[med-svn] [Git][med-team/python-parasail][master] 7 commits: Trim patch
Nilesh Patra
gitlab at salsa.debian.org
Fri Nov 6 06:36:09 GMT 2020
Nilesh Patra pushed to branch master at Debian Med / python-parasail
Commits:
ebc56c47 by Nilesh Patra at 2020-11-06T12:01:20+05:30
Trim patch
- - - - -
5895ea6b by Nilesh Patra at 2020-11-06T12:01:40+05:30
routine-update: New upstream version
- - - - -
bdf4e7cf by Nilesh Patra at 2020-11-06T12:01:41+05:30
New upstream version 1.2.1
- - - - -
c8afbc4c by Nilesh Patra at 2020-11-06T12:01:43+05:30
Update upstream source from tag 'upstream/1.2.1'
Update to upstream version '1.2.1'
with Debian dir 2c3d198c824e16e470c733598d048ff76b1d4f96
- - - - -
feddf076 by Nilesh Patra at 2020-11-06T12:01:44+05:30
routine-update: debhelper-compat 13
- - - - -
dfa52b18 by Nilesh Patra at 2020-11-06T12:03:31+05:30
Add myself to uploaders
- - - - -
781a7f2b by Nilesh Patra at 2020-11-06T12:03:37+05:30
Upload to unstable
- - - - -
9 changed files:
- .travis.yml
- CHANGELOG.rst
- debian/changelog
- debian/control
- debian/patches/find-parasail-so-file-from-system.patch
- parasail/__init__.py
- parasail/bindings_v2.py
- tests/test_ssw.py
- tools/ctypesgen2.py
Changes:
=====================================
.travis.yml
=====================================
@@ -14,14 +14,19 @@ jobs:
- choco install python --version 3.7.5
- export PATH="/c/Python37:/c/Python37/Scripts:$PATH"
+# all three OSes agree about 'pip3'
+# 'python' points to Python 2.7 on macOS but points to Python 3.7 on Linux and Windows
+# 'python3' is a 'command not found' error on Windows but 'py' works on Windows only
env:
global:
- CIBW_BUILD="cp37-*"
- - CIBW_TEST_COMMAND="python -m unittest discover {project}/tests"
+ - CIBW_TEST_COMMAND_MACOS="python3 -m unittest discover {project}/tests"
+ - CIBW_TEST_COMMAND_LINUX="python3 -m unittest discover {project}/tests"
+ - CIBW_TEST_COMMAND_WINDOWS="python -m unittest discover {project}/tests"
- TWINE_USERNAME=__token__
install:
- - python -m pip install twine cibuildwheel==1.1.0 wheel
+ - pip3 install twine cibuildwheel==1.6.4 wheel
- wget -O parasail-master.zip https://github.com/jeffdaily/parasail/archive/master.zip
script:
@@ -29,4 +34,4 @@ script:
- if [[ "$TRAVIS_OS_NAME" = "windows" ]]; then python setup.py sdist -d wheelhouse; fi
after_success:
- - if [[ $TRAVIS_TAG ]]; then python -m twine upload wheelhouse/*; fi
+ - if [[ $TRAVIS_TAG ]]; then python3 -m twine upload wheelhouse/* || python -m twine upload wheelhouse/* ; fi
=====================================
CHANGELOG.rst
=====================================
@@ -10,6 +10,11 @@ Unreleased_
-----------
The Unreleased section will be empty for tagged releases. Unreleased functionality appears in the develop branch.
+-------------------
+1.2.1_ - 2020-11-03
+-------------------
+- Fix #54 bug in ssw_init()
+
-----------------
1.2_ - 2020-02-26
-----------------
@@ -143,27 +148,28 @@ The Unreleased section will be empty for tagged releases. Unreleased functionali
-------------------
First tagged release. The 'master' branch always represents the latest stable code. Tagged releases correspond to pypi releases.
-.. _Unreleased: https://github.com/jeffdaily/parasail-python/compare/v1.2...master
-.. _1.2: https://github.com/jeffdaily/parasail-python/compare/v1.1.20...v1.2
-.. _1.1.20: https://github.com/jeffdaily/parasail-python/compare/v1.1.19...v1.1.20
-.. _1.1.19: https://github.com/jeffdaily/parasail-python/compare/v1.1.18...v1.1.19
-.. _1.1.18: https://github.com/jeffdaily/parasail-python/compare/v1.1.17...v1.1.18
-.. _1.1.17: https://github.com/jeffdaily/parasail-python/compare/v1.1.16...v1.1.17
-.. _1.1.16: https://github.com/jeffdaily/parasail-python/compare/v1.1.15...v1.1.16
-.. _1.1.15: https://github.com/jeffdaily/parasail-python/compare/v1.1.14...v1.1.15
-.. _1.1.14: https://github.com/jeffdaily/parasail-python/compare/v1.1.13...v1.1.14
-.. _1.1.13: https://github.com/jeffdaily/parasail-python/compare/v1.1.12...v1.1.13
-.. _1.1.12: https://github.com/jeffdaily/parasail-python/compare/v1.1.11...v1.1.12
-.. _1.1.11: https://github.com/jeffdaily/parasail-python/compare/v1.1.10...v1.1.11
-.. _1.1.10: https://github.com/jeffdaily/parasail-python/compare/v1.1.9...v1.1.10
-.. _1.1.9: https://github.com/jeffdaily/parasail-python/compare/v1.1.8...v1.1.9
-.. _1.1.8: https://github.com/jeffdaily/parasail-python/compare/v1.1.7...v1.1.8
-.. _1.1.7: https://github.com/jeffdaily/parasail-python/compare/v1.1.6...v1.1.7
-.. _1.1.6: https://github.com/jeffdaily/parasail-python/compare/v1.1.5...v1.1.6
-.. _1.1.5: https://github.com/jeffdaily/parasail-python/compare/v1.1.4...v1.1.5
-.. _1.1.4: https://github.com/jeffdaily/parasail-python/compare/v1.1.3...v1.1.4
-.. _1.1.3: https://github.com/jeffdaily/parasail-python/compare/v1.1.2...v1.1.3
-.. _1.1.2: https://github.com/jeffdaily/parasail-python/compare/v1.1.1...v1.1.2
-.. _1.1.1: https://github.com/jeffdaily/parasail-python/compare/v1.1.0...v1.1.1
-.. _1.1.0: https://github.com/jeffdaily/parasail-python/releases/tag/v1.1.0
+.. _Unreleased: https://github.com/jeffdaily/parasail-python/compare/v1.2.1...master
+.. _1.2.1: https://github.com/jeffdaily/parasail-python/compare/v1.2...v1.2.1
+.. _1.2: https://github.com/jeffdaily/parasail-python/compare/v1.1.20...v1.2
+.. _1.1.20: https://github.com/jeffdaily/parasail-python/compare/v1.1.19...v1.1.20
+.. _1.1.19: https://github.com/jeffdaily/parasail-python/compare/v1.1.18...v1.1.19
+.. _1.1.18: https://github.com/jeffdaily/parasail-python/compare/v1.1.17...v1.1.18
+.. _1.1.17: https://github.com/jeffdaily/parasail-python/compare/v1.1.16...v1.1.17
+.. _1.1.16: https://github.com/jeffdaily/parasail-python/compare/v1.1.15...v1.1.16
+.. _1.1.15: https://github.com/jeffdaily/parasail-python/compare/v1.1.14...v1.1.15
+.. _1.1.14: https://github.com/jeffdaily/parasail-python/compare/v1.1.13...v1.1.14
+.. _1.1.13: https://github.com/jeffdaily/parasail-python/compare/v1.1.12...v1.1.13
+.. _1.1.12: https://github.com/jeffdaily/parasail-python/compare/v1.1.11...v1.1.12
+.. _1.1.11: https://github.com/jeffdaily/parasail-python/compare/v1.1.10...v1.1.11
+.. _1.1.10: https://github.com/jeffdaily/parasail-python/compare/v1.1.9...v1.1.10
+.. _1.1.9: https://github.com/jeffdaily/parasail-python/compare/v1.1.8...v1.1.9
+.. _1.1.8: https://github.com/jeffdaily/parasail-python/compare/v1.1.7...v1.1.8
+.. _1.1.7: https://github.com/jeffdaily/parasail-python/compare/v1.1.6...v1.1.7
+.. _1.1.6: https://github.com/jeffdaily/parasail-python/compare/v1.1.5...v1.1.6
+.. _1.1.5: https://github.com/jeffdaily/parasail-python/compare/v1.1.4...v1.1.5
+.. _1.1.4: https://github.com/jeffdaily/parasail-python/compare/v1.1.3...v1.1.4
+.. _1.1.3: https://github.com/jeffdaily/parasail-python/compare/v1.1.2...v1.1.3
+.. _1.1.2: https://github.com/jeffdaily/parasail-python/compare/v1.1.1...v1.1.2
+.. _1.1.1: https://github.com/jeffdaily/parasail-python/compare/v1.1.0...v1.1.1
+.. _1.1.0: https://github.com/jeffdaily/parasail-python/releases/tag/v1.1.0
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+python-parasail (1.2.1-1) unstable; urgency=medium
+
+ * New upstream version
+ * debhelper-compat 13 (routine-update)
+
+ -- Nilesh Patra <npatra974 at gmail.com> Fri, 06 Nov 2020 12:01:50 +0530
+
python-parasail (1.2-3) unstable; urgency=medium
* Re-add libparasail-dev to Depends to make sure libparasail.so
=====================================
debian/control
=====================================
@@ -2,8 +2,8 @@ Source: python-parasail
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper-compat (= 12),
+Uploaders: Andreas Tille <tille at debian.org>, Nilesh Patra <npatra974 at gmail.com>
+Build-Depends: debhelper-compat (= 13),
dh-python,
python3,
python3-setuptools,
=====================================
debian/patches/find-parasail-so-file-from-system.patch
=====================================
@@ -2,17 +2,6 @@ Description: Fix package to find libparasail.so from the system
Author: Nilesh Patra <npatra974 at gmail.com>
Last-Update: Thu, 23 Apr 2020 01:41:10 +0530
---- a/parasail/__init__.py
-+++ b/parasail/__init__.py
-@@ -43,7 +43,7 @@
- global _lib
- global _libpath
- _libpath = None
-- for env_var in ["PARASAIL_LIBPATH", "LD_LIBRARY_PATH", "DYLD_LIBRARY_PATH", "PATH"]:
-+ for env_var in ["PARASAIL_LIBPATH", "LD_LIBRARY_PATH", "DYLD_LIBRARY_PATH", "PATH", "DEB_HOST_MULTIARCH"]:
- if env_var in os.environ:
- if _verbose: print("searching {} for {}".format(env_var,_libname))
- for path in re.split("[:;]", os.environ[env_var]):
--- a/setup.py
+++ b/setup.py
@@ -422,7 +422,6 @@
=====================================
parasail/__init__.py
=====================================
@@ -6,7 +6,7 @@ import sys
import numpy
-__version__ = "1.2"
+__version__ = "1.2.1"
__title__ = "parasail"
__description__ = "pairwise sequence alignment library"
__uri__ = "https://github.com/jeffdaily/parasail-python"
=====================================
parasail/bindings_v2.py
=====================================
@@ -973,7 +973,8 @@ def ssw_profile(profile, s2, open, extend):
return None
def ssw_init(s1, matrix, score_size):
- return Profile(_lib.parasail_ssw_init(b(s1), len(s1), matrix, score_size), matrix)
+ s1b = b(s1)
+ return Profile(_lib.parasail_ssw_init(s1b, len(s1), matrix, score_size), matrix, s1b)
_lib.parasail_sequences_from_file.argtype = [ctypes.c_char_p]
_lib.parasail_sequences_from_file.restype = c_sequences_p
=====================================
tests/test_ssw.py
=====================================
@@ -4,7 +4,6 @@ from unittest import TestCase, main, expectedFailure
class Tests(TestCase):
- @expectedFailure
def test1(self):
p = parasail.ssw_init("asdf", parasail.blosum62, 1)
r = parasail.ssw_profile(p, "asdf", 10, 1)
=====================================
tools/ctypesgen2.py
=====================================
@@ -982,7 +982,8 @@ def ssw_profile(profile, s2, open, extend):
return None
def ssw_init(s1, matrix, score_size):
- return Profile(_lib.parasail_ssw_init(b(s1), len(s1), matrix, score_size), matrix)
+ s1b = b(s1)
+ return Profile(_lib.parasail_ssw_init(s1b, len(s1), matrix, score_size), matrix, s1b)
_lib.parasail_sequences_from_file.argtype = [ctypes.c_char_p]
_lib.parasail_sequences_from_file.restype = c_sequences_p
View it on GitLab: https://salsa.debian.org/med-team/python-parasail/-/compare/d9e31f027193723792b2f2b9a9af5d675081a95d...781a7f2b8c725af25091bb7bde5eddacd55bf39a
--
View it on GitLab: https://salsa.debian.org/med-team/python-parasail/-/compare/d9e31f027193723792b2f2b9a9af5d675081a95d...781a7f2b8c725af25091bb7bde5eddacd55bf39a
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