R-pandoc (empty) → 0.1

raw patch · 6 files changed

+214/−0 lines, 6 filesdep +R-pandocdep +basedep +directorysetup-changed

Dependencies added: R-pandoc, base, directory, filepath, pandoc-types, process, split

Files

LICENSE +30/−0
R-pandoc.cabal +40/−0
README.md +59/−0
Setup.hs +2/−0
src/Main.hs +5/−0
src/Text/Pandoc/R.hs +78/−0

+ LICENSE view

@@ -0,0 +1,30 @@+Copyright (c) 2015 Corentin Dupont++All rights reserved.++Redistribution and use in source and binary forms, with or without+modification, are permitted provided that the following conditions are met:++    * Redistributions of source code must retain the above copyright+      notice, this list of conditions and the following disclaimer.++    * Redistributions in binary form must reproduce the above+      copyright notice, this list of conditions and the following+      disclaimer in the documentation and/or other materials provided+      with the distribution.++    * Neither the name of Brent Yorgey nor the names of other+      contributors may be used to endorse or promote products derived+      from this software without specific prior written permission.++THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

+ R-pandoc.cabal view

@@ -0,0 +1,40 @@+name: R-pandoc+version: 0.1+cabal-version: >=1.10+build-type: Simple+license: BSD3+license-file: LICENSE+maintainer: corentin.dupont@gmail.com+bug-reports: http://github.com/cdupont/R-pandoc/issues+synopsis: A pandoc filter to express R plots inside markdown+category: Text+author: Corentin Dupont+extra-source-files: README.md++source-repository head+    type: git+    location: http://github.com/cdupont/R-pandoc.git++library+    build-depends:+        base         >=4.6  && <4.9,+        pandoc-types >=1.12 && <1.13,+        directory    >=1.2  && <1.3,+        filepath     >=1.3  && <1.5,+        process      >=1.2  && <1.3,+        split        >=0.2  && <0.3+    exposed-modules: Text.Pandoc.R+    exposed: True+    buildable: True+    default-language: Haskell2010+    hs-source-dirs: src+    ghc-options: -Wall++executable R-pandoc+    build-depends:+        base         >=4.6  && <4.9,+        pandoc-types >=1.12 && <1.13,+        R-pandoc     ==0.1+    main-is: src/Main.hs+    buildable: True+    default-language: Haskell2010

+ README.md view

@@ -0,0 +1,59 @@++Please note that this repo is work in progress.++[![Build Status](https://travis-ci.org/cdupont/R-pandoc.svg?branch=master)](https://travis-ci.org/cdupont/R-pandoc)++A [pandoc](http://johnmacfarlane.net/pandoc/) filter to embbed R plots inside markdown documents.++## Usage++Install R:++    sudo apt-get install r-base+++Create a file called `demo.md` with the following text:++``` markdown+Here is a nice plot:+    ~~~ {.Rplot}+    require(stats)+    D = 150+    T = 10+    t = seq(0, 80, 0.01)+    x = -D*exp(-(t/T))+D+    v = (D/T)*exp(-(t/T))+    plot(t, x, type="l", main="position through time", xlab="time (s)", ylab="position (m)", xlim=c(0,80), ylim=c(0, D+10),  xaxs = "i", yaxs = "i")+    ~~~+```++Now run:+``` shell+    pandoc -t html demo.md --filter R-pandoc -o demo.html -s+```++The file demo.html should now have a nice plot included:++![plot](img/Rplot.png)+++## Details++`R-pandoc` compiles code blocks containing R plots+and includes the resulting images in the pandoc markup.  It is meant+to be run as a+[pandoc filter](http://johnmacfarlane.net/pandoc/scripting.html) as+shown above.++`R-pandoc` is aware of two code block classes.  A block with+the `Rplot` class will be replaced by the resulting plot---the code+will not appear in the output.  ++## Installing+++``` shell+    git clone https://github.com/cdupont/R-pandoc.git+    cd R-pandoc+    cabal install+```

+ Setup.hs view

@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain

+ src/Main.hs view

@@ -0,0 +1,5 @@+import           Text.Pandoc.JSON+import           Text.Pandoc.R++main :: IO ()+main = toJSONFilter (insertRplots "plots")

+ src/Text/Pandoc/R.hs view

@@ -0,0 +1,78 @@+++module Text.Pandoc.R where++import           Control.Applicative+import           Control.Monad+import           Data.List           (delete)+import           Data.List.Split+import           Data.Maybe+import           System.Directory    (createDirectoryIfMissing, doesFileExist, removeFile, renameFile)+import           System.Exit         (ExitCode (..))+import           System.FilePath     ((<.>), (</>), pathSeparator)+import           System.IO           (hPutStrLn, stderr)+import           System.Process+import           Text.Pandoc.Generic+import           Text.Pandoc.JSON++rClass, fileAttr, defFile, defRplot, tmpRFile :: String+rClass = "Rplot"+fileAttr = "files"+defFile = "Rplot.png"+defRplot = "Rplots.pdf"+tmpRFile = "plot.R"++renderRPandoc :: FilePath -> Pandoc -> IO Pandoc+renderRPandoc f p = bottomUpM (insertRplots f) p++insertRplots :: FilePath -> Block -> IO Block+insertRplots outDir block@(CodeBlock (ident, classes, attrs) code) = do+   --hPutStrLn stderr $ "insertRplots classes: " ++ (show classes) ++ " attrs: " ++ (show attrs) ++ " ident: " ++ (show ident)+   if rClass `elem` classes then do+      let imgFiles = case lookup fileAttr attrs of+           Just is -> splitOn "," is+           Nothing   -> [defFile]+      d <- renderRPlot code+      when (imgFiles == [defFile]) $ void $ convertDefault+      imgFiles' <- moveFiles imgFiles outDir+      return $ if d then Plain (map insertImage imgFiles') else block+   else return block+insertRplots _ block = return block++insertImage :: FilePath -> Inline+insertImage file = Image [] (file,"")++--plot the R graph+--the files created will be the one specified in the R code with commands such as:+--png(filename="fig1.png")+--if no filename is specified, a file "Rplots.pdf" is generated.+renderRPlot :: String -> IO Bool+renderRPlot rcode = do+   writeFile tmpRFile rcode+   (code,stdout,stderr) <- readProcessWithExitCode "R" ["CMD", "BATCH", "--no-save", "--quiet", tmpRFile] ""+   when (code /= ExitSuccess) $ do+      putStrLnErr $ "R exited with: " ++ (show code)+      putStrLnErr stdout+      putStrLnErr stderr+   whenM (doesFileExist tmpRFile) $ removeFile tmpRFile+   whenM (doesFileExist "plot.Rout") $ removeFile "plot.Rout"+   return $ (code==ExitSuccess)++moveFiles :: [FilePath] -> FilePath -> IO [FilePath]+moveFiles files outDir = do+   createDirectoryIfMissing False outDir+   mapM_ (\a -> whenM (doesFileExist a) $ renameFile a (outDir </> a)) files+   return $ map ((pathSeparator : outDir) </>) files++convertDefault :: IO Bool+convertDefault = do+   (code,_,_) <- readProcessWithExitCode "convert" [defRplot, defFile] ""+   whenM (doesFileExist defRplot) $ void $ removeFile defRplot+   return $ (code==ExitSuccess)++putStrLnErr = hPutStrLn stderr++whenM :: Monad m => m Bool -> m () -> m ()+whenM cond a = do+  c <- cond+  if c then a else (return ())