Version 0.1.3.1. Fixed reading of insertion code for residues in MAE (#34)

Co-authored-by: Bogdan Neterebskii <[email protected]>
Co-authored-by: Maxim Koltsov <[email protected]>

Author: 3 people

.travis.yml

@@ -1,23 +1,28 @@
 sudo: false
-language: haskell
+language: generic
+
+env:
+  global:
+      # HACKAGE_PASSWORD
+    - secure: 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
 
 # Caching so the next build will be fast too.
 cache:
   directories:
   - $HOME/.stack
 
-matrix:
-  include:
-    - ghc: 8.6.4
-      env: STACK_YAML="$TRAVIS_BUILD_DIR/stack.yaml"
-
 before_install:
-- mkdir -p ~/.local/bin
-- export PATH=$HOME/.local/bin:$PATH
-- travis_retry curl -L https://www.stackage.org/stack/linux-x86_64 | tar xz --wildcards --strip-components=1 -C ~/.local/bin '*/stack'
+  - curl -sSL https://get.haskellstack.org/ | sh
+  - stack --version
 
 install:
-  - travis_wait 60 stack --no-terminal --system-ghc test --only-snapshot
+  - stack build --test --bench --only-dependencies
 
-script:
-  - stack --no-terminal --system-ghc test --pedantic
+jobs:
+  include:
+    - stage: Build and test
+      script: stack build --pedantic --test --bench --no-run-benchmarks
+    - stage: Hackage deploy
+      # n is for "store credentials" question
+      script: echo -e "ozzzzz\n${HACKAGE_PASSWORD}\nn" | stack upload --pvp-bounds both .
+      if: tag IS present

ChangeLog.md

@@ -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`.

package.yaml

@@ -1,5 +1,5 @@
 name:                cobot-io
-version:             0.1.3.0
+version:             0.1.3.1
 github:              "less-wrong/cobot-io"
 license:             BSD3
 category:            Bio

src/Bio/MAE.hs

@@ -140,7 +140,7 @@ instance StructureModels Mae where
                 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

@@ -145,5 +145,4 @@ firstPDBModel filepath = do
 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