Hello community, here is the log from the commit of package ghc-fasta for openSUSE:Factory checked in at 2017-03-31 15:07:35 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/ghc-fasta (Old) and /work/SRC/openSUSE:Factory/.ghc-fasta.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "ghc-fasta" Fri Mar 31 15:07:35 2017 rev:2 rq:482173 version:0.10.4.2 Changes: -------- --- /work/SRC/openSUSE:Factory/ghc-fasta/ghc-fasta.changes 2017-03-16 09:35:37.772925320 +0100 +++ /work/SRC/openSUSE:Factory/.ghc-fasta.new/ghc-fasta.changes 2017-03-31 15:07:36.844276205 +0200 @@ -1,0 +2,10 @@ +Mon Feb 20 08:43:02 UTC 2017 - [email protected] + +- Update to version 0.10.4.2 with cabal2obs. + +------------------------------------------------------------------- +Sun Feb 12 14:14:12 UTC 2017 - [email protected] + +- Update to version 0.10.4.1 with cabal2obs. + +------------------------------------------------------------------- Old: ---- fasta-0.10.4.0.tar.gz New: ---- fasta-0.10.4.2.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ ghc-fasta.spec ++++++ --- /var/tmp/diff_new_pack.8P9FV6/_old 2017-03-31 15:07:37.412195915 +0200 +++ /var/tmp/diff_new_pack.8P9FV6/_new 2017-03-31 15:07:37.416195349 +0200 @@ -1,7 +1,7 @@ # # spec file for package ghc-fasta # -# Copyright (c) 2016 SUSE LINUX GmbH, Nuernberg, Germany. +# Copyright (c) 2017 SUSE LINUX GmbH, Nuernberg, Germany. # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -18,7 +18,7 @@ %global pkg_name fasta Name: ghc-%{pkg_name} -Version: 0.10.4.0 +Version: 0.10.4.2 Release: 0 Summary: A simple, mindless parser for fasta files License: GPL-3.0+ ++++++ fasta-0.10.4.0.tar.gz -> fasta-0.10.4.2.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/fasta-0.10.4.0/fasta.cabal new/fasta-0.10.4.2/fasta.cabal --- old/fasta-0.10.4.0/fasta.cabal 2016-07-07 15:09:51.000000000 +0200 +++ new/fasta-0.10.4.2/fasta.cabal 2017-02-13 16:17:49.000000000 +0100 @@ -10,7 +10,7 @@ -- PVP summary: +-+------- breaking API changes -- | | +----- non-breaking API additions -- | | | +--- code changes with no API change -version: 0.10.4.0 +version: 0.10.4.2 -- A short (one-line) description of the package. synopsis: A simple, mindless parser for fasta files. diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/fasta-0.10.4.0/src/Data/Fasta/ByteString/Lazy/Parse.hs new/fasta-0.10.4.2/src/Data/Fasta/ByteString/Lazy/Parse.hs --- old/fasta-0.10.4.0/src/Data/Fasta/ByteString/Lazy/Parse.hs 2015-10-20 21:46:09.000000000 +0200 +++ new/fasta-0.10.4.2/src/Data/Fasta/ByteString/Lazy/Parse.hs 2017-02-13 16:17:28.000000000 +0100 @@ -171,12 +171,13 @@ where toFasta x = FastaSequence { fastaHeader = B.fromChunks . take 1 - . SB.lines + . lines' $ x , fastaSeq = B.fromChunks . tail - . SB.lines + . lines' $ x } + lines' = SB.lines . SB.filter (/= '\r') -- | Parse a CLIP fasta file into strict text sequences for pipes. pipesCLIPFasta :: (MonadIO m) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/fasta-0.10.4.0/src/Data/Fasta/ByteString/Lazy/Utility.hs new/fasta-0.10.4.2/src/Data/Fasta/ByteString/Lazy/Utility.hs --- old/fasta-0.10.4.0/src/Data/Fasta/ByteString/Lazy/Utility.hs 2016-07-07 15:08:26.000000000 +0200 +++ new/fasta-0.10.4.2/src/Data/Fasta/ByteString/Lazy/Utility.hs 2017-02-10 21:11:06.000000000 +0100 @@ -10,8 +10,10 @@ ) where -- Built in +import Data.Maybe -- Cabal +import Control.Lens import qualified Data.ByteString.Lazy.Char8 as BL -- Local @@ -21,7 +23,10 @@ -- | Gets a 1 indexed field from the header of a fasta sequence using a certain -- delimiter. getField :: Int -> Char -> FastaSequence -> BL.ByteString -getField field delim = (!! (field - 1)) . BL.split delim . fastaHeader +getField field delim = fromMaybe (error "getField: Field out of bounds in fasta header") + . preview (ix $ field - 1) + . BL.split delim + . fastaHeader -- | Gets the complement of the sequence. compl :: FastaSequence -> FastaSequence diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/fasta-0.10.4.0/src/Data/Fasta/ByteString/Parse.hs new/fasta-0.10.4.2/src/Data/Fasta/ByteString/Parse.hs --- old/fasta-0.10.4.0/src/Data/Fasta/ByteString/Parse.hs 2015-10-20 21:45:58.000000000 +0200 +++ new/fasta-0.10.4.2/src/Data/Fasta/ByteString/Parse.hs 2017-02-13 16:15:54.000000000 +0100 @@ -168,8 +168,9 @@ $ p ) >-> P.map toFasta where - toFasta x = FastaSequence { fastaHeader = head . B.lines $ x - , fastaSeq = B.concat . tail . B.lines $ x } + toFasta x = FastaSequence { fastaHeader = head . lines' $ x + , fastaSeq = B.concat . tail . lines' $ x } + lines' = B.lines . B.filter (/= '\r') -- | Parse a CLIP fasta file into strict text sequences for pipes. pipesCLIPFasta :: (MonadIO m) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/fasta-0.10.4.0/src/Data/Fasta/ByteString/Utility.hs new/fasta-0.10.4.2/src/Data/Fasta/ByteString/Utility.hs --- old/fasta-0.10.4.0/src/Data/Fasta/ByteString/Utility.hs 2016-07-07 15:09:05.000000000 +0200 +++ new/fasta-0.10.4.2/src/Data/Fasta/ByteString/Utility.hs 2017-02-10 21:09:19.000000000 +0100 @@ -10,8 +10,10 @@ ) where -- Built in +import Data.Maybe -- Cabal +import Control.Lens import qualified Data.ByteString.Char8 as B -- Local @@ -21,7 +23,10 @@ -- | Gets a 1 indexed field from the header of a fasta sequence using a certain -- delimiter. getField :: Int -> Char -> FastaSequence -> B.ByteString -getField field delim = (!! (field - 1)) . B.split delim . fastaHeader +getField field delim = fromMaybe (error "getField: Field out of bounds in fasta header") + . preview (ix $ field - 1) + . B.split delim + . fastaHeader -- | Gets the complement of the sequence. compl :: FastaSequence -> FastaSequence diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/fasta-0.10.4.0/src/Data/Fasta/String/Utility.hs new/fasta-0.10.4.2/src/Data/Fasta/String/Utility.hs --- old/fasta-0.10.4.0/src/Data/Fasta/String/Utility.hs 2016-07-07 15:10:30.000000000 +0200 +++ new/fasta-0.10.4.2/src/Data/Fasta/String/Utility.hs 2017-02-10 21:09:54.000000000 +0100 @@ -10,8 +10,10 @@ ) where -- Built in +import Data.Maybe -- Cabal +import Control.Lens import qualified Data.List.Split as Split -- Local @@ -21,7 +23,10 @@ -- | Gets a 1 indexed field from the header of a fasta sequence using a certain -- delimiter. getField :: Int -> Char -> FastaSequence -> String -getField field delim = (!! (field - 1)) . Split.splitWhen (== delim) . fastaHeader +getField field delim = fromMaybe (error "getField: Field out of bounds in fasta header") + . preview (ix $ field - 1) + . Split.splitWhen (== delim) + . fastaHeader -- | Gets the complement of the sequence. compl :: FastaSequence -> FastaSequence diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/fasta-0.10.4.0/src/Data/Fasta/Text/Lazy/Parse.hs new/fasta-0.10.4.2/src/Data/Fasta/Text/Lazy/Parse.hs --- old/fasta-0.10.4.0/src/Data/Fasta/Text/Lazy/Parse.hs 2015-10-20 21:53:39.000000000 +0200 +++ new/fasta-0.10.4.2/src/Data/Fasta/Text/Lazy/Parse.hs 2017-02-13 16:16:52.000000000 +0100 @@ -167,12 +167,13 @@ where toFasta x = FastaSequence { fastaHeader = T.fromChunks . take 1 - . ST.lines + . lines' $ x , fastaSeq = T.fromChunks . tail - . ST.lines + . lines' $ x } + lines' = ST.lines . ST.filter (/= '\r') -- | Parse a CLIP fasta file into a pipe pipesCLIPFasta :: (MonadIO m) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/fasta-0.10.4.0/src/Data/Fasta/Text/Lazy/Utility.hs new/fasta-0.10.4.2/src/Data/Fasta/Text/Lazy/Utility.hs --- old/fasta-0.10.4.0/src/Data/Fasta/Text/Lazy/Utility.hs 2016-07-07 15:10:49.000000000 +0200 +++ new/fasta-0.10.4.2/src/Data/Fasta/Text/Lazy/Utility.hs 2017-02-10 21:10:31.000000000 +0100 @@ -10,8 +10,10 @@ ) where -- Built in +import Data.Maybe -- Cabal +import Control.Lens import qualified Data.Text.Lazy as T -- Local @@ -21,7 +23,10 @@ -- | Gets a 1 indexed field from the header of a fasta sequence using a certain -- delimiter. getField :: Int -> Char -> FastaSequence -> T.Text -getField field delim = (!! (field - 1)) . T.split (== delim) . fastaHeader +getField field delim = fromMaybe (error "getField: Field out of bounds in fasta header") + . preview (ix $ field - 1) + . T.split (== delim) + . fastaHeader -- | Gets the complement of the sequence. compl :: FastaSequence -> FastaSequence diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/fasta-0.10.4.0/src/Data/Fasta/Text/Parse.hs new/fasta-0.10.4.2/src/Data/Fasta/Text/Parse.hs --- old/fasta-0.10.4.0/src/Data/Fasta/Text/Parse.hs 2015-10-20 21:59:29.000000000 +0200 +++ new/fasta-0.10.4.2/src/Data/Fasta/Text/Parse.hs 2017-02-13 16:14:18.000000000 +0100 @@ -161,8 +161,9 @@ $ p ) >-> P.map toFasta where - toFasta x = FastaSequence { fastaHeader = head . T.lines $ x - , fastaSeq = T.concat . tail . T.lines $ x } + toFasta x = FastaSequence { fastaHeader = head . lines' $ x + , fastaSeq = T.concat . tail . lines' $ x } + lines' = T.lines . T.filter (/= '\r') -- | Parse a CLIP fasta file into a pipe pipesCLIPFasta :: (MonadIO m) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/fasta-0.10.4.0/src/Data/Fasta/Text/Utility.hs new/fasta-0.10.4.2/src/Data/Fasta/Text/Utility.hs --- old/fasta-0.10.4.0/src/Data/Fasta/Text/Utility.hs 2016-07-07 15:10:39.000000000 +0200 +++ new/fasta-0.10.4.2/src/Data/Fasta/Text/Utility.hs 2017-02-10 21:09:18.000000000 +0100 @@ -10,8 +10,10 @@ ) where -- Built in +import Data.Maybe -- Cabal +import Control.Lens import qualified Data.Text as T -- Local @@ -21,7 +23,10 @@ -- | Gets a 1 indexed field from the header of a fasta sequence using a certain -- delimiter. getField :: Int -> Char -> FastaSequence -> T.Text -getField field delim = (!! (field - 1)) . T.split (== delim) . fastaHeader +getField field delim = fromMaybe (error "getField: Field out of bounds in fasta header") + . preview (ix $ field - 1) + . T.split (== delim) + . fastaHeader -- | Gets the complement of the sequence. compl :: FastaSequence -> FastaSequence
