[med-svn] [Git][med-team/libncl][master] 5 commits: Use 2to3 to port from Python2 to Python3
Andreas Tille
gitlab at salsa.debian.org
Mon Dec 16 09:04:16 GMT 2019
Andreas Tille pushed to branch master at Debian Med / libncl
Commits:
cea2cee4 by Andreas Tille at 2019-12-16T07:30:41Z
Use 2to3 to port from Python2 to Python3
- - - - -
f7b9543f by Andreas Tille at 2019-12-16T07:31:18Z
Build-Depends: python3
- - - - -
cfdfc5a9 by Andreas Tille at 2019-12-16T07:32:54Z
routine-update: Standards-Version: 4.4.1
- - - - -
63fec481 by Andreas Tille at 2019-12-16T07:33:02Z
Set upstream metadata fields: Bug-Database, Repository, Repository-Browse.
- - - - -
0bc34fd4 by Andreas Tille at 2019-12-16T09:03:33Z
Thanks to Andrey Rahmatullin for this fix
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/2to3.patch
- debian/patches/series
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+libncl (2.1.21+git20190531.feceb81-2) unstable; urgency=medium
+
+ * Use 2to3 to port from Python2 to Python3
+ Closes: #943083
+ * Standards-Version: 4.4.1
+ * Set upstream metadata fields: Bug-Database, Repository, Repository-
+ Browse.
+
+ -- Andreas Tille <tille at debian.org> Mon, 16 Dec 2019 08:33:03 +0100
+
libncl (2.1.21+git20190531.feceb81-1) unstable; urgency=medium
* Fix symbols file
=====================================
debian/control
=====================================
@@ -5,8 +5,8 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
d-shlibs,
- python
-Standards-Version: 4.4.0
+ python3
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/libncl
Vcs-Git: https://salsa.debian.org/med-team/libncl.git
Homepage: https://github.com/mtholder/ncl
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,180 @@
+Description: Use 2to3 to port from Python2 to Python3
+Bug-Debian: https://bugs.debian.org/943083
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 16 Dec 2019 08:27:49 +0100
+
+--- a/config/ax_python_module.m4
++++ b/config/ax_python_module.m4
+@@ -16,9 +16,9 @@ dnl @license AllPermissive
+ AC_DEFUN([AC_PYTHON_MODULE],[
+ if test -z "PYTHON"
+ then
+- AC_PATH_PROG([PYTHON], [python], [], [$PATH])
++ AC_PATH_PROG([PYTHON], [python3], [], [$PATH])
+ fi
+- AC_MSG_CHECKING(python module: $1)
++ AC_MSG_CHECKING(python3 module: $1)
+ if test -z "$PYTHON"
+ then
+ false
+--- a/configure.ac
++++ b/configure.ac
+@@ -139,7 +139,7 @@ AC_CHECK_FUNCS([memmove strchr strtol])
+ # the install-check requires python with subprocess to actually perform a check
+ # these tests should not cause failure of configure if python is not found.
+ ################################################################################
+-AC_PATH_PROG([PYTHON], [python], [], [$PATH])
++AC_PATH_PROG([PYTHON], [python3], [], [$PATH])
+ AC_PYTHON_MODULE([subprocess], [], [])
+ AC_SUBST(PYTHON)
+
+--- a/misc/generate_codon_recode.py
++++ b/misc/generate_codon_recode.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import sys
+ f = open(sys.argv[1], "rU")
+ bases = "ACGT"
+--- a/misc/genetic_codes.py
++++ b/misc/genetic_codes.py
+@@ -1,8 +1,8 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # Parsing of information from ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt
+ # into code for NCL's (alphabetical) order of codons
+ import sys
+-from cStringIO import StringIO
++from io import StringIO
+
+ codes = []
+
+@@ -15,7 +15,7 @@ class Code(object):
+ assert len(self.aa) == len(self.nuc_order[1])
+ assert len(self.aa) == len(self.nuc_order[2])
+ gen_code = {}
+- for codon_n in xrange(len(self.aa)):
++ for codon_n in range(len(self.aa)):
+ aa = self.aa[codon_n]
+ f = self.nuc_order[0][codon_n]
+ s = self.nuc_order[1][codon_n]
+@@ -243,11 +243,11 @@ for n, code in enumerate(codes):
+ l = code.to_order_ind(desired_order)
+ if n == 0:
+ x = l
+- for j in xrange(64):
++ for j in range(64):
+ sys.stdout.write('\taaInd[%d] = %d;\n' % (j, l[j]))
+ else:
+ sys.stdout.write('\tif (codeIndex = %s) {\n' % code.name)
+- for j in xrange(64):
++ for j in range(64):
+ if l[j] != x[j]:
+ sys.stdout.write('\t\taaInd[%d] = %d;\n' % (j, l[j]))
+ sys.stdout.write('\t}\n')
+--- a/swig_configure.ac
++++ b/swig_configure.ac
+@@ -54,7 +54,7 @@ AC_ARG_WITH(
+ [swig],
+ AC_HELP_STRING(
+ [--with-swig=yes],
+- [Compiles NCL for use with SWIG bindings for use with languages other than C++ - currently only python examples are included]
++ [Compiles NCL for use with SWIG bindings for use with languages other than C++ - currently only python3 examples are included]
+ ),
+ [
+ if test "$withval" = "yes"; then
+@@ -134,7 +134,7 @@ AC_CHECK_FUNCS([memmove strchr strtol])
+ # the install-check requires python with subprocess to actually perform a check
+ # these tests should not cause failure of configure if python is not found.
+ ################################################################################
+-AC_PATH_PROG([PYTHON], [python], [], [$PATH])
++AC_PATH_PROG([PYTHON], [python3], [], [$PATH])
+ AC_PYTHON_MODULE([subprocess], [], [])
+ AC_SUBST(PYTHON)
+
+--- a/test/roundTripNCLTest.py
++++ b/test/roundTripNCLTest.py
+@@ -1,10 +1,10 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import sys
+ import os
+ import subprocess
+ import filecmp
+ import itertools
+-import cStringIO
++import io
+ import shutil
+
+ def runTest(inArgPath,
+@@ -38,7 +38,7 @@ def runTest(inArgPath,
+ inFiles = [os.path.basename(inArgPath)]
+
+ if not inFiles:
+- print >>sys.stderr, "No files to test (looking for " + " ".join(fileNamePatterns) + " files)"
++ print("No files to test (looking for " + " ".join(fileNamePatterns) + " files)", file=sys.stderr)
+ sys.exit(0)
+
+ if compareOut:
+@@ -110,15 +110,15 @@ def runTest(inArgPath,
+ n = 1
+ while True:
+ try:
+- eLine = eit.next()
++ eLine = next(eit)
+ try:
+- oLine = oit.next()
++ oLine = next(oit)
+ except StopIteration:
+ oLine = ""
+ except StopIteration:
+ eLine = ""
+ try:
+- oLine = oit.next()
++ oLine = next(oit)
+ except StopIteration:
+ break
+ if eLine != oLine:
+@@ -128,7 +128,7 @@ def runTest(inArgPath,
+ sys.exit(basicMsg + fileInfo + diff)
+ e.close()
+ o.close()
+- print >>sys.stderr, sys.argv[0], ": Call to", normalizer, "succeeded for", inFile
++ print(sys.argv[0], ": Call to", normalizer, "succeeded for", inFile, file=sys.stderr)
+ if os.path.exists(tf):
+ os.remove(tf)
+
+@@ -209,7 +209,7 @@ if options.auto:
+ m = "%s does not exist." % resourceFilePath
+ if options.batch != "~/.ncl_round_triprc":
+ sys.exit(m)
+- print(m + " Test stepped skipped.")
++ print((m + " Test stepped skipped."))
+ sys.exit(0)
+ resourceFileStream = open(resourceFilePath, "rU")
+ else:
+@@ -229,7 +229,7 @@ else:
+ fs = "%s\n%s\n" % (args[1], args[2])
+ else:
+ fs = "%s\n" % (args[1])
+- resourceFileStream = cStringIO.StringIO(fs)
++ resourceFileStream = io.StringIO(fs)
+ normalizer = os.path.abspath(args[0])
+ if not os.path.exists(normalizer):
+ sys.exit(normalizer + " does not exist")
+@@ -240,13 +240,13 @@ try:
+ while True:
+ inputParentPath = "#"
+ while len(inputParentPath) < 1 or inputParentPath.strip().startswith("#"):
+- inputParentPath = lineIter.next().strip()
++ inputParentPath = next(lineIter).strip()
+ if options.invalid:
+ outputParentPath = None
+ else:
+ outputParentPath = "#"
+ while len(outputParentPath) < 1 or outputParentPath.strip().startswith("#"):
+- outputParentPath = lineIter.next().strip()
++ outputParentPath = next(lineIter).strip()
+ #print "next round: ", inputParentPath,"\n ", outputParentPath
+ if options.x:
+ extra_args = ['-x']
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
fix_rpath_issue.patch
set_soname_version.patch
spelling.patch
+2to3.patch
=====================================
debian/upstream/metadata
=====================================
@@ -1,22 +1,23 @@
Reference:
- - Author: Paul O. Lewis
- Title: >
+- Author: Paul O. Lewis
+ Title: >
NCL: a C++ class library for interpreting data files in NEXUS format
- Journal: Bioinformatics
- Year: 2003
- Volume: 19
- Number: 17
- Pages: 2330-2331
- DOI: 10.1093/bioinformatics/btg319
- PMID: 14630669
- URL: "https://academic.oup.com/bioinformatics/article/19/17/2330/\
- 206304/NCL-a-C-class-library-for-interpreting-data-files"
- eprint: "https://academic.oup.com/bioinformatics/article-pdf/\
- 19/17/2330/539234/btg319.pdf"
+ Journal: Bioinformatics
+ Year: 2003
+ Volume: 19
+ Number: 17
+ Pages: 2330-2331
+ DOI: 10.1093/bioinformatics/btg319
+ PMID: 14630669
+ URL: "https://academic.oup.com/bioinformatics/article/19/17/2330/206304/NCL-a-C-class-library-for-interpreting-data-files"
+ eprint: "https://academic.oup.com/bioinformatics/article-pdf/19/17/2330/539234/btg319.pdf"
Registry:
- - Name: OMICtools
- Entry: OMICS_20523
- - Name: bio.tools
- Entry: NA
- - Name: SciCrunch
- Entry: NA
+- Name: OMICtools
+ Entry: OMICS_20523
+- Name: bio.tools
+ Entry: NA
+- Name: SciCrunch
+ Entry: NA
+Bug-Database: https://github.com/mtholder/ncl/issues
+Repository: https://github.com/mtholder/ncl.git
+Repository-Browse: https://github.com/mtholder/ncl
View it on GitLab: https://salsa.debian.org/med-team/libncl/compare/17dde8e9c60394fe682ec3fd12f6c5294d68daf7...0bc34fd4f53a74ad879b59d4d25e2eb8d5b26dd3
--
View it on GitLab: https://salsa.debian.org/med-team/libncl/compare/17dde8e9c60394fe682ec3fd12f6c5294d68daf7...0bc34fd4f53a74ad879b59d4d25e2eb8d5b26dd3
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