[med-svn] [Git][med-team/python-pyfaidx][master] 4 commits: Add patch to fix FTBFS

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / python-pyfaidx


Commits:
c5f6145c by Nilesh Patra at 2022-02-17T22:26:06+05:30
Add patch to fix FTBFS

- - - - -
61cebfa0 by Nilesh Patra at 2022-02-17T22:30:00+05:30
Add B-D on python3-biopython

- - - - -
70aaa746 by Nilesh Patra at 2022-02-17T22:31:47+05:30
Revert "Update patches"

This reverts commit 8c6f2831c1d107a5a6d8bb902672c4ba01f6ecf7.

- - - - -
cf2d24aa by Nilesh Patra at 2022-02-17T22:33:57+05:30
Properly re-diff locale patch

- - - - -


4 changed files:

- debian/control
- + debian/patches/fix-pkg-resources.patch
- debian/patches/series
- + debian/patches/test-locale-to-c.patch


Changes:

=====================================
debian/control
=====================================
@@ -9,6 +9,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-all,
                python3-coverage,
                python3-setuptools,
+               python3-biopython,
                python3-numpy <!nocheck>,
                python3-pkg-resources <!nocheck>,
                python3-pytest <!nocheck>,


=====================================
debian/patches/fix-pkg-resources.patch
=====================================
@@ -0,0 +1,29 @@
+Description: pkg-resources only works once the package has been installed and breaks
+ in-place testing. Workaround it by making it n/a if not found
+Author: Nilesh Patra <nilesh at debian.org>
+Forwarded: not-needed
+Last-Update: 2022-02-17
+--- a/pyfaidx/__init__.py
++++ b/pyfaidx/__init__.py
+@@ -6,6 +6,7 @@
+ from __future__ import division
+ 
+ import os
++import pkg_resources
+ import re
+ import string
+ import sys
+@@ -25,8 +26,11 @@
+     from collections import OrderedDict
+ except ImportError:  #python 2.6
+     from ordereddict import OrderedDict
+-    
+-__version__ = get_distribution("pyfaidx").version
++
++try:
++    __version__ = get_distribution("pyfaidx").version
++except (ImportError, pkg_resources.DistributionNotFound):
++    __version__ = 'n/a'
+ 
+ if sys.version_info > (3, ):
+     buffer = memoryview


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,4 @@
+test-locale-to-c.patch
 remove-ignore-docstring.patch
 no_setuptools-scm.patch
+fix-pkg-resources.patch


=====================================
debian/patches/test-locale-to-c.patch
=====================================
@@ -0,0 +1,25 @@
+Description: Test locale to C
+ Change the testing locale "C", for avoiding the case in which the
+ additional locale set "en_US.utf8" is not available.
+Author: Sao I Kuan <saoikuan at gmail.com>
+Forwarded: not-needed
+Last-Update: 2020-09-30
+
+--- a/tests/test_feature_indexing.py
++++ b/tests/test_feature_indexing.py
+@@ -318,7 +318,7 @@
+     import platform
+     
+     if platform.system() == "Linux":
+-        new_locale = 'en_US.utf8'
++        new_locale = 'C'
+     elif platform.system() == "Darwin":
+         new_locale = 'en_US.UTF-8'
+     
+@@ -349,4 +349,4 @@
+             fasta_out.write("CTCCGGGCCCAT\nATAAAGCCTAAA\n")
+         faidx = Faidx(fasta_path)
+     finally:
+-        shutil.rmtree(tmp_dir)
+\ No newline at end of file
++        shutil.rmtree(tmp_dir)



View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/compare/707ff65c7f1d0a8320fa8dd428b0873f931c92f9...cf2d24aaa46dbdfce4b9336dfb801f514403dd28

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/compare/707ff65c7f1d0a8320fa8dd428b0873f931c92f9...cf2d24aaa46dbdfce4b9336dfb801f514403dd28
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