March 2017 - openSUSE Commits - openSUSE Mailing Lists

commit ghc-reform-blaze for openSUSE:Factory
by root＠hilbert.suse.de 31 Mar '17

31 Mar '17

Hello community, here is the log from the commit of package ghc-reform-blaze for openSUSE:Factory checked in at 2017-03-31 15:07:38 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/ghc-reform-blaze (Old) and /work/SRC/openSUSE:Factory/.ghc-reform-blaze.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "ghc-reform-blaze" Fri Mar 31 15:07:38 2017 rev:2 rq:482174 version:0.2.4.3 Changes: -------- --- /work/SRC/openSUSE:Factory/ghc-reform-blaze/ghc-reform-blaze.changes 2017-03-16 09:35:17.347817397 +0100 +++ /work/SRC/openSUSE:Factory/.ghc-reform-blaze.new/ghc-reform-blaze.changes 2017-03-31 15:07:38.752006497 +0200 @@ -1,0 +2,5 @@ +Sun Feb 12 14:16:56 UTC 2017 - psimons(a)suse.com + +- Update to version 0.2.4.3 with cabal2obs. + +------------------------------------------------------------------- Old: ---- 1.cabal reform-blaze-0.2.4.1.tar.gz New: ---- reform-blaze-0.2.4.3.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ ghc-reform-blaze.spec ++++++ --- /var/tmp/diff_new_pack.EpgYki/_old 2017-03-31 15:07:39.343922814 +0200 +++ /var/tmp/diff_new_pack.EpgYki/_new 2017-03-31 15:07:39.343922814 +0200 @@ -1,7 +1,7 @@ # # spec file for package ghc-reform-blaze # -# 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 @@ -18,23 +18,20 @@ %global pkg_name reform-blaze Name: ghc-%{pkg_name} -Version: 0.2.4.1 +Version: 0.2.4.3 Release: 0 Summary: Add support for using blaze-html with Reform License: BSD-3-Clause -Group: System/Libraries +Group: Development/Languages/Other Url: https://hackage.haskell.org/package/%{pkg_name} Source0: https://hackage.haskell.org/package/%{pkg_name}-%{version}/%{pkg_name}-%{ve… -Source1: https://hackage.haskell.org/package/%{pkg_name}-%{version}/revision/1.cabal BuildRequires: ghc-Cabal-devel -# Begin cabal-rpm deps: BuildRequires: ghc-blaze-html-devel BuildRequires: ghc-blaze-markup-devel BuildRequires: ghc-reform-devel BuildRequires: ghc-rpm-macros BuildRequires: ghc-text-devel BuildRoot: %{_tmppath}/%{name}-%{version}-build -# End cabal-rpm deps %description Reform is a library for building and validating forms using applicative @@ -53,17 +50,13 @@ %prep %setup -q -n %{pkg_name}-%{version} -cp -p %{SOURCE1} %{pkg_name}.cabal - %build %ghc_lib_build - %install %ghc_lib_install - %post devel %ghc_pkg_recache ++++++ reform-blaze-0.2.4.1.tar.gz -> reform-blaze-0.2.4.3.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/reform-blaze-0.2.4.1/reform-blaze.cabal new/reform-blaze-0.2.4.3/reform-blaze.cabal --- old/reform-blaze-0.2.4.1/reform-blaze.cabal 2015-12-18 22:14:02.000000000 +0100 +++ new/reform-blaze-0.2.4.3/reform-blaze.cabal 2017-02-10 04:07:40.000000000 +0100 @@ -1,5 +1,5 @@ Name: reform-blaze -Version: 0.2.4.1 +Version: 0.2.4.3 Synopsis: Add support for using blaze-html with Reform Description: Reform is a library for building and validating forms using applicative functors. This package add support for using reform with blaze-html. Homepage: http://www.happstack.com/ @@ -22,8 +22,8 @@ Text.Reform.Blaze.String Text.Reform.Blaze.Text - Build-depends: base >4 && <5, - blaze-markup >= 0.5 && < 0.8, - blaze-html >= 0.5 && < 0.9, + Build-depends: base >4.5 && <5, + blaze-markup >= 0.5 && < 0.9, + blaze-html >= 0.5 && < 0.10, reform == 0.2.*, text >= 0.11 && < 1.3

1 0

commit ghc-fasta for openSUSE:Factory
by root＠hilbert.suse.de 31 Mar '17

31 Mar '17

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 - psimons(a)suse.com + +- Update to version 0.10.4.2 with cabal2obs. + +------------------------------------------------------------------- +Sun Feb 12 14:14:12 UTC 2017 - psimons(a)suse.com + +- 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

1 0

commit ghc-bytestring-progress for openSUSE:Factory
by root＠hilbert.suse.de 31 Mar '17

31 Mar '17

Hello community, here is the log from the commit of package ghc-bytestring-progress for openSUSE:Factory checked in at 2017-03-31 15:07:33 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/ghc-bytestring-progress (Old) and /work/SRC/openSUSE:Factory/.ghc-bytestring-progress.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "ghc-bytestring-progress" Fri Mar 31 15:07:33 2017 rev:2 rq:482172 version:1.0.7 Changes: -------- --- /work/SRC/openSUSE:Factory/ghc-bytestring-progress/ghc-bytestring-progress.changes 2017-03-16 09:35:40.200581577 +0100 +++ /work/SRC/openSUSE:Factory/.ghc-bytestring-progress.new/ghc-bytestring-progress.changes 2017-03-31 15:07:34.588595105 +0200 @@ -1,0 +2,5 @@ +Tue Oct 11 08:49:34 UTC 2016 - psimons(a)suse.com + +- Update to version 1.0.7 with cabal2obs. + +------------------------------------------------------------------- Old: ---- bytestring-progress-1.0.6.tar.gz New: ---- bytestring-progress-1.0.7.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ ghc-bytestring-progress.spec ++++++ --- /var/tmp/diff_new_pack.Aq3GpD/_old 2017-03-31 15:07:35.328490501 +0200 +++ /var/tmp/diff_new_pack.Aq3GpD/_new 2017-03-31 15:07:35.332489935 +0200 @@ -1,7 +1,7 @@ # # spec file for package ghc-bytestring-progress # -# 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 bytestring-progress Name: ghc-%{pkg_name} -Version: 1.0.6 +Version: 1.0.7 Release: 0 Summary: A library for tracking the consumption of a lazy ByteString License: BSD-3-Clause ++++++ bytestring-progress-1.0.6.tar.gz -> bytestring-progress-1.0.7.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/bytestring-progress-1.0.6/System/ProgressBar/ByteString.hs new/bytestring-progress-1.0.7/System/ProgressBar/ByteString.hs --- old/bytestring-progress-1.0.6/System/ProgressBar/ByteString.hs 2016-06-06 20:28:32.000000000 +0200 +++ new/bytestring-progress-1.0.7/System/ProgressBar/ByteString.hs 2016-10-03 01:10:17.000000000 +0200 @@ -10,7 +10,7 @@ import Data.ByteString.Lazy.Progress import System.IO(Handle,hSetBuffering,hPutChar,hPutStr,BufferMode(..)) import System.IO(openFile,hFileSize,IOMode(..)) -import System.ProgressBar +import System.ProgressBar(Label, mkProgressBar) type ℤ = Integer diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/bytestring-progress-1.0.6/bytestring-progress.cabal new/bytestring-progress-1.0.7/bytestring-progress.cabal --- old/bytestring-progress-1.0.6/bytestring-progress.cabal 2016-06-06 20:28:32.000000000 +0200 +++ new/bytestring-progress-1.0.7/bytestring-progress.cabal 2016-10-03 01:10:17.000000000 +0200 @@ -1,5 +1,5 @@ Name: bytestring-progress -Version: 1.0.6 +Version: 1.0.7 Build-Type: Simple Cabal-Version: >= 1.6 License: BSD3 @@ -29,7 +29,7 @@ Exposed-Modules: Data.ByteString.Lazy.Progress if flag(use-system-progressbar) - Build-Depends: terminal-progress-bar >= 0.0.1 && < 0.0.2 + Build-Depends: terminal-progress-bar >= 0.0.1 && < 0.2.0 Exposed-Modules: System.ProgressBar.ByteString

1 0

commit ghc-active for openSUSE:Factory
by root＠hilbert.suse.de 31 Mar '17

31 Mar '17

Hello community, here is the log from the commit of package ghc-active for openSUSE:Factory checked in at 2017-03-31 15:07:30 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/ghc-active (Old) and /work/SRC/openSUSE:Factory/.ghc-active.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "ghc-active" Fri Mar 31 15:07:30 2017 rev:2 rq:482171 version:0.2.0.12 Changes: -------- --- /work/SRC/openSUSE:Factory/ghc-active/ghc-active.changes 2017-03-16 09:35:20.451377951 +0100 +++ /work/SRC/openSUSE:Factory/.ghc-active.new/ghc-active.changes 2017-03-31 15:07:31.201074020 +0200 @@ -1,0 +2,5 @@ +Sun Feb 12 14:10:02 UTC 2017 - psimons(a)suse.com + +- Update to version 0.2.0.12 with cabal2obs. + +------------------------------------------------------------------- Old: ---- active-0.2.0.10.tar.gz New: ---- active-0.2.0.12.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ ghc-active.spec ++++++ --- /var/tmp/diff_new_pack.XqQUfA/_old 2017-03-31 15:07:31.840983552 +0200 +++ /var/tmp/diff_new_pack.XqQUfA/_new 2017-03-31 15:07:31.840983552 +0200 @@ -1,7 +1,7 @@ # # spec file for package ghc-active # -# 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 @@ -19,11 +19,11 @@ %global pkg_name active %bcond_with tests Name: ghc-%{pkg_name} -Version: 0.2.0.10 +Version: 0.2.0.12 Release: 0 Summary: Abstractions for animation License: BSD-3-Clause -Group: System/Libraries +Group: Development/Languages/Other Url: https://hackage.haskell.org/package/%{pkg_name} Source0: https://hackage.haskell.org/package/%{pkg_name}-%{version}/%{pkg_name}-%{ve… BuildRequires: ghc-Cabal-devel @@ -55,19 +55,15 @@ %prep %setup -q -n %{pkg_name}-%{version} - %build %ghc_lib_build - %install %ghc_lib_install - %check %cabal_test - %post devel %ghc_pkg_recache @@ -80,6 +76,6 @@ %files devel -f %{name}-devel.files %defattr(-,root,root,-) -%doc README.markdown +%doc CHANGES README.markdown %changelog ++++++ active-0.2.0.10.tar.gz -> active-0.2.0.12.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/active-0.2.0.10/CHANGES new/active-0.2.0.12/CHANGES --- old/active-0.2.0.10/CHANGES 2016-07-02 03:37:56.000000000 +0200 +++ new/active-0.2.0.12/CHANGES 2016-10-14 23:41:33.000000000 +0200 @@ -1,3 +1,11 @@ +## [0.2.0.12](https://github.com/diagrams/active/tree/v0.2.0.12) (2016-10-14) + +- allow `lens-4.15` + +## [v0.2.0.11](https://github.com/diagrams/active/tree/v0.2.0.11) (2016-08-01) + +- update test suite for `QuickCheck-2.9` + ## [v0.2.0.10](https://github.com/diagrams/active/tree/v0.2.0.10) (2016-07-01) - allow `semigroupoids-5.1` diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/active-0.2.0.10/LICENSE new/active-0.2.0.12/LICENSE --- old/active-0.2.0.10/LICENSE 2016-07-02 03:37:56.000000000 +0200 +++ new/active-0.2.0.12/LICENSE 2016-10-14 23:41:33.000000000 +0200 @@ -2,6 +2,7 @@ Andy Gill <andygill(a)ku.edu> Ben Gamari <ben(a)smart-cactus.org> +Bollu <siddu.druid(a)gmail.com> Brent Yorgey <byorgey(a)gmail.com> Christopher Chalmers <c.chalmers(a)me.com> Daniel Bergey <bergey(a)alum.mit.edu> diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/active-0.2.0.10/active.cabal new/active-0.2.0.12/active.cabal --- old/active-0.2.0.10/active.cabal 2016-07-02 03:37:56.000000000 +0200 +++ new/active-0.2.0.12/active.cabal 2016-10-14 23:41:33.000000000 +0200 @@ -1,18 +1,18 @@ name: active -version: 0.2.0.10 +version: 0.2.0.12 synopsis: Abstractions for animation description: "Active" abstraction for animated things with finite start and end times. license: BSD3 license-file: LICENSE author: Brent Yorgey -maintainer: byorgey(a)cis.upenn.edu +maintainer: byorgey(a)gmail.com copyright: (c) 2011-2015 Brent Yorgey category: Data build-type: Simple cabal-version: >=1.10 extra-source-files: CHANGES, README.markdown, diagrams/*.svg extra-doc-files: diagrams/*.svg -tested-with: GHC == 7.6.3, GHC == 7.8.4, GHC == 7.10.2 +tested-with: GHC == 7.6.3, GHC == 7.8.4, GHC == 7.10.2, GHC == 8.0.1 bug-reports: https://github.com/diagrams/active/issues source-repository head type: git @@ -24,7 +24,7 @@ vector >= 0.10, semigroups >= 0.1 && < 0.19, semigroupoids >= 1.2 && < 5.2, - lens >= 4.0 && < 4.15, + lens >= 4.0 && < 4.16, linear >= 1.14 && < 1.21 hs-source-dirs: src default-language: Haskell2010 @@ -36,8 +36,9 @@ vector >= 0.10, semigroups >= 0.1 && < 0.19, semigroupoids >= 1.2 && < 5.2, - lens >= 4.0 && < 4.15, + lens >= 4.0 && < 4.16, linear >= 1.14 && < 1.21, - QuickCheck >= 2.4.2 && < 2.9 + QuickCheck >= 2.9 && < 2.10 + other-modules: Data.Active hs-source-dirs: src, test default-language: Haskell2010 diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/active-0.2.0.10/test/active-tests.hs new/active-0.2.0.12/test/active-tests.hs --- old/active-0.2.0.10/test/active-tests.hs 2016-07-02 03:37:56.000000000 +0200 +++ new/active-0.2.0.12/test/active-tests.hs 2016-10-14 23:41:33.000000000 +0200 @@ -51,16 +51,13 @@ {-# ANN main ("HLint: ignore Eta reduce" :: String) #-} -- eta reducing qc breaks it -instance Arbitrary Any where - arbitrary = Any <$> arbitrary - -instance (Arbitrary n, Fractional n, Real n) => Arbitrary (Time n) where +instance (Fractional n) => Arbitrary (Time n) where arbitrary = fromRational <$> arbitrary -instance (CoArbitrary n, Real n) => CoArbitrary (Time n) where +instance (Real n) => CoArbitrary (Time n) where coarbitrary t = coarbitrary (toRational t) -instance (Arbitrary n, Fractional n, Real n) => Arbitrary (Duration n) where +instance (Fractional n) => Arbitrary (Duration n) where arbitrary = (fromRational . abs) <$> arbitrary instance Arbitrary a => Arbitrary (Dynamic a) where

1 0

commit ghc-ClustalParser for openSUSE:Factory
by root＠hilbert.suse.de 31 Mar '17

31 Mar '17

Hello community, here is the log from the commit of package ghc-ClustalParser for openSUSE:Factory checked in at 2017-03-31 15:07:29 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/ghc-ClustalParser (Old) and /work/SRC/openSUSE:Factory/.ghc-ClustalParser.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "ghc-ClustalParser" Fri Mar 31 15:07:29 2017 rev:2 rq:482169 version:1.2.1 Changes: -------- --- /work/SRC/openSUSE:Factory/ghc-ClustalParser/ghc-ClustalParser.changes 2017-03-16 09:35:54.446564427 +0100 +++ /work/SRC/openSUSE:Factory/.ghc-ClustalParser.new/ghc-ClustalParser.changes 2017-03-31 15:07:30.301201240 +0200 @@ -1,0 +2,5 @@ +Sun Feb 12 14:12:30 UTC 2017 - psimons(a)suse.com + +- Update to version 1.2.1 with cabal2obs. + +------------------------------------------------------------------- Old: ---- ClustalParser-1.1.4.tar.gz New: ---- ClustalParser-1.2.1.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ ghc-ClustalParser.spec ++++++ --- /var/tmp/diff_new_pack.cekxdv/_old 2017-03-31 15:07:30.837125473 +0200 +++ /var/tmp/diff_new_pack.cekxdv/_new 2017-03-31 15:07:30.841124908 +0200 @@ -19,10 +19,10 @@ %global pkg_name ClustalParser %bcond_with tests Name: ghc-%{pkg_name} -Version: 1.1.4 +Version: 1.2.1 Release: 0 Summary: Libary for parsing Clustal tools output -License: GPL-3.0 +License: GPL-3.0+ Group: Development/Languages/Other Url: https://hackage.haskell.org/package/%{pkg_name} Source0: https://hackage.haskell.org/package/%{pkg_name}-%{version}/%{pkg_name}-%{ve… @@ -32,6 +32,7 @@ BuildRequires: ghc-either-unwrap-devel BuildRequires: ghc-parsec-devel BuildRequires: ghc-rpm-macros +BuildRequires: ghc-text-devel BuildRequires: ghc-vector-devel BuildRoot: %{_tmppath}/%{name}-%{version}-build %if %{with tests} ++++++ ClustalParser-1.1.4.tar.gz -> ClustalParser-1.2.1.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/ClustalParser-1.1.4/ClustalParser.cabal new/ClustalParser-1.2.1/ClustalParser.cabal --- old/ClustalParser-1.1.4/ClustalParser.cabal 2016-05-30 11:45:48.000000000 +0200 +++ new/ClustalParser-1.2.1/ClustalParser.cabal 2017-02-06 19:20:52.000000000 +0100 @@ -5,7 +5,7 @@ -- PVP summary: +-+------- breaking API changes -- | | +----- non-breaking API additions -- | | | +--- code changes with no API change -version: 1.1.4 +version: 1.2.1 synopsis: Libary for parsing Clustal tools output description: Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna, cmalign . @@ -18,7 +18,7 @@ Cmalign is a multiple sequence alignment program based on RNA family models and produces ,among others, clustal output. It is part of infernal <http://infernal.janelia.org/>. -license: GPL +license: GPL-3.0 license-file: LICENSE author: Florian Eggenhofer maintainer: egg(a)tbi.univie.ac.at @@ -36,8 +36,8 @@ source-repository this type: git - location: https://github.com/eggzilla/ClustalParser/tree/1.1.4 - tag: 1.1.4 + location: https://github.com/eggzilla/ClustalParser/tree/1.2.1 + tag: 1.2.1 library -- Modules exported by the library. @@ -45,7 +45,7 @@ other-modules: Bio.ClustalData -- Other library packages from which modules are imported. - build-depends: base >=4.5 && <5, parsec>=3.1.9, vector + build-depends: base >=4.5 && <5, parsec>=3.1.9, vector, text -- compiler options ghc-options: -Wall -O2 -fno-warn-unused-do-bind -- Directories containing source files. @@ -58,7 +58,7 @@ ghc-options: -Wall -O2 test-suite hspec - build-depends: base, parsec, ClustalParser, hspec >= 1.8 + build-depends: base, parsec, ClustalParser, hspec >= 1.8, text hs-source-dirs: test-suite main-is: Spec.hs type: exitcode-stdio-1.0 diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/ClustalParser-1.1.4/ClustalParserTest.hs new/ClustalParser-1.2.1/ClustalParserTest.hs --- old/ClustalParser-1.1.4/ClustalParserTest.hs 2016-05-30 11:45:48.000000000 +0200 +++ new/ClustalParser-1.2.1/ClustalParserTest.hs 2017-02-06 19:20:52.000000000 +0100 @@ -1,7 +1,9 @@ +--runghc -package-db --ghc-arg=.cabal-sandbox/x86_64-linux-ghc-8.0.1-packages.conf.d ClustalParserTest.hs struct-multiline.mlocarna module Main where import System.Environment (getArgs) import Bio.ClustalParser +--import Data.Either.Unwrap main :: IO () main = do @@ -10,4 +12,5 @@ -- read Clustal outputfile parsedinput <- readStructuralClustalAlignment input_file print parsedinput + --print $ structuralAlignmentEntries (fromRight parsedinput) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/ClustalParser-1.1.4/changelog new/ClustalParser-1.2.1/changelog --- old/ClustalParser-1.1.4/changelog 2016-05-30 11:45:48.000000000 +0200 +++ new/ClustalParser-1.2.1/changelog 2017-02-06 19:20:52.000000000 +0100 @@ -1,4 +1,8 @@ -*-change-log-*- +1.2.1 Florian Eggenhofer <egg(a)cs.uni-freiburg.de> 06. February 2017 + * Structural alignment parser now works with multiline consensus structures +1.2.0 Florian Eggenhofer <egg(a)cs.uni-freiburg.de> 07. January 2017 + * Changed datastructures for sequence identifers and sequences to Data.Text 1.1.4 Florian Eggenhofer <egg(a)cs.uni-freiburg.de> 30. May 2016 * Fixed a bug in output of clustal alignments with sequence length of 60 1.1.3 Florian Eggenhofer <florian.eggenhofer(a)univie.ac.at> 4. July 2015 diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/ClustalParser-1.1.4/src/Bio/ClustalData.hs new/ClustalParser-1.2.1/src/Bio/ClustalData.hs --- old/ClustalParser-1.1.4/src/Bio/ClustalData.hs 2016-05-30 11:45:48.000000000 +0200 +++ new/ClustalParser-1.2.1/src/Bio/ClustalData.hs 2017-02-06 19:20:52.000000000 +0100 @@ -3,26 +3,27 @@ module Bio.ClustalData where import qualified Data.Vector as V - +import qualified Data.Text as T + -- | Data type for clustal summary, containing information about the alignment process, usually printed to STDOUT data ClustalSummary = ClustalSummary { - clustalw2version :: String, - sequenceFormat :: String, + clustalw2version :: T.Text, + sequenceFormat :: T.Text, parametersOfInputSequences :: [SequenceParameters], pairwiseAlignmentSummaries :: [PairwiseAlignmentSummary], - guideTreeFileName :: String, + guideTreeFileName :: T.Text, groupNumber :: Int, groupSummaries :: [GroupSummary], alignmentScore :: Int, - alignmentFileName :: String + alignmentFileName :: T.Text } deriving (Show, Eq) data SequenceParameters = SequenceParameters { inputSequenceIndex :: Int, - inputSequenceIdentifier :: String, + inputSequenceIdentifier :: T.Text, inputSequenceLength :: Int } deriving (Show, Eq) @@ -47,7 +48,7 @@ data ClustalAlignment = ClustalAlignment { alignmentEntries :: [ClustalAlignmentEntry], - conservationTrack :: String + conservationTrack :: T.Text } deriving (Eq) @@ -56,30 +57,30 @@ | not (null _alignmentEntries) = header ++ alignmentString | otherwise = header where header = "CLUSTAL W (1.8) multiple sequence alignment\n\n\n" - longestSequenceIdLength = (maximum (map length (map entrySequenceIdentifier _alignmentEntries))) + 1 - totalSequenceLength = length (entryAlignedSequence (head _alignmentEntries)) + longestSequenceIdLength = (maximum (map T.length (map entrySequenceIdentifier _alignmentEntries))) + 1 + totalSequenceLength = T.length (entryAlignedSequence (head _alignmentEntries)) alignmentString = showAlignment totalSequenceLength longestSequenceIdLength 0 _alignmentEntries _conservationTrack -showAlignment :: Int -> Int -> Int -> [ClustalAlignmentEntry] -> String -> String +showAlignment :: Int -> Int -> Int -> [ClustalAlignmentEntry] -> T.Text -> String showAlignment totalSequenceLength longestSequenceIdLength currentWindowPosition _alignmentEntries _conservationTrack | totalSequenceLength == 0 = [] | currentWindowPosition < totalSequenceLength = showAlignmentBlock longestSequenceIdLength currentWindowPosition _alignmentEntries _conservationTrack ++ (showAlignment totalSequenceLength longestSequenceIdLength (currentWindowPosition + 60) _alignmentEntries _conservationTrack) | currentWindowPosition == totalSequenceLength = [] - | otherwise = "" + | otherwise = "" -showAlignmentBlock :: Int -> Int -> [ClustalAlignmentEntry] -> String -> String +showAlignmentBlock :: Int -> Int -> [ClustalAlignmentEntry] -> T.Text -> String showAlignmentBlock longestSequenceIdLength currentWindowPosition _alignmentEntries _conservationTrack = blockString where blockString = entries ++ extraTrack ++ "\n" entries = concatMap (showAlignmentLine longestSequenceIdLength currentWindowPosition) _alignmentEntries - extraTrack = concat (replicate longestSequenceIdLength " ") ++ V.toList (V.slice currentWindowPosition 60 (V.fromList _conservationTrack)) ++ "\n" + extraTrack = concat (replicate longestSequenceIdLength " ") ++ V.toList (V.slice currentWindowPosition 60 (V.fromList (T.unpack _conservationTrack))) ++ "\n" showAlignmentLine :: Int -> Int -> ClustalAlignmentEntry -> String -showAlignmentLine longestSequenceIdLength currentWindowPosition _alignmentEntry = (entrySequenceIdentifier _alignmentEntry) ++ concat (replicate (longestSequenceIdLength - length (entrySequenceIdentifier _alignmentEntry)) " ") ++ V.toList (V.slice currentWindowPosition 60 (V.fromList (entryAlignedSequence _alignmentEntry))) ++ "\n" +showAlignmentLine longestSequenceIdLength currentWindowPosition _alignmentEntry = T.unpack (entrySequenceIdentifier _alignmentEntry) ++ concat (replicate (longestSequenceIdLength - T.length (entrySequenceIdentifier _alignmentEntry)) " ") ++ V.toList (V.slice currentWindowPosition 60 (V.fromList (T.unpack (entryAlignedSequence _alignmentEntry)))) ++ "\n" data ClustalAlignmentEntry = ClustalAlignmentEntry { - entrySequenceIdentifier :: String, - entryAlignedSequence :: String + entrySequenceIdentifier :: T.Text, + entryAlignedSequence :: T.Text } deriving (Show, Eq) @@ -91,18 +92,18 @@ deriving (Show, Eq) data ClustalAlignmentEntrySlice = ClustalAlignmentEntrySlice - { - entrySequenceSliceIdentifier :: String, - entryAlignedSliceSequence :: String, - spacerLength :: Int - } - deriving (Show, Eq) + { + entrySequenceSliceIdentifier :: String, + entryAlignedSliceSequence :: String, + spacerLength :: Int + } + deriving (Show, Eq) -- | Data structure for structural Clustal alignment format data StructuralClustalAlignment = StructuralClustalAlignment { structuralAlignmentEntries :: [ClustalAlignmentEntry], - secondaryStructureTrack :: String, + secondaryStructureTrack :: T.Text, energy :: Double } deriving (Eq) @@ -112,15 +113,15 @@ | not (null _alignmentEntries) = header ++ alignmentString | otherwise = header where header = "CLUSTAL W \n\n" - longestSequenceIdLength = (maximum (map length (map entrySequenceIdentifier _alignmentEntries))) + 1 - totalSequenceLength = length (entryAlignedSequence (head _alignmentEntries)) + longestSequenceIdLength = (maximum (map T.length (map entrySequenceIdentifier _alignmentEntries))) + 1 + totalSequenceLength = T.length (entryAlignedSequence (head _alignmentEntries)) alignmentString = showAlignment totalSequenceLength longestSequenceIdLength 0 _alignmentEntries _secondaryStructureTrack -data StructuralClustalAlignmentSlice = StructuralClustalAlignmentSlice - { - structuralEntrySlices :: [StructuralClustalAlignmentEntrySlice] - } - deriving (Show, Eq) +-- data StructuralClustalAlignmentSlice = StructuralClustalAlignmentSlice +-- { +-- structuralEntrySlices :: [StructuralClustalAlignmentEntrySlice] +-- } +-- deriving (Show, Eq) data StructuralClustalAlignmentEntrySlice = StructuralClustalAlignmentEntrySlice { diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/ClustalParser-1.1.4/src/Bio/ClustalParser.hs new/ClustalParser-1.2.1/src/Bio/ClustalParser.hs --- old/ClustalParser-1.1.4/src/Bio/ClustalParser.hs 2016-05-30 11:45:48.000000000 +0200 +++ new/ClustalParser-1.2.1/src/Bio/ClustalParser.hs 2017-02-06 19:20:52.000000000 +0100 @@ -14,7 +14,7 @@ import Text.ParserCombinators.Parsec import Control.Monad import Data.List - +import qualified Data.Text as T readDouble :: String -> Double readDouble = read @@ -69,7 +69,7 @@ newline newline eof - return $ ClustalSummary version sequenceFormat' sequenceParametersList pairwiseAlignmentSummaryList guideTreeFileName' (readInt numberOfGroups) groupSummaryList (readInt alignmentScore') alignmentFileName' + return $ ClustalSummary (T.pack version) (T.pack sequenceFormat') sequenceParametersList pairwiseAlignmentSummaryList (T.pack guideTreeFileName') (readInt numberOfGroups) groupSummaryList (readInt alignmentScore') (T.pack alignmentFileName') genParserGroupSummary :: GenParser Char st GroupSummary genParserGroupSummary = do @@ -109,7 +109,7 @@ space string "bp" newline - return $ SequenceParameters (readInt sequenceIndexParam) sequenceIdentifierParam (readInt sequenceLengthParam) + return $ SequenceParameters (readInt sequenceIndexParam) (T.pack sequenceIdentifierParam) (readInt sequenceLengthParam) -- | Parse the input as ClustalAlignment datatype genParserClustalAlignment :: GenParser Char st ClustalAlignment @@ -123,18 +123,17 @@ mergealignmentSlices :: [ClustalAlignmentSlice] -> ClustalAlignment mergealignmentSlices slices = alignment - where entrySlicesList = map entrySlices slices -- list of lists of entry slices - sequenceIdentifiers = nub (map entrySequenceSliceIdentifier (head entrySlicesList)) - alignmentEntriesListBySlice = map (map entryAlignedSliceSequence) entrySlicesList - transposedAlignmentEntriesListbySlice = transpose alignmentEntriesListBySlice - mergedAlignmentSequenceEntries = map concat transposedAlignmentEntriesListbySlice - mergedAlignmentEntries = map constructAlignmentEntries (zip sequenceIdentifiers mergedAlignmentSequenceEntries) - conservationTrackSlices = map conservationTrackSlice slices - mergedConservationTrack = concat conservationTrackSlices - alignment = ClustalAlignment mergedAlignmentEntries mergedConservationTrack - -constructAlignmentEntries :: (String, String) -> ClustalAlignmentEntry -constructAlignmentEntries (entryIdentifier,entrySequence) = ClustalAlignmentEntry entryIdentifier entrySequence + where entrySlicesList = concatMap entrySlices slices -- list of lists of entry slices + sequenceIdentifiers = nub (map entrySequenceSliceIdentifier entrySlicesList) + mergedAlignmentEntries = map (constructAlignmentEntries entrySlicesList) sequenceIdentifiers + mergedConservationTrack = concatMap conservationTrackSlice slices + alignment = ClustalAlignment mergedAlignmentEntries (T.pack mergedConservationTrack) + +constructAlignmentEntries :: [ClustalAlignmentEntrySlice] -> String -> ClustalAlignmentEntry +constructAlignmentEntries slices entryIdentifier= entry + where currentSlices = filter (\a -> entrySequenceSliceIdentifier a == entryIdentifier) slices + entrySequence = concatMap entryAlignedSliceSequence currentSlices + entry = ClustalAlignmentEntry (T.pack entryIdentifier) (T.pack entrySequence) genParserClustalAlignmentSlice :: GenParser Char st ClustalAlignmentSlice genParserClustalAlignmentSlice = do @@ -165,16 +164,21 @@ secondaryStructure <- genSecondaryStructure energy' <- genParseEnergy eof - return (mergeStructuralAlignmentSlices alignmentSlices secondaryStructure energy') + return (mergeStructuralAlignmentSlices (concat alignmentSlices) secondaryStructure energy') genSecondaryStructure :: GenParser Char st String genSecondaryStructure = do string "alifold" - many1 space - secondaryStructure <- many1 (oneOf ".()") - space - return secondaryStructure + secondaryStructure <- many1 (try genSecondaryStructureSlice) + return (concat secondaryStructure) +genSecondaryStructureSlice :: GenParser Char st String +genSecondaryStructureSlice = do + many1 space + secondaryStructureSlice <- many1 (try (oneOf ".()")) + choice [try (string "\n"),try (string " ")] + return secondaryStructureSlice + genParseEnergy :: GenParser Char st Double genParseEnergy = do string "(" @@ -203,24 +207,23 @@ many1 newline return "" -mergeStructuralAlignmentSlices :: [StructuralClustalAlignmentSlice] -> String -> Double -> StructuralClustalAlignment +mergeStructuralAlignmentSlices :: [StructuralClustalAlignmentEntrySlice] -> String -> Double -> StructuralClustalAlignment mergeStructuralAlignmentSlices slices secondaryStructure energy' = alignment - where entrySlicesList = map structuralEntrySlices slices -- list of lists of entry slices - sequenceIdentifiers = (map structuralEntrySequenceSliceIdentifier (head entrySlicesList)) - alignmentEntriesListBySlice = map (map structuralEntryAlignedSliceSequence) entrySlicesList - transposedAlignmentEntriesListbySlice = transpose alignmentEntriesListBySlice - mergedAlignmentSequenceEntries = map concat transposedAlignmentEntriesListbySlice - mergedAlignmentEntries = map constructStructuralAlignmentEntries (zip sequenceIdentifiers mergedAlignmentSequenceEntries) - alignment = StructuralClustalAlignment mergedAlignmentEntries secondaryStructure energy' - -constructStructuralAlignmentEntries :: (String, String) -> ClustalAlignmentEntry -constructStructuralAlignmentEntries (entryIdentifier,entrySequence) = ClustalAlignmentEntry entryIdentifier entrySequence + where sequenceIdentifiers = nub (map structuralEntrySequenceSliceIdentifier slices) + mergedAlignmentEntries = map (constructStructuralAlignmentEntries slices) sequenceIdentifiers + alignment = StructuralClustalAlignment mergedAlignmentEntries (T.pack secondaryStructure) energy' + +constructStructuralAlignmentEntries :: [StructuralClustalAlignmentEntrySlice] -> String -> ClustalAlignmentEntry +constructStructuralAlignmentEntries slices entryIdentifier= entry + where currentSlices = filter (\a -> structuralEntrySequenceSliceIdentifier a == entryIdentifier) slices + entrySequence = concatMap structuralEntryAlignedSliceSequence currentSlices + entry = ClustalAlignmentEntry (T.pack entryIdentifier) (T.pack entrySequence) -genParserStructuralClustalAlignmentSlice :: GenParser Char st StructuralClustalAlignmentSlice +genParserStructuralClustalAlignmentSlice :: GenParser Char st [StructuralClustalAlignmentEntrySlice] genParserStructuralClustalAlignmentSlice = do entrySlices' <- many1 (try genParserStructuralClustalEntrySlice) optional newline - return $ StructuralClustalAlignmentSlice entrySlices' + return entrySlices' genParserStructuralClustalEntrySlice :: GenParser Char st StructuralClustalAlignmentEntrySlice genParserStructuralClustalEntrySlice = do @@ -237,30 +240,30 @@ parseClustalAlignment = parse genParserClustalAlignment "genParserClustalAlignment" -- | Parse Clustal alignment (.aln) from filehandle -readClustalAlignment :: String -> IO (Either ParseError ClustalAlignment) +readClustalAlignment :: String -> IO (Either ParseError ClustalAlignment) readClustalAlignment = parseFromFile genParserClustalAlignment -- | Parse Clustal alignment (.aln) with secondary structure in dot-bracket notation from String (as produced by mlocarna) -parseStructuralClustalAlignment :: String -> Either ParseError StructuralClustalAlignment +parseStructuralClustalAlignment :: String -> Either ParseError StructuralClustalAlignment parseStructuralClustalAlignment = parse genParserStructuralClustalAlignment "genParserStructuralClustalAlignment" -- | Parse Clustal alignment (.aln) with secondary structure in dot-bracket notation from filehandle (as produced by mlocarna) -readStructuralClustalAlignment :: String -> IO (Either ParseError StructuralClustalAlignment) +readStructuralClustalAlignment :: String -> IO (Either ParseError StructuralClustalAlignment) readStructuralClustalAlignment = parseFromFile genParserStructuralClustalAlignment -- | Parse Clustal summary (printed to STDOUT) from String -parseClustalSummary :: String -> Either ParseError ClustalSummary +parseClustalSummary :: String -> Either ParseError ClustalSummary parseClustalSummary = parse genParserClustalSummary "genParserClustalSummary" -- | Parse Clustal summary (printed to STDOUT) from file -readClustalSummary :: String -> IO (Either ParseError ClustalSummary) +readClustalSummary :: String -> IO (Either ParseError ClustalSummary) readClustalSummary = parseFromFile genParserClustalSummary -- | Parse nucleotide sequence. Allowed letters according to IUPAC -parseNucleotideSequence :: GenParser Char st String -parseNucleotideSequence = do - nucleotideSequence <- many1 (oneOf "RYSWKMBDHVNATUGCryswkmbdhvnatugc") - return $ nucleotideSequence +--parseNucleotideSequence :: GenParser Char st String +--parseNucleotideSequence = do +-- nucleotideSequence <- many1 (oneOf "RYSWKMBDHVNATUGCryswkmbdhvnatugc") +-- return $ nucleotideSequence -- | Parse nucleotide alignment entry. Allowed letters according to IUPAC and commonly used gap characters parseNucleotideAlignmentEntry :: GenParser Char st String @@ -269,13 +272,13 @@ return $ entry -- | Parse protein amino acid code sequence. Allowed letters according to IUPAC -parseProteinSequence :: GenParser Char st String -parseProteinSequence = do - proteinSequence <- many1 (oneOf "ABCDEFGHIKLMNPQRSTVWXYZabcdefghiklmnpqrstvwxyz") - return $ proteinSequence +--parseProteinSequence :: GenParser Char st String +--parseProteinSequence = do +-- proteinSequence <- many1 (oneOf "ABCDEFGHIKLMNPQRSTVWXYZabcdefghiklmnpqrstvwxyz") +-- return $ proteinSequence -- | Parse protein amino acid code alignment entry. Allowed letters according to IUPAC and commonly used gap characters -parseProteinAlignmentEntry :: GenParser Char st String -parseProteinAlignmentEntry = do - entry <- many1 (oneOf "~_-.ABCDEFGHIKLMNPQRSTVWXYZabcdefghiklmnpqrstvwxyz") - return $ entry +--parseProteinAlignmentEntry :: GenParser Char st String +--parseProteinAlignmentEntry = do +-- entry <- many1 (oneOf "~_-.ABCDEFGHIKLMNPQRSTVWXYZabcdefghiklmnpqrstvwxyz") +-- return $ entry

1 0

commit arbtt for openSUSE:Factory
by root＠hilbert.suse.de 31 Mar '17

31 Mar '17

Hello community, here is the log from the commit of package arbtt for openSUSE:Factory checked in at 2017-03-31 15:07:26 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/arbtt (Old) and /work/SRC/openSUSE:Factory/.arbtt.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "arbtt" Fri Mar 31 15:07:26 2017 rev:2 rq:482168 version:0.9.0.12 Changes: -------- --- /work/SRC/openSUSE:Factory/arbtt/arbtt.changes 2017-03-16 09:35:50.267156208 +0100 +++ /work/SRC/openSUSE:Factory/.arbtt.new/arbtt.changes 2017-03-31 15:07:27.693569897 +0200 @@ -1,0 +2,10 @@ +Sun Jan 8 21:14:00 UTC 2017 - psimons(a)suse.com + +- Update to version 0.9.0.12 with cabal2obs. + +------------------------------------------------------------------- +Fri Dec 16 17:59:49 UTC 2016 - psimons(a)suse.com + +- Update to version 0.9.0.11 with cabal2obs. + +------------------------------------------------------------------- Old: ---- arbtt-0.9.0.10.tar.gz New: ---- arbtt-0.9.0.12.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ arbtt.spec ++++++ --- /var/tmp/diff_new_pack.UFTERj/_old 2017-03-31 15:07:28.857405358 +0200 +++ /var/tmp/diff_new_pack.UFTERj/_new 2017-03-31 15:07:28.861404793 +0200 @@ -1,7 +1,7 @@ # # spec file for package arbtt # -# 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 @@ %bcond_with tests Name: arbtt -Version: 0.9.0.10 +Version: 0.9.0.12 Release: 0 Summary: Automatic Rule-Based Time Tracker License: GPL-1.0+ ++++++ arbtt-0.9.0.10.tar.gz -> arbtt-0.9.0.12.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/arbtt-0.9.0.10/arbtt.cabal new/arbtt-0.9.0.12/arbtt.cabal --- old/arbtt-0.9.0.10/arbtt.cabal 2016-08-16 20:33:43.000000000 +0200 +++ new/arbtt-0.9.0.12/arbtt.cabal 2017-01-03 21:23:31.000000000 +0100 @@ -1,5 +1,5 @@ name: arbtt -version: 0.9.0.10 +version: 0.9.0.12 license: GPL license-file: LICENSE category: Desktop @@ -42,7 +42,7 @@ build-depends: base >= 4.7 && < 4.10, filepath, directory, transformers, utf8-string, - aeson >= 0.6 && < 1.1, + aeson >= 0.6 && < 1.2, binary >= 0.5, bytestring, deepseq @@ -105,7 +105,7 @@ binary >= 0.5, deepseq, bytestring, utf8-string, strict, transformers, directory, filepath, - aeson >= 0.6 && < 1.1, + aeson >= 0.6 && < 1.2, array == 0.4.* || == 0.5.*, terminal-progress-bar, bytestring-progress @@ -147,7 +147,7 @@ base >= 4.7 && < 4.10, parsec == 3.*, containers == 0.5.*, - aeson >= 0.6 && < 1.1, + aeson >= 0.6 && < 1.2, array == 0.4.* || == 0.5.*, binary >= 0.5, deepseq, bytestring, utf8-string, strict, @@ -261,9 +261,9 @@ Build-depends: base >= 4.7 && < 4.10 , tasty >= 0.7 && < 0.12 - , tasty-golden >= 2.2.0.2 && <= 2.4 + , tasty-golden >= 2.2.0.2 && < 2.4 , tasty-hunit >= 0.2 && < 0.11 - , process-extras == 0.2.* || == 0.3.* || == 0.4.* + , process-extras >= 0.2 && < 0.8 , deepseq , binary >= 0.5 , bytestring

1 0

commit audacity for openSUSE:Factory
by root＠hilbert.suse.de 31 Mar '17

31 Mar '17

Hello community, here is the log from the commit of package audacity for openSUSE:Factory checked in at 2017-03-31 15:07:24 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/audacity (Old) and /work/SRC/openSUSE:Factory/.audacity.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "audacity" Fri Mar 31 15:07:24 2017 rev:72 rq:482035 version:2.1.3 Changes: -------- --- /work/SRC/openSUSE:Factory/audacity/audacity.changes 2017-03-20 17:10:27.158331486 +0100 +++ /work/SRC/openSUSE:Factory/.audacity.new/audacity.changes 2017-03-31 15:07:25.117934030 +0200 @@ -1,0 +2,5 @@ +Wed Mar 22 15:29:45 UTC 2017 - davejplater(a)gmail.com + +- Added requires for flac > 1.3.0. + +------------------------------------------------------------------- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ audacity.spec ++++++ --- /var/tmp/diff_new_pack.Z9R6AO/_old 2017-03-31 15:07:26.753702771 +0200 +++ /var/tmp/diff_new_pack.Z9R6AO/_new 2017-03-31 15:07:26.757702206 +0200 @@ -84,6 +84,8 @@ Recommends: libavformat Recommends: libavutil Recommends: libmp3lame0 +Requires: libFLAC++6 >= 1.3.1 +Requires: libFLAC8 >= 1.3.1 %if %{with mad} BuildRequires: pkgconfig(mad) %endif

1 0

commit baka-mplayer for openSUSE:Factory
by root＠hilbert.suse.de 31 Mar '17

31 Mar '17

Hello community, here is the log from the commit of package baka-mplayer for openSUSE:Factory checked in at 2017-03-31 15:07:22 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/baka-mplayer (Old) and /work/SRC/openSUSE:Factory/.baka-mplayer.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "baka-mplayer" Fri Mar 31 15:07:22 2017 rev:2 rq:481953 version:2.0.4 Changes: -------- --- /work/SRC/openSUSE:Factory/baka-mplayer/baka-mplayer.changes 2017-03-13 15:33:43.372246595 +0100 +++ /work/SRC/openSUSE:Factory/.baka-mplayer.new/baka-mplayer.changes 2017-03-31 15:07:24.054084432 +0200 @@ -1,0 +2,5 @@ +Tue Mar 21 16:05:43 UTC 2017 - olaf(a)aepfle.de + +- Remove Category "Utilities" from desktop file + +------------------------------------------------------------------- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ baka-mplayer.spec ++++++ --- /var/tmp/diff_new_pack.4xexP8/_old 2017-03-31 15:07:24.733988311 +0200 +++ /var/tmp/diff_new_pack.4xexP8/_new 2017-03-31 15:07:24.737987745 +0200 @@ -58,7 +58,7 @@ %install make install INSTALL_ROOT=%{buildroot} -%suse_update_desktop_file %{name} Utility +%suse_update_desktop_file %{name} AudioVideo Video Player %post %desktop_database_post

1 0

commit gnumeric for openSUSE:Factory
by root＠hilbert.suse.de 31 Mar '17

31 Mar '17

Hello community, here is the log from the commit of package gnumeric for openSUSE:Factory checked in at 2017-03-31 15:07:19 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/gnumeric (Old) and /work/SRC/openSUSE:Factory/.gnumeric.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "gnumeric" Fri Mar 31 15:07:19 2017 rev:105 rq:481946 version:1.12.34 Changes: -------- --- /work/SRC/openSUSE:Factory/gnumeric/gnumeric.changes 2017-02-09 11:19:40.924557502 +0100 +++ /work/SRC/openSUSE:Factory/.gnumeric.new/gnumeric.changes 2017-03-31 15:07:22.318329826 +0200 @@ -1,0 +2,23 @@ +Tue Mar 21 10:08:37 UTC 2017 - dimstar(a)opensuse.org + +- Update to version 1.12.34: + + Fix hyperlinks import from ODF (bgo#779635). + + Fix xlsx export of chart series names (bgo#778618). + + Always export a transparent fill style in charts (bgo#779160). + + Doc fixes. + + Fix xlsx import with missing header/footer (bgo#778292). + + Minor xlsx import improvements with alias colors. + + Test suite improvements. + + Improve Excel handling of hyperlinks. + + Hyperlinks improvements (bgo#706671). + + Plug leaks. + + Fix issues with sheet-local names. + + ssdiff improvements with hyperlinks, input messages, + conditional formats, and validations. + + Make exit code from ssdiff follow diff's. + + Fix ssdiff with inter-sheet references. + + Fix style border colour sharing. +- Drop gnumeric-1.12.33-destdir.patch and + gnumeric-1.12.33-docbook.patch: fixed upstream. + +------------------------------------------------------------------- Old: ---- gnumeric-1.12.33-destdir.patch gnumeric-1.12.33-docbook.patch gnumeric-1.12.33.tar.xz New: ---- gnumeric-1.12.34.tar.xz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ gnumeric.spec ++++++ --- /var/tmp/diff_new_pack.aBhz0a/_old 2017-03-31 15:07:23.782122881 +0200 +++ /var/tmp/diff_new_pack.aBhz0a/_new 2017-03-31 15:07:23.786122316 +0200 @@ -17,17 +17,13 @@ Name: gnumeric -Version: 1.12.33 +Version: 1.12.34 Release: 0 Summary: Spreadsheet Application License: GPL-2.0 or GPL-3.0 Group: Productivity/Office/Spreadsheets Url: http://www.gnumeric.org/ Source0: http://download.gnome.org/sources/gnumeric/1.12/%{name}-%{version}.tar.xz -# PATCH-FIX-UPSTREAM gnumeric-1.12.33-destdir.patch firebird209(a)gmail.com -- Fix compilation, destdir of helpfiles. -Patch0: gnumeric-1.12.33-destdir.patch -# PATCH-FIX-UPSTREAM gnumeric-1.12.33-docbook.patch firebird209(a)gmail.com -- Fixes some problems with non-ascii parameter names. -Patch1: gnumeric-1.12.33-docbook.patch BuildRequires: bison BuildRequires: docbook-dtds BuildRequires: fdupes @@ -106,10 +102,6 @@ %lang_package %prep %setup -q -# Destdir fix for Gnumeric 1.12.33 -%patch0 -p1 -# Use xml-dtd -%patch1 -p1 %if !0%{?is_opensuse} translation-update-upstream translation-update-upstream po-functions gnumeric-functions ++++++ gnumeric-1.12.33.tar.xz -> gnumeric-1.12.34.tar.xz ++++++ /work/SRC/openSUSE:Factory/gnumeric/gnumeric-1.12.33.tar.xz /work/SRC/openSUSE:Factory/.gnumeric.new/gnumeric-1.12.34.tar.xz differ: char 27, line 1

1 0

commit goffice for openSUSE:Factory
by root＠hilbert.suse.de 31 Mar '17

31 Mar '17

Hello community, here is the log from the commit of package goffice for openSUSE:Factory checked in at 2017-03-31 15:07:18 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/goffice (Old) and /work/SRC/openSUSE:Factory/.goffice.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "goffice" Fri Mar 31 15:07:18 2017 rev:87 rq:481945 version:0.10.34 Changes: -------- --- /work/SRC/openSUSE:Factory/goffice/goffice.changes 2017-02-24 02:55:12.385425158 +0100 +++ /work/SRC/openSUSE:Factory/.goffice.new/goffice.changes 2017-03-31 15:07:19.570718272 +0200 @@ -1,0 +2,6 @@ +Tue Mar 21 10:06:16 UTC 2017 - dimstar(a)opensuse.org + +- Update to version 0.10.34: + + Fix rich-text format problem. + +------------------------------------------------------------------- Old: ---- goffice-0.10.33.tar.xz New: ---- goffice-0.10.34.tar.xz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ goffice.spec ++++++ --- /var/tmp/diff_new_pack.nHXxSO/_old 2017-03-31 15:07:20.458592748 +0200 +++ /var/tmp/diff_new_pack.nHXxSO/_new 2017-03-31 15:07:20.462592182 +0200 @@ -17,7 +17,7 @@ Name: goffice -Version: 0.10.33 +Version: 0.10.34 Release: 0 Summary: GLib/GTK+ Set of Document-Centric Objects and Utilities License: GPL-2.0 or GPL-3.0 ++++++ goffice-0.10.33.tar.xz -> goffice-0.10.34.tar.xz ++++++ ++++ 6372 lines of diff (skipped)

1 0