[med-svn] [Git][med-team/metastudent][master] Do not ask for installation of pp-popularity-contest
Andreas Tille
gitlab at salsa.debian.org
Mon Feb 1 13:08:54 GMT 2021
Andreas Tille pushed to branch master at Debian Med / metastudent
Commits:
81b541e8 by Andreas Tille at 2021-02-01T14:08:36+01:00
Do not ask for installation of pp-popularity-contest
- - - - -
2 changed files:
- debian/changelog
- debian/patches/2to3.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+metastudent (2.0.1-9) UNRELEASED; urgency=medium
+
+ * Do not ask for installation of pp-popularity-contest
+
+ -- Andreas Tille <tille at debian.org> Mon, 01 Feb 2021 14:05:36 +0100
+
metastudent (2.0.1-8) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/2to3.patch
=====================================
@@ -5,11 +5,9 @@ Bug-Debian: https://bugs.debian.org/937017
Last-Update: 2019-09-17
---
-Index: metastudent/metastudent
-===================================================================
---- metastudent.orig/metastudent 2019-09-17 01:14:50.567566834 +0100
-+++ metastudent/metastudent 2019-09-17 01:14:50.555566892 +0100
-@@ -25,701 +25,756 @@
+--- a/metastudent
++++ b/metastudent
+@@ -25,701 +25,753 @@ import os
from shutil import copy2, rmtree
import random
import math
@@ -1285,9 +1283,6 @@ Index: metastudent/metastudent
+ metastudentPkgPath = getPkgPath()
+ dataPkgPath = os.path.join(sys.prefix, "share", "metastudent-data")
+
-+ if subprocess.getstatusoutput('pp_popcon_cnt -p metastudent')[0] != 0:
-+ print("The Rost Lab recommends you install the pp-popularity-contest package that provides pp_popcon_cnt:\n\nsudo apt-get install pp-popularity-contest\n", file=sys.stderr)
-+
+ try:
+ opts, args = getopt(sys.argv[1:], "hi:o:", ["debug", "help", "silent", "keep-temp", "temp-dir=", "version", "config=",
+ "output-blast", "no-names", "with-images", "blast-kickstart-databases=", "ontologies=", "blast-only", "all-predictions"])
@@ -1434,16 +1429,14 @@ Index: metastudent/metastudent
"""
=pod
-@@ -868,4 +923,3 @@
+@@ -868,4 +920,3 @@ Tobias Hamp <hampt at rostlab.org>
=cut
"""
-
-Index: metastudent/metastudentPkg/BlastWrapper.py
-===================================================================
---- metastudent.orig/metastudentPkg/BlastWrapper.py 2019-09-17 01:14:50.567566834 +0100
-+++ metastudent/metastudentPkg/BlastWrapper.py 2019-09-17 01:14:50.559566873 +0100
-@@ -6,70 +6,69 @@
+--- a/metastudentPkg/BlastWrapper.py
++++ b/metastudentPkg/BlastWrapper.py
+@@ -6,70 +6,69 @@ Created on May 18, 2010
class blastallParameters:
@@ -1577,10 +1570,8 @@ Index: metastudent/metastudentPkg/BlastWrapper.py
+ " 2>" + blastParameters.getOutputFilePath()+".err"
+ return returnString
-Index: metastudent/metastudentPkg/Logger.py
-===================================================================
---- metastudent.orig/metastudentPkg/Logger.py 2019-09-17 01:14:50.567566834 +0100
-+++ metastudent/metastudentPkg/Logger.py 2019-09-17 01:14:50.559566873 +0100
+--- a/metastudentPkg/Logger.py
++++ b/metastudentPkg/Logger.py
@@ -3,31 +3,29 @@
# Copyright (c) 2011-2012 Tobias Hamp <hampt at rostlab.org>
@@ -1630,11 +1621,9 @@ Index: metastudent/metastudentPkg/Logger.py
+ print(msg, file=sys.stderr)
+ # cls.internalLogger.info(msg)
-Index: metastudent/metastudentPkg/commons.py
-===================================================================
---- metastudent.orig/metastudentPkg/commons.py 2019-09-17 01:14:50.567566834 +0100
-+++ metastudent/metastudentPkg/commons.py 2019-09-17 01:14:50.559566873 +0100
-@@ -10,6 +10,7 @@
+--- a/metastudentPkg/commons.py
++++ b/metastudentPkg/commons.py
+@@ -10,6 +10,7 @@ import sys
import shlex
import time
from multiprocessing.pool import Pool
@@ -1642,7 +1631,7 @@ Index: metastudent/metastudentPkg/commons.py
mfRoot = "GO:0003674"
bpRoot = "GO:0008150"
-@@ -17,342 +18,340 @@
+@@ -17,342 +18,340 @@ ccRoot = "GO:0005575"
whiteSpaceCode = "~"
@@ -2287,11 +2276,9 @@ Index: metastudent/metastudentPkg/commons.py
+ self.targetToTermToScore[sortedTargets[i]] = result
+ return self
-Index: metastudent/metastudentPkg/generateTermNameMapping.py
-===================================================================
---- metastudent.orig/metastudentPkg/generateTermNameMapping.py 2019-09-17 01:14:50.567566834 +0100
-+++ metastudent/metastudentPkg/generateTermNameMapping.py 2019-09-17 01:14:50.559566873 +0100
-@@ -2,16 +2,16 @@
+--- a/metastudentPkg/generateTermNameMapping.py
++++ b/metastudentPkg/generateTermNameMapping.py
+@@ -2,16 +2,16 @@ import sys
def convertGotermtxtToNameMapping(gotermtxtFilePath, nameMappingFilePath):
@@ -2321,10 +2308,8 @@ Index: metastudent/metastudentPkg/generateTermNameMapping.py
+
+# if __name__ == "__main__":
+# convertGotermtxtToNameMapping(sys.argv[1], sys.argv[2])
-Index: metastudent/metastudentPkg/lib/groupA/DataPreprocessing/splitDB.py
-===================================================================
---- metastudent.orig/metastudentPkg/lib/groupA/DataPreprocessing/splitDB.py 2019-09-17 01:14:50.567566834 +0100
-+++ metastudent/metastudentPkg/lib/groupA/DataPreprocessing/splitDB.py 2019-09-17 01:14:50.559566873 +0100
+--- a/metastudentPkg/lib/groupA/DataPreprocessing/splitDB.py
++++ b/metastudentPkg/lib/groupA/DataPreprocessing/splitDB.py
@@ -2,30 +2,31 @@
import sys
@@ -2365,7 +2350,7 @@ Index: metastudent/metastudentPkg/lib/groupA/DataPreprocessing/splitDB.py
buffer = ""
for line in infile:
if line.startswith('>'):
-@@ -34,31 +35,31 @@
+@@ -34,31 +35,31 @@ def main():
entrycount += 1
else:
buffer += line
@@ -2407,10 +2392,8 @@ Index: metastudent/metastudentPkg/lib/groupA/DataPreprocessing/splitDB.py
if __name__ == "__main__":
try:
main()
-Index: metastudent/metastudentPkg/lib/groupA/parser/group2_blastParser.py
-===================================================================
---- metastudent.orig/metastudentPkg/lib/groupA/parser/group2_blastParser.py 2019-09-17 01:14:50.567566834 +0100
-+++ metastudent/metastudentPkg/lib/groupA/parser/group2_blastParser.py 2019-09-17 01:14:50.559566873 +0100
+--- a/metastudentPkg/lib/groupA/parser/group2_blastParser.py
++++ b/metastudentPkg/lib/groupA/parser/group2_blastParser.py
@@ -3,20 +3,21 @@
import sys
@@ -2437,7 +2420,7 @@ Index: metastudent/metastudentPkg/lib/groupA/parser/group2_blastParser.py
for line in infile:
if line.startswith("Results from round 2"):
for line in infile:
-@@ -31,29 +32,28 @@
+@@ -31,29 +32,28 @@ def main():
else:
outfile.write(go + "\n")
break
@@ -2473,10 +2456,8 @@ Index: metastudent/metastudentPkg/lib/groupA/parser/group2_blastParser.py
if __name__ == "__main__":
try:
main()
-Index: metastudent/metastudentPkg/lib/groupA/parser/group2_goParserSwissprot.py
-===================================================================
---- metastudent.orig/metastudentPkg/lib/groupA/parser/group2_goParserSwissprot.py 2019-09-17 01:14:50.567566834 +0100
-+++ metastudent/metastudentPkg/lib/groupA/parser/group2_goParserSwissprot.py 2019-09-17 01:14:50.559566873 +0100
+--- a/metastudentPkg/lib/groupA/parser/group2_goParserSwissprot.py
++++ b/metastudentPkg/lib/groupA/parser/group2_goParserSwissprot.py
@@ -3,27 +3,28 @@
import sys
@@ -2511,7 +2492,7 @@ Index: metastudent/metastudentPkg/lib/groupA/parser/group2_goParserSwissprot.py
if go == '':
go = '>' + tmpline[1].lstrip()[4:]
else:
-@@ -35,25 +36,26 @@
+@@ -35,25 +36,26 @@ def main():
# if GO and SQ has been found in one block (separated by '//') the GOs and SQ is written into the outfile
if go != '':
outfile.write(go+'\n'+sq+'\n')
@@ -2550,10 +2531,8 @@ Index: metastudent/metastudentPkg/lib/groupA/parser/group2_goParserSwissprot.py
if __name__ == "__main__":
try:
main()
-Index: metastudent/metastudentPkg/lib/groupA/parser/group2_goStatistics.py
-===================================================================
---- metastudent.orig/metastudentPkg/lib/groupA/parser/group2_goStatistics.py 2019-09-17 01:14:50.567566834 +0100
-+++ metastudent/metastudentPkg/lib/groupA/parser/group2_goStatistics.py 2019-09-17 01:14:50.559566873 +0100
+--- a/metastudentPkg/lib/groupA/parser/group2_goStatistics.py
++++ b/metastudentPkg/lib/groupA/parser/group2_goStatistics.py
@@ -3,21 +3,22 @@
import sys
import math
@@ -2581,7 +2560,7 @@ Index: metastudent/metastudentPkg/lib/groupA/parser/group2_goStatistics.py
# deriving the needed numbers
for line in infile:
if line.startswith('>'):
-@@ -26,22 +27,21 @@
+@@ -26,22 +27,21 @@ def main():
if len(gos) == 1:
seqWithOneGo += 1
goCount += len(gos)
@@ -2612,11 +2591,9 @@ Index: metastudent/metastudentPkg/lib/groupA/parser/group2_goStatistics.py
if __name__ == "__main__":
-Index: metastudent/metastudentPkg/runMethods.py
-===================================================================
---- metastudent.orig/metastudentPkg/runMethods.py 2019-09-17 01:14:50.567566834 +0100
-+++ metastudent/metastudentPkg/runMethods.py 2019-09-17 01:14:50.559566873 +0100
-@@ -5,9 +5,9 @@
+--- a/metastudentPkg/runMethods.py
++++ b/metastudentPkg/runMethods.py
+@@ -5,9 +5,9 @@ Created on Mar 17, 2012
'''
import os
@@ -2629,7 +2606,7 @@ Index: metastudent/metastudentPkg/runMethods.py
from metastudentPkg.commons import p, splitBigFastaFile
import sys
import shlex
-@@ -16,206 +16,212 @@
+@@ -16,206 +16,212 @@ import time
def runBlast(inputFilePath, blastDatabasePath, outputFilePath, tmpDir, eValue, iters, configMap):
@@ -3040,11 +3017,9 @@ Index: metastudent/metastudentPkg/runMethods.py
- return predFilesContent
+ return predFilesContent
-Index: metastudent/setup.py
-===================================================================
---- metastudent.orig/setup.py 2019-09-17 01:14:50.567566834 +0100
-+++ metastudent/setup.py 2019-09-17 01:14:50.563566854 +0100
-@@ -11,21 +11,23 @@
+--- a/setup.py
++++ b/setup.py
+@@ -11,21 +11,23 @@ import shutil
import tempfile
@@ -3081,7 +3056,7 @@ Index: metastudent/setup.py
# if "/.svn" not in path and "dataset_201012" not in path:
# for filename in files:
# filenameSplit = filename.split(".")
-@@ -36,70 +38,73 @@
+@@ -36,70 +38,73 @@ executables=set(["CafaWrapper3.pl","exer
# dataFiles.append(os.path.relpath(os.path.join(path, filename), pkgPath))
for path, dirs, files in os.walk(os.path.join(pkgPath, "lib")):
View it on GitLab: https://salsa.debian.org/med-team/metastudent/-/commit/81b541e8f2fcd71da97ae9aba408a4056372c383
--
View it on GitLab: https://salsa.debian.org/med-team/metastudent/-/commit/81b541e8f2fcd71da97ae9aba408a4056372c383
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