/data.csv-    -    tests/includes/bokeh.py-    tests/includes/ggplot2.r-    tests/includes/gnuplot.gp-    tests/includes/graphviz.dot-    tests/includes/mathplot.m-    tests/includes/matlabplot.m-    tests/includes/matplotlib.py-    tests/includes/octave.m-    tests/includes/plotly-python.py-    tests/includes/plotly-r.r-    tests/includes/plotsjl.jl-    tests/includes/plantuml.txt-    tests/includes/sagemath.sage-    tests/includes/d2-dd.d2--source-repository head-    type: git-    location: https://github.com/LaurentRDC/pandoc-plot--library-    exposed-modules:-        Text.Pandoc.Filter.Plot-        Text.Pandoc.Filter.Plot.Internal-    other-modules:-        Paths_pandoc_plot-        Text.Pandoc.Filter.Plot.Clean-        Text.Pandoc.Filter.Plot.Configuration-        Text.Pandoc.Filter.Plot.Parse-        Text.Pandoc.Filter.Plot.Scripting-        Text.Pandoc.Filter.Plot.Scripting.Template-        Text.Pandoc.Filter.Plot.Renderers-        Text.Pandoc.Filter.Plot.Renderers.Prelude-        Text.Pandoc.Filter.Plot.Renderers.Matplotlib-        Text.Pandoc.Filter.Plot.Renderers.PlotlyPython-        Text.Pandoc.Filter.Plot.Renderers.PlotlyR-        Text.Pandoc.Filter.Plot.Renderers.Matlab-        Text.Pandoc.Filter.Plot.Renderers.Mathematica-        Text.Pandoc.Filter.Plot.Renderers.Octave-        Text.Pandoc.Filter.Plot.Renderers.GGPlot2-        Text.Pandoc.Filter.Plot.Renderers.GNUPlot-        Text.Pandoc.Filter.Plot.Renderers.Graphviz-        Text.Pandoc.Filter.Plot.Renderers.Bokeh-        Text.Pandoc.Filter.Plot.Renderers.Plotsjl-        Text.Pandoc.Filter.Plot.Renderers.PlantUML-        Text.Pandoc.Filter.Plot.Renderers.SageMath-        Text.Pandoc.Filter.Plot.Renderers.D2-        Text.Pandoc.Filter.Plot.Monad-        Text.Pandoc.Filter.Plot.Monad.Logging-        Text.Pandoc.Filter.Plot.Monad.Types-        Text.Pandoc.Filter.Plot.Embed-    autogen-modules:-        Paths_pandoc_plot-    hs-source-dirs:-        src-    ghc-options: -        -Wall -        -Wcompat-        -Widentities-        -Wincomplete-uni-patterns-        -Wincomplete-record-updates-        -Wredundant-constraints-        -fhide-source-paths-        -Wmissing-export-lists-        -Wpartial-fields-    build-depends:-          aeson              >= 2     && < 3-        , base               >= 4.11  && < 5-        , bytestring-        , containers-        , data-default  -        , directory          >= 1.2.7 && < 2-        , filepath           >= 1.4   && < 2-        , hashable           >= 1     && < 2-        , pandoc             >= 3     && < 4-        , pandoc-types       >= 1.23  && < 1.24-        , lifted-async       >= 0.10  && < 1-        , lifted-base        >= 0.2   && < 1-        , shakespeare        >= 2.0   && < 3-        , tagsoup            >= 0.14  && < 1-        , template-haskell   >  2.7   && < 3-        , text               >= 1     && < 3-        , typed-process      >= 0.2.1 && < 1-        , yaml               >= 0.8   && < 1-        , mtl                >= 2.2   && < 3-    if !os(windows)-        build-depends:  unix >= 2.4 && < 2.9-    default-language: Haskell2010--executable pandoc-plot-    main-is: Main.hs-    other-modules:-        ManPage-        ExampleConfig-        OpenFile-        Paths_pandoc_plot-    hs-source-dirs:-        executable-    ghc-options: -Wall -Wcompat -threaded -rtsopts -with-rtsopts=-N-    build-depends:-          base                  >= 4.11 && <5-        , containers-        , directory-        , filepath-        , gitrev                >= 1    && < 2-        , optparse-applicative  >= 0.14 && < 0.19-        , pandoc-        , pandoc-plot-        , pandoc-types          >= 1.21 && < 2-        , template-haskell      >  2.7  && < 3-        , typed-process-        , text-    default-language: Haskell2010--test-suite tests-    type: exitcode-stdio-1.0-    hs-source-dirs:  tests-    main-is:         Main.hs-    other-modules:   Common-    build-depends:   base-                   , containers-                   , directory-                   , filepath-                   , hspec-expectations-                   , pandoc-types-                   , pandoc-plot-                   , tasty-                   , tasty-hunit-                   , tasty-hspec-                   , text-    default-language: Haskell2010+cabal-version:  2.2
+name:           pandoc-plot
+version:        1.8.0
+synopsis:       A Pandoc filter to include figures generated from code blocks using your plotting toolkit of choice.
+description:    A Pandoc filter to include figures generated from code blocks. 
+                Keep the document and code in the same location. Output is 
+                captured and included as a figure.
+category:       Text
+copyright:      (c) 2019-present Laurent P. René de Cotret
+homepage:       https://github.com/LaurentRDC/pandoc-plot#readme
+bug-reports:    https://github.com/LaurentRDC/pandoc-plot/issues
+author:         Laurent P. René de Cotret
+maintainer:     Laurent P. René de Cotret
+license:        GPL-2.0-or-later
+license-file:   LICENSE
+build-type:     Simple
+tested-with:    GHC == 8.10.4, 
+                GHC == 9.0.1, 
+                GHC == 9.2.1, 
+                GHC == 9.2.2,
+                GHC == 9.4.4,
+                GHC == 9.6.1,
+                GHC == 9.6.3
+extra-source-files:
+    CHANGELOG.md
+    LICENSE
+    README.md
+    MANUAL.md
+    docs/MANUAL.html
+    example-config.yml
+
+    data/srctemplate.html
+
+    tests/fixtures/.config-meta.yml
+    tests/fixtures/.empty-config.yml
+    tests/fixtures/.verbose-config.yml
+    tests/fixtures/plotfile.py
+    tests/fixtures/data.csv
+    
+    tests/includes/bokeh.py
+    tests/includes/ggplot2.r
+    tests/includes/gnuplot.gp
+    tests/includes/graphviz.dot
+    tests/includes/mathplot.m
+    tests/includes/matlabplot.m
+    tests/includes/matplotlib.py
+    tests/includes/octave.m
+    tests/includes/plotly-python.py
+    tests/includes/plotly-r.r
+    tests/includes/plotsjl.jl
+    tests/includes/plantuml.txt
+    tests/includes/sagemath.sage
+    tests/includes/d2-dd.d2
+
+source-repository head
+    type: git
+    location: https://github.com/LaurentRDC/pandoc-plot
+
+library
+    exposed-modules:
+        Text.Pandoc.Filter.Plot
+        Text.Pandoc.Filter.Plot.Internal
+    other-modules:
+        Paths_pandoc_plot
+        Text.Pandoc.Filter.Plot.Clean
+        Text.Pandoc.Filter.Plot.Configuration
+        Text.Pandoc.Filter.Plot.Parse
+        Text.Pandoc.Filter.Plot.Scripting
+        Text.Pandoc.Filter.Plot.Scripting.Template
+        Text.Pandoc.Filter.Plot.Renderers
+        Text.Pandoc.Filter.Plot.Renderers.Prelude
+        Text.Pandoc.Filter.Plot.Renderers.Matplotlib
+        Text.Pandoc.Filter.Plot.Renderers.PlotlyPython
+        Text.Pandoc.Filter.Plot.Renderers.PlotlyR
+        Text.Pandoc.Filter.Plot.Renderers.Matlab
+        Text.Pandoc.Filter.Plot.Renderers.Mathematica
+        Text.Pandoc.Filter.Plot.Renderers.Octave
+        Text.Pandoc.Filter.Plot.Renderers.GGPlot2
+        Text.Pandoc.Filter.Plot.Renderers.GNUPlot
+        Text.Pandoc.Filter.Plot.Renderers.Graphviz
+        Text.Pandoc.Filter.Plot.Renderers.Bokeh
+        Text.Pandoc.Filter.Plot.Renderers.Plotsjl
+        Text.Pandoc.Filter.Plot.Renderers.PlantUML
+        Text.Pandoc.Filter.Plot.Renderers.SageMath
+        Text.Pandoc.Filter.Plot.Renderers.D2
+        Text.Pandoc.Filter.Plot.Renderers.Asymptote
+        Text.Pandoc.Filter.Plot.Monad
+        Text.Pandoc.Filter.Plot.Monad.Logging
+        Text.Pandoc.Filter.Plot.Monad.Types
+        Text.Pandoc.Filter.Plot.Embed
+    autogen-modules:
+        Paths_pandoc_plot
+    hs-source-dirs:
+        src
+    ghc-options: 
+        -Wall 
+        -Wcompat
+        -Widentities
+        -Wincomplete-uni-patterns
+        -Wincomplete-record-updates
+        -Wredundant-constraints
+        -fhide-source-paths
+        -Wmissing-export-lists
+        -Wpartial-fields
+    build-depends:
+          aeson              >= 2     && < 3
+        , base               >= 4.11  && < 5
+        , bytestring
+        , containers
+        , data-default  
+        , directory          >= 1.2.7 && < 2
+        , filepath           >= 1.4   && < 2
+        , hashable           >= 1     && < 2
+        , pandoc             >= 3     && < 4
+        , pandoc-types       >= 1.23  && < 1.24
+        , lifted-async       >= 0.10  && < 1
+        , lifted-base        >= 0.2   && < 1
+        , shakespeare        >= 2.0   && < 3
+        , tagsoup            >= 0.14  && < 1
+        , template-haskell   >  2.7   && < 3
+        , text               >= 1     && < 3
+        , typed-process      >= 0.2.1 && < 1
+        , yaml               >= 0.8   && < 1
+        , mtl                >= 2.2   && < 3
+    if !os(windows)
+        build-depends:  unix >= 2.4 && < 2.9
+    default-language: Haskell2010
+
+executable pandoc-plot
+    main-is: Main.hs
+    other-modules:
+        ManPage
+        ExampleConfig
+        OpenFile
+        Paths_pandoc_plot
+    hs-source-dirs:
+        executable
+    ghc-options: -Wall -Wcompat -threaded -rtsopts -with-rtsopts=-N
+    build-depends:
+          base                  >= 4.11 && <5
+        , containers
+        , directory
+        , filepath
+        , gitrev                >= 1    && < 2
+        , optparse-applicative  >= 0.14 && < 0.19
+        , pandoc
+        , pandoc-plot
+        , pandoc-types          >= 1.21 && < 2
+        , template-haskell      >  2.7  && < 3
+        , typed-process
+        , text
+    default-language: Haskell2010
+
+test-suite tests
+    type: exitcode-stdio-1.0
+    hs-source-dirs:  tests
+    main-is:         Main.hs
+    other-modules:   Common
+    build-depends:   base
+                   , containers
+                   , directory
+                   , filepath
+                   , hspec-expectations
+                   , pandoc-types
+                   , pandoc-plot
+                   , tasty
+                   , tasty-hunit
+                   , tasty-hspec
+                   , text
+    default-language: Haskell2010

@@ -1,242 +1,242 @@-{-# LANGUAGE FlexibleContexts #-}-{-# LANGUAGE LambdaCase #-}-{-# LANGUAGE OverloadedStrings #-}---- |--- Module      : $header$--- Description : Pandoc filter to create figures from code blocks using your plotting toolkit of choice--- Copyright   : (c) Laurent P René de Cotret, 2019 - present--- License     : GNU GPL, version 2 or above--- Maintainer  : laurent.decotret@outlook.com--- Stability   : unstable--- Portability : portable------ This module defines a Pandoc filter @plotFilter@ and related functions--- that can be used to walk over a Pandoc document and generate figures from--- code blocks, using a multitude of plotting toolkits.------ The syntax for code blocks is simple. Code blocks with the appropriate class--- attribute will trigger the filter, e.g. @matplotlib@ for matplotlib-based Python plots.------ Here is an example, in Markdown, for a plot in MATLAB:------ @--- This is a paragraph.------ ```{.matlabplot}--- figure()--- plot([1,2,3,4,5], [1,2,3,4,5], '-k')--- ```--- @------ or a using GNUPlot:------ @--- ```{.gnuplot format=png caption="Sinusoidal function" source=true}--- sin(x)------ set xlabel "x"--- set ylabel "y"--- ```--- @------ The code block will be reworked into a script and the output figure will be captured. Optionally, the source code---  used to generate the figure will be linked in the caption.------ Here are /some/ of the possible attributes what pandoc-plot understands for ALL toolkits:------     * @directory=...@ : Directory where to save the figure. This path should be specified with---       respect to the current working directory, and not with respect to the document.---     * @source=true|false@ : Whether or not to link the source code of this figure in the caption.---       Ideal for web pages, for example. Default is false.---     * @format=...@: Format of the generated figure. This can be an extension or an acronym,---       e.g. @format=PNG@.---     * @caption="..."@: Specify a plot caption (or alternate text). Format---       for captions is specified in the documentation for the @Configuration@ type.---     * @dpi=...@: Specify a value for figure resolution, or dots-per-inch. Certain toolkits ignore this.---     * @dependencies=[...]@: Specify files/directories on which a figure depends, e.g. data file.---       Figures will be re-rendered if one of those file/directory changes. These paths should---       be specified with respect to the current working directory, and not with respect to the document.---     * @preamble=...@: Path to a file to include before the code block. Ideal to avoid repetition over---       many figures.---     * @file=...@: Path to a file from which to read the content of the figure. The content of the---       code block will be ignored. This path should be specified with respect to the current working---       directory, and not with respect to the document.------ All attributes are described in the online documentation, linked on the home page.-module Text.Pandoc.Filter.Plot-  ( -- * Operating on whole Pandoc documents-    plotFilter,-    plotTransform,--    -- * Cleaning output directories-    cleanOutputDirs,--    -- * Runtime configuration-    configuration,-    defaultConfiguration,-    Configuration (..),-    Verbosity (..),-    LogSink (..),-    SaveFormat (..),-    Script,--    -- * Determining available plotting toolkits-    Toolkit (..),-    availableToolkits,-    unavailableToolkits,-    toolkits,-    supportedSaveFormats,--    -- * Version information-    pandocPlotVersion,--    -- * For embedding, testing and internal purposes ONLY. Might change without notice.-    make,-    makeEither,-    PandocPlotError (..),-  )-where--import Control.Concurrent (getNumCapabilities)-import Control.Monad (when)-import Data.Functor ((<&>))-import Data.Map (singleton)-import Data.Text (Text, pack, unpack)-import Data.Version (Version)-import Paths_pandoc_plot (version)-import Text.Pandoc.Definition (Block, Format, Meta (..), MetaValue (..), Pandoc (..))-import Text.Pandoc.Filter.Plot.Internal-  ( Configuration (..),-    FigureSpec,-    LogSink (..),-    ParseFigureResult (..),-    PlotM,-    RuntimeEnv (envConfig),-    SaveFormat (..),-    Script,-    ScriptResult (..),-    Toolkit (..),-    Verbosity (..),-    asks,-    asksConfig,-    availableToolkits,-    cleanOutputDirs,-    configuration,-    debug,-    defaultConfiguration,-    mapConcurrentlyN,-    parseFigureSpec,-    runPlotM,-    runScriptIfNecessary,-    supportedSaveFormats,-    throwStrictError,-    toFigure,-    toolkits,-    unavailableToolkits,-  )-import Text.Pandoc.Walk (walkM)---- | Walk over an entire Pandoc document, transforming appropriate code blocks--- into figures. This function will operate on blocks in parallel if possible.------ If the target conversion format is known, then this function can provide better--- defaults and error messages. For example, hyperlinks to source code will only be created--- if the final target format supports it (e.g. HTML).------ Failing to render a figure does not stop the filter, so that you may run the filter--- on documents without having all necessary toolkits installed. In this case, error--- messages are printed to stderr, and blocks are left unchanged.------ @since 1.3.0-plotFilter ::-  -- | Configuration for default values-  Configuration ->-  -- | Final converted format, if known-  Maybe Format ->-  -- | Input document-  Pandoc ->-  IO Pandoc-plotFilter conf mfmt (Pandoc meta blocks) = do-  maxproc <- getNumCapabilities-  runPlotM mfmt conf $ do-    debug $ mconcat ["Starting a new run, utilizing at most ", pack . show $ maxproc, " processes."]-    mapConcurrentlyN maxproc make blocks <&> Pandoc newMeta-  where-    -- This variable is needed for pandoc's default LaTeX template,-    -- so that graphicx gets used.-    newMeta = meta <> Meta (singleton "graphics" $ MetaBool True)---- | Walk over an entire Pandoc document, transforming appropriate code blocks--- into figures. This function will operate on blocks in parallel if possible.------ Failing to render a figure does not stop the filter, so that you may run the filter--- on documents without having all necessary toolkits installed. In this case, error--- messages are printed to stderr, and blocks are left unchanged.------ __Note that this function is DEPRECATED in favour of @plotFilter@. It will be--- removed in the next major update (v2+).__-plotTransform ::-  -- | Configuration for default values-  Configuration ->-  -- | Input document-  Pandoc ->-  IO Pandoc-{-# DEPRECATED-  plotTransform-  [ "plotTransform has been deprecated in favour of plotFilter, which is aware of conversion format.",-    "plotTransform will be removed in an upcoming major update."-  ]-  #-}-plotTransform conf = plotFilter conf Nothing---- | The version of the pandoc-plot package.------ @since 0.8.0.0-pandocPlotVersion :: Version-pandocPlotVersion = version---- | Try to process the block with `pandoc-plot`. If a failure happens (or the block)--- was not meant to become a figure, return the block as-is unless running in strict mode.--- In strict mode, any failure (for example, due to a missing plotting toolkit) will halt execution.------ New in version 1.2.0: this function will detect nested code blocks, for example in @Div@ blocks.-make :: Block -> PlotM Block-make = walkM $ \blk -> either (onError blk) return =<< makeEither blk-  where-    onError :: Block -> PandocPlotError -> PlotM Block-    onError b e = do-      whenStrict $ throwStrictError (pack . show $ e)-      return b--    whenStrict f = asksConfig strictMode >>= \s -> when s f---- | Try to process the block with `pandoc-plot`, documenting the error.--- This function does not transform code blocks nested in--- other blocks (e.g. @Divs@)-makeEither :: Block -> PlotM (Either PandocPlotError Block)-makeEither block =-  parseFigureSpec block-    >>= \case-      NotAFigure -> return $ Right block-      PFigure fs -> runScriptIfNecessary fs >>= handleResult fs-      MissingToolkit tk -> return $ Left $ ToolkitNotInstalledError tk-      UnsupportedSaveFormat tk sv -> return $ Left $ IncompatibleSaveFormatError sv tk-  where-    -- Logging of errors has been taken care of in @runScriptIfNecessary@-    handleResult :: FigureSpec -> ScriptResult -> PlotM (Either PandocPlotError Block)-    handleResult _ (ScriptFailure cmd code _) = return $ Left (ScriptRuntimeError cmd code)-    handleResult _ (ScriptChecksFailed msg) = return $ Left (ScriptChecksFailedError msg)-    handleResult spec ScriptSuccess = asks envConfig >>= \c -> Right <$> toFigure (captionFormat c) spec--data PandocPlotError-  = ScriptRuntimeError Text Int-  | ScriptChecksFailedError Text-  | ToolkitNotInstalledError Toolkit-  | IncompatibleSaveFormatError SaveFormat Toolkit--instance Show PandocPlotError where-  show (ScriptRuntimeError _ exitcode) = "ERROR (pandoc-plot) The script failed with exit code " <> show exitcode <> "."-  show (ScriptChecksFailedError msg) = "ERROR (pandoc-plot) A script check failed with message: " <> unpack msg <> "."-  show (ToolkitNotInstalledError tk) = "ERROR (pandoc-plot) The " <> show tk <> " toolkit is required but not installed."-  show (IncompatibleSaveFormatError tk sv) = "ERROR (pandoc-plot) Save format " <> show sv <> " not supported by the " <> show tk <> " toolkit."+{-# LANGUAGE FlexibleContexts #-}
+{-# LANGUAGE LambdaCase #-}
+{-# LANGUAGE OverloadedStrings #-}
+
+-- |
+-- Module      : $header$
+-- Description : Pandoc filter to create figures from code blocks using your plotting toolkit of choice
+-- Copyright   : (c) Laurent P René de Cotret, 2019 - present
+-- License     : GNU GPL, version 2 or above
+-- Maintainer  : laurent.decotret@outlook.com
+-- Stability   : unstable
+-- Portability : portable
+--
+-- This module defines a Pandoc filter @plotFilter@ and related functions
+-- that can be used to walk over a Pandoc document and generate figures from
+-- code blocks, using a multitude of plotting toolkits.
+--
+-- The syntax for code blocks is simple. Code blocks with the appropriate class
+-- attribute will trigger the filter, e.g. @matplotlib@ for matplotlib-based Python plots.
+--
+-- Here is an example, in Markdown, for a plot in MATLAB:
+--
+-- @
+-- This is a paragraph.
+--
+-- ```{.matlabplot}
+-- figure()
+-- plot([1,2,3,4,5], [1,2,3,4,5], '-k')
+-- ```
+-- @
+--
+-- or a using GNUPlot:
+--
+-- @
+-- ```{.gnuplot format=png caption="Sinusoidal function" source=true}
+-- sin(x)
+--
+-- set xlabel "x"
+-- set ylabel "y"
+-- ```
+-- @
+--
+-- The code block will be reworked into a script and the output figure will be captured. Optionally, the source code
+--  used to generate the figure will be linked in the caption.
+--
+-- Here are /some/ of the possible attributes what pandoc-plot understands for ALL toolkits:
+--
+--     * @directory=...@ : Directory where to save the figure. This path should be specified with
+--       respect to the current working directory, and not with respect to the document.
+--     * @source=true|false@ : Whether or not to link the source code of this figure in the caption.
+--       Ideal for web pages, for example. Default is false.
+--     * @format=...@: Format of the generated figure. This can be an extension or an acronym,
+--       e.g. @format=PNG@.
+--     * @caption="..."@: Specify a plot caption (or alternate text). Format
+--       for captions is specified in the documentation for the @Configuration@ type.
+--     * @dpi=...@: Specify a value for figure resolution, or dots-per-inch. Certain toolkits ignore this.
+--     * @dependencies=[...]@: Specify files/directories on which a figure depends, e.g. data file.
+--       Figures will be re-rendered if one of those file/directory changes. These paths should
+--       be specified with respect to the current working directory, and not with respect to the document.
+--     * @preamble=...@: Path to a file to include before the code block. Ideal to avoid repetition over
+--       many figures.
+--     * @file=...@: Path to a file from which to read the content of the figure. The content of the
+--       code block will be ignored. This path should be specified with respect to the current working
+--       directory, and not with respect to the document.
+--
+-- All attributes are described in the online documentation, linked on the home page.
+module Text.Pandoc.Filter.Plot
+  ( -- * Operating on whole Pandoc documents
+    plotFilter,
+    plotTransform,
+
+    -- * Cleaning output directories
+    cleanOutputDirs,
+
+    -- * Runtime configuration
+    configuration,
+    defaultConfiguration,
+    Configuration (..),
+    Verbosity (..),
+    LogSink (..),
+    SaveFormat (..),
+    Script,
+
+    -- * Determining available plotting toolkits
+    Toolkit (..),
+    availableToolkits,
+    unavailableToolkits,
+    toolkits,
+    supportedSaveFormats,
+
+    -- * Version information
+    pandocPlotVersion,
+
+    -- * For embedding, testing and internal purposes ONLY. Might change without notice.
+    make,
+    makeEither,
+    PandocPlotError (..),
+  )
+where
+
+import Control.Concurrent (getNumCapabilities)
+import Control.Monad (when)
+import Data.Functor ((<&>))
+import Data.Map (singleton)
+import Data.Text (Text, pack, unpack)
+import Data.Version (Version)
+import Paths_pandoc_plot (version)
+import Text.Pandoc.Definition (Block, Format, Meta (..), MetaValue (..), Pandoc (..))
+import Text.Pandoc.Filter.Plot.Internal
+  ( Configuration (..),
+    FigureSpec,
+    LogSink (..),
+    ParseFigureResult (..),
+    PlotM,
+    RuntimeEnv (envConfig),
+    SaveFormat (..),
+    Script,
+    ScriptResult (..),
+    Toolkit (..),
+    Verbosity (..),
+    asks,
+    asksConfig,
+    availableToolkits,
+    cleanOutputDirs,
+    configuration,
+    debug,
+    defaultConfiguration,
+    mapConcurrentlyN,
+    parseFigureSpec,
+    runPlotM,
+    runScriptIfNecessary,
+    supportedSaveFormats,
+    throwStrictError,
+    toFigure,
+    toolkits,
+    unavailableToolkits,
+  )
+import Text.Pandoc.Walk (walkM)
+
+-- | Walk over an entire Pandoc document, transforming appropriate code blocks
+-- into figures. This function will operate on blocks in parallel if possible.
+--
+-- If the target conversion format is known, then this function can provide better
+-- defaults and error messages. For example, hyperlinks to source code will only be created
+-- if the final target format supports it (e.g. HTML).
+--
+-- Failing to render a figure does not stop the filter, so that you may run the filter
+-- on documents without having all necessary toolkits installed. In this case, error
+-- messages are printed to stderr, and blocks are left unchanged.
+--
+-- @since 1.3.0
+plotFilter ::
+  -- | Configuration for default values
+  Configuration ->
+  -- | Final converted format, if known
+  Maybe Format ->
+  -- | Input document
+  Pandoc ->
+  IO Pandoc
+plotFilter conf mfmt (Pandoc meta blocks) = do
+  maxproc <- getNumCapabilities
+  runPlotM mfmt conf $ do
+    debug $ mconcat ["Starting a new run, utilizing at most ", pack . show $ maxproc, " processes."]
+    mapConcurrentlyN maxproc make blocks <&> Pandoc newMeta
+  where
+    -- This variable is needed for pandoc's default LaTeX template,
+    -- so that graphicx gets used.
+    newMeta = meta <> Meta (singleton "graphics" $ MetaBool True)
+
+-- | Walk over an entire Pandoc document, transforming appropriate code blocks
+-- into figures. This function will operate on blocks in parallel if possible.
+--
+-- Failing to render a figure does not stop the filter, so that you may run the filter
+-- on documents without having all necessary toolkits installed. In this case, error
+-- messages are printed to stderr, and blocks are left unchanged.
+--
+-- __Note that this function is DEPRECATED in favour of @plotFilter@. It will be
+-- removed in the next major update (v2+).__
+plotTransform ::
+  -- | Configuration for default values
+  Configuration ->
+  -- | Input document
+  Pandoc ->
+  IO Pandoc
+{-# DEPRECATED
+  plotTransform
+  [ "plotTransform has been deprecated in favour of plotFilter, which is aware of conversion format.",
+    "plotTransform will be removed in an upcoming major update."
+  ]
+  #-}
+plotTransform conf = plotFilter conf Nothing
+
+-- | The version of the pandoc-plot package.
+--
+-- @since 0.8.0.0
+pandocPlotVersion :: Version
+pandocPlotVersion = version
+
+-- | Try to process the block with `pandoc-plot`. If a failure happens (or the block)
+-- was not meant to become a figure, return the block as-is unless running in strict mode.
+-- In strict mode, any failure (for example, due to a missing plotting toolkit) will halt execution.
+--
+-- New in version 1.2.0: this function will detect nested code blocks, for example in @Div@ blocks.
+make :: Block -> PlotM Block
+make = walkM $ \blk -> either (onError blk) return =<< makeEither blk
+  where
+    onError :: Block -> PandocPlotError -> PlotM Block
+    onError b e = do
+      whenStrict $ throwStrictError (pack . show $ e)
+      return b
+
+    whenStrict f = asksConfig strictMode >>= \s -> when s f
+
+-- | Try to process the block with `pandoc-plot`, documenting the error.
+-- This function does not transform code blocks nested in
+-- other blocks (e.g. @Divs@)
+makeEither :: Block -> PlotM (Either PandocPlotError Block)
+makeEither block =
+  parseFigureSpec block
+    >>= \case
+      NotAFigure -> return $ Right block
+      PFigure fs -> runScriptIfNecessary fs >>= handleResult fs
+      MissingToolkit tk -> return $ Left $ ToolkitNotInstalledError tk
+      UnsupportedSaveFormat tk sv -> return $ Left $ IncompatibleSaveFormatError sv tk
+  where
+    -- Logging of errors has been taken care of in @runScriptIfNecessary@
+    handleResult :: FigureSpec -> ScriptResult -> PlotM (Either PandocPlotError Block)
+    handleResult _ (ScriptFailure cmd code _) = return $ Left (ScriptRuntimeError cmd code)
+    handleResult _ (ScriptChecksFailed msg) = return $ Left (ScriptChecksFailedError msg)
+    handleResult spec ScriptSuccess = asks envConfig >>= \c -> Right <$> toFigure (captionFormat c) spec
+
+data PandocPlotError
+  = ScriptRuntimeError Text Int
+  | ScriptChecksFailedError Text
+  | ToolkitNotInstalledError Toolkit
+  | IncompatibleSaveFormatError SaveFormat Toolkit
+
+instance Show PandocPlotError where
+  show (ScriptRuntimeError _ exitcode) = "ERROR (pandoc-plot) The script failed with exit code " <> show exitcode <> "."
+  show (ScriptChecksFailedError msg) = "ERROR (pandoc-plot) A script check failed with message: " <> unpack msg <> "."
+  show (ToolkitNotInstalledError tk) = "ERROR (pandoc-plot) The " <> show tk <> " toolkit is required but not installed."
+  show (IncompatibleSaveFormatError tk sv) = "ERROR (pandoc-plot) Save format " <> show sv <> " not supported by the " <> show tk <> " toolkit."

@@ -1,165 +1,165 @@-{-# LANGUAGE FlexibleContexts #-}-{-# LANGUAGE OverloadedStrings #-}---- |--- Module      : $header$--- Copyright   : (c) Laurent P René de Cotret, 2019 - present--- License     : GNU GPL, version 2 or above--- Maintainer  : laurent.decotret@outlook.com--- Stability   : internal--- Portability : portable------ Utilities to clean pandoc-plot output directories.-module Text.Pandoc.Filter.Plot.Clean-  ( cleanOutputDirs,-    outputDirs,-    readDoc,-  )-where---- TODO: forConcurrently-import Control.Monad (forM)-import qualified Data.ByteString.Lazy as B-import Data.Char (toLower)-import Data.Default (def)-import Data.List (nub)-import Data.Maybe (catMaybes, fromMaybe)-import Data.Text (Text, pack)-import qualified Data.Text.IO as Text-import System.Directory (removePathForcibly)-import System.FilePath (takeExtension)-import Text.Pandoc.Class (runIO)-import Text.Pandoc.Definition (Block, Pandoc)-import Text.Pandoc.Error (handleError)-import Text.Pandoc.Filter.Plot.Monad-import Text.Pandoc.Filter.Plot.Parse-import Text.Pandoc.Format (FlavoredFormat (..))-import qualified Text.Pandoc.Options as P-import qualified Text.Pandoc.Readers as P-import Text.Pandoc.Walk (Walkable, query)---- | Clean all output related to pandoc-plot. This includes output directories specified--- in the configuration and in the document/block, as well as log files.--- Note that *all* files in pandoc-plot output directories will be removed.------ The cleaned directories are returned.-cleanOutputDirs ::-  (Walkable Block b) =>-  Configuration ->-  b ->-  IO [FilePath]-cleanOutputDirs conf doc = do-  dirs <- runPlotM Nothing conf . cleanOutputDirsM $ doc-  -- Deletion of the log file must be done outside of PlotM-  -- to ensure the log file has been closed.-  case logSink conf of-    LogFile path -> removePathForcibly path-    _ -> return ()-  return dirs---- | Analyze a document to determine where would the pandoc-plot output directories be.-outputDirs ::-  (Walkable Block b) =>-  b ->-  PlotM [FilePath]-outputDirs = fmap (nub . catMaybes) . sequence . query (\b -> [hasDirectory <$> parseFigureSpec b])-  where-    hasDirectory :: ParseFigureResult -> Maybe FilePath-    hasDirectory (PFigure fs) = Just $ directory fs-    hasDirectory _ = Nothing---- | PlotM version of @cleanOutputDirs@-cleanOutputDirsM ::-  (Walkable Block b) =>-  b ->-  PlotM [FilePath]-cleanOutputDirsM doc = do-  directories <- outputDirs doc-  forM directories $ \fp -> do-    info $ "Removing directory " <> pack fp-    -- It is important to use `removePathForcibly` here, because it does-    -- not throw exceptions if the directory doesn't exist. This means-    -- we do not have to check in advance if directories are nested in our-    -- list of directories.-    liftIO $ removePathForcibly fp-    return fp---- | Read a document, guessing what extensions and reader options are appropriate. If--- the file cannot be read for any reason, an error is thrown.-readDoc :: FilePath -> IO Pandoc-readDoc fp =-  handleError-    =<< runIO-      ( do-          let fmt = fromMaybe mempty (formatFromFilePath fp)-          (reader, exts) <- P.getReader $ FlavoredFormat fmt mempty-          let readerOpts = def {P.readerExtensions = exts}-          case reader of-            P.TextReader fct -> do-              t <- liftIO $ Text.readFile fp-              fct readerOpts t-            P.ByteStringReader bst -> do-              b <- liftIO $ B.readFile fp-              bst readerOpts b-      )---- | Determine format based on file extension--- Note : this is exactly the heuristic used by pandoc here:--- https://github.com/jgm/pandoc/blob/master/src/Text/Pandoc/App/FormatHeuristics.hs------ However, this is not exported, so it must be re-defined here.-formatFromFilePath :: FilePath -> Maybe Text-formatFromFilePath x =-  case takeExtension (map toLower x) of-    ".adoc" -> Just "asciidoc"-    ".asciidoc" -> Just "asciidoc"-    ".context" -> Just "context"-    ".ctx" -> Just "context"-    ".db" -> Just "docbook"-    ".doc" -> Just "doc" -- so we get an "unknown reader" error-    ".docx" -> Just "docx"-    ".dokuwiki" -> Just "dokuwiki"-    ".epub" -> Just "epub"-    ".fb2" -> Just "fb2"-    ".htm" -> Just "html"-    ".html" -> Just "html"-    ".icml" -> Just "icml"-    ".json" -> Just "json"-    ".latex" -> Just "latex"-    ".lhs" -> Just "markdown+lhs"-    ".ltx" -> Just "latex"-    ".markdown" -> Just "markdown"-    ".mkdn" -> Just "markdown"-    ".mkd" -> Just "markdown"-    ".mdwn" -> Just "markdown"-    ".mdown" -> Just "markdown"-    ".Rmd" -> Just "markdown"-    ".md" -> Just "markdown"-    ".ms" -> Just "ms"-    ".muse" -> Just "muse"-    ".native" -> Just "native"-    ".odt" -> Just "odt"-    ".opml" -> Just "opml"-    ".org" -> Just "org"-    ".pdf" -> Just "pdf" -- so we get an "unknown reader" error-    ".pptx" -> Just "pptx"-    ".roff" -> Just "ms"-    ".rst" -> Just "rst"-    ".rtf" -> Just "rtf"-    ".s5" -> Just "s5"-    ".t2t" -> Just "t2t"-    ".tei" -> Just "tei"-    ".tei.xml" -> Just "tei"-    ".tex" -> Just "latex"-    ".texi" -> Just "texinfo"-    ".texinfo" -> Just "texinfo"-    ".text" -> Just "markdown"-    ".textile" -> Just "textile"-    ".txt" -> Just "markdown"-    ".wiki" -> Just "mediawiki"-    ".xhtml" -> Just "html"-    ".ipynb" -> Just "ipynb"-    ".csv" -> Just "csv"-    ".bib" -> Just "biblatex"-    ['.', y] | y `elem` ['1' .. '9'] -> Just "man"-    _ -> Nothing+{-# LANGUAGE FlexibleContexts #-}
+{-# LANGUAGE OverloadedStrings #-}
+
+-- |
+-- Module      : $header$
+-- Copyright   : (c) Laurent P René de Cotret, 2019 - present
+-- License     : GNU GPL, version 2 or above
+-- Maintainer  : laurent.decotret@outlook.com
+-- Stability   : internal
+-- Portability : portable
+--
+-- Utilities to clean pandoc-plot output directories.
+module Text.Pandoc.Filter.Plot.Clean
+  ( cleanOutputDirs,
+    outputDirs,
+    readDoc,
+  )
+where
+
+-- TODO: forConcurrently
+import Control.Monad (forM)
+import qualified Data.ByteString.Lazy as B
+import Data.Char (toLower)
+import Data.Default (def)
+import Data.List (nub)
+import Data.Maybe (catMaybes, fromMaybe)
+import Data.Text (Text, pack)
+import qualified Data.Text.IO as Text
+import System.Directory (removePathForcibly)
+import System.FilePath (takeExtension)
+import Text.Pandoc.Class (runIO)
+import Text.Pandoc.Definition (Block, Pandoc)
+import Text.Pandoc.Error (handleError)
+import Text.Pandoc.Filter.Plot.Monad
+import Text.Pandoc.Filter.Plot.Parse
+import Text.Pandoc.Format (FlavoredFormat (..))
+import qualified Text.Pandoc.Options as P
+import qualified Text.Pandoc.Readers as P
+import Text.Pandoc.Walk (Walkable, query)
+
+-- | Clean all output related to pandoc-plot. This includes output directories specified
+-- in the configuration and in the document/block, as well as log files.
+-- Note that *all* files in pandoc-plot output directories will be removed.
+--
+-- The cleaned directories are returned.
+cleanOutputDirs ::
+  (Walkable Block b) =>
+  Configuration ->
+  b ->
+  IO [FilePath]
+cleanOutputDirs conf doc = do
+  dirs <- runPlotM Nothing conf . cleanOutputDirsM $ doc
+  -- Deletion of the log file must be done outside of PlotM
+  -- to ensure the log file has been closed.
+  case logSink conf of
+    LogFile path -> removePathForcibly path
+    _ -> return ()
+  return dirs
+
+-- | Analyze a document to determine where would the pandoc-plot output directories be.
+outputDirs ::
+  (Walkable Block b) =>
+  b ->
+  PlotM [FilePath]
+outputDirs = fmap (nub . catMaybes) . sequence . query (\b -> [hasDirectory <$> parseFigureSpec b])
+  where
+    hasDirectory :: ParseFigureResult -> Maybe FilePath
+    hasDirectory (PFigure fs) = Just $ directory fs
+    hasDirectory _ = Nothing
+
+-- | PlotM version of @cleanOutputDirs@
+cleanOutputDirsM ::
+  (Walkable Block b) =>
+  b ->
+  PlotM [FilePath]
+cleanOutputDirsM doc = do
+  directories <- outputDirs doc
+  forM directories $ \fp -> do
+    info $ "Removing directory " <> pack fp
+    -- It is important to use `removePathForcibly` here, because it does
+    -- not throw exceptions if the directory doesn't exist. This means
+    -- we do not have to check in advance if directories are nested in our
+    -- list of directories.
+    liftIO $ removePathForcibly fp
+    return fp
+
+-- | Read a document, guessing what extensions and reader options are appropriate. If
+-- the file cannot be read for any reason, an error is thrown.
+readDoc :: FilePath -> IO Pandoc
+readDoc fp =
+  handleError
+    =<< runIO
+      ( do
+          let fmt = fromMaybe mempty (formatFromFilePath fp)
+          (reader, exts) <- P.getReader $ FlavoredFormat fmt mempty
+          let readerOpts = def {P.readerExtensions = exts}
+          case reader of
+            P.TextReader fct -> do
+              t <- liftIO $ Text.readFile fp
+              fct readerOpts t
+            P.ByteStringReader bst -> do
+              b <- liftIO $ B.readFile fp
+              bst readerOpts b
+      )
+
+-- | Determine format based on file extension
+-- Note : this is exactly the heuristic used by pandoc here:
+-- https://github.com/jgm/pandoc/blob/master/src/Text/Pandoc/App/FormatHeuristics.hs
+--
+-- However, this is not exported, so it must be re-defined here.
+formatFromFilePath :: FilePath -> Maybe Text
+formatFromFilePath x =
+  case takeExtension (map toLower x) of
+    ".adoc" -> Just "asciidoc"
+    ".asciidoc" -> Just "asciidoc"
+    ".context" -> Just "context"
+    ".ctx" -> Just "context"
+    ".db" -> Just "docbook"
+    ".doc" -> Just "doc" -- so we get an "unknown reader" error
+    ".docx" -> Just "docx"
+    ".dokuwiki" -> Just "dokuwiki"
+    ".epub" -> Just "epub"
+    ".fb2" -> Just "fb2"
+    ".htm" -> Just "html"
+    ".html" -> Just "html"
+    ".icml" -> Just "icml"
+    ".json" -> Just "json"
+    ".latex" -> Just "latex"
+    ".lhs" -> Just "markdown+lhs"
+    ".ltx" -> Just "latex"
+    ".markdown" -> Just "markdown"
+    ".mkdn" -> Just "markdown"
+    ".mkd" -> Just "markdown"
+    ".mdwn" -> Just "markdown"
+    ".mdown" -> Just "markdown"
+    ".Rmd" -> Just "markdown"
+    ".md" -> Just "markdown"
+    ".ms" -> Just "ms"
+    ".muse" -> Just "muse"
+    ".native" -> Just "native"
+    ".odt" -> Just "odt"
+    ".opml" -> Just "opml"
+    ".org" -> Just "org"
+    ".pdf" -> Just "pdf" -- so we get an "unknown reader" error
+    ".pptx" -> Just "pptx"
+    ".roff" -> Just "ms"
+    ".rst" -> Just "rst"
+    ".rtf" -> Just "rtf"
+    ".s5" -> Just "s5"
+    ".t2t" -> Just "t2t"
+    ".tei" -> Just "tei"
+    ".tei.xml" -> Just "tei"
+    ".tex" -> Just "latex"
+    ".texi" -> Just "texinfo"
+    ".texinfo" -> Just "texinfo"
+    ".text" -> Just "markdown"
+    ".textile" -> Just "textile"
+    ".txt" -> Just "markdown"
+    ".wiki" -> Just "mediawiki"
+    ".xhtml" -> Just "html"
+    ".ipynb" -> Just "ipynb"
+    ".csv" -> Just "csv"
+    ".bib" -> Just "biblatex"
+    ['.', y] | y `elem` ['1' .. '9'] -> Just "man"
+    _ -> Nothing

@@ -1,399 +1,414 @@-{-# LANGUAGE OverloadedStrings #-}-{-# LANGUAGE RecordWildCards #-}---- |--- Module      : $header$--- Copyright   : (c) Laurent P René de Cotret, 2019 - present--- License     : GNU GPL, version 2 or above--- Maintainer  : laurent.decotret@outlook.com--- Stability   : internal--- Portability : portable------ Reading configuration from file-module Text.Pandoc.Filter.Plot.Configuration-  ( configuration,-    configurationPathMeta,-    defaultConfiguration,-  )-where--import Data.Aeson (FromJSON (parseJSON), Key, Value (Null, Object), (.!=), (.:?))-import Data.String (IsString (..))-import Data.Text (Text, unpack)-import qualified Data.Text.IO as TIO-import Data.Yaml.Config (ignoreEnv, loadYamlSettings)-import System.FilePath (normalise)-import Text.Pandoc.Definition (Format (..), Inline (..), MetaValue (..), Pandoc (..), lookupMeta)-import Text.Pandoc.Filter.Plot.Monad---- | Read configuration from a YAML file. The--- keys are exactly the same as for code blocks.------ If a key is not present, its value will be set--- to the default value. Parsing errors result in thrown exceptions.-configuration :: FilePath -> IO Configuration-configuration fp = loadYamlSettings [normalise fp] [] ignoreEnv >>= renderConfig---- | Default configuration values.------ @since 0.5.0.0-defaultConfiguration :: Configuration-defaultConfiguration =-  Configuration-    { defaultDirectory = "plots/",-      defaultWithSource = False,-      defaultDPI = 80,-      defaultSaveFormat = PNG,-      defaultDependencies = mempty,-      captionFormat = Format "markdown+tex_math_dollars",-      sourceCodeLabel = "Source code",-      strictMode = False,-      logVerbosity = Warning,-      logSink = StdErr,-      -- Preambles-      matplotlibPreamble = mempty,-      plotlyPythonPreamble = mempty,-      plotlyRPreamble = mempty,-      matlabPreamble = mempty,-      mathematicaPreamble = mempty,-      octavePreamble = mempty,-      ggplot2Preamble = mempty,-      gnuplotPreamble = mempty,-      graphvizPreamble = mempty,-      bokehPreamble = mempty,-      plotsjlPreamble = mempty,-      plantumlPreamble = mempty,-      sagemathPreamble = mempty,-      d2Preamble = mempty,-      -- Executables-      matplotlibExe = python,-      matlabExe = "matlab",-      plotlyPythonExe = python,-      plotlyRExe = "Rscript",-      mathematicaExe = "math",-      octaveExe = "octave",-      ggplot2Exe = "Rscript",-      gnuplotExe = "gnuplot",-      graphvizExe = "dot",-      bokehExe = python,-      plotsjlExe = "julia",-      plantumlExe = "java",-      sagemathExe = "sage",-      d2Exe = "d2",-      -- Command line arguments-      matplotlibCmdArgs = mempty,-      matlabCmdArgs = mempty,-      plotlyPythonCmdArgs = mempty,-      plotlyRCmdArgs = mempty,-      mathematicaCmdArgs = mempty,-      octaveCmdArgs = mempty,-      ggplot2CmdArgs = mempty,-      gnuplotCmdArgs = mempty,-      graphvizCmdArgs = mempty,-      bokehCmdArgs = mempty,-      plotsjlCmdArgs = mempty,-      plantumlCmdArgs = "-jar plantuml.jar",-      sagemathCmdArgs = mempty,-      d2CmdArgs = mempty,-      -- Extras-      matplotlibTightBBox = False,-      matplotlibTransparent = False-    }-  where-    python = if isWindows then "python" else "python3"---- | Extact path to configuration from the metadata in a Pandoc document.--- The path to the configuration file should be under the @plot-configuration@ key.--- In case there is no such metadata, return the default configuration.------ For example, at the top of a markdown file:------ @--- ------ title: My document--- author: John Doe--- plot-configuration: /path/to/file.yml--- ------ @------ The same can be specified via the command line using Pandoc's @-M@ flag:------ > pandoc --filter pandoc-plot -M plot-configuration="path/to/file.yml" ...------ @since 0.6.0.0-configurationPathMeta :: Pandoc -> Maybe FilePath-configurationPathMeta (Pandoc meta _) =-  lookupMeta "plot-configuration" meta >>= getPath-  where-    getPath (MetaString t) = Just (unpack t)-    getPath (MetaInlines [Str s]) = Just (unpack s)-    getPath _ = Nothing---- We define a precursor type because preambles are best specified as file paths,--- but we want to read those files before building a full--- @Configuration@ value.-data ConfigPrecursor = ConfigPrecursor-  { _defaultDirectory :: !FilePath,-    _defaultWithSource :: !Bool,-    _defaultDPI :: !Int,-    _defaultSaveFormat :: !SaveFormat,-    _defaultDependencies :: ![FilePath],-    _captionFormat :: !Format,-    _sourceCodeLabel :: !Text,-    _strictMode :: !Bool,-    _logPrec :: !LoggingPrecursor,-    _matplotlibPrec :: !MatplotlibPrecursor,-    _matlabPrec :: !MatlabPrecursor,-    _plotlyPythonPrec :: !PlotlyPythonPrecursor,-    _plotlyRPrec :: !PlotlyRPrecursor,-    _mathematicaPrec :: !MathematicaPrecursor,-    _octavePrec :: !OctavePrecursor,-    _ggplot2Prec :: !GGPlot2Precursor,-    _gnuplotPrec :: !GNUPlotPrecursor,-    _graphvizPrec :: !GraphvizPrecursor,-    _bokehPrec :: !BokehPrecursor,-    _plotsjlPrec :: !PlotsjlPrecursor,-    _plantumlPrec :: !PlantUMLPrecursor,-    _sagemathPrec :: !SageMathPrecursor,-    _d2Prec :: !D2Precursor-  }--defaultConfigPrecursor :: ConfigPrecursor-defaultConfigPrecursor =-  ConfigPrecursor-    { _defaultDirectory = defaultDirectory defaultConfiguration,-      _defaultWithSource = defaultWithSource defaultConfiguration,-      _defaultDPI = defaultDPI defaultConfiguration,-      _defaultSaveFormat = defaultSaveFormat defaultConfiguration,-      _defaultDependencies = defaultDependencies defaultConfiguration,-      _captionFormat = captionFormat defaultConfiguration,-      _sourceCodeLabel = sourceCodeLabel defaultConfiguration,-      _strictMode = strictMode defaultConfiguration,-      _logPrec = LoggingPrecursor (logVerbosity defaultConfiguration) Nothing, -- _logFilePath=Nothing implies log to stderr-      _matplotlibPrec = MatplotlibPrecursor Nothing (matplotlibTightBBox defaultConfiguration) (matplotlibTransparent defaultConfiguration) (matplotlibExe defaultConfiguration) (matplotlibCmdArgs defaultConfiguration),-      _matlabPrec = MatlabPrecursor Nothing (matlabExe defaultConfiguration) (matlabCmdArgs defaultConfiguration),-      _plotlyPythonPrec = PlotlyPythonPrecursor Nothing (plotlyPythonExe defaultConfiguration) (plotlyPythonCmdArgs defaultConfiguration),-      _plotlyRPrec = PlotlyRPrecursor Nothing (plotlyRExe defaultConfiguration) (plotlyRCmdArgs defaultConfiguration),-      _mathematicaPrec = MathematicaPrecursor Nothing (mathematicaExe defaultConfiguration) (mathematicaCmdArgs defaultConfiguration),-      _octavePrec = OctavePrecursor Nothing (octaveExe defaultConfiguration) (octaveCmdArgs defaultConfiguration),-      _ggplot2Prec = GGPlot2Precursor Nothing (ggplot2Exe defaultConfiguration) (ggplot2CmdArgs defaultConfiguration),-      _gnuplotPrec = GNUPlotPrecursor Nothing (gnuplotExe defaultConfiguration) (gnuplotCmdArgs defaultConfiguration),-      _graphvizPrec = GraphvizPrecursor Nothing (graphvizExe defaultConfiguration) (graphvizCmdArgs defaultConfiguration),-      _bokehPrec = BokehPrecursor Nothing (bokehExe defaultConfiguration) (bokehCmdArgs defaultConfiguration),-      _plotsjlPrec = PlotsjlPrecursor Nothing (plotsjlExe defaultConfiguration) (plotsjlCmdArgs defaultConfiguration),-      _plantumlPrec = PlantUMLPrecursor Nothing (plantumlExe defaultConfiguration) (plantumlCmdArgs defaultConfiguration),-      _sagemathPrec = SageMathPrecursor Nothing (sagemathExe defaultConfiguration) (sagemathCmdArgs defaultConfiguration),-      _d2Prec = D2Precursor Nothing (d2Exe defaultConfiguration) (d2CmdArgs defaultConfiguration)-    }--data LoggingPrecursor = LoggingPrecursor-  { _logVerbosity :: !Verbosity,-    _logFilePath :: !(Maybe FilePath)-  }---- Separate YAML clauses have their own types.-data MatplotlibPrecursor = MatplotlibPrecursor-  { _matplotlibPreamble :: !(Maybe FilePath),-    _matplotlibTightBBox :: !Bool,-    _matplotlibTransparent :: !Bool,-    _matplotlibExe :: !FilePath,-    _matplotlibCmdArgs :: !Text-  }--data MatlabPrecursor = MatlabPrecursor {_matlabPreamble :: !(Maybe FilePath), _matlabExe :: !FilePath, _matlabCmdArgs :: !Text}--data PlotlyPythonPrecursor = PlotlyPythonPrecursor {_plotlyPythonPreamble :: !(Maybe FilePath), _plotlyPythonExe :: !FilePath, _plotlyPythonCmdArgs :: !Text}--data PlotlyRPrecursor = PlotlyRPrecursor {_plotlyRPreamble :: !(Maybe FilePath), _plotlyRExe :: !FilePath, _plotlyRCmdArgs :: !Text}--data MathematicaPrecursor = MathematicaPrecursor {_mathematicaPreamble :: !(Maybe FilePath), _mathematicaExe :: !FilePath, _mathematicaCmdArgs :: !Text}--data OctavePrecursor = OctavePrecursor {_octavePreamble :: !(Maybe FilePath), _octaveExe :: !FilePath, _octaveCmdArgs :: !Text}--data GGPlot2Precursor = GGPlot2Precursor {_ggplot2Preamble :: !(Maybe FilePath), _ggplot2Exe :: !FilePath, _ggplot2CmdArgs :: !Text}--data GNUPlotPrecursor = GNUPlotPrecursor {_gnuplotPreamble :: !(Maybe FilePath), _gnuplotExe :: !FilePath, _gnuplotCmdArgs :: !Text}--data GraphvizPrecursor = GraphvizPrecursor {_graphvizPreamble :: !(Maybe FilePath), _graphvizExe :: !FilePath, _graphvizCmdArgs :: !Text}--data BokehPrecursor = BokehPrecursor {_bokehPreamble :: !(Maybe FilePath), _bokehExe :: !FilePath, _bokehCmdArgs :: !Text}--data PlotsjlPrecursor = PlotsjlPrecursor {_plotsjlPreamble :: !(Maybe FilePath), _plotsjlExe :: !FilePath, _plotsjlCmdArgs :: !Text}--data PlantUMLPrecursor = PlantUMLPrecursor {_plantumlPreamble :: !(Maybe FilePath), _plantumlExe :: !FilePath, _plantumlCmdArgs :: !Text}--data SageMathPrecursor = SageMathPrecursor {_sagemathPreamble :: !(Maybe FilePath), _sagemathExe :: !FilePath, _sagemathCmdArgs :: !Text}--data D2Precursor = D2Precursor {_d2Preamble :: !(Maybe FilePath), _d2Exe :: !FilePath, _d2CmdArgs :: !Text}--instance FromJSON LoggingPrecursor where-  parseJSON (Object v) =-    LoggingPrecursor-      <$> v .:? "verbosity" .!= logVerbosity defaultConfiguration-      <*> v .:? "filepath"-  parseJSON _ = fail $ mconcat ["Could not parse logging configuration. "]--asKey :: InclusionKey -> Key-asKey = fromString . show--instance FromJSON MatplotlibPrecursor where-  parseJSON (Object v) =-    MatplotlibPrecursor-      <$> v .:? asKey PreambleK-      <*> v .:? asKey MatplotlibTightBBoxK .!= matplotlibTightBBox defaultConfiguration-      <*> v .:? asKey MatplotlibTransparentK .!= matplotlibTransparent defaultConfiguration-      <*> v .:? asKey ExecutableK .!= matplotlibExe defaultConfiguration-      <*> v .:? asKey CommandLineArgsK .!= matplotlibCmdArgs defaultConfiguration-  parseJSON _ = fail $ mconcat ["Could not parse ", show Matplotlib, " configuration."]--instance FromJSON MatlabPrecursor where-  parseJSON (Object v) = MatlabPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= matlabExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= matlabCmdArgs defaultConfiguration-  parseJSON _ = fail $ mconcat ["Could not parse ", show Matlab, " configuration."]--instance FromJSON PlotlyPythonPrecursor where-  parseJSON (Object v) = PlotlyPythonPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= plotlyPythonExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= plotlyPythonCmdArgs defaultConfiguration-  parseJSON _ = fail $ mconcat ["Could not parse ", show PlotlyPython, " configuration."]--instance FromJSON PlotlyRPrecursor where-  parseJSON (Object v) = PlotlyRPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= plotlyRExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= plotlyRCmdArgs defaultConfiguration-  parseJSON _ = fail $ mconcat ["Could not parse ", show PlotlyR, " configuration."]--instance FromJSON MathematicaPrecursor where-  parseJSON (Object v) = MathematicaPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= mathematicaExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= mathematicaCmdArgs defaultConfiguration-  parseJSON _ = fail $ mconcat ["Could not parse ", show Mathematica, " configuration."]--instance FromJSON OctavePrecursor where-  parseJSON (Object v) = OctavePrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= octaveExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= octaveCmdArgs defaultConfiguration-  parseJSON _ = fail $ mconcat ["Could not parse ", show Octave, " configuration."]--instance FromJSON GGPlot2Precursor where-  parseJSON (Object v) = GGPlot2Precursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= ggplot2Exe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= ggplot2CmdArgs defaultConfiguration-  parseJSON _ = fail $ mconcat ["Could not parse ", show GGPlot2, " configuration."]--instance FromJSON GNUPlotPrecursor where-  parseJSON (Object v) = GNUPlotPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= gnuplotExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= gnuplotCmdArgs defaultConfiguration-  parseJSON _ = fail $ mconcat ["Could not parse ", show GNUPlot, " configuration."]--instance FromJSON GraphvizPrecursor where-  parseJSON (Object v) = GraphvizPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= graphvizExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= graphvizCmdArgs defaultConfiguration-  parseJSON _ = fail $ mconcat ["Could not parse ", show Graphviz, " configuration."]--instance FromJSON BokehPrecursor where-  parseJSON (Object v) = BokehPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= bokehExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= bokehCmdArgs defaultConfiguration-  parseJSON _ = fail $ mconcat ["Could not parse ", show Bokeh, " configuration."]--instance FromJSON PlotsjlPrecursor where-  parseJSON (Object v) = PlotsjlPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= plotsjlExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= plotsjlCmdArgs defaultConfiguration-  parseJSON _ = fail $ mconcat ["Could not parse ", show Plotsjl, " configuration."]--instance FromJSON PlantUMLPrecursor where-  parseJSON (Object v) = PlantUMLPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= plantumlExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= plantumlCmdArgs defaultConfiguration-  parseJSON _ = fail $ mconcat ["Could not parse ", show PlantUML, " configuration."]--instance FromJSON SageMathPrecursor where-  parseJSON (Object v) = SageMathPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= sagemathExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= sagemathCmdArgs defaultConfiguration-  parseJSON _ = fail $ mconcat ["Could not parse ", show SageMath, " configuration."]--instance FromJSON D2Precursor where-  parseJSON (Object v) = D2Precursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= d2Exe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= d2CmdArgs defaultConfiguration-  parseJSON _ = fail $ mconcat ["Could not parse ", show SageMath, " configuration."]--toolkitAsKey :: Toolkit -> Key-toolkitAsKey = fromString . unpack . cls--instance FromJSON ConfigPrecursor where-  parseJSON Null = return defaultConfigPrecursor -- In case of empty file-  parseJSON (Object v) = do-    _defaultDirectory <- v .:? asKey DirectoryK .!= _defaultDirectory defaultConfigPrecursor-    _defaultWithSource <- v .:? asKey WithSourceK .!= _defaultWithSource defaultConfigPrecursor-    _defaultDPI <- v .:? asKey DpiK .!= _defaultDPI defaultConfigPrecursor-    _defaultSaveFormat <- v .:? asKey SaveFormatK .!= _defaultSaveFormat defaultConfigPrecursor-    _defaultDependencies <- v .:? asKey DependenciesK .!= _defaultDependencies defaultConfigPrecursor-    _captionFormat <- v .:? asKey CaptionFormatK .!= _captionFormat defaultConfigPrecursor-    _sourceCodeLabel <- v .:? asKey SourceCodeLabelK .!= _sourceCodeLabel defaultConfigPrecursor-    _strictMode <- v .:? asKey StrictModeK .!= _strictMode defaultConfigPrecursor-    _logPrec <- v .:? "logging" .!= _logPrec defaultConfigPrecursor--    _matplotlibPrec <- v .:? toolkitAsKey Matplotlib .!= _matplotlibPrec defaultConfigPrecursor-    _matlabPrec <- v .:? toolkitAsKey Matlab .!= _matlabPrec defaultConfigPrecursor-    _plotlyPythonPrec <- v .:? toolkitAsKey PlotlyPython .!= _plotlyPythonPrec defaultConfigPrecursor-    _plotlyRPrec <- v .:? toolkitAsKey PlotlyR .!= _plotlyRPrec defaultConfigPrecursor-    _mathematicaPrec <- v .:? toolkitAsKey Mathematica .!= _mathematicaPrec defaultConfigPrecursor-    _octavePrec <- v .:? toolkitAsKey Octave .!= _octavePrec defaultConfigPrecursor-    _ggplot2Prec <- v .:? toolkitAsKey GGPlot2 .!= _ggplot2Prec defaultConfigPrecursor-    _gnuplotPrec <- v .:? toolkitAsKey GNUPlot .!= _gnuplotPrec defaultConfigPrecursor-    _graphvizPrec <- v .:? toolkitAsKey Graphviz .!= _graphvizPrec defaultConfigPrecursor-    _bokehPrec <- v .:? toolkitAsKey Bokeh .!= _bokehPrec defaultConfigPrecursor-    _plotsjlPrec <- v .:? toolkitAsKey Plotsjl .!= _plotsjlPrec defaultConfigPrecursor-    _plantumlPrec <- v .:? toolkitAsKey PlantUML .!= _plantumlPrec defaultConfigPrecursor-    _sagemathPrec <- v .:? toolkitAsKey SageMath .!= _sagemathPrec defaultConfigPrecursor-    _d2Prec <- v .:? toolkitAsKey D2 .!= _d2Prec defaultConfigPrecursor--    return $ ConfigPrecursor {..}-  parseJSON _ = fail "Could not parse configuration."--renderConfig :: ConfigPrecursor -> IO Configuration-renderConfig ConfigPrecursor {..} = do-  let defaultDirectory = _defaultDirectory-      defaultWithSource = _defaultWithSource-      defaultDPI = _defaultDPI-      defaultSaveFormat = _defaultSaveFormat-      defaultDependencies = _defaultDependencies-      captionFormat = _captionFormat-      sourceCodeLabel = _sourceCodeLabel-      strictMode = _strictMode--      logVerbosity = _logVerbosity _logPrec-      logSink = maybe StdErr LogFile (_logFilePath _logPrec)--      matplotlibTightBBox = _matplotlibTightBBox _matplotlibPrec-      matplotlibTransparent = _matplotlibTransparent _matplotlibPrec--      matplotlibExe = _matplotlibExe _matplotlibPrec-      matlabExe = _matlabExe _matlabPrec-      plotlyPythonExe = _plotlyPythonExe _plotlyPythonPrec-      plotlyRExe = _plotlyRExe _plotlyRPrec-      mathematicaExe = _mathematicaExe _mathematicaPrec-      octaveExe = _octaveExe _octavePrec-      ggplot2Exe = _ggplot2Exe _ggplot2Prec-      gnuplotExe = _gnuplotExe _gnuplotPrec-      graphvizExe = _graphvizExe _graphvizPrec-      bokehExe = _bokehExe _bokehPrec-      plotsjlExe = _plotsjlExe _plotsjlPrec-      plantumlExe = _plantumlExe _plantumlPrec-      sagemathExe = _sagemathExe _sagemathPrec-      d2Exe = _d2Exe _d2Prec--      matplotlibCmdArgs = _matplotlibCmdArgs _matplotlibPrec-      matlabCmdArgs = _matlabCmdArgs _matlabPrec-      plotlyPythonCmdArgs = _plotlyPythonCmdArgs _plotlyPythonPrec-      plotlyRCmdArgs = _plotlyRCmdArgs _plotlyRPrec-      mathematicaCmdArgs = _mathematicaCmdArgs _mathematicaPrec-      octaveCmdArgs = _octaveCmdArgs _octavePrec-      ggplot2CmdArgs = _ggplot2CmdArgs _ggplot2Prec-      gnuplotCmdArgs = _gnuplotCmdArgs _gnuplotPrec-      graphvizCmdArgs = _graphvizCmdArgs _graphvizPrec-      bokehCmdArgs = _bokehCmdArgs _bokehPrec-      plotsjlCmdArgs = _plotsjlCmdArgs _plotsjlPrec-      plantumlCmdArgs = _plantumlCmdArgs _plantumlPrec-      sagemathCmdArgs = _sagemathCmdArgs _sagemathPrec-      d2CmdArgs = _d2CmdArgs _d2Prec--  matplotlibPreamble <- readPreamble (_matplotlibPreamble _matplotlibPrec)-  matlabPreamble <- readPreamble (_matlabPreamble _matlabPrec)-  plotlyPythonPreamble <- readPreamble (_plotlyPythonPreamble _plotlyPythonPrec)-  plotlyRPreamble <- readPreamble (_plotlyRPreamble _plotlyRPrec)-  mathematicaPreamble <- readPreamble (_mathematicaPreamble _mathematicaPrec)-  octavePreamble <- readPreamble (_octavePreamble _octavePrec)-  ggplot2Preamble <- readPreamble (_ggplot2Preamble _ggplot2Prec)-  gnuplotPreamble <- readPreamble (_gnuplotPreamble _gnuplotPrec)-  graphvizPreamble <- readPreamble (_graphvizPreamble _graphvizPrec)-  bokehPreamble <- readPreamble (_bokehPreamble _bokehPrec)-  plotsjlPreamble <- readPreamble (_plotsjlPreamble _plotsjlPrec)-  plantumlPreamble <- readPreamble (_plantumlPreamble _plantumlPrec)-  sagemathPreamble <- readPreamble (_sagemathPreamble _sagemathPrec)-  d2Preamble <- readPreamble (_d2Preamble _d2Prec)--  return Configuration {..}-  where-    readPreamble = maybe mempty TIO.readFile+{-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE RecordWildCards #-}
+
+-- |
+-- Module      : $header$
+-- Copyright   : (c) Laurent P René de Cotret, 2019 - present
+-- License     : GNU GPL, version 2 or above
+-- Maintainer  : laurent.decotret@outlook.com
+-- Stability   : internal
+-- Portability : portable
+--
+-- Reading configuration from file
+module Text.Pandoc.Filter.Plot.Configuration
+  ( configuration,
+    configurationPathMeta,
+    defaultConfiguration,
+  )
+where
+
+import Data.Aeson (FromJSON (parseJSON), Key, Value (Null, Object), (.!=), (.:?))
+import Data.String (IsString (..))
+import Data.Text (Text, unpack)
+import qualified Data.Text.IO as TIO
+import Data.Yaml.Config (ignoreEnv, loadYamlSettings)
+import System.FilePath (normalise)
+import Text.Pandoc.Definition (Format (..), Inline (..), MetaValue (..), Pandoc (..), lookupMeta)
+import Text.Pandoc.Filter.Plot.Monad
+
+-- | Read configuration from a YAML file. The
+-- keys are exactly the same as for code blocks.
+--
+-- If a key is not present, its value will be set
+-- to the default value. Parsing errors result in thrown exceptions.
+configuration :: FilePath -> IO Configuration
+configuration fp = loadYamlSettings [normalise fp] [] ignoreEnv >>= renderConfig
+
+-- | Default configuration values.
+--
+-- @since 0.5.0.0
+defaultConfiguration :: Configuration
+defaultConfiguration =
+  Configuration
+    { defaultDirectory = "plots/",
+      defaultWithSource = False,
+      defaultDPI = 80,
+      defaultSaveFormat = PNG,
+      defaultDependencies = mempty,
+      captionFormat = Format "markdown+tex_math_dollars",
+      sourceCodeLabel = "Source code",
+      strictMode = False,
+      logVerbosity = Warning,
+      logSink = StdErr,
+      -- Preambles
+      matplotlibPreamble = mempty,
+      plotlyPythonPreamble = mempty,
+      plotlyRPreamble = mempty,
+      matlabPreamble = mempty,
+      mathematicaPreamble = mempty,
+      octavePreamble = mempty,
+      ggplot2Preamble = mempty,
+      gnuplotPreamble = mempty,
+      graphvizPreamble = mempty,
+      bokehPreamble = mempty,
+      plotsjlPreamble = mempty,
+      plantumlPreamble = mempty,
+      sagemathPreamble = mempty,
+      d2Preamble = mempty,
+      asyPreamble = mempty,
+      -- Executables
+      matplotlibExe = python,
+      matlabExe = "matlab",
+      plotlyPythonExe = python,
+      plotlyRExe = "Rscript",
+      mathematicaExe = "math",
+      octaveExe = "octave",
+      ggplot2Exe = "Rscript",
+      gnuplotExe = "gnuplot",
+      graphvizExe = "dot",
+      bokehExe = python,
+      plotsjlExe = "julia",
+      plantumlExe = "java",
+      sagemathExe = "sage",
+      d2Exe = "d2",
+      asyExe = "asy",
+      -- Command line arguments
+      matplotlibCmdArgs = mempty,
+      matlabCmdArgs = mempty,
+      plotlyPythonCmdArgs = mempty,
+      plotlyRCmdArgs = mempty,
+      mathematicaCmdArgs = mempty,
+      octaveCmdArgs = mempty,
+      ggplot2CmdArgs = mempty,
+      gnuplotCmdArgs = mempty,
+      graphvizCmdArgs = mempty,
+      bokehCmdArgs = mempty,
+      plotsjlCmdArgs = mempty,
+      plantumlCmdArgs = "-jar plantuml.jar",
+      sagemathCmdArgs = mempty,
+      d2CmdArgs = mempty,
+      asyCmdArgs = mempty,
+      -- Extras
+      matplotlibTightBBox = False,
+      matplotlibTransparent = False
+    }
+  where
+    python = if isWindows then "python" else "python3"
+
+-- | Extact path to configuration from the metadata in a Pandoc document.
+-- The path to the configuration file should be under the @plot-configuration@ key.
+-- In case there is no such metadata, return the default configuration.
+--
+-- For example, at the top of a markdown file:
+--
+-- @
+-- ---
+-- title: My document
+-- author: John Doe
+-- plot-configuration: /path/to/file.yml
+-- ---
+-- @
+--
+-- The same can be specified via the command line using Pandoc's @-M@ flag:
+--
+-- > pandoc --filter pandoc-plot -M plot-configuration="path/to/file.yml" ...
+--
+-- @since 0.6.0.0
+configurationPathMeta :: Pandoc -> Maybe FilePath
+configurationPathMeta (Pandoc meta _) =
+  lookupMeta "plot-configuration" meta >>= getPath
+  where
+    getPath (MetaString t) = Just (unpack t)
+    getPath (MetaInlines [Str s]) = Just (unpack s)
+    getPath _ = Nothing
+
+-- We define a precursor type because preambles are best specified as file paths,
+-- but we want to read those files before building a full
+-- @Configuration@ value.
+data ConfigPrecursor = ConfigPrecursor
+  { _defaultDirectory :: !FilePath,
+    _defaultWithSource :: !Bool,
+    _defaultDPI :: !Int,
+    _defaultSaveFormat :: !SaveFormat,
+    _defaultDependencies :: ![FilePath],
+    _captionFormat :: !Format,
+    _sourceCodeLabel :: !Text,
+    _strictMode :: !Bool,
+    _logPrec :: !LoggingPrecursor,
+    _matplotlibPrec :: !MatplotlibPrecursor,
+    _matlabPrec :: !MatlabPrecursor,
+    _plotlyPythonPrec :: !PlotlyPythonPrecursor,
+    _plotlyRPrec :: !PlotlyRPrecursor,
+    _mathematicaPrec :: !MathematicaPrecursor,
+    _octavePrec :: !OctavePrecursor,
+    _ggplot2Prec :: !GGPlot2Precursor,
+    _gnuplotPrec :: !GNUPlotPrecursor,
+    _graphvizPrec :: !GraphvizPrecursor,
+    _bokehPrec :: !BokehPrecursor,
+    _plotsjlPrec :: !PlotsjlPrecursor,
+    _plantumlPrec :: !PlantUMLPrecursor,
+    _sagemathPrec :: !SageMathPrecursor,
+    _d2Prec :: !D2Precursor,
+    _asyPrec :: !AsyPrecursor
+  }
+
+defaultConfigPrecursor :: ConfigPrecursor
+defaultConfigPrecursor =
+  ConfigPrecursor
+    { _defaultDirectory = defaultDirectory defaultConfiguration,
+      _defaultWithSource = defaultWithSource defaultConfiguration,
+      _defaultDPI = defaultDPI defaultConfiguration,
+      _defaultSaveFormat = defaultSaveFormat defaultConfiguration,
+      _defaultDependencies = defaultDependencies defaultConfiguration,
+      _captionFormat = captionFormat defaultConfiguration,
+      _sourceCodeLabel = sourceCodeLabel defaultConfiguration,
+      _strictMode = strictMode defaultConfiguration,
+      _logPrec = LoggingPrecursor (logVerbosity defaultConfiguration) Nothing, -- _logFilePath=Nothing implies log to stderr
+      _matplotlibPrec = MatplotlibPrecursor Nothing (matplotlibTightBBox defaultConfiguration) (matplotlibTransparent defaultConfiguration) (matplotlibExe defaultConfiguration) (matplotlibCmdArgs defaultConfiguration),
+      _matlabPrec = MatlabPrecursor Nothing (matlabExe defaultConfiguration) (matlabCmdArgs defaultConfiguration),
+      _plotlyPythonPrec = PlotlyPythonPrecursor Nothing (plotlyPythonExe defaultConfiguration) (plotlyPythonCmdArgs defaultConfiguration),
+      _plotlyRPrec = PlotlyRPrecursor Nothing (plotlyRExe defaultConfiguration) (plotlyRCmdArgs defaultConfiguration),
+      _mathematicaPrec = MathematicaPrecursor Nothing (mathematicaExe defaultConfiguration) (mathematicaCmdArgs defaultConfiguration),
+      _octavePrec = OctavePrecursor Nothing (octaveExe defaultConfiguration) (octaveCmdArgs defaultConfiguration),
+      _ggplot2Prec = GGPlot2Precursor Nothing (ggplot2Exe defaultConfiguration) (ggplot2CmdArgs defaultConfiguration),
+      _gnuplotPrec = GNUPlotPrecursor Nothing (gnuplotExe defaultConfiguration) (gnuplotCmdArgs defaultConfiguration),
+      _graphvizPrec = GraphvizPrecursor Nothing (graphvizExe defaultConfiguration) (graphvizCmdArgs defaultConfiguration),
+      _bokehPrec = BokehPrecursor Nothing (bokehExe defaultConfiguration) (bokehCmdArgs defaultConfiguration),
+      _plotsjlPrec = PlotsjlPrecursor Nothing (plotsjlExe defaultConfiguration) (plotsjlCmdArgs defaultConfiguration),
+      _plantumlPrec = PlantUMLPrecursor Nothing (plantumlExe defaultConfiguration) (plantumlCmdArgs defaultConfiguration),
+      _sagemathPrec = SageMathPrecursor Nothing (sagemathExe defaultConfiguration) (sagemathCmdArgs defaultConfiguration),
+      _d2Prec = D2Precursor Nothing (d2Exe defaultConfiguration) (d2CmdArgs defaultConfiguration),
+      _asyPrec = AsyPrecursor Nothing (asyExe defaultConfiguration) (asyCmdArgs defaultConfiguration)
+    }
+
+data LoggingPrecursor = LoggingPrecursor
+  { _logVerbosity :: !Verbosity,
+    _logFilePath :: !(Maybe FilePath)
+  }
+
+-- Separate YAML clauses have their own types.
+data MatplotlibPrecursor = MatplotlibPrecursor
+  { _matplotlibPreamble :: !(Maybe FilePath),
+    _matplotlibTightBBox :: !Bool,
+    _matplotlibTransparent :: !Bool,
+    _matplotlibExe :: !FilePath,
+    _matplotlibCmdArgs :: !Text
+  }
+
+data MatlabPrecursor = MatlabPrecursor {_matlabPreamble :: !(Maybe FilePath), _matlabExe :: !FilePath, _matlabCmdArgs :: !Text}
+
+data PlotlyPythonPrecursor = PlotlyPythonPrecursor {_plotlyPythonPreamble :: !(Maybe FilePath), _plotlyPythonExe :: !FilePath, _plotlyPythonCmdArgs :: !Text}
+
+data PlotlyRPrecursor = PlotlyRPrecursor {_plotlyRPreamble :: !(Maybe FilePath), _plotlyRExe :: !FilePath, _plotlyRCmdArgs :: !Text}
+
+data MathematicaPrecursor = MathematicaPrecursor {_mathematicaPreamble :: !(Maybe FilePath), _mathematicaExe :: !FilePath, _mathematicaCmdArgs :: !Text}
+
+data OctavePrecursor = OctavePrecursor {_octavePreamble :: !(Maybe FilePath), _octaveExe :: !FilePath, _octaveCmdArgs :: !Text}
+
+data GGPlot2Precursor = GGPlot2Precursor {_ggplot2Preamble :: !(Maybe FilePath), _ggplot2Exe :: !FilePath, _ggplot2CmdArgs :: !Text}
+
+data GNUPlotPrecursor = GNUPlotPrecursor {_gnuplotPreamble :: !(Maybe FilePath), _gnuplotExe :: !FilePath, _gnuplotCmdArgs :: !Text}
+
+data GraphvizPrecursor = GraphvizPrecursor {_graphvizPreamble :: !(Maybe FilePath), _graphvizExe :: !FilePath, _graphvizCmdArgs :: !Text}
+
+data BokehPrecursor = BokehPrecursor {_bokehPreamble :: !(Maybe FilePath), _bokehExe :: !FilePath, _bokehCmdArgs :: !Text}
+
+data PlotsjlPrecursor = PlotsjlPrecursor {_plotsjlPreamble :: !(Maybe FilePath), _plotsjlExe :: !FilePath, _plotsjlCmdArgs :: !Text}
+
+data PlantUMLPrecursor = PlantUMLPrecursor {_plantumlPreamble :: !(Maybe FilePath), _plantumlExe :: !FilePath, _plantumlCmdArgs :: !Text}
+
+data SageMathPrecursor = SageMathPrecursor {_sagemathPreamble :: !(Maybe FilePath), _sagemathExe :: !FilePath, _sagemathCmdArgs :: !Text}
+
+data D2Precursor = D2Precursor {_d2Preamble :: !(Maybe FilePath), _d2Exe :: !FilePath, _d2CmdArgs :: !Text}
+
+data AsyPrecursor = AsyPrecursor {_asyPreamble :: !(Maybe FilePath), _asyExe :: !FilePath, _asyCmdArgs :: !Text}
+
+instance FromJSON LoggingPrecursor where
+  parseJSON (Object v) =
+    LoggingPrecursor
+      <$> v .:? "verbosity" .!= logVerbosity defaultConfiguration
+      <*> v .:? "filepath"
+  parseJSON _ = fail $ mconcat ["Could not parse logging configuration. "]
+
+asKey :: InclusionKey -> Key
+asKey = fromString . show
+
+instance FromJSON MatplotlibPrecursor where
+  parseJSON (Object v) =
+    MatplotlibPrecursor
+      <$> v .:? asKey PreambleK
+      <*> v .:? asKey MatplotlibTightBBoxK .!= matplotlibTightBBox defaultConfiguration
+      <*> v .:? asKey MatplotlibTransparentK .!= matplotlibTransparent defaultConfiguration
+      <*> v .:? asKey ExecutableK .!= matplotlibExe defaultConfiguration
+      <*> v .:? asKey CommandLineArgsK .!= matplotlibCmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show Matplotlib, " configuration."]
+
+instance FromJSON MatlabPrecursor where
+  parseJSON (Object v) = MatlabPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= matlabExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= matlabCmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show Matlab, " configuration."]
+
+instance FromJSON PlotlyPythonPrecursor where
+  parseJSON (Object v) = PlotlyPythonPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= plotlyPythonExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= plotlyPythonCmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show PlotlyPython, " configuration."]
+
+instance FromJSON PlotlyRPrecursor where
+  parseJSON (Object v) = PlotlyRPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= plotlyRExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= plotlyRCmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show PlotlyR, " configuration."]
+
+instance FromJSON MathematicaPrecursor where
+  parseJSON (Object v) = MathematicaPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= mathematicaExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= mathematicaCmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show Mathematica, " configuration."]
+
+instance FromJSON OctavePrecursor where
+  parseJSON (Object v) = OctavePrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= octaveExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= octaveCmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show Octave, " configuration."]
+
+instance FromJSON GGPlot2Precursor where
+  parseJSON (Object v) = GGPlot2Precursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= ggplot2Exe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= ggplot2CmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show GGPlot2, " configuration."]
+
+instance FromJSON GNUPlotPrecursor where
+  parseJSON (Object v) = GNUPlotPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= gnuplotExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= gnuplotCmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show GNUPlot, " configuration."]
+
+instance FromJSON GraphvizPrecursor where
+  parseJSON (Object v) = GraphvizPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= graphvizExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= graphvizCmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show Graphviz, " configuration."]
+
+instance FromJSON BokehPrecursor where
+  parseJSON (Object v) = BokehPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= bokehExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= bokehCmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show Bokeh, " configuration."]
+
+instance FromJSON PlotsjlPrecursor where
+  parseJSON (Object v) = PlotsjlPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= plotsjlExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= plotsjlCmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show Plotsjl, " configuration."]
+
+instance FromJSON PlantUMLPrecursor where
+  parseJSON (Object v) = PlantUMLPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= plantumlExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= plantumlCmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show PlantUML, " configuration."]
+
+instance FromJSON SageMathPrecursor where
+  parseJSON (Object v) = SageMathPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= sagemathExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= sagemathCmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show SageMath, " configuration."]
+
+instance FromJSON D2Precursor where
+  parseJSON (Object v) = D2Precursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= d2Exe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= d2CmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show SageMath, " configuration."]
+
+instance FromJSON AsyPrecursor where
+  parseJSON (Object v) = AsyPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= asyExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= asyCmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show Asymptote, " configuration."]
+
+toolkitAsKey :: Toolkit -> Key
+toolkitAsKey = fromString . unpack . cls
+
+instance FromJSON ConfigPrecursor where
+  parseJSON Null = return defaultConfigPrecursor -- In case of empty file
+  parseJSON (Object v) = do
+    _defaultDirectory <- v .:? asKey DirectoryK .!= _defaultDirectory defaultConfigPrecursor
+    _defaultWithSource <- v .:? asKey WithSourceK .!= _defaultWithSource defaultConfigPrecursor
+    _defaultDPI <- v .:? asKey DpiK .!= _defaultDPI defaultConfigPrecursor
+    _defaultSaveFormat <- v .:? asKey SaveFormatK .!= _defaultSaveFormat defaultConfigPrecursor
+    _defaultDependencies <- v .:? asKey DependenciesK .!= _defaultDependencies defaultConfigPrecursor
+    _captionFormat <- v .:? asKey CaptionFormatK .!= _captionFormat defaultConfigPrecursor
+    _sourceCodeLabel <- v .:? asKey SourceCodeLabelK .!= _sourceCodeLabel defaultConfigPrecursor
+    _strictMode <- v .:? asKey StrictModeK .!= _strictMode defaultConfigPrecursor
+    _logPrec <- v .:? "logging" .!= _logPrec defaultConfigPrecursor
+
+    _matplotlibPrec <- v .:? toolkitAsKey Matplotlib .!= _matplotlibPrec defaultConfigPrecursor
+    _matlabPrec <- v .:? toolkitAsKey Matlab .!= _matlabPrec defaultConfigPrecursor
+    _plotlyPythonPrec <- v .:? toolkitAsKey PlotlyPython .!= _plotlyPythonPrec defaultConfigPrecursor
+    _plotlyRPrec <- v .:? toolkitAsKey PlotlyR .!= _plotlyRPrec defaultConfigPrecursor
+    _mathematicaPrec <- v .:? toolkitAsKey Mathematica .!= _mathematicaPrec defaultConfigPrecursor
+    _octavePrec <- v .:? toolkitAsKey Octave .!= _octavePrec defaultConfigPrecursor
+    _ggplot2Prec <- v .:? toolkitAsKey GGPlot2 .!= _ggplot2Prec defaultConfigPrecursor
+    _gnuplotPrec <- v .:? toolkitAsKey GNUPlot .!= _gnuplotPrec defaultConfigPrecursor
+    _graphvizPrec <- v .:? toolkitAsKey Graphviz .!= _graphvizPrec defaultConfigPrecursor
+    _bokehPrec <- v .:? toolkitAsKey Bokeh .!= _bokehPrec defaultConfigPrecursor
+    _plotsjlPrec <- v .:? toolkitAsKey Plotsjl .!= _plotsjlPrec defaultConfigPrecursor
+    _plantumlPrec <- v .:? toolkitAsKey PlantUML .!= _plantumlPrec defaultConfigPrecursor
+    _sagemathPrec <- v .:? toolkitAsKey SageMath .!= _sagemathPrec defaultConfigPrecursor
+    _d2Prec <- v .:? toolkitAsKey D2 .!= _d2Prec defaultConfigPrecursor
+    _asyPrec <- v .:? toolkitAsKey Asymptote .!= _asyPrec defaultConfigPrecursor
+
+    return $ ConfigPrecursor {..}
+  parseJSON _ = fail "Could not parse configuration."
+
+renderConfig :: ConfigPrecursor -> IO Configuration
+renderConfig ConfigPrecursor {..} = do
+  let defaultDirectory = _defaultDirectory
+      defaultWithSource = _defaultWithSource
+      defaultDPI = _defaultDPI
+      defaultSaveFormat = _defaultSaveFormat
+      defaultDependencies = _defaultDependencies
+      captionFormat = _captionFormat
+      sourceCodeLabel = _sourceCodeLabel
+      strictMode = _strictMode
+
+      logVerbosity = _logVerbosity _logPrec
+      logSink = maybe StdErr LogFile (_logFilePath _logPrec)
+
+      matplotlibTightBBox = _matplotlibTightBBox _matplotlibPrec
+      matplotlibTransparent = _matplotlibTransparent _matplotlibPrec
+
+      matplotlibExe = _matplotlibExe _matplotlibPrec
+      matlabExe = _matlabExe _matlabPrec
+      plotlyPythonExe = _plotlyPythonExe _plotlyPythonPrec
+      plotlyRExe = _plotlyRExe _plotlyRPrec
+      mathematicaExe = _mathematicaExe _mathematicaPrec
+      octaveExe = _octaveExe _octavePrec
+      ggplot2Exe = _ggplot2Exe _ggplot2Prec
+      gnuplotExe = _gnuplotExe _gnuplotPrec
+      graphvizExe = _graphvizExe _graphvizPrec
+      bokehExe = _bokehExe _bokehPrec
+      plotsjlExe = _plotsjlExe _plotsjlPrec
+      plantumlExe = _plantumlExe _plantumlPrec
+      sagemathExe = _sagemathExe _sagemathPrec
+      d2Exe = _d2Exe _d2Prec
+      asyExe = _asyExe _asyPrec
+
+      matplotlibCmdArgs = _matplotlibCmdArgs _matplotlibPrec
+      matlabCmdArgs = _matlabCmdArgs _matlabPrec
+      plotlyPythonCmdArgs = _plotlyPythonCmdArgs _plotlyPythonPrec
+      plotlyRCmdArgs = _plotlyRCmdArgs _plotlyRPrec
+      mathematicaCmdArgs = _mathematicaCmdArgs _mathematicaPrec
+      octaveCmdArgs = _octaveCmdArgs _octavePrec
+      ggplot2CmdArgs = _ggplot2CmdArgs _ggplot2Prec
+      gnuplotCmdArgs = _gnuplotCmdArgs _gnuplotPrec
+      graphvizCmdArgs = _graphvizCmdArgs _graphvizPrec
+      bokehCmdArgs = _bokehCmdArgs _bokehPrec
+      plotsjlCmdArgs = _plotsjlCmdArgs _plotsjlPrec
+      plantumlCmdArgs = _plantumlCmdArgs _plantumlPrec
+      sagemathCmdArgs = _sagemathCmdArgs _sagemathPrec
+      d2CmdArgs = _d2CmdArgs _d2Prec
+      asyCmdArgs = _asyCmdArgs _asyPrec
+
+  matplotlibPreamble <- readPreamble (_matplotlibPreamble _matplotlibPrec)
+  matlabPreamble <- readPreamble (_matlabPreamble _matlabPrec)
+  plotlyPythonPreamble <- readPreamble (_plotlyPythonPreamble _plotlyPythonPrec)
+  plotlyRPreamble <- readPreamble (_plotlyRPreamble _plotlyRPrec)
+  mathematicaPreamble <- readPreamble (_mathematicaPreamble _mathematicaPrec)
+  octavePreamble <- readPreamble (_octavePreamble _octavePrec)
+  ggplot2Preamble <- readPreamble (_ggplot2Preamble _ggplot2Prec)
+  gnuplotPreamble <- readPreamble (_gnuplotPreamble _gnuplotPrec)
+  graphvizPreamble <- readPreamble (_graphvizPreamble _graphvizPrec)
+  bokehPreamble <- readPreamble (_bokehPreamble _bokehPrec)
+  plotsjlPreamble <- readPreamble (_plotsjlPreamble _plotsjlPrec)
+  plantumlPreamble <- readPreamble (_plantumlPreamble _plantumlPrec)
+  sagemathPreamble <- readPreamble (_sagemathPreamble _sagemathPrec)
+  d2Preamble <- readPreamble (_d2Preamble _d2Prec)
+  asyPreamble <- readPreamble (_asyPreamble _asyPrec)
+
+  return Configuration {..}
+  where
+    readPreamble = maybe mempty TIO.readFile