elynx-tree 0.7.0.1 → 0.7.1.0

raw patch · 5 files changed

+26/−8 lines, 5 filesdep −double-conversionPVP ok

version bump matches the API change (PVP)

Dependencies removed: double-conversion

API changes (from Hackage documentation)

Files

• ChangeLog.md +7/−0
• elynx-tree.cabal +1/−2
• src/ELynx/Tree/Import/Newick.hs +16/−1
• src/ELynx/Tree/Mrca.hs +1/−1
• src/ELynx/Tree/Name.hs +1/−4

@@ -5,6 +5,13 @@ ## Unreleased changes  +## Version 0.7.1.0++-   Be less strict with quoted identifiers/names in phylogenetic trees.+-   Be less strict with FASTA identifiers.+-   Update tooling (GHC 9.2.4).++ ## Version 0.7.0.1  -   Random 1.2: Parallel functions now require an \`IOGenM\` random number

@@ -1,6 +1,6 @@ cabal-version:      3.0 name:               elynx-tree-version:            0.7.0.1+version:            0.7.1.0 synopsis:           Handle phylogenetic trees description:   Examine, compare, and simulate phylogenetic trees in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>.@@ -84,7 +84,6 @@     , containers     , data-default-class     , deepseq-    , double-conversion     , elynx-nexus     , math-functions     , parallel

@@ -145,8 +145,23 @@  -- A name can be any string of printable characters except blanks, colons, -- semicolons, parentheses, and square brackets (and commas).+nameNotQuoted :: Parser Name+nameNotQuoted = Name . BL.fromStrict <$> takeWhile nameChar <?> "nameNoQuotes"++noClosingQuote :: Char -> Bool+noClosingQuote c = c /= '\''++nameQuoted :: Parser Name+nameQuoted = (<?> "nameQuotes") $ do+  _ <- char '\''+  n <- Name . BL.fromStrict <$> takeWhile noClosingQuote <?> "nameQuoted"+  _ <- char '\''+  pure n++-- A name can be any string of printable characters except blanks, colons,+-- semicolons, parentheses, and square brackets (and commas). name :: Parser Name-name = Name . BL.fromStrict <$> takeWhile nameChar <?> "name"+name = nameQuoted <|> nameNotQuoted <?> "name"  phylo :: Parser Phylo phylo = Phylo <$> optional branchLengthStandard <*> optional branchSupportStandard <?> "phylo"

@@ -104,7 +104,7 @@           [] -> Just $ Right $ S.singleton x           (l : r : _) -> Just $ Right $ S.fromList [head $ leaves l, head $ leaves r]           _ -> Just $ Left $ "findNode: degree two node found" <> show n-      | otherwise = case catMaybes $ map (go x) ts of+      | otherwise = case mapMaybe (go x) ts of           [] -> Nothing           [z] -> Just z           -- Use 'error' because this should never happen since we check for

@@ -25,9 +25,6 @@ import qualified Data.ByteString.Char8 as BS import qualified Data.ByteString.Lazy.Char8 as BL import Data.Default.Class--- TODO: 2021-09-02: Native conversion is being implemented at the moment.--- Remove external library when this is available.-import qualified Data.Double.Conversion.ByteString as BC import Data.String  -- | Node name.@@ -64,7 +61,7 @@   getName = Name . BB.toLazyByteString . BB.intDec  instance HasName Double where-  getName = Name . BL.fromStrict . BC.toShortest+  getName = Name . BB.toLazyByteString . BB.doubleDec  instance HasName Char where   getName = Name . BB.toLazyByteString . BB.char8