[med-svn] [Git][med-team/minia][master] 3 commits: Use 2to3 to port from Python2 to Python3
Andreas Tille
gitlab at salsa.debian.org
Mon Dec 16 08:54:35 GMT 2019
Andreas Tille pushed to branch master at Debian Med / minia
Commits:
add5770f by Andreas Tille at 2019-12-16T08:23:37Z
Use 2to3 to port from Python2 to Python3
- - - - -
4cc33eb5 by Andreas Tille at 2019-12-16T08:26:45Z
Latest update also fixed autopkgtest issue
- - - - -
fa6e0cee by Andreas Tille at 2019-12-16T08:30:03Z
Upload to unstable
- - - - -
8 changed files:
- debian/changelog
- + debian/patches/2to3.patch
- debian/patches/link_libraries.patch
- debian/patches/no_install_to_wrong_dir.patch
- debian/patches/series
- debian/patches/skip-rpath.patch
- debian/patches/use_debian_packaged_gatb-core.patch
- debian/tests/control
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+minia (3.2.1+git20191130.5b131b9-2) unstable; urgency=medium
+
+ * Use 2to3 to port from Python2 to Python3
+ Closes: #943115
+ * Latest update also fixed autopkgtest issue
+ Closes: #939894
+
+ -- Andreas Tille <tille at debian.org> Mon, 16 Dec 2019 09:26:55 +0100
+
minia (3.2.1+git20191130.5b131b9-1) unstable; urgency=medium
[ Andreas Tille ]
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,114 @@
+Description: Use 2to3 to port from Python2 to Python3
+Bug-Debian: https://bugs.debian.org/943115
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 16 Dec 2019 09:21:08 +0100
+
+--- a/scripts/convertToGFA.py
++++ b/scripts/convertToGFA.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ '''****************************************************************************
+
+@@ -20,8 +20,8 @@
+
+ '''****************************************************************************
+
+-* To run the program, pass three arguments with the python script on command line.
+-* For example - python convertToGFA.py inputFileName outputFileName kmerSize
++* To run the program, pass three arguments with the python3 script on command line.
++* For example - python3 convertToGFA.py inputFileName outputFileName kmerSize
+
+ * Logic - It reads through the fasta file with all the unitigs information
+ * and link information and outputs it in the GFA format.
+--- a/scripts/debug_1seq_tip_removal.py
++++ b/scripts/debug_1seq_tip_removal.py
+@@ -16,7 +16,7 @@ for line in fasta:
+ seq = line.strip()
+ is_error = False
+ is_genome = False
+- for i in xrange(len(seq)-k+1):
++ for i in range(len(seq)-k+1):
+ kmer = seq[i:i+k]
+ if kmer not in genome[0] and kmer not in genome[1]:
+ is_error = True
+@@ -24,9 +24,9 @@ for line in fasta:
+ is_genome = True
+
+ if is_error and is_genome:
+- print "mix of erroneous kmers and true genomic kmers inside the same assembled contig!!"
+- print id
+- print seq
++ print("mix of erroneous kmers and true genomic kmers inside the same assembled contig!!")
++ print(id)
++ print(seq)
+ exit(1)
+ else:
+- print id,is_error,is_genome
++ print(id,is_error,is_genome)
+--- a/scripts/duplicate_sequences_according_abundance.py
++++ b/scripts/duplicate_sequences_according_abundance.py
+@@ -8,7 +8,7 @@ for line in fasta:
+ #print abundance
+ id=line
+ else:
+- for i in xrange(int(abundance)):
+- print id,
+- print line,
++ for i in range(int(abundance)):
++ print(id, end=' ')
++ print(line, end=' ')
+
+--- a/scripts/ilots_stats.py
++++ b/scripts/ilots_stats.py
+@@ -37,4 +37,4 @@ for ctg in ctg_connect:
+ else:
+ nb_ilots += 1
+
+-print "contigs input", nb_ctg/2, "connected", nb_connected, "ilots", nb_ilots
++print("contigs input", nb_ctg/2, "connected", nb_connected, "ilots", nb_ilots)
+--- a/scripts/max_mem_usage_from_log.py
++++ b/scripts/max_mem_usage_from_log.py
+@@ -10,4 +10,4 @@ for line in sys.stdin:
+ mem=int(s[i-1])
+ max_mem=max(mem,max_mem)
+
+-print max_mem
++print(max_mem)
+--- a/scripts/strip_bcalm_links.py
++++ b/scripts/strip_bcalm_links.py
+@@ -3,11 +3,11 @@ file=sys.argv[1]
+ for line in open(file):
+ line=line.strip()
+ if not line.startswith(">"):
+- print(line.strip())
++ print((line.strip()))
+ continue
+ if "L:" in line:
+ s = line.split("L:")
+ else:
+ s = [line.strip()]
+- print(s[0])
++ print((s[0]))
+
+--- a/test/compare_fasta.py
++++ b/test/compare_fasta.py
+@@ -32,5 +32,5 @@ if len(s1) == len(s2) and len(s1) == 1:
+ else:
+ print("BAD: one sequence doesn't exactly match the other")
+
+-print("NOT EQUAL: %d sequence(s) in %s not in %s" % (len(s1.difference(s2)), fasta1, fasta2))
++print(("NOT EQUAL: %d sequence(s) in %s not in %s" % (len(s1.difference(s2)), fasta1, fasta2)))
+ sys.exit(1)
+--- a/test/simple_test.sh
++++ b/test/simple_test.sh
+@@ -35,7 +35,7 @@ function test()
+ else
+ eval $bindir/minia $args
+ fi
+- python compare_fasta.py "$file".solution.fa "$file".contigs.fa
++ python3 compare_fasta.py "$file".solution.fa "$file".contigs.fa
+ }
+
+ # Test One
=====================================
debian/patches/link_libraries.patch
=====================================
@@ -4,7 +4,7 @@ Description: Link against Debian packaged gatbcore
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -72,15 +72,17 @@
+@@ -74,15 +74,17 @@ cmake_policy(SET CMP0009 NEW) # fixes cm
include_directories (${PROGRAM_SOURCE_DIR})
file (GLOB_RECURSE ProjectFiles ${PROGRAM_SOURCE_DIR}/*)
=====================================
debian/patches/no_install_to_wrong_dir.patch
=====================================
@@ -4,7 +4,7 @@ Description: Failed to fix these install dirs, deactivate completely and use dh_
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -127,9 +127,9 @@
+@@ -129,9 +129,9 @@ SET (CPACK_SOURCE_IGNORE_FILES
)
# We copy the project binary to the 'bin' directory
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ link_libraries.patch
no_install_to_wrong_dir.patch
skip-rpath.patch
fix_path_in_tests.patch
+2to3.patch
=====================================
debian/patches/skip-rpath.patch
=====================================
@@ -4,7 +4,7 @@ Description: Do not set rpath
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -75,6 +75,7 @@ file (GLOB_RECURSE ProjectFiles ${PROG
+@@ -77,6 +77,7 @@ file (GLOB_RECURSE ProjectFiles ${PROG
include(GNUInstallDirs)
LINK_DIRECTORIES( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial )
add_executable(${PROJECT_NAME} ${ProjectFiles})
@@ -12,7 +12,7 @@ Description: Do not set rpath
target_link_libraries(${PROJECT_NAME} gatbcore hdf5 )
# merci
-@@ -82,6 +83,7 @@ set (MERCI_SOURCE_DIR ${PROJECT_SOURCE_D
+@@ -84,6 +85,7 @@ set (MERCI_SOURCE_DIR ${PROJECT_SOURCE_D
include_directories (${MERCI_SOURCE_DIR})
file (GLOB_RECURSE MerciFiles ${MERCI_SOURCE_DIR}/*.cpp)
add_executable("merci" ${MerciFiles})
=====================================
debian/patches/use_debian_packaged_gatb-core.patch
=====================================
@@ -3,7 +3,7 @@ Last-Update: Mon, 21 Jan 2019 09:01:19 +0100
Description: Use cmake input file of Debian packaged gatb-core
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -28,20 +28,6 @@
+@@ -28,20 +28,6 @@ IF (DEFINED JENKINS_TAG)
SET (gatb-tool-version ${JENKINS_TAG})
ENDIF()
@@ -24,7 +24,7 @@ Description: Use cmake input file of Debian packaged gatb-core
################################################################################
# Define cmake modules directory
################################################################################
-@@ -66,7 +52,7 @@
+@@ -66,7 +52,7 @@ SET (GATB_CORE_EXCLUDE_TESTS 1)
SET (GATB_CORE_EXCLUDE_EXAMPLES 1)
# GATB CORE
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @, samtools, python, bandage
+Depends: @, samtools, python3, bandage
Restrictions: allow-stderr
View it on GitLab: https://salsa.debian.org/med-team/minia/compare/b6cc8e8152b5fda7949ea2f3878aa62d47dd7730...fa6e0ceebb96e86e2e01f53f4e219ed8dfb91a1d
--
View it on GitLab: https://salsa.debian.org/med-team/minia/compare/b6cc8e8152b5fda7949ea2f3878aa62d47dd7730...fa6e0ceebb96e86e2e01f53f4e219ed8dfb91a1d
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