diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -2,6 +2,11 @@ ## [Unreleased] +## [0.1.3.2] - 2020-04-15 +### Changed +- Resolver version up. +- Moving from `less-wrong` to `biocad`. + ## [0.1.3.1] - 2020-04-02 ### Fixed - Reading of insertion code for residues in MAE. diff --git a/cobot-io.cabal b/cobot-io.cabal --- a/cobot-io.cabal +++ b/cobot-io.cabal @@ -1,16 +1,16 @@ cabal-version: 1.12 name: cobot-io -version: 0.1.3.1 +version: 0.1.3.2 license: BSD3 license-file: LICENSE -copyright: 2018-2019, Less Wrong Bio +copyright: 2020, Biocad maintainer: pavel@yakovlev.me author: Pavel Yakovlev, Bogdan Neterebskii, Alexander Sadovnikov -homepage: https://github.com/less-wrong/cobot-io#readme -bug-reports: https://github.com/less-wrong/cobot-io/issues +homepage: https://github.com/biocad/cobot-io#readme +bug-reports: https://github.com/biocad/cobot-io/issues synopsis: Biological data file formats and IO description: - Please see the README on GitHub at + Please see the README on GitHub at category: Bio build-type: Simple extra-source-files: @@ -19,7 +19,7 @@ source-repository head type: git - location: https://github.com/less-wrong/cobot-io + location: https://github.com/biocad/cobot-io library exposed-modules: @@ -85,9 +85,9 @@ lens >=4.16 && <5.0, linear ==1.20.*, mtl >=2.2.1 && <2.3.0, - split >=0.2.3.3 && <0.3, + split >=0.2.3.4 && <0.3, text >=1.2.2.1 && <1.3, - vector >=0.12.0.3 && <0.13 + vector >=0.12.1.2 && <0.13 test-suite cobot-io-test type: exitcode-stdio-1.0 @@ -123,7 +123,7 @@ containers >=0.5.7.1 && <0.7, data-msgpack >=0.0.9 && <0.1, deepseq ==1.4.*, - directory >=1.3.3.0 && <1.4, + directory >=1.3.6.0 && <1.4, hspec >=2.4.1 && <2.8, http-conduit ==2.3.*, hyraxAbif >=0.2.3.15 && <0.2.4.0, @@ -131,6 +131,6 @@ linear ==1.20.*, mtl >=2.2.1 && <2.3.0, neat-interpolation ==0.3.*, - split >=0.2.3.3 && <0.3, + split >=0.2.3.4 && <0.3, text >=1.2.2.1 && <1.3, - vector >=0.12.0.3 && <0.13 + vector >=0.12.1.2 && <0.13 diff --git a/src/Bio/ABI/Decode.hs b/src/Bio/ABI/Decode.hs --- a/src/Bio/ABI/Decode.hs +++ b/src/Bio/ABI/Decode.hs @@ -9,8 +9,7 @@ import Data.ByteString.Lazy as BSL (ByteString, fromStrict) import Data.ByteString.Lazy.Char8 as BSL8 (unpack) import Data.Char (ord) -import Data.List (elem, find) -import Data.Maybe (maybe) +import Data.List (find) import Data.Text (Text) import Hyrax.Abif (Abif (..), Directory (..)) import Hyrax.Abif.Read (getAbif) diff --git a/src/Bio/MMTF.hs b/src/Bio/MMTF.hs --- a/src/Bio/MMTF.hs +++ b/src/Bio/MMTF.hs @@ -16,9 +16,8 @@ import Data.Bifunctor (Bifunctor (..)) import Data.ByteString.Lazy (ByteString) import Data.Int (Int32) -import Data.List (mapAccumL, zip3, zip4) +import Data.List (mapAccumL, zip4) import Data.MessagePack (unpack) -import Data.Monoid ((<>)) import Data.String (IsString (..)) import Data.Text (Text) import Data.Vector (Vector, empty, toList, (!)) diff --git a/src/Bio/MMTF/Decode/MessagePack.hs b/src/Bio/MMTF/Decode/MessagePack.hs --- a/src/Bio/MMTF/Decode/MessagePack.hs +++ b/src/Bio/MMTF/Decode/MessagePack.hs @@ -2,13 +2,12 @@ module Bio.MMTF.Decode.MessagePack where -import Data.ByteString.Lazy (ByteString, fromStrict) -import Data.Map.Strict (Map, fromList) -import qualified Data.Map.Strict as M (lookup) +import Data.ByteString.Lazy (ByteString, fromStrict) +import Data.Map.Strict (Map, fromList) +import qualified Data.Map.Strict as M (lookup) import Data.MessagePack -import Data.Monoid ((<>)) -import Data.Text (Text) -import qualified Data.Text as T (unpack) +import Data.Text (Text) +import qualified Data.Text as T (unpack) #if !MIN_VERSION_base(4,13,0) -- Data.MessagePack includes MonadFail constraints only for GHC-8.8+, so we can't use diff --git a/src/Bio/PDB/Parser.hs b/src/Bio/PDB/Parser.hs --- a/src/Bio/PDB/Parser.hs +++ b/src/Bio/PDB/Parser.hs @@ -16,7 +16,6 @@ import qualified Data.List as L (groupBy) import Data.Map.Strict (Map, fromListWithKey) import Data.Maybe (catMaybes) -import Data.Monoid ((<>)) import Data.Text as T (Text, concat, pack, stripEnd) import qualified Data.Vector as V (Vector, concat, fromList, singleton) import GHC.Generics () diff --git a/src/Bio/Sequence/Class.hs b/src/Bio/Sequence/Class.hs --- a/src/Bio/Sequence/Class.hs +++ b/src/Bio/Sequence/Class.hs @@ -45,7 +45,6 @@ import Bio.Sequence.Utilities (Range, checkRange, unsafeEither) import Control.Lens import Control.Monad.Except (MonadError, throwError) -import Data.Bifunctor (bimap) import Data.Kind (Constraint) import qualified Data.List as L (length, null) import Data.Text (Text) diff --git a/src/Bio/Sequence/Functions/Sequence.hs b/src/Bio/Sequence/Functions/Sequence.hs --- a/src/Bio/Sequence/Functions/Sequence.hs +++ b/src/Bio/Sequence/Functions/Sequence.hs @@ -18,7 +18,6 @@ import Bio.Sequence.Utilities (Range, checkRange, unsafeEither) import Control.Lens import Control.Monad.Except (MonadError, throwError) -import Data.Bifunctor (bimap) import qualified Data.Foldable as F (length, null, toList) import qualified Data.List as L (drop, take) import Data.Maybe (fromMaybe) diff --git a/src/Bio/Uniprot/Parser.hs b/src/Bio/Uniprot/Parser.hs --- a/src/Bio/Uniprot/Parser.hs +++ b/src/Bio/Uniprot/Parser.hs @@ -16,7 +16,6 @@ import Data.Bifunctor (second) import Data.Char (isSpace) import Data.Functor (($>)) -import Data.Monoid ((<>)) import Data.Text (Text, append, isPrefixOf, null, pack, splitOn, unpack)