Merge pull request #73 from biocad/maksbotan/megaparsec-9.3

Allow megaparsec >= 9.3.1

.github/workflows/haskell-ci.yml

@@ -1,16 +1,16 @@
 # This GitHub workflow config has been generated by a script via
 #
-#   haskell-ci 'github' 'cobot-io.cabal'
+#   haskell-ci 'github' 'cabal.project'
 #
 # To regenerate the script (for example after adjusting tested-with) run
 #
 #   haskell-ci regenerate
 #
 # For more information, see https://github.com/haskell-CI/haskell-ci
 #
-# version: 0.16.6
+# version: 0.17.20231110
 #
-# REGENDATA ("0.16.6",["github","cobot-io.cabal"])
+# REGENDATA ("0.17.20231110",["github","cabal.project"])
 #
 name: Haskell-CI
 on:
@@ -32,11 +32,26 @@ jobs:
     strategy:
       matrix:
         include:
+          - compiler: ghc-9.8.1
+            compilerKind: ghc
+            compilerVersion: 9.8.1
+            setup-method: ghcup
+            allow-failure: true
+          - compiler: ghc-9.6.3
+            compilerKind: ghc
+            compilerVersion: 9.6.3
+            setup-method: ghcup
+            allow-failure: false
+          - compiler: ghc-9.4.8
+            compilerKind: ghc
+            compilerVersion: 9.4.8
+            setup-method: ghcup
+            allow-failure: false
           - compiler: ghc-9.2.8
             compilerKind: ghc
             compilerVersion: 9.2.8
             setup-method: ghcup
-            allow-failure: true
+            allow-failure: false
           - compiler: ghc-9.0.2
             compilerKind: ghc
             compilerVersion: 9.0.2
@@ -54,10 +69,10 @@ jobs:
           apt-get update
           apt-get install -y --no-install-recommends gnupg ca-certificates dirmngr curl git software-properties-common libtinfo5
           mkdir -p "$HOME/.ghcup/bin"
-          curl -sL https://downloads.haskell.org/ghcup/0.1.19.2/x86_64-linux-ghcup-0.1.19.2 > "$HOME/.ghcup/bin/ghcup"
+          curl -sL https://downloads.haskell.org/ghcup/0.1.20.0/x86_64-linux-ghcup-0.1.20.0 > "$HOME/.ghcup/bin/ghcup"
           chmod a+x "$HOME/.ghcup/bin/ghcup"
           "$HOME/.ghcup/bin/ghcup" install ghc "$HCVER" || (cat "$HOME"/.ghcup/logs/*.* && false)
-          "$HOME/.ghcup/bin/ghcup" install cabal 3.10.1.0 || (cat "$HOME"/.ghcup/logs/*.* && false)
+          "$HOME/.ghcup/bin/ghcup" install cabal 3.10.2.0 || (cat "$HOME"/.ghcup/logs/*.* && false)
         env:
           HCKIND: ${{ matrix.compilerKind }}
           HCNAME: ${{ matrix.compiler }}
@@ -69,11 +84,13 @@ jobs:
           echo "CABAL_DIR=$HOME/.cabal" >> "$GITHUB_ENV"
           echo "CABAL_CONFIG=$HOME/.cabal/config" >> "$GITHUB_ENV"
           HCDIR=/opt/$HCKIND/$HCVER
-          HC=$HOME/.ghcup/bin/$HCKIND-$HCVER
+          HC=$("$HOME/.ghcup/bin/ghcup" whereis ghc "$HCVER")
+          HCPKG=$(echo "$HC" | sed 's#ghc$#ghc-pkg#')
+          HADDOCK=$(echo "$HC" | sed 's#ghc$#haddock#')
           echo "HC=$HC" >> "$GITHUB_ENV"
-          echo "HCPKG=$HOME/.ghcup/bin/$HCKIND-pkg-$HCVER" >> "$GITHUB_ENV"
-          echo "HADDOCK=$HOME/.ghcup/bin/haddock-$HCVER" >> "$GITHUB_ENV"
-          echo "CABAL=$HOME/.ghcup/bin/cabal-3.10.1.0 -vnormal+nowrap" >> "$GITHUB_ENV"
+          echo "HCPKG=$HCPKG" >> "$GITHUB_ENV"
+          echo "HADDOCK=$HADDOCK" >> "$GITHUB_ENV"
+          echo "CABAL=$HOME/.ghcup/bin/cabal-3.10.2.0 -vnormal+nowrap" >> "$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"
@@ -168,6 +185,9 @@ jobs:
           echo "package cobot-io" >> cabal.project
           echo "    ghc-options: -Werror=missing-methods" >> cabal.project
           cat >> cabal.project <<EOF
+          allow-newer: hyraxAbif:text
+          allow-newer: hyraxAbif:bytestring
+
           package cobot-io
             ghc-options: -Wall -Werror -fkeep-going
           EOF

ChangeLog.md

@@ -2,6 +2,9 @@
 
 ## [Unreleased]
 
+## [0.1.5.3] - 2023-12-08
+- Update tests and dependencies.
+
 ## [0.1.5.2] - 2023-11-09
 - Add Ord for Fasta and related types.
 

cabal.haskell-ci

@@ -2,6 +2,6 @@ distribution: focal
 
 branches: master
 
-allow-failures: >=9.2
+allow-failures: >=9.8
 
 local-ghc-options: -Wall -Werror -fkeep-going

cabal.project

@@ -0,0 +1,3 @@
+packages: *.cabal
+
+allow-newer: hyraxAbif:text, hyraxAbif:bytestring

package.yaml

@@ -1,5 +1,5 @@
 name:                cobot-io
-version:             0.1.5.2
+version:             0.1.5.3
 github:              "biocad/cobot-io"
 license:             BSD3
 category:            Bio
@@ -23,10 +23,9 @@ tested-with: |
   GHC ==8.10.7
    || ==9.0.2
    || ==9.2.8
-
-# hyraxAbif does not support text >= 1.3 yet
-#   || ==9.4.5
-#   || ==9.6.2
+   || ==9.4.8
+   || ==9.6.3
+   || ==9.8.1
 
 # Metadata used when publishing your package
 
@@ -40,11 +39,11 @@ dependencies:
 - array >= 0.5 && < 0.6
 - attoparsec >= 0.10 && < 0.15
 - binary >= 0.8.3.0 && < 1.0
-- bytestring >= 0.10.8.1 && < 0.12
+- bytestring >= 0.10.8.1 && < 0.13
 - cobot >= 0.1.1.7
 - containers >= 0.5.7.1 && < 0.7
 - data-msgpack >= 0.0.9 && < 0.1
-- deepseq >= 1.4 && < 1.5
+- deepseq >= 1.4 && < 1.6
 - filepath
 - http-conduit >= 2.3 && < 2.4
 - hyraxAbif >= 0.2.3.27 && < 0.2.5.0
@@ -54,7 +53,7 @@ dependencies:
 - mtl >= 2.2.1 && < 2.4
 - parser-combinators >= 1.2.1
 - split
-- text >= 1.2.2.1 && < 2.1
+- text >= 1.2.2.1 && < 2.2
 - vector
 
 library:
@@ -97,9 +96,7 @@ tests:
     - cobot-io
     - directory
     - QuickCheck >= 2.9.2 && < 2.15
-    - hspec >= 2.4.1 && < 2.11
+    - hspec >= 2.4.1 && < 2.12
     - neat-interpolation >= 0.3
     - linear
-# megaparsec-9.3 changed something in error messages
-# so that our tests do not pass.
-    - megaparsec < 9.3
+    - megaparsec

src/Bio/Uniprot/Parser.hs

@@ -1,3 +1,4 @@
+{-# LANGUAGE CPP #-}
 {-# LANGUAGE TupleSections #-}
 {-# OPTIONS_GHC -fno-warn-unused-do-bind #-}
 {-# OPTIONS_GHC -fno-warn-name-shadowing #-}
@@ -9,8 +10,13 @@ module Bio.Uniprot.Parser where
 import           Prelude              hiding (null)
 import qualified Prelude              as P (concat, init, last, null, tail)
 
-import           Bio.Uniprot.Type
+#if MIN_VERSION_base(4, 18, 0)
+import           Control.Applicative  ((<|>))
+#else
 import           Control.Applicative  (liftA2, (<|>))
+#endif
+
+import           Bio.Uniprot.Type
 import           Control.Monad        (unless)
 import           Data.Attoparsec.Text
 import           Data.Bifunctor       (second)

test/FASTASpec.hs

@@ -2,15 +2,18 @@
 
 module FASTASpec where
 
-import Bio.FASTA              (fastaP, fromFile, toFile)
-import Bio.FASTA.Parser       (parseOnly)
-import Bio.FASTA.Type         (Fasta, FastaItem (..))
-import Bio.Sequence           (bareSequence)
-import Control.Monad.IO.Class (liftIO)
-import Data.Text.IO           (readFile)
-import Prelude                hiding (readFile, writeFile)
-import System.Directory       (removeFile)
-import Test.Hspec
+import           Control.Monad.IO.Class (liftIO)
+import           Data.Bifunctor         (first)
+import qualified Data.Text              as T
+import           Data.Text.IO           (readFile)
+import           Prelude                hiding (readFile, writeFile)
+import           System.Directory       (removeFile)
+import           Test.Hspec
+
+import Bio.FASTA        (fastaP, fromFile, toFile)
+import Bio.FASTA.Parser (parseOnly)
+import Bio.FASTA.Type   (Fasta, FastaItem (..))
+import Bio.Sequence     (bareSequence)
 
 correctFasta1 :: Fasta Char
 correctFasta1 = [ FastaItem "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")
@@ -70,7 +73,7 @@ parseBadFile path cf =
     it ("correctly parses bad fasta from file " <> path) $ do
         res <- liftIO (readFile path)
         let badRes = parseOnly fastaP res
-        badRes `shouldBe` cf
+        noSpaces badRes `shouldBe` noSpaces cf
 
 writeFile :: FilePath -> Fasta Char -> Spec
 writeFile path cf =
@@ -79,3 +82,7 @@ writeFile path cf =
         fasta <- fromFile path
         removeFile path
         fasta `shouldBe` cf
+
+-- | megaparsec >= 9.3 added more spaces to error messages, so that our old ones do not match.
+noSpaces :: Either String a -> Either String a
+noSpaces = first $ T.unpack . T.replace " " "" . T.pack