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commit 153fa1d84e6e6b9db77370a85222acea1270f6dc Author: Sascha Steinbiss <sa...@debian.org> Date: Tue Jan 30 12:31:13 2018 +0100 clean up unused patches --- debian/changelog | 1 + debian/patches/disable_spades_tests.patch | 17 ----------------- debian/patches/fix-spades-call.patch | 20 -------------------- debian/patches/relax-pysam-version.patch | 25 ------------------------- debian/patches/rename-cdhit.patch | 14 -------------- debian/patches/rename_test_input.patch | 16 ---------------- 6 files changed, 1 insertion(+), 92 deletions(-) diff --git a/debian/changelog b/debian/changelog index 069d415..82b36d6 100644 --- a/debian/changelog +++ b/debian/changelog @@ -6,6 +6,7 @@ ariba (2.10.3+ds-2) unstable; urgency=medium * Require Python3 version in d/control. * Clean up test override target in d/rules. * Remove obsolete Testsuite entry in d/control. + * Clean up unused patches from patch dir. -- Sascha Steinbiss <sa...@debian.org> Tue, 30 Jan 2018 10:28:08 +0100 diff --git a/debian/patches/disable_spades_tests.patch b/debian/patches/disable_spades_tests.patch deleted file mode 100644 index 924414c..0000000 --- a/debian/patches/disable_spades_tests.patch +++ /dev/null @@ -1,17 +0,0 @@ -Description: disable SPAdes specific test - This patch disables tests still requiring SPAdes support, as the - dependency on SPAdes has been dropped from 2.0.0+ds-1 on. -Author: Sascha Steinbiss <sa...@debian.org> ---- a/ariba/tests/assembly_test.py -+++ b/ariba/tests/assembly_test.py -@@ -21,8 +21,8 @@ - self.assertEqual(got, 42) - - -- def test_check_spades_log_file(self): -- '''test _check_spades_log_file''' -+ def _test_check_spades_log_file(self): -+ '''_test _check_spades_log_file''' - good_file = os.path.join(data_dir, 'assembly_test_check_spades_log_file.log.good') - bad_file = os.path.join(data_dir, 'assembly_test_check_spades_log_file.log.bad') - self.assertTrue(assembly.Assembly._check_spades_log_file(good_file)) diff --git a/debian/patches/fix-spades-call.patch b/debian/patches/fix-spades-call.patch deleted file mode 100644 index 6acc01f..0000000 --- a/debian/patches/fix-spades-call.patch +++ /dev/null @@ -1,20 +0,0 @@ -Description: fix SPAdes call - In Debian, spades.py is an alternative name for spades, a wrapper - around a script located elsewhere. ARIBA assumes it's the original - Python script and tries to call it as an argument of 'python2'. - This is no longer necessary in Debian; it will determine its Python - version by itself. -Author: Sascha Steinbiss <sa...@debian.org> ---- a/ariba/external_progs.py -+++ b/ariba/external_progs.py -@@ -72,8 +72,8 @@ - # python3.4, not python2. SPAdes throws an error about not being - # compatible with python3.4. - # This means we need to explicitly run SPAdes with python2. -- if prog == 'spades' and self.progs[prog] is not None: -- self.progs[prog] = 'python2 ' + self.progs[prog] -+ #if prog == 'spades' and self.progs[prog] is not None: -+ # self.progs[prog] = 'python2 ' + self.progs[prog] - if self.progs[prog] is None: - if prog in optional_progs: - warnings.append(prog + ' not found in path. Looked for ' + prog_exe + '. But it is optional so will be skipped during assembly') diff --git a/debian/patches/relax-pysam-version.patch b/debian/patches/relax-pysam-version.patch deleted file mode 100644 index b31458f..0000000 --- a/debian/patches/relax-pysam-version.patch +++ /dev/null @@ -1,25 +0,0 @@ -Description: relax pysam version - Pysam was restricted by upstream to <0.8.3 because newer versions fail - to build when installed via pip. This is no longer necessary in Debian. -Author: Sascha Steinbiss <sa...@debian.org> ---- a/setup.py -+++ b/setup.py -@@ -20,7 +20,7 @@ - install_requires=[ - 'openpyxl >= 1.6.2', - 'pyfastaq >= 3.12.0', -- 'pysam >= 0.8.1, <= 0.8.3', -+ 'pysam >= 0.8.1', - 'pymummer>=0.6.1', - ], - license='GPLv3', ---- a/ariba/versions.py -+++ b/ariba/versions.py -@@ -12,7 +12,6 @@ - } - - package_max_versions = { -- 'pysam': '0.8.3', - } - - diff --git a/debian/patches/rename-cdhit.patch b/debian/patches/rename-cdhit.patch deleted file mode 100644 index ddac598..0000000 --- a/debian/patches/rename-cdhit.patch +++ /dev/null @@ -1,14 +0,0 @@ -Description: use Debian name for CD-HIT - Debian's CD-HIT-EST executable is named cdhit-est, not cd-hit-est. -Author: Sascha Steinbiss <sa...@debian.org> ---- a/ariba/external_progs.py -+++ b/ariba/external_progs.py -@@ -11,7 +11,7 @@ - - prog_to_default = { - 'bowtie2': 'bowtie2', -- 'cdhit': 'cd-hit-est', -+ 'cdhit': 'cdhit-est', - #'cdhit2d': 'cd-hit-est-2d', - #'gapfiller': 'GapFiller.pl', - 'mash': 'mash', diff --git a/debian/patches/rename_test_input.patch b/debian/patches/rename_test_input.patch deleted file mode 100644 index 5d319db..0000000 --- a/debian/patches/rename_test_input.patch +++ /dev/null @@ -1,16 +0,0 @@ -Description: rename test input - This patch makes sure the correct file name is used for a - negative test targeting the fermi-lite extension. Trying to read a - nonexistent file leads to a failing assertion in fermi-lite's mrope.c. -Author: Sascha Steinbiss <sa...@debian.org> ---- a/ariba/tests/assembly_test.py -+++ b/ariba/tests/assembly_test.py -@@ -47,7 +47,7 @@ - - def test_run_fermilite_fails(self): - '''test _run_fermilite when it fails''' -- reads = os.path.join(data_dir, 'assembly_run_fermilite_fails.reads.fq') -+ reads = os.path.join(data_dir, 'assembly_run_fermilite_fail.reads.fq') - tmp_fa = 'tmp.test_run_fermilite_fails.fa' - tmp_log = 'tmp.test_run_fermilite_fails.log' - expected_log = os.path.join(data_dir, 'assembly_run_fermilite_fails.expected.log') -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit