BLD Update to LTS-22.6

ngless-toolkit · Feb 22, 2024 · cb010b8 · cb010b8
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diff --git a/NGLess/BuiltinModules/AsReads.hs b/NGLess/BuiltinModules/AsReads.hs
@@ -1,4 +1,4 @@
-{- Copyright 2015-2018 NGLess Authors
+{- Copyright 2015-2024 NGLess Authors
  - License: MIT
  -}
 
@@ -18,7 +18,8 @@ import qualified Data.Conduit.Combinators as CC
 import qualified Data.Conduit.Algorithms.Async as CAlg
 import Control.Monad.Trans.Resource (release)
 import Data.Conduit ((.|))
-import Control.Monad.Except
+import Control.Monad
+import Control.Monad.IO.Class (liftIO)
 import System.IO
 import Data.Default (def)
 import Data.IORef (newIORef, writeIORef, readIORef)

diff --git a/NGLess/BuiltinModules/Assemble.hs b/NGLess/BuiltinModules/Assemble.hs
@@ -1,4 +1,4 @@
-{- Copyright 2017-2022 NGLess Authors
+{- Copyright 2017-2024 NGLess Authors
  - License: MIT
  -}
 
@@ -8,7 +8,7 @@ module BuiltinModules.Assemble
 
 import qualified Data.Text as T
 import           System.FilePath ((</>))
-import           Control.Monad.Except (liftIO)
+import           Control.Monad.IO.Class (liftIO)
 import           Data.Default (def)
 import           GHC.Conc (getNumCapabilities)
 import           Control.Monad.Trans.Resource (release)

diff --git a/NGLess/BuiltinModules/Checks.hs b/NGLess/BuiltinModules/Checks.hs
@@ -1,4 +1,4 @@
-{- Copyright 2016-2022 NGLess Authors
+{- Copyright 2016-2024 NGLess Authors
  - License: MIT
  -}
 
@@ -11,7 +11,8 @@ module BuiltinModules.Checks
 import qualified Data.Text as T
 import           Data.Default (def)
 import Control.Monad.Extra (whenJust)
-import Control.Monad.Except
+import Control.Monad
+import Control.Monad.IO.Class
 import System.Directory
 import System.FilePath (takeDirectory)
 

diff --git a/NGLess/BuiltinModules/ORFFind.hs b/NGLess/BuiltinModules/ORFFind.hs
@@ -1,4 +1,4 @@
-{- Copyright 2017-2022 NGLess Authors
+{- Copyright 2017-2024 NGLess Authors
  - License: MIT
  -}
 
@@ -8,7 +8,7 @@ module BuiltinModules.ORFFind
 
 import qualified Data.Text as T
 import           System.IO (hClose)
-import           Control.Monad.Except (liftIO)
+import           Control.Monad.IO.Class (liftIO)
 import           Data.Default (def)
 
 import Language

diff --git a/NGLess/BuiltinModules/QCStats.hs b/NGLess/BuiltinModules/QCStats.hs
@@ -1,4 +1,4 @@
-{- Copyright 2017-2019 NGLess Authors
+{- Copyright 2017-2024 NGLess Authors
  - License: MIT
  -}
 
@@ -13,7 +13,7 @@ module BuiltinModules.QCStats
 
 import qualified Data.Text as T
 import           Data.Default (def)
-import Control.Monad.Except
+import           Control.Monad.IO.Class
 import System.IO
 
 import Language

diff --git a/NGLess/Data/FastQ.hs b/NGLess/Data/FastQ.hs
@@ -1,6 +1,6 @@
 {-# LANGUAGE FlexibleContexts, ScopedTypeVariables, MultiWayIf #-}
 {-# LANGUAGE TemplateHaskell, QuasiQuotes, CPP #-}
-{- Copyright 2013-2019 NGLess Authors
+{- Copyright 2013-2024 NGLess Authors
  - License: MIT
  -}
 
@@ -38,7 +38,10 @@ import Data.Conduit.Combinators qualified as CC
 import           Control.DeepSeq (NFData(..))
 import           Data.Conduit ((.|))
 import           Data.Conduit.Algorithms.Async (conduitPossiblyCompressedFile)
+import           Control.Monad.IO.Class
+import Control.Monad (forM, forM_, when)
 import Control.Monad.Except
+import Control.Monad.Trans.Class (lift)
 import Control.Monad.Trans.Resource
 import Control.Exception
 

diff --git a/NGLess/Data/Fasta.hs b/NGLess/Data/Fasta.hs
@@ -14,6 +14,7 @@ import qualified Data.ByteString.Char8 as B8
 import qualified Data.Conduit as C
 import           Data.Conduit ((.|))
 import           Data.Word
+import           Control.Monad.IO.Class
 import           Control.Monad.Except
 import           Control.DeepSeq
 

diff --git a/NGLess/Data/Sam.hs b/NGLess/Data/Sam.hs
@@ -44,6 +44,7 @@ import Control.Error (note)
 import Control.DeepSeq
 
 import Data.Maybe
+import           Control.Monad.IO.Class
 import Control.Monad.Except
 import NGLess.NGError
 import Utils.Utils

diff --git a/NGLess/Interpretation/FastQ.hs b/NGLess/Interpretation/FastQ.hs
@@ -1,4 +1,4 @@
-{- Copyright 2013-2020 NGLess Authors
+{- Copyright 2013-2024 NGLess Authors
  - License: MIT
  -}
 {-# LANGUAGE FlexibleContexts, MultiWayIf, CPP #-}
@@ -32,7 +32,9 @@ import           Data.Conduit.Algorithms.Async (withPossiblyCompressedFile)
 import qualified Data.Conduit.Algorithms.Utils as CAlg
 import           Control.Monad.Trans.Resource (runResourceT)
 import Control.Exception (try)
-import Control.Monad.Except
+import Control.Monad
+import Control.Monad.Trans.Class
+import Control.Monad.IO.Class
 import Data.Maybe
 import Data.Word
 

diff --git a/NGLess/Interpretation/Map.hs b/NGLess/Interpretation/Map.hs
@@ -1,4 +1,4 @@
-{- Copyright 2013-2022 NGLess Authors
+{- Copyright 2013-2024 NGLess Authors
  - License: MIT
  -}
 {-# LANGUAGE FlexibleContexts #-}
@@ -15,7 +15,7 @@ import qualified Data.ByteString as B
 import qualified Data.ByteString.Char8 as B8
 import qualified Data.ByteString.Builder as BB
 import           Control.Monad
-import           Control.Monad.Except
+import           Control.Monad.IO.Class
 
 import qualified Data.Conduit.List as CL
 import qualified Data.Conduit.Binary as CB
@@ -25,6 +25,7 @@ import qualified Data.Conduit.Algorithms.Async as CAlg
 import           Data.Conduit ((.|))
 import           Data.Conduit.Algorithms.Utils (awaitJust)
 import           Control.Monad.Extra (unlessM)
+import           Control.Monad.Trans.Class
 import           Data.List (sort)
 
 

diff --git a/NGLess/Interpretation/Write.hs b/NGLess/Interpretation/Write.hs
@@ -30,6 +30,8 @@ import           Data.Default (Default(..))
 import           Data.Maybe
 import           Data.String.Utils (replace, endswith)
 import           Control.Monad.IO.Unlift (MonadUnliftIO)
+import           Control.Monad.IO.Class
+import           Control.Monad
 import           Control.Monad.Except
 import           Control.Monad.Catch (MonadMask)
 import           System.IO (Handle, stdout)

diff --git a/NGLess/Language.hs b/NGLess/Language.hs
@@ -28,6 +28,7 @@ module Language
 {- This module defines the internal representation the language -}
 import qualified Data.Text as T
 import           Data.Either.Extra (eitherToMaybe)
+import           Control.Monad (forM)
 import           Control.Monad.Extra (whenJust)
 import           Control.Monad.Writer
 import           System.FilePath ((</>))

diff --git a/NGLess/NGLess/NGError.hs b/NGLess/NGLess/NGError.hs
@@ -15,11 +15,13 @@ module NGLess.NGError
 
 import           Control.DeepSeq
 import           Control.Monad.Except
+import           Control.Monad.IO.Class
 import           Control.Monad.Trans.Resource
 import           Control.Monad.Primitive
 import           Control.Monad.Catch
 import           Control.Exception
 
+
 -- This file should be a leaf in the import graph (i.e., not import any other NGLess modules)
 
 -- | An error in evaluating an ngless script

diff --git a/NGLess/Parse.hs b/NGLess/Parse.hs
@@ -1,4 +1,4 @@
-{- Copyright 2013-2021 NGLess Authors
+{- Copyright 2013-2024 NGLess Authors
  - License: MIT
  -}
 {-# LANGUAGE CPP #-}
@@ -165,7 +165,7 @@ funccall = try paired <|> FunctionCall <$>
 funcblock = optionMaybe (Block <$> (reserved "using" *> operator '|' *> variable <* operator '|' <* operator ':') <*> block)
 
 paired = FunctionCall
-            <$> (match_word "paired" $> (FuncName "paired"))
+            <$> (match_word "paired" $> FuncName "paired")
             <*> (operator '(' *> innerexpression <* operator ',')
             <*> pairedKwArgs
             <*> pure Nothing

diff --git a/NGLess/StandardModules/Parallel.hs b/NGLess/StandardModules/Parallel.hs
@@ -1,4 +1,4 @@
-{- Copyright 2016-2022 NGLess Authors
+{- Copyright 2016-2024 NGLess Authors
  - License: MIT
  -}
 
@@ -38,11 +38,11 @@ import qualified Data.Conduit.TQueue as CA
 import qualified Data.Conduit.Algorithms as CAlg
 import qualified Data.Conduit.Algorithms.Async as CAlg
 import           Data.Conduit.Algorithms.Async (conduitPossiblyCompressedFile)
+import           Control.Monad
 import           Control.Monad.ST (runST)
 import           Control.Monad.Except (throwError)
 import           Control.Monad.Extra (allM, unlessM)
 import           Control.DeepSeq
-import           Data.Traversable
 import           Control.Monad.Trans.Class
 import           System.AtomicWrite.Writer.Text (atomicWriteFile)
 import           System.Random.Shuffle (shuffleM)
@@ -83,11 +83,11 @@ import           Utils.LockFile (LockParameters(..))
 syncFile :: FilePath -> IO ()
 #ifndef WINDOWS
 syncFile fname = do
-    bracket (openFd fname ReadWrite Nothing defaultFileFlags)
+    bracket (openFd fname ReadWrite defaultFileFlags)
         closeFd
         fileSynchronise
     -- The code below will not work on Windows
-    bracket (openFd (takeDirectory fname) ReadOnly Nothing defaultFileFlags)
+    bracket (openFd (takeDirectory fname) ReadOnly defaultFileFlags)
         closeFd
         fileSynchronise
 

diff --git a/NGLess/Transform.hs b/NGLess/Transform.hs
@@ -12,7 +12,7 @@ module Transform
 
 import qualified Data.Text as T
 import Control.Monad.Trans.Cont
-import Control.Monad.Except
+import Control.Monad
 import Control.Monad.Writer
 import Control.Monad.RWS
 import Control.Arrow (first, second)

diff --git a/NGLess/Types.hs b/NGLess/Types.hs
@@ -18,6 +18,7 @@ import Data.Maybe
 import Control.Monad.State.Strict
 import Control.Monad.Trans.Except
 import Control.Monad.Reader (ReaderT(..), asks)
+import Control.Monad
 import Control.Monad.Writer
 import           Control.Applicative ((<|>))
 import           Data.String (fromString)

diff --git a/NGLess/Utils/LockFile.hs b/NGLess/Utils/LockFile.hs
@@ -29,6 +29,8 @@ import Data.Time (NominalDiffTime
                  , getCurrentTime
                  , diffUTCTime
                  )
+import Control.Monad.IO.Class
+import Control.Monad
 import Control.Monad.Except
 import Control.Exception
 import Control.Concurrent (threadDelay)

diff --git a/NGLess/Utils/Samtools.hs b/NGLess/Utils/Samtools.hs
@@ -1,4 +1,4 @@
-{- Copyright 2015-2022 NGLess Authors
+{- Copyright 2015-2024 NGLess Authors
  - License: MIT
  -}
 
@@ -23,7 +23,8 @@ import qualified Control.Concurrent.Async as A
 import qualified UnliftIO as U
 import           Data.Conduit ((.|))
 import           Data.Conduit.Algorithms.Async (conduitPossiblyCompressedFile)
-import           Control.Monad.Except
+import           Control.Monad.IO.Class
+import           Control.Monad.Trans.Class
 import           Control.Concurrent (getNumCapabilities, setNumCapabilities)
 import           Data.List (isSuffixOf)
 import           System.Process (proc)

diff --git a/NGLess/Validation.hs b/NGLess/Validation.hs
@@ -1,4 +1,4 @@
-{- Copyright 2013-2022 NGLess Authors
+{- Copyright 2013-2024 NGLess Authors
  - License: MIT
  -}
 {-# LANGUAGE FlexibleContexts #-}
@@ -13,6 +13,7 @@ import qualified Data.Text.Read as T
 import           Data.Either.Combinators (rightToMaybe)
 import           Control.Monad.Extra (whenJust)
 import           Control.Monad.Writer.Strict
+import           Control.Monad
 import           Control.Monad.RWS
 import           Data.List (find, isSuffixOf)
 import           Data.Maybe

diff --git a/NGLess/ValidationIO.hs b/NGLess/ValidationIO.hs
@@ -1,4 +1,4 @@
-{- Copyright 2013-2021 NGLess Authors
+{- Copyright 2013-2024 NGLess Authors
  - License: MIT
  -}
 
@@ -40,7 +40,7 @@ findFunctionIO fname = asks (flip findFunction fname) >>= \case
 -- | Run as many checks as possible (including non-pure, IO consuming, checks)
 validateIO :: [Module] -> Script -> NGLessIO (Maybe [T.Text])
 validateIO mods sc = do
-        err <- runReaderT (execWriterT (mapM ($sc) checks)) mods
+        err <- runReaderT (execWriterT (mapM ($ sc) checks)) mods
         case err of
             [] -> return Nothing
             errors -> return (Just errors)

diff --git a/build-scripts/ngless-static-embed-dependencies.nix b/build-scripts/ngless-static-embed-dependencies.nix
@@ -2,9 +2,9 @@
 let
   sources = {
     haskellNix = builtins.fetchTarball {
-        name = "haskell-nix-snap";
-        url = "https://github.com/input-output-hk/haskell.nix/archive/fadf9227afcdd93eedc656ba380f6a55d08fa650.tar.gz";
-        sha256 = "0bxk9gdw393gm9h2vr9lh70488n7pzj060ik1s2q54d2ydb44xfn";
+      name = "haskell-nix-snap";
+      url = "https://github.com/input-output-hk/haskell.nix/archive/c689f01730e5b6c6c16d3947a15689569844c38c.tar.gz";
+      sha256 = "09lw2419a5dd9g0ja31hjfqf6d4bzcgr5mrqx0vrvlksmp7a1kzk";
     };
   };
 
@@ -24,7 +24,7 @@ let
 in pkgs.haskell-nix.stackProject {
   name = "NGLess";
   src = (import ./sources-with-static-dependencies.nix) ;
-  stack-sha256 = "159b7sfkjfv5m0ppfb9lkr4vcplb152s3b7j6g9jhg9kcd9w0rmi";
+  stack-sha256 = "1lcj0vvrsyfq2fj014hf6q8qlg0rxvc387wkpb4kgclkhkwx7jg3";
   materialized = ./sources-with-static-dependencies.materialized;
   inherit checkMaterialization;
 }

diff --git a/build-scripts/release.materialized/NGLess.nix b/build-scripts/release.materialized/NGLess.nix
@@ -113,7 +113,7 @@
             ]);
         buildable = true;
         modules = [ "Paths_NGLess" ];
-        cSources = [ "NGLess/Dependencies/embedded.c" "NGLess/Data/FastQ.c" ];
+        cSources = [ "NGLess/Data/FastQ.c" "NGLess/Dependencies/embedded.c" ];
         hsSourceDirs = [ "NGLess/" ];
         };
       exes = {
@@ -191,7 +191,6 @@
               (hsPkgs."unix" or (errorHandler.buildDepError "unix"))
               ]);
           buildable = true;
-          cSources = [ "NGLess/Dependencies/embedded.c" "NGLess/Data/FastQ.c" ];
           hsSourceDirs = [ "Execs" ];
           mainPath = (([ "Main.hs" ] ++ [
             ""
@@ -279,7 +278,7 @@
               ]);
           buildable = true;
           modules = [ "Paths_NGLess" ];
-          cSources = [ "NGLess/Dependencies/embedded.c" "NGLess/Data/FastQ.c" ];
+          cSources = [ "NGLess/Data/FastQ.c" "NGLess/Dependencies/embedded.c" ];
           hsSourceDirs = [ "NGLess" "Tests-Src/" ];
           mainPath = [ "Tests.hs" ];
           };
@@ -361,7 +360,6 @@
               (hsPkgs."unix" or (errorHandler.buildDepError "unix"))
               ]);
           buildable = true;
-          cSources = [ "NGLess/Dependencies/embedded.c" "NGLess/Data/FastQ.c" ];
           hsSourceDirs = [ "Execs/" ];
           };
         };

diff --git a/build-scripts/release.materialized/default.nix b/build-scripts/release.materialized/default.nix
@@ -2,11 +2,12 @@
   extras = hackage:
     {
       packages = {
+        "conduit-algorithms" = (((hackage.conduit-algorithms)."0.0.14.0").revisions).default;
         NGLess = ./NGLess.nix;
         int-interval-map = ./.stack-to-nix.cache.0;
         };
       };
-  resolver = "lts-20.1";
+  resolver = "lts-22.6";
   modules = [
     ({ lib, ... }:
       { packages = {}; })