[med-svn] [Git][med-team/python-parasail][upstream] New upstream version 1.2.1

Fri Nov 6 06:36:14 GMT 2020


Nilesh Patra pushed to branch upstream at Debian Med / python-parasail


Commits:
bdf4e7cf by Nilesh Patra at 2020-11-06T12:01:41+05:30
New upstream version 1.2.1
- - - - -


6 changed files:

- .travis.yml
- CHANGELOG.rst
- 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
 


=====================================
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/-/commit/bdf4e7cf939eb6c3d99ce8008a64e99396e2739b

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View it on GitLab: https://salsa.debian.org/med-team/python-parasail/-/commit/bdf4e7cf939eb6c3d99ce8008a64e99396e2739b
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