Merge pull request #72 from biocad/maksbotan/update-haskell-ci

haskell-ci regenerate

Author: maksbotan

.github/workflows/haskell-ci.yml

@@ -8,9 +8,9 @@
 #
 # For more information, see https://github.com/haskell-CI/haskell-ci
 #
-# version: 0.14.3
+# version: 0.16.6
 #
-# REGENDATA ("0.14.3",["github","cobot-io.cabal"])
+# REGENDATA ("0.16.6",["github","cobot-io.cabal"])
 #
 name: Haskell-CI
 on:
@@ -23,7 +23,7 @@ on:
 jobs:
   linux:
     name: Haskell-CI - Linux - ${{ matrix.compiler }}
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     timeout-minutes:
       60
     container:
@@ -32,14 +32,9 @@ jobs:
     strategy:
       matrix:
         include:
-          - compiler: ghc-9.4.4
+          - compiler: ghc-9.2.8
             compilerKind: ghc
-            compilerVersion: 9.4.4
-            setup-method: ghcup
-            allow-failure: true
-          - compiler: ghc-9.2.5
-            compilerKind: ghc
-            compilerVersion: 9.2.5
+            compilerVersion: 9.2.8
             setup-method: ghcup
             allow-failure: true
           - compiler: ghc-9.0.2
@@ -59,10 +54,10 @@ jobs:
           apt-get update
           apt-get install -y --no-install-recommends gnupg ca-certificates dirmngr curl git software-properties-common libtinfo5
           mkdir -p "$HOME/.ghcup/bin"
-          curl -sL https://downloads.haskell.org/ghcup/0.1.17.5/x86_64-linux-ghcup-0.1.17.5 > "$HOME/.ghcup/bin/ghcup"
+          curl -sL https://downloads.haskell.org/ghcup/0.1.19.2/x86_64-linux-ghcup-0.1.19.2 > "$HOME/.ghcup/bin/ghcup"
           chmod a+x "$HOME/.ghcup/bin/ghcup"
-          "$HOME/.ghcup/bin/ghcup" install ghc "$HCVER"
-          "$HOME/.ghcup/bin/ghcup" install cabal 3.6.2.0
+          "$HOME/.ghcup/bin/ghcup" install ghc "$HCVER" || (cat "$HOME"/.ghcup/logs/*.* && false)
+          "$HOME/.ghcup/bin/ghcup" install cabal 3.10.1.0 || (cat "$HOME"/.ghcup/logs/*.* && false)
         env:
           HCKIND: ${{ matrix.compilerKind }}
           HCNAME: ${{ matrix.compiler }}
@@ -78,7 +73,7 @@ jobs:
           echo "HC=$HC" >> "$GITHUB_ENV"
           echo "HCPKG=$HOME/.ghcup/bin/$HCKIND-pkg-$HCVER" >> "$GITHUB_ENV"
           echo "HADDOCK=$HOME/.ghcup/bin/haddock-$HCVER" >> "$GITHUB_ENV"
-          echo "CABAL=$HOME/.ghcup/bin/cabal-3.6.2.0 -vnormal+nowrap" >> "$GITHUB_ENV"
+          echo "CABAL=$HOME/.ghcup/bin/cabal-3.10.1.0 -vnormal+nowrap" >> "$GITHUB_ENV"
           HCNUMVER=$(${HC} --numeric-version|perl -ne '/^(\d+)\.(\d+)\.(\d+)(\.(\d+))?$/; print(10000 * $1 + 100 * $2 + ($3 == 0 ? $5 != 1 : $3))')
           echo "HCNUMVER=$HCNUMVER" >> "$GITHUB_ENV"
           echo "ARG_TESTS=--enable-tests" >> "$GITHUB_ENV"
@@ -128,8 +123,8 @@ jobs:
       - name: install cabal-plan
         run: |
           mkdir -p $HOME/.cabal/bin
-          curl -sL https://github.com/haskell-hvr/cabal-plan/releases/download/v0.6.2.0/cabal-plan-0.6.2.0-x86_64-linux.xz > cabal-plan.xz
-          echo 'de73600b1836d3f55e32d80385acc055fd97f60eaa0ab68a755302685f5d81bc  cabal-plan.xz' | sha256sum -c -
+          curl -sL https://github.com/haskell-hvr/cabal-plan/releases/download/v0.7.3.0/cabal-plan-0.7.3.0-x86_64-linux.xz > cabal-plan.xz
+          echo 'f62ccb2971567a5f638f2005ad3173dba14693a45154c1508645c52289714cb2  cabal-plan.xz' | sha256sum -c -
           xz -d < cabal-plan.xz > $HOME/.cabal/bin/cabal-plan
           rm -f cabal-plan.xz
           chmod a+x $HOME/.cabal/bin/cabal-plan
@@ -142,7 +137,7 @@ jobs:
           chmod a+x $HOME/.cabal/bin/hpack
           hpack --version
       - name: checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           path: source
       - name: generate cabal file
@@ -183,8 +178,8 @@ jobs:
         run: |
           $CABAL v2-build $ARG_COMPILER $ARG_TESTS $ARG_BENCH --dry-run all
           cabal-plan
-      - name: cache
-        uses: actions/cache@v2
+      - name: restore cache
+        uses: actions/cache/restore@v3
         with:
           key: ${{ runner.os }}-${{ matrix.compiler }}-${{ github.sha }}
           path: ~/.cabal/store
@@ -208,8 +203,14 @@ jobs:
           ${CABAL} -vnormal check
       - name: haddock
         run: |
-          $CABAL v2-haddock $ARG_COMPILER --with-haddock $HADDOCK $ARG_TESTS $ARG_BENCH all
+          $CABAL v2-haddock --disable-documentation --haddock-all $ARG_COMPILER --with-haddock $HADDOCK $ARG_TESTS $ARG_BENCH all
       - name: unconstrained build
         run: |
           rm -f cabal.project.local
           $CABAL v2-build $ARG_COMPILER --disable-tests --disable-benchmarks all
+      - name: save cache
+        uses: actions/cache/save@v3
+        if: always()
+        with:
+          key: ${{ runner.os }}-${{ matrix.compiler }}-${{ github.sha }}
+          path: ~/.cabal/store

package.yaml

@@ -22,8 +22,11 @@ extra-source-files:
 tested-with: |
   GHC ==8.10.7
    || ==9.0.2
-   || ==9.2.5
-   || ==9.4.4
+   || ==9.2.8
+
+# hyraxAbif does not support text >= 1.3 yet
+#   || ==9.4.5
+#   || ==9.6.2
 
 # Metadata used when publishing your package
 
@@ -97,3 +100,6 @@ tests:
     - hspec >= 2.4.1 && < 2.11
     - neat-interpolation >= 0.3
     - linear
+# megaparsec-9.3 changed something in error messages
+# so that our tests do not pass.
+    - megaparsec < 9.3

test/FASTASpec.hs

@@ -43,36 +43,37 @@ badFasta8 :: Either String (Fasta Char)
 badFasta8 = Left "input.fasta:21:5:\n   |\n21 | CMV + enhMCK + prcTnT-2\r\n   |     ^^\nunexpected \"+ \"\nexpecting end of input, end of line, or letter\n"
 
 fastaSpec :: Spec
-fastaSpec = describe "Fasta files parser." $ do
-    parseFile "test/FASTA/order1.fasta" correctFasta1
-    writeFile "test/FASTA/input.fasta" correctFasta1
-    parseBadFile "test/FASTA/order2.fasta" badFasta2
-    parseFile "test/FASTA/order3.fasta" correctFasta3
-    writeFile "test/FASTA/input.fasta" correctFasta3
-    parseBadFile "test/FASTA/order4.fasta" badFasta4
-    parseFile  "test/FASTA/order5.fasta" correctFasta5
-    writeFile "test/FASTA/input.fasta" correctFasta5
-    parseBadFile "test/FASTA/order6.fasta" badFasta6
-    parseBadFile "test/FASTA/order7.fasta" badFasta7
-    parseBadFile "test/FASTA/order8.fasta" badFasta8
+fastaSpec = describe "Fasta files parser" $ do
+    describe "fromFile" $ do
+      parseFile "test/FASTA/order1.fasta" correctFasta1
+      parseBadFile "test/FASTA/order2.fasta" badFasta2
+      parseFile "test/FASTA/order3.fasta" correctFasta3
+      parseBadFile "test/FASTA/order4.fasta" badFasta4
+      parseFile  "test/FASTA/order5.fasta" correctFasta5
+      parseBadFile "test/FASTA/order6.fasta" badFasta6
+      parseBadFile "test/FASTA/order7.fasta" badFasta7
+      parseBadFile "test/FASTA/order8.fasta" badFasta8
+
+    describe "toFile" $ do
+      writeFile "test/FASTA/input.fasta" correctFasta5
+      writeFile "test/FASTA/input.fasta" correctFasta1
+      writeFile "test/FASTA/input.fasta" correctFasta3
 
 parseFile :: FilePath -> Fasta Char -> Spec
-parseFile path cf = do
-    describe "fromFile" $ do
-        it "correctly parses fasta from file" $ do
-            fasta <- fromFile path
-            fasta `shouldBe` cf
+parseFile path cf =
+    it ("correctly parses good fasta from file " <> path) $ do
+        fasta <- fromFile path
+        fasta `shouldBe` cf
 
 parseBadFile :: FilePath -> Either String (Fasta Char) -> Spec
-parseBadFile path cf = do
-    describe "fromFile" $ do
-         it "correctly parses fasta from file" $ do
-            res <- liftIO (readFile path)
-            let badRes = parseOnly fastaP res
-            badRes `shouldBe` cf
+parseBadFile path cf =
+    it ("correctly parses bad fasta from file " <> path) $ do
+        res <- liftIO (readFile path)
+        let badRes = parseOnly fastaP res
+        badRes `shouldBe` cf
 
 writeFile :: FilePath -> Fasta Char -> Spec
-writeFile path cf = describe "writeFile" $ do
+writeFile path cf =
     it "correctly write fasta into file" $ do
         toFile cf path
         fasta <- fromFile path