[med-svn] [ariba] 05/07: clean up unused patches
Sascha Steinbiss
satta at debian.org
Tue Jan 30 11:39:00 UTC 2018
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository ariba.
commit 153fa1d84e6e6b9db77370a85222acea1270f6dc
Author: Sascha Steinbiss <satta at 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 <satta at 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 <satta at 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 <satta at 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 <satta at 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 <satta at 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 <satta at 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
More information about the debian-med-commit
mailing list