cobot-io 0.1.3.10 → 0.1.3.11

raw patch · 3 files changed

+16/−12 lines, 3 filesdep ~linearPVP ok

version bump matches the API change (PVP)

Dependency ranges changed: linear

API changes (from Hackage documentation)

Files

• ChangeLog.md +4/−0
• cobot-io.cabal +4/−4
• test/MAESpec.hs +8/−8

@@ -2,6 +2,10 @@  ## [Unreleased] +## [0.1.3.11] - 2020-11-08+### Changed+- Allow `linear-0.21`.+ ## [0.1.3.10] - 2020-11-06 ### Fixed - `SOURCE` and `ORIGIN` in GB parser.

@@ -4,10 +4,10 @@ -- -- see: https://github.com/sol/hpack ----- hash: 7812eda294db70053683641ccf7a28ce152e843de09376f47a6bc6d2d1a86db2+-- hash: 4a6f3015c17c537b110962a77c5d6d5da84a9a9a01620acfb07850485afca69a  name:           cobot-io-version:        0.1.3.10+version:        0.1.3.11 synopsis:       Biological data file formats and IO description:    Please see the README on GitHub at <https://github.com/biocad/cobot-io#readme> category:       Bio@@ -86,7 +86,7 @@     , 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+    , linear >=1.20 && <1.22     , mtl >=2.2.1 && <2.3.0     , split     , text >=1.2.2.1 && <1.3@@ -133,7 +133,7 @@     , 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+    , linear     , mtl >=2.2.1 && <2.3.0     , neat-interpolation >=0.3     , split

@@ -27,20 +27,20 @@         let secondChainResidues Model{..} = (chainResidues $ modelChains V.! 1)          it "two chains" $ \Model{..} -> length modelChains `shouldBe` 2-        -        it "residue numbers" $ \m@Model{..} -> do++        it "residue numbers" $ \m -> do             fmap resName (firstChainResidues m) `shouldBe` V.fromList ["ACE", "ASP", "ILE", "LYS"]             fmap resName (secondChainResidues m) `shouldBe` V.fromList ["GLU", "LEU", "VAL", "ARG", "PRO", "GLY", "ALA", "LEU", "VAL"]-        -        it "residue names" $ \m@Model{..} -> do++        it "residue names" $ \m -> do             fmap resNumber (firstChainResidues m) `shouldBe` V.fromList [0, 1, 2, 3]             fmap resNumber (secondChainResidues m) `shouldBe` V.fromList [10, 11, 12, 13, 13, 15, 16, 17, 18] -- 13 is doubled because the second 13 has 'A' insertion code -        it "residue insertion codes" $ \m@Model{..} -> do+        it "residue insertion codes" $ \m -> do             fmap resInsertionCode (firstChainResidues m) `shouldBe` V.fromList [' ', ' ', ' ', ' ']             fmap resInsertionCode (secondChainResidues m) `shouldBe` V.fromList [' ', ' ', ' ', ' ', 'A', ' ', ' ', ' ', ' '] -        it "atoms count" $ \m@Model{..} -> do+        it "atoms count" $ \m -> do             sum (fmap (length . resAtoms) (firstChainResidues m)) `shouldBe` 62             sum (fmap (length . resAtoms) (secondChainResidues m)) `shouldBe` 140 @@ -68,7 +68,7 @@         let residue1 m = firstChainResidues m V.! 3         let residue2 m = secondChainResidues m V.! 0 -        it "atoms in residues" $ \m@Model{..} -> do+        it "atoms in residues" $ \m -> do             let atoms1 = resAtoms $ residue1 m             let atoms2 = resAtoms $ residue2 m @@ -94,7 +94,7 @@                                                          , V3 (-10.322000) 11.996000 16.297000, V3 (-9.798000) 11.676000 19.305000, V3 (-10.128000) 10.318000 18.313000, V3 (-12.084000) 12.633000 18.684000, V3 (-12.123000) 11.111000 19.544000                                                          ] -        it "bonds in residues" $ \m@Model{..} -> do+        it "bonds in residues" $ \m -> do             toSet (resBonds $ residue1 m) `shouldBe` toSet (V.fromList $ toBond LocalID . (\(x, y, o) -> (x - 37, y - 37, o)) <$> filter (\(x, y, _) -> x - 1 `elem` [37 .. 58] && y - 1 `elem` [37 .. 58]) allBonds)             toSet (resBonds $ residue2 m) `shouldBe` toSet (V.fromList $ toBond LocalID . (\(x, y, o) -> (x - 59, y - 59, o)) <$> filter (\(x, y, _) -> x - 1 `elem` [59 .. 73] && y - 1 `elem` [59 .. 73]) allBonds)     where