cobot-io 0.1.3.0 → 0.1.3.1
raw patch · 4 files changed
+132/−133 lines, 4 filesdep ~directorydep ~neat-interpolationdep ~splitPVP ok
version bump matches the API change (PVP)
Dependency ranges changed: directory, neat-interpolation, split, vector
API changes (from Hackage documentation)
Files
- ChangeLog.md +4/−0
- cobot-io.cabal +126/−130
- src/Bio/MAE.hs +1/−1
- test/PDBSpec.hs +1/−2
ChangeLog.md view
@@ -2,6 +2,10 @@ ## [Unreleased] +## [0.1.3.1] - 2020-04-02+### Fixed+- Reading of insertion code for residues in MAE.+ ## [0.1.3.0] - 2020-03-27 ### Added - Residue index in `Structure`.
cobot-io.cabal view
@@ -1,140 +1,136 @@ cabal-version: 1.12---- This file has been generated from package.yaml by hpack version 0.31.2.------ see: https://github.com/sol/hpack------ hash: a5a2fbb335e61a22b55a3d74cd08557730ea19a8b93005c693a4576dad82e498--name: cobot-io-version: 0.1.3.0-synopsis: Biological data file formats and IO-description: Please see the README on GitHub at <https://github.com/less-wrong/cobot-io#readme>-category: Bio-homepage: https://github.com/less-wrong/cobot-io#readme-bug-reports: https://github.com/less-wrong/cobot-io/issues-author: Pavel Yakovlev, Bogdan Neterebskii, Alexander Sadovnikov-maintainer: pavel@yakovlev.me-copyright: 2018-2019, Less Wrong Bio-license: BSD3-license-file: LICENSE-build-type: Simple+name: cobot-io+version: 0.1.3.1+license: BSD3+license-file: LICENSE+copyright: 2018-2019, Less Wrong Bio+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+synopsis: Biological data file formats and IO+description:+ Please see the README on GitHub at <https://github.com/less-wrong/cobot-io#readme>+category: Bio+build-type: Simple extra-source-files: README.md ChangeLog.md source-repository head- type: git- location: https://github.com/less-wrong/cobot-io+ type: git+ location: https://github.com/less-wrong/cobot-io library- exposed-modules:- Bio.ABI- Bio.ABI.Clean- Bio.ABI.Decode- Bio.FASTA- Bio.FASTA.Parser- Bio.FASTA.Type- Bio.FASTA.Writer- Bio.GB- Bio.GB.Parser- Bio.GB.Type- Bio.GB.Writer- Bio.MAE- Bio.MAE.Parser- Bio.MAE.Type- Bio.MMTF- Bio.MMTF.Decode- Bio.MMTF.Decode.Codec- Bio.MMTF.Decode.MessagePack- Bio.MMTF.MessagePack- Bio.MMTF.Type- Bio.PDB- Bio.PDB.BondRestoring- Bio.PDB.Functions- Bio.PDB.Parser- Bio.PDB.Reader- Bio.PDB.Type- Bio.Sequence- Bio.Sequence.Basecalled- Bio.Sequence.Basecalled.Type- Bio.Sequence.Class- Bio.Sequence.Functions.Marking- Bio.Sequence.Functions.Sequence- Bio.Sequence.Functions.Weight- Bio.Sequence.Utilities- Bio.Structure- Bio.Structure.Functions- Bio.Uniprot- Bio.Uniprot.Parser- Bio.Uniprot.Type- other-modules:- Paths_cobot_io- hs-source-dirs:- src- default-extensions: DeriveGeneric DeriveFunctor DeriveFoldable DeriveAnyClass FlexibleInstances InstanceSigs MultiParamTypeClasses RecordWildCards ScopedTypeVariables OverloadedStrings TypeApplications TypeFamilies DataKinds ConstraintKinds TypeOperators TemplateHaskell FlexibleContexts- build-depends:- array >=0.5 && <0.6- , attoparsec >=0.10 && <0.14- , base >=4.7 && <5- , binary >=0.8.3.0 && <1.0- , bytestring >=0.10.8.1 && <0.11- , containers >=0.5.7.1 && <0.7- , data-msgpack >=0.0.9 && <0.1- , deepseq >=1.4 && <1.5- , http-conduit >=2.3 && <2.4- , hyraxAbif >=0.2.3.15 && <0.2.4.0- , lens >=4.16 && <5.0- , linear >=1.20 && <1.21- , mtl >=2.2.1 && <2.3.0- , split- , text >=1.2.2.1 && <1.3- , vector- default-language: Haskell2010+ exposed-modules:+ Bio.ABI+ Bio.ABI.Clean+ Bio.ABI.Decode+ Bio.FASTA+ Bio.FASTA.Parser+ Bio.FASTA.Type+ Bio.FASTA.Writer+ Bio.GB+ Bio.GB.Parser+ Bio.GB.Type+ Bio.GB.Writer+ Bio.MAE+ Bio.MAE.Parser+ Bio.MAE.Type+ Bio.MMTF+ Bio.MMTF.Decode+ Bio.MMTF.Decode.Codec+ Bio.MMTF.Decode.MessagePack+ Bio.MMTF.MessagePack+ Bio.MMTF.Type+ Bio.PDB+ Bio.PDB.BondRestoring+ Bio.PDB.Functions+ Bio.PDB.Parser+ Bio.PDB.Reader+ Bio.PDB.Type+ Bio.Sequence+ Bio.Sequence.Basecalled+ Bio.Sequence.Basecalled.Type+ Bio.Sequence.Class+ Bio.Sequence.Functions.Marking+ Bio.Sequence.Functions.Sequence+ Bio.Sequence.Functions.Weight+ Bio.Sequence.Utilities+ Bio.Structure+ Bio.Structure.Functions+ Bio.Uniprot+ Bio.Uniprot.Parser+ Bio.Uniprot.Type+ hs-source-dirs: src+ other-modules:+ Paths_cobot_io+ default-language: Haskell2010+ default-extensions: DeriveGeneric DeriveFunctor DeriveFoldable+ DeriveAnyClass FlexibleInstances InstanceSigs MultiParamTypeClasses+ RecordWildCards ScopedTypeVariables OverloadedStrings+ TypeApplications TypeFamilies DataKinds ConstraintKinds+ TypeOperators TemplateHaskell FlexibleContexts+ build-depends:+ array ==0.5.*,+ attoparsec >=0.10 && <0.14,+ base >=4.7 && <5,+ binary >=0.8.3.0 && <1.0,+ bytestring >=0.10.8.1 && <0.11,+ containers >=0.5.7.1 && <0.7,+ data-msgpack >=0.0.9 && <0.1,+ deepseq ==1.4.*,+ http-conduit ==2.3.*,+ hyraxAbif >=0.2.3.15 && <0.2.4.0,+ lens >=4.16 && <5.0,+ linear ==1.20.*,+ mtl >=2.2.1 && <2.3.0,+ split >=0.2.3.3 && <0.3,+ text >=1.2.2.1 && <1.3,+ vector >=0.12.0.3 && <0.13 test-suite cobot-io-test- type: exitcode-stdio-1.0- main-is: Spec.hs- other-modules:- ABISpec- FastaParserSpec- FASTASpec- FastaWriterSpec- GBParserSpec- GBWriterSpec- MAEParserSpec- MAESpec- MMTFSpec- PDBParserSpec- PDBSpec- SequenceSpec- StructureSpec- UniprotSpec- Paths_cobot_io- hs-source-dirs:- test- default-extensions: OverloadedStrings TypeFamilies- ghc-options: -threaded -rtsopts -with-rtsopts=-N- build-depends:- QuickCheck >=2.9.2 && <2.14- , array >=0.5 && <0.6- , attoparsec >=0.10 && <0.14- , base >=4.7 && <5- , binary >=0.8.3.0 && <1.0- , bytestring >=0.10.8.1 && <0.11- , cobot-io- , containers >=0.5.7.1 && <0.7- , data-msgpack >=0.0.9 && <0.1- , deepseq >=1.4 && <1.5- , directory- , hspec >=2.4.1 && <2.8- , http-conduit >=2.3 && <2.4- , hyraxAbif >=0.2.3.15 && <0.2.4.0- , lens >=4.16 && <5.0- , linear >=1.20 && <1.21- , mtl >=2.2.1 && <2.3.0- , neat-interpolation >=0.3- , split- , text >=1.2.2.1 && <1.3- , vector- default-language: Haskell2010+ type: exitcode-stdio-1.0+ main-is: Spec.hs+ hs-source-dirs: test+ other-modules:+ ABISpec+ FastaParserSpec+ FASTASpec+ FastaWriterSpec+ GBParserSpec+ GBWriterSpec+ MAEParserSpec+ MAESpec+ MMTFSpec+ PDBParserSpec+ PDBSpec+ SequenceSpec+ StructureSpec+ UniprotSpec+ Paths_cobot_io+ default-language: Haskell2010+ default-extensions: OverloadedStrings TypeFamilies+ ghc-options: -threaded -rtsopts -with-rtsopts=-N+ build-depends:+ QuickCheck >=2.9.2 && <2.14,+ array ==0.5.*,+ attoparsec >=0.10 && <0.14,+ base >=4.7 && <5,+ binary >=0.8.3.0 && <1.0,+ bytestring >=0.10.8.1 && <0.11,+ cobot-io -any,+ containers >=0.5.7.1 && <0.7,+ data-msgpack >=0.0.9 && <0.1,+ deepseq ==1.4.*,+ directory >=1.3.3.0 && <1.4,+ hspec >=2.4.1 && <2.8,+ http-conduit ==2.3.*,+ hyraxAbif >=0.2.3.15 && <0.2.4.0,+ lens >=4.16 && <5.0,+ linear ==1.20.*,+ mtl >=2.2.1 && <2.3.0,+ neat-interpolation ==0.3.*,+ split >=0.2.3.3 && <0.3,+ text >=1.2.2.1 && <1.3,+ vector >=0.12.0.3 && <0.13
src/Bio/MAE.hs view
@@ -140,7 +140,7 @@ where name = stripQuotes $ unsafeGetFromContents "s_m_pdb_residue_name" h residueNumber = unsafeGetFromContents "i_m_residue_number" h- insertionCode = unsafeGetFromContents "s_m_insertion_code" h+ insertionCode = getFromContents defaultInsertionCode "s_m_insertion_code" h atoms = V.fromList $ fmap indexToAtom group localInds = [0 .. length group - 1]
test/PDBSpec.hs view
@@ -145,5 +145,4 @@ firstMaeModel :: (MonadIO m) => FilePath -> m Model firstMaeModel filepath = do eitherMae <- modelsFromMaeFile filepath- -- `evaluate . force` fails for some reason- pure . V.head $ fromRight undefined eitherMae+ liftIO . ef . V.head $ fromRight undefined eitherMae