[med-svn] [Git][med-team/idba][master] 7 commits: Run build time test
Andreas Tille
gitlab at salsa.debian.org
Thu Nov 28 11:43:26 GMT 2019
Andreas Tille pushed to branch master at Debian Med / idba
Commits:
f9f6e53e by Andreas Tille at 2019-11-28T09:07:02Z
Run build time test
- - - - -
736fd302 by Andreas Tille at 2019-11-28T09:10:37Z
Use 2to3 to port Python2 to Python3 scripts
- - - - -
d56f79d8 by Andreas Tille at 2019-11-28T09:11:01Z
debhelper-compat 12
- - - - -
78bfd987 by Andreas Tille at 2019-11-28T09:11:09Z
Standards-Version: 4.4.1
- - - - -
286ebd30 by Andreas Tille at 2019-11-28T09:11:17Z
Set upstream metadata fields: Bug-Submit, Repository, Repository-Browse.
- - - - -
61daa6ab by Andreas Tille at 2019-11-28T11:05:46Z
Really run build time tests
- - - - -
81deea10 by Andreas Tille at 2019-11-28T11:11:47Z
Upload to unstable
- - - - -
8 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/2to3.patch
- debian/patches/series
- + debian/patches/use_debian_packaged_googletest.patch
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,19 @@
-idba (1.1.3-4) UNRELEASED; urgency=medium
+idba (1.1.3-5) unstable; urgency=medium
+ [ Jelmer Vernooij ]
* Use secure copyright file specification URI.
* Trim trailing whitespace.
- -- Jelmer Vernooij <jelmer at debian.org> Sun, 14 Oct 2018 19:43:45 +0000
+ [ Andreas Tille ]
+ * Run build time test
+ * Use 2to3 to port Python2 to Python3 scripts
+ Closes: #945684
+ * debhelper-compat 12
+ * Standards-Version: 4.4.1
+ * Set upstream metadata fields: Bug-Submit, Repository, Repository-
+ Browse.
+
+ -- Andreas Tille <tille at debian.org> Thu, 28 Nov 2019 12:08:11 +0100
idba (1.1.3-3) unstable; urgency=medium
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,8 +3,10 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.2.1
+Build-Depends: debhelper-compat (= 12),
+ libgtest-dev <!nocheck>,
+ python3 <!nocheck>
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/idba
Vcs-Git: https://salsa.debian.org/med-team/idba.git
Homepage: https://github.com/loneknightpy/idba
@@ -13,7 +15,7 @@ Package: idba
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- python
+ python3
Description: iterative De Bruijn Graph short read assemblers
IDBA stands for iterative de Bruijn graph assembler. In computational
sequence biology, an assembler solves the puzzle coming from large
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,126 @@
+Description: Use 2to3 to port Python2 to Python3 scripts
+Bug-Debian: https://bugs.debian.org/945684
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 28 Nov 2019 10:05:54 +0100
+
+--- a/script/run-unittest.py
++++ b/script/run-unittest.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/python
++#!/usr/bin/python3
+ ##
+ # @file run-unittest.py
+ # @brief Scan test directory and run all unit tests.
+--- a/script/scan.py
++++ b/script/scan.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/python
++#!/usr/bin/python3
+ ##
+ # @file scan.py
+ # @brief Scan src directory recursively to build Makefile.am automatically.
+@@ -15,11 +15,11 @@ install = []
+ noninstall = []
+
+ def Usage():
+- print "Usage: scan.py {bin, lib, test}\n"
++ print("Usage: scan.py {bin, lib, test}\n")
+
+
+ def ParamsToString(params):
+- return "".join(["%s = %s\n" % (k, v) for k, v in params.items()])
++ return "".join(["%s = %s\n" % (k, v) for k, v in list(params.items())])
+
+ def Scan(paths, pattern):
+ files = []
+@@ -62,11 +62,11 @@ if __name__ == "__main__":
+ + "-I$(top_srcdir)/gtest_src "
+
+ if (sys.argv[1] == "lib"):
+- print ParamsToString(params)
++ print(ParamsToString(params))
+ #print "noinst_LIBRARIES = libcommon.a libassembly.a\n"
+
+ #print ScanLibrary("libcommon.a", ["include/common", "src/common"], "\.cpp$|\.h$"), "\n"
+- print ScanLibrary("libassembly.a",
++ print(ScanLibrary("libassembly.a",
+ [#"src/common", "src/common",
+ "src/basic",
+ "src/container",
+@@ -74,16 +74,16 @@ if __name__ == "__main__":
+ "src/sequence",
+ "src/graph",
+ "src/assembly", ],
+- "\.cpp$|\.h$"), "\n"
++ "\.cpp$|\.h$"), "\n")
+
+- print "noinst_LIBRARIES = \\\n\t" + " \\\n\t".join(noninstall), "\n"
++ print("noinst_LIBRARIES = \\\n\t" + " \\\n\t".join(noninstall), "\n")
+
+ elif (sys.argv[1] == "lib-test"):
+- print ParamsToString(params)
++ print(ParamsToString(params))
+ #print "noinst_LIBRARIES = libcommon.a libassembly.a\n"
+
+ #print ScanLibrary("libcommon.a", ["include/common", "src/common"], "\.cpp$|\.h$"), "\n"
+- print ScanLibrary("libassembly.a",
++ print(ScanLibrary("libassembly.a",
+ [#"src/common", "src/common",
+ "src/basic",
+ "src/container",
+@@ -91,39 +91,39 @@ if __name__ == "__main__":
+ "src/sequence",
+ "src/graph",
+ "src/assembly", ],
+- "\.cpp$|\.h$"), "\n"
++ "\.cpp$|\.h$"), "\n")
+
+- print ScanLibrary("libgtest.a",
++ print(ScanLibrary("libgtest.a",
+ [ "gtest_src/gtest" ],
+- "\.cpp$|\.h$|.cc$"), "\n"
++ "\.cpp$|\.h$|.cc$"), "\n")
+
+- print "noinst_LIBRARIES = \\\n\t" + " \\\n\t".join(noninstall), "\n"
++ print("noinst_LIBRARIES = \\\n\t" + " \\\n\t".join(noninstall), "\n")
+
+ elif (sys.argv[1] == "bin"):
+ params["LIBS"] = "$(top_srcdir)/lib/libassembly.a @LIBS@";
+- print ParamsToString(params)
+- print ScanBinary(["src/tools"], "\.cpp$"), "\n"
+- print ScanBinary(["src/release"], "\.cpp$"), "\n"
++ print(ParamsToString(params))
++ print(ScanBinary(["src/tools"], "\.cpp$"), "\n")
++ print(ScanBinary(["src/release"], "\.cpp$"), "\n")
+
+ SetInstall("idba_hybrid")
+- print "bin_PROGRAMS = \\\n\t" + " \\\n\t".join(install), "\n"
+- print "noinst_PROGRAMS = \\\n\t" + " \\\n\t".join(noninstall), "\n"
++ print("bin_PROGRAMS = \\\n\t" + " \\\n\t".join(install), "\n")
++ print("noinst_PROGRAMS = \\\n\t" + " \\\n\t".join(noninstall), "\n")
+
+ elif (sys.argv[1] == "release"):
+ params["LIBS"] = "$(top_srcdir)/lib/libassembly.a @LIBS@";
+- print ParamsToString(params)
+- print ScanBinary(["src/release"], "\.cpp$"), "\n"
++ print(ParamsToString(params))
++ print(ScanBinary(["src/release"], "\.cpp$"), "\n")
+
+ SetInstall("idba_hybrid")
+- print "bin_PROGRAMS = \\\n\t" + " \\\n\t".join(install), "\n"
+- print "noinst_PROGRAMS = \\\n\t" + " \\\n\t".join(noninstall), "\n"
++ print("bin_PROGRAMS = \\\n\t" + " \\\n\t".join(install), "\n")
++ print("noinst_PROGRAMS = \\\n\t" + " \\\n\t".join(noninstall), "\n")
+
+ elif (sys.argv[1] == "test"):
+ params["LIBS"] = "$(top_srcdir)/lib/libassembly.a $(top_srcdir)/lib/libgtest.a @LIBS@";
+- print ParamsToString(params)
+- print ScanBinary(["src/test"], "\.cpp$"), "\n"
++ print(ParamsToString(params))
++ print(ScanBinary(["src/test"], "\.cpp$"), "\n")
+
+- print "noinst_PROGRAMS = \\\n\t" + " \\\n\t".join(noninstall), "\n"
++ print("noinst_PROGRAMS = \\\n\t" + " \\\n\t".join(noninstall), "\n")
+
+
+
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,5 @@
install_all_idba_flavours.patch
use-atomic-for-mips.patch
spelling.patch
+2to3.patch
+use_debian_packaged_googletest.patch
=====================================
debian/patches/use_debian_packaged_googletest.patch
=====================================
@@ -0,0 +1,42 @@
+Description: Use Debian packaged googletest library
+Bug-Debian: https://bugs.debian.org/945684
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 28 Nov 2019 10:05:54 +0100
+
+--- a/test/Makefile.am
++++ b/test/Makefile.am
+@@ -1,20 +1,20 @@
+ AM_LDFLAGS = -fopenmp -pthread
+-LIBS = $(top_srcdir)/lib/libassembly.a $(top_srcdir)/lib/libgtest.a @LIBS@
++LIBS = $(top_srcdir)/lib/libassembly.a -lgtest @LIBS@
+ AM_CXXFLAGS = -Wall -O3 -fopenmp -pthread
+-INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/gtest_src
++INCLUDES = -I$(top_srcdir)/src
+
+-compact_sequence_unittest_SOURCES = $(top_srcdir)/src/test/compact_sequence_unittest.cpp
+-hash_table_unittest_SOURCES = $(top_srcdir)/src/test/hash_table_unittest.cpp
+-bit_edges_unittest_SOURCES = $(top_srcdir)/src/test/bit_edges_unittest.cpp
+-kmer_unittest_SOURCES = $(top_srcdir)/src/test/kmer_unittest.cpp
+-hash_set_unittest_SOURCES = $(top_srcdir)/src/test/hash_set_unittest.cpp
+-atomic_integer_unittest_SOURCES = $(top_srcdir)/src/test/atomic_integer_unittest.cpp
+-vertex_status_unittest_SOURCES = $(top_srcdir)/src/test/vertex_status_unittest.cpp
+-histgram_unittest_SOURCES = $(top_srcdir)/src/test/histgram_unittest.cpp
+-managed_list_unittest_SOURCES = $(top_srcdir)/src/test/managed_list_unittest.cpp
+-sequence_unittest_SOURCES = $(top_srcdir)/src/test/sequence_unittest.cpp
+-short_sequence_unittest_SOURCES = $(top_srcdir)/src/test/short_sequence_unittest.cpp
+-hash_map_unittest_SOURCES = $(top_srcdir)/src/test/hash_map_unittest.cpp
++compact_sequence_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/compact_sequence_unittest.cpp
++hash_table_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/hash_table_unittest.cpp
++bit_edges_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/bit_edges_unittest.cpp
++kmer_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/kmer_unittest.cpp
++hash_set_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/hash_set_unittest.cpp
++atomic_integer_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/atomic_integer_unittest.cpp
++vertex_status_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/vertex_status_unittest.cpp
++histgram_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/histgram_unittest.cpp
++managed_list_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/managed_list_unittest.cpp
++sequence_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/sequence_unittest.cpp
++short_sequence_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/short_sequence_unittest.cpp
++hash_map_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/hash_map_unittest.cpp
+
+ check_PROGRAMS = \
+ compact_sequence_unittest \
=====================================
debian/rules
=====================================
@@ -17,3 +17,9 @@ override_dh_install:
# for the moment the role of these scripts is totally unknown but they do not seem to be necessary
mv debian/$(DEB_SOURCE)/usr/bin/*.py debian/$(DEB_SOURCE)/usr/lib/idba/
mv debian/$(DEB_SOURCE)/usr/bin/validate_blat* debian/$(DEB_SOURCE)/usr/lib/idba/
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ # $(MAKE) unittest
+ cd test && $(MAKE) check
+endif
=====================================
debian/upstream/metadata
=====================================
@@ -1,46 +1,46 @@
Reference:
- - Author: >
- Yu Peng and Henry C. M. Leung and S. M. Yiu and Francis Y. L. Chin
- Title: >
- IDBA-UD: a de novo assembler for single-cell and metagenomic
- sequencing data with highly uneven depth
- Journal: Bioinformatics
- Year: 2012
- Volume: 28
- Number: 11
- Pages: 1420-1428
- DOI: 10.1093/bioinformatics/bts174
- PMID: 22495754
- URL: http://bioinformatics.oxfordjournals.org/content/28/11/1420.full
- eprint: "http://bioinformatics.oxfordjournals.org/content/\
- 28/11/1420.full.pdf+html"
- - Author: >
+- Author: >
+ Yu Peng and Henry C. M. Leung and S. M. Yiu and Francis Y. L. Chin
+ Title: >
+ IDBA-UD: a de novo assembler for single-cell and metagenomic
+ sequencing data with highly uneven depth
+ Journal: Bioinformatics
+ Year: 2012
+ Volume: 28
+ Number: 11
+ Pages: 1420-1428
+ DOI: 10.1093/bioinformatics/bts174
+ PMID: 22495754
+ URL: http://bioinformatics.oxfordjournals.org/content/28/11/1420.full
+ eprint: "http://bioinformatics.oxfordjournals.org/content/28/11/1420.full.pdf+html"
+- Author: >
Yu Peng and Henry C. M. Leung and Siu-Ming Yiu and Ming-Ju Lv and
Xin-Guang Zhu and Francis Y. L. Chin
- Title: >
+ Title: >
IDBA-tran: a more robust de novo de Bruijn graph assembler for
transcriptomes with uneven expression levels
- Journal: Bioinformatics
- Year: 2013
- Month: Jul
- Day: 1
- Volume: 29
- Number: 13
- Pages: i326-i334
- DOI: 10.1093/bioinformatics/btt219
- PMID: 23813001
- URL: "https://academic.oup.com/bioinformatics/article-lookup/doi/\
- 10.1093/bioinformatics/btt219"
- eprint: "https://academic.oup.com/bioinformatics/article-pdf/\
- 29/13/i326/18534891/btt219.pdf"
+ Journal: Bioinformatics
+ Year: 2013
+ Month: Jul
+ Day: 1
+ Volume: 29
+ Number: 13
+ Pages: i326-i334
+ DOI: 10.1093/bioinformatics/btt219
+ PMID: 23813001
+ URL: "https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btt219"
+ eprint: "https://academic.oup.com/bioinformatics/article-pdf/29/13/i326/18534891/btt219.pdf"
Registry:
- - Name: bio.tools
- Entry: IDBA
- - Name: OMICtools
- Entry: OMICS_01423
- - Name: OMICtools
- Entry: OMICS_01318
- - Name: SciCrunch
- Entry: SCR_011912
- - Name: conda:bioconda
- Entry: idba
+- Name: bio.tools
+ Entry: IDBA
+- Name: OMICtools
+ Entry: OMICS_01423
+- Name: OMICtools
+ Entry: OMICS_01318
+- Name: SciCrunch
+ Entry: SCR_011912
+- Name: conda:bioconda
+ Entry: idba
+Repository: https://github.com/loneknightpy/idba
+Bug-Submit: loneknightpy at gmail.com
+Repository-Browse: https://github.com/loneknightpy/idba
View it on GitLab: https://salsa.debian.org/med-team/idba/compare/0a4786dc325711ceb4e64cbb1dcb4357da6f1a72...81deea10b02034b4d664d60b1a873bf0eb278bd6
--
View it on GitLab: https://salsa.debian.org/med-team/idba/compare/0a4786dc325711ceb4e64cbb1dcb4357da6f1a72...81deea10b02034b4d664d60b1a873bf0eb278bd6
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20191128/4105d930/attachment-0001.html>
More information about the debian-med-commit
mailing list