commit ghc-ViennaRNAParser for openSUSE:Factory

Hello community, here is the log from the commit of package ghc-ViennaRNAParser for openSUSE:Factory checked in at 2017-04-14 13:34:28 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/ghc-ViennaRNAParser (Old) and /work/SRC/openSUSE:Factory/.ghc-ViennaRNAParser.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "ghc-ViennaRNAParser" Fri Apr 14 13:34:28 2017 rev:2 rq:483917 version:1.3.2 Changes: -------- --- /work/SRC/openSUSE:Factory/ghc-ViennaRNAParser/ghc-ViennaRNAParser.changes 2017-03-24 02:07:09.319167852 +0100 +++ /work/SRC/openSUSE:Factory/.ghc-ViennaRNAParser.new/ghc-ViennaRNAParser.changes 2017-04-14 13:34:29.734742253 +0200 @@ -1,0 +2,5 @@ +Sun Feb 12 14:18:43 UTC 2017 - psimons@suse.com + +- Update to version 1.3.2 with cabal2obs. + +------------------------------------------------------------------- Old: ---- ViennaRNAParser-1.2.9.tar.gz New: ---- ViennaRNAParser-1.3.2.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ ghc-ViennaRNAParser.spec ++++++ --- /var/tmp/diff_new_pack.Ymu2pr/_old 2017-04-14 13:34:30.874581165 +0200 +++ /var/tmp/diff_new_pack.Ymu2pr/_new 2017-04-14 13:34:30.878580600 +0200 @@ -19,7 +19,7 @@ %global pkg_name ViennaRNAParser %bcond_with tests Name: ghc-%{pkg_name} -Version: 1.2.9 +Version: 1.3.2 Release: 0 Summary: Libary for parsing ViennaRNA package output License: GPL-3.0 @@ -27,6 +27,7 @@ Url: https://hackage.haskell.org/package/%{pkg_name} Source0: https://hackage.haskell.org/package/%{pkg_name}-%{version}/%{pkg_name}-%{version}.tar.gz BuildRequires: ghc-Cabal-devel +BuildRequires: ghc-ParsecTools-devel BuildRequires: ghc-parsec-devel BuildRequires: ghc-process-devel BuildRequires: ghc-rpm-macros @@ -43,7 +44,7 @@ For more information on the ViennaRNA package refer to http://www.tbi.univie.ac.at/RNA/. -The libary is tested with Version 2.2.4 of the ViennaRNA package. +The libary is tested with Version 2.3.2 of the ViennaRNA package. %package devel Summary: Haskell %{pkg_name} library development files ++++++ ViennaRNAParser-1.2.9.tar.gz -> ViennaRNAParser-1.3.2.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/ViennaRNAParser-1.2.9/ViennaRNAParser.cabal new/ViennaRNAParser-1.3.2/ViennaRNAParser.cabal --- old/ViennaRNAParser-1.2.9/ViennaRNAParser.cabal 2016-03-23 19:54:17.000000000 +0100 +++ new/ViennaRNAParser-1.3.2/ViennaRNAParser.cabal 2017-01-20 10:12:13.000000000 +0100 @@ -5,13 +5,13 @@ -- PVP summary: +-+------- breaking API changes -- | | +----- non-breaking API additions -- | | | +--- code changes with no API change -version: 1.2.9 +version: 1.3.2 synopsis: Libary for parsing ViennaRNA package output description: Currently contains parsers and datatypes for: RNAalifold, RNAcode, RNAdistance, RNAcofold, RNAfold, RNAplex, RNAup, RNAz. . For more information on the ViennaRNA package refer to http://www.tbi.univie.ac.at/RNA/. . - The libary is tested with Version 2.2.4 of the ViennaRNA package. + The libary is tested with Version 2.3.2 of the ViennaRNA package. license: GPL license-file: LICENSE author: Florian Eggenhofer @@ -30,8 +30,8 @@ source-repository this type: git - location: https://github.com/eggzilla/ViennaRNAParser/tree/1.2.9 - tag: 1.2.9 + location: https://github.com/eggzilla/ViennaRNAParser/tree/1.3.2 + tag: 1.3.2 library -- Modules exported by the library. @@ -58,7 +58,7 @@ ghc-options: -Wall -O2 -fno-warn-unused-do-bind -- Other library packages from which modules are imported. - build-depends: base >=4.5 && <5, parsec>=3.1.9, process, transformers + build-depends: base >=4.5 && <5, parsec>=3.1.9, process, transformers, ParsecTools -- Directories containing source files. hs-source-dirs: src diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/ViennaRNAParser-1.2.9/changelog new/ViennaRNAParser-1.3.2/changelog --- old/ViennaRNAParser-1.2.9/changelog 2016-03-23 19:54:17.000000000 +0100 +++ new/ViennaRNAParser-1.3.2/changelog 2017-01-20 10:12:13.000000000 +0100 @@ -1,4 +1,11 @@ -*-change-log-*- +1.3.2 Florian Eggenhofer 20. January 2017 + * Fix for RNAalifold systemcall function +1.3.1 Florian Eggenhofer 23. October 2016 + * Improvements to RNAcode parser, + * Improvements to travis testing +1.3.0 Florian Eggenhofer 6. September 2016 + * Added support for new prefilter fields in RNAplex output 1.2.8 Florian Eggenhofer 11. February 2016 * Fixed special character parsing of identifiers in RNAcode 1.2.7 Florian Eggenhofer 4. January 2016 diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/ViennaRNAParser-1.2.9/src/Bio/RNAalifoldParser.hs new/ViennaRNAParser-1.3.2/src/Bio/RNAalifoldParser.hs --- old/ViennaRNAParser-1.2.9/src/Bio/RNAalifoldParser.hs 2016-03-23 19:54:17.000000000 +0100 +++ new/ViennaRNAParser-1.3.2/src/Bio/RNAalifoldParser.hs 2017-01-20 10:12:13.000000000 +0100 @@ -17,7 +17,7 @@ --- | Run external RNAalifold command and read the output into the corresponding datatype systemRNAalifold :: String -> String -> String -> IO ExitCode -systemRNAalifold options inputFilePath outputFilePath = system ("RNAalifold " ++ options ++ " < " ++ inputFilePath ++ " > " ++ outputFilePath) +systemRNAalifold options inputFilePath outputFilePath = system ("RNAalifold " ++ options ++ " " ++ inputFilePath ++ " > " ++ outputFilePath) -- | Parse the consenus of RNAz results genParserRNAalifold :: GenParser Char st RNAalifold diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/ViennaRNAParser-1.2.9/src/Bio/RNAcodeData.hs new/ViennaRNAParser-1.3.2/src/Bio/RNAcodeData.hs --- old/ViennaRNAParser-1.2.9/src/Bio/RNAcodeData.hs 2016-03-23 19:54:17.000000000 +0100 +++ new/ViennaRNAParser-1.3.2/src/Bio/RNAcodeData.hs 2017-01-20 10:12:13.000000000 +0100 @@ -22,8 +22,9 @@ data RNAcodeHit = RNAcodeHit { hss :: Int, - frame :: Double, - length :: Int, + strand :: Char, + frame :: Int, + hitLength :: Int, from :: Int, to :: Int, name :: String, diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/ViennaRNAParser-1.2.9/src/Bio/RNAcodeParser.hs new/ViennaRNAParser-1.3.2/src/Bio/RNAcodeParser.hs --- old/ViennaRNAParser-1.2.9/src/Bio/RNAcodeParser.hs 2016-03-23 19:54:17.000000000 +0100 +++ new/ViennaRNAParser-1.3.2/src/Bio/RNAcodeParser.hs 2017-01-20 10:12:13.000000000 +0100 @@ -19,6 +19,7 @@ import qualified Control.Exception.Base as CE import Text.Parsec.Language (haskell) import Control.Applicative ((<*>),(<$>),(<$),pure) +import Text.Parsec.Numbers -- | Run external RNAcode command and read the output into the corresponding datatype systemRNAcode :: String -> String -> String -> IO ExitCode @@ -33,21 +34,29 @@ -- | Parse the input as RNAcodeHit genParseRNAcodeTabularHit :: GenParser Char st RNAcodeHit genParseRNAcodeTabularHit = do - _hss <- natural haskell - _frame <- integer haskell - _length <- natural haskell - _from <- natural haskell - _to <- natural haskell - _name <- identifier haskell - --_name <- identifier haskell + _hss <- parseIntegral + tab + _strand <- oneOf "+-" + tab + _frame <- parseIntegral + tab + _length <- parseIntegral + tab + _from <- parseIntegral + tab + _to <-parseIntegral + tab _name <- many1 (oneOf "AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz1234567890_-") - string ("\t") - _start <- natural haskell - _end <- natural haskell - _score <- many1 (oneOf "1234567890e.-+") - many space - _pvalue <- float haskell - return $ RNAcodeHit (fromInteger _hss) (fromInteger _frame) (fromInteger _length) (fromInteger _from) (fromInteger _to) _name (fromInteger _start) (fromInteger _end) (read _score ::Double) _pvalue + tab + _start <- parseIntegral + tab + _end <- parseIntegral + tab + _score <- parseFloat + tab + _pvalue <- parseFloat + newline + return $ RNAcodeHit _hss _strand _frame _length _from _to _name _start _end _score _pvalue -- | Parse the input as RNAcode datatype @@ -82,20 +91,29 @@ genParseRNAcodeHit :: GenParser Char st RNAcodeHit genParseRNAcodeHit = do many (char ' ') - _hss <- natural haskell - _frame <- integer haskell - _length <- natural haskell - _from <- natural haskell - _to <- natural haskell - --_name <- identifier haskell + _hss <- parseIntegral + tab + _strand <- oneOf "+-" + tab + _frame <- parseIntegral + tab + _length <- parseIntegral + tab + _from <- parseIntegral + tab + _to <- parseIntegral + tab _name <- many1 (oneOf "AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz1234567890_-") - string ("\t") - _start <- natural haskell - _end <- natural haskell - _score <- float haskell - _pvalue <- many1 (try (choice [digit,char '.'])) + tab + _start <- parseIntegral + tab + _end <- parseIntegral + tab + _score <- parseFloat + tab + _pvalue <- parseFloat newline - return $ RNAcodeHit (fromInteger _hss) (fromInteger _frame) (fromInteger _length) (fromInteger _from) (fromInteger _to) _name (fromInteger _start) (fromInteger _end) _score (read _pvalue :: Double) + return $ RNAcodeHit _hss _strand _frame _length _from _to _name _start _end _score _pvalue -- | parse RNAcode from input string parseRNAcode :: String -> Either ParseError RNAcode @@ -109,7 +127,7 @@ -- | parse RNAcode from input string parseRNAcodeTabular :: String -> Either ParseError RNAcode -parseRNAcodeTabular = parse genParseRNAcodeTabular "parseRNAcode" +parseRNAcodeTabular = parse genParseRNAcodeTabular "parseRNAcodeTabular" -- | parse RNAcode from input filePath readRNAcodeTabular :: String -> IO (Either ParseError RNAcode) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/ViennaRNAParser-1.2.9/src/Bio/RNAplexData.hs new/ViennaRNAParser-1.3.2/src/Bio/RNAplexData.hs --- old/ViennaRNAParser-1.2.9/src/Bio/RNAplexData.hs 2016-03-23 19:54:17.000000000 +0100 +++ new/ViennaRNAParser-1.3.2/src/Bio/RNAplexData.hs 2017-01-20 10:12:13.000000000 +0100 @@ -17,6 +17,9 @@ duplexEnergy :: Double, duplexEnergyWithoutAccessiblity :: Maybe Double, queryAccessiblity :: Maybe Double, - targetAccessibility :: Maybe Double + targetAccessibility :: Maybe Double, + prefilterStart :: Maybe Int, + prefilterStop :: Maybe Int, + prefilterEnergy :: Maybe Double } deriving (Show, Eq) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/ViennaRNAParser-1.2.9/src/Bio/RNAplexParser.hs new/ViennaRNAParser-1.3.2/src/Bio/RNAplexParser.hs --- old/ViennaRNAParser-1.2.9/src/Bio/RNAplexParser.hs 2016-03-23 19:54:17.000000000 +0100 +++ new/ViennaRNAParser-1.3.2/src/Bio/RNAplexParser.hs 2017-01-20 10:12:13.000000000 +0100 @@ -9,7 +9,8 @@ import Bio.RNAplexData import Bio.ViennaRNAParserLibrary -import Text.ParserCombinators.Parsec +import Text.ParserCombinators.Parsec +import Text.Parsec.Numbers import Control.Monad -- | Parse the input as list of RNAplexInteraction datatype @@ -30,34 +31,44 @@ newline _secondaryStructure <- many1 (oneOf "&().,") many1 space - _targetDuplexBegin <- many1 digit + _targetDuplexBegin <- parseIntegral char ',' - _targetDuplexEnd <- many1 digit + _targetDuplexEnd <- parseIntegral many1 space char ':' many1 space - _queryDuplexBegin <- many1 digit + _queryDuplexBegin <- parseIntegral char ',' - _queryDuplexEnd <- many1 digit + _queryDuplexEnd <- parseIntegral many1 space char '(' - optional space - _duplexEnergy <- many1 (noneOf (" )")) - optional space + optional (string " ") + _duplexEnergy <- parseFloat + optional (string " ") optional (char '=') - optional space - _duplexEnergyWithoutAccessiblity <- optionMaybe (try (many1 (noneOf (" )")))) - optional space + optional (string " ") + _duplexEnergyWithoutAccessiblity <- optionMaybe (try parseFloat) + optional (string " ") optional (char '+') - optional (many1 space) - _queryAccessiblity <- optionMaybe (try (many1 (noneOf (" )")))) - optional space + optional (many1 (string " ")) + _queryAccessiblity <- optionMaybe (try parseFloat) + optional (string " ") optional (char '+') optional (many1 space) - _targetAccessibility <- optionMaybe (try (many1 (noneOf (")")))) + _targetAccessibility <- optionMaybe (try parseFloat) char ')' + many (oneOf " ") + optional (string "i:") + _prefilterStart <- optionMaybe (try parseIntegral) + optional (string ",") + optional (string "j:") + _prefilterEnd <- optionMaybe (try parseIntegral) + many (oneOf " ") + optional (string "<") + _prefilterEnergy <- optionMaybe (try parseFloat) + optional (string ">") newline - return $ RNAplexInteraction _targetIdentifier _queryIdentifier _secondaryStructure (readInt _targetDuplexBegin) (readInt _targetDuplexEnd) (readInt _queryDuplexBegin) (readInt _queryDuplexEnd) (readDouble _duplexEnergy) (liftM readDouble _duplexEnergyWithoutAccessiblity) (liftM readDouble _queryAccessiblity) (liftM readDouble _targetAccessibility) + return $ RNAplexInteraction _targetIdentifier _queryIdentifier _secondaryStructure _targetDuplexBegin _targetDuplexEnd _queryDuplexBegin _queryDuplexEnd _duplexEnergy _duplexEnergyWithoutAccessiblity _queryAccessiblity _targetAccessibility _prefilterStart _prefilterEnd _prefilterEnergy -- | parse RNAplexOutput from input string parseRNAplex :: [Char] -> Either ParseError [RNAplexInteraction]