Updating GHC support to 9.0.* & 9.2.*, minor release

Author: recursion-ninja

ChangeLog.md

@@ -1,5 +1,15 @@
 # Revision history for commutative-multi-string-alignment
 
-## 0.1.0.0 -- 2018-03-18
+## 1.1.0 -- 2022-02-23
+
+* Added support for GHC `9.0.*` and `9.2.*`
+* Added test suites
+* Added reproducibility script, to replicate results of published paper
+* Added preprint LaTeX files for [![DOI:10.1186/s12859-020-03595-2](https://zenodo.org/badge/DOI/10.1186/s12859-020-03595-2.svg)](https://doi.org/10.1186/s12859-020-03595-2)
+* Added `LICENSE`
+* Updated `README`
+
+
+## 0.1.0 -- 2018-03-18
 
 * First version. No functionality, just compiles.

cabal.project

@@ -6,4 +6,4 @@ allow-newer:
 
 packages: .
 
-with-compiler: ghc-8.10.7
+with-compiler: ghc-9.2.1

efficient-implied-alignment.cabal

@@ -3,7 +3,7 @@ category:       Algorithms
 build-type:     Simple
 
 name:           efficient-implied-alignment
-version:        1.0.0
+version:        1.1.0
 
 author:         Alex Washburn
 maintainer:     [email protected]
@@ -26,8 +26,9 @@ bug-reports:    https://github.com/recursion-ninja/efficient-implied-alignment/i
 
 tested-with:
     GHC == 8.8.4
-    GHC == 8.10.4
-    GHC == 9.0.1
+    GHC == 8.10.7
+    GHC == 9.0.2
+    GHC == 9.2.1
 
 extra-source-files:
     ChangeLog.md
@@ -68,7 +69,6 @@ common ghc-flags
 --    -Wmissing-deriving-strategies
     -Wmissing-fields
     -Wmissing-home-modules
-    -Wmissing-monadfail-instances
     -Wmissing-signatures
     -Wnoncanonical-monad-instances
     -Wnoncanonical-monoid-instances
@@ -90,7 +90,6 @@ common ghc-flags
       -Wderiving-defaults
       -Wunused-packages
 
-
 library
 
   import:
@@ -107,7 +106,6 @@ library
     , deepseq
     , dlist
     , hashable
-    , integer-gmp
     , keys
     , lens
     , matrices
@@ -121,7 +119,6 @@ library
     , scientific
     , semigroupoids
     , text               >=1.2
-    , transformers
     , validation
     , vector
     , vector-instances >=3.4
@@ -261,7 +258,6 @@ executable draw-pre-order-figure
     , diagrams-lib
     , diagrams-svg
     , keys
-    , lens
 
   default-language: Haskell2010
 

src/Alignment/Internal.hs

@@ -131,7 +131,7 @@ deriveAlignment pAlignment pContext cContext = alignment
   where
     alignment = extractVector {-- . traceResult --} $ foldlWithKey f ([], toList cContext, toList pContext) pAlignment
 
-    extractVector e@ (x,ys,zs) =
+    extractVector e@(x,ys,zs) =
         case (ys, zs) of
           ([],[]) -> fromNonEmpty . NE.fromList $ reverse x
           _       -> error $ unlines

src/Alignment/Pairwise/Internal.hs

@@ -468,7 +468,7 @@ insertGaps gap lGaps rGaps meds
         ins = insertElement gap gap
         del = deleteElement gap gap
 
-        xs !> i = maybe (error "Tried to index an empty alignment context when reinserting gaps") (!i) xs
+        xs !> i = maybe (error "Tried to index an empty alignment context when reinserting gaps") (! i) xs
 
         newVector = EV.create $ do
           mVec <- MV.unsafeNew newLength

src/Numeric/Extended/Natural.hs

@@ -132,7 +132,7 @@ instance Num ExtendedNatural where
       | lhs <= rhs      = minBound
       | otherwise       = Cost $ x - y
 
-    lhs@(Cost x) * rhs@ (Cost y)
+    lhs@(Cost x) * rhs@(Cost y)
       -- If either value is infinite,
       -- then the product is infinite
       | lhs    == infinity  = infinity

stack.yaml

@@ -1,6 +1,6 @@
 allow-newer: true
 
-compiler: ghc-8.10.4
+compiler: ghc-9.2.1
 
 compiler-check: match-exact