[med-svn] [Git][med-team/kineticstools][master] 3 commits: * d/patches/remove-pkg-resources.patch: Add patch to replace the usages of

[Emmanuel Arias (@eamanu)]

Emmanuel Arias pushed to branch master at Debian Med / kineticstools


Commits:
ccce34da by Emmanuel Arias at 2025-01-22T18:43:25-03:00
* d/patches/remove-pkg-resources.patch: Add patch to replace the usages of
  pkg_resources with importlib.resources.
  - Thanks Vladimir Petko for the patch.

- - - - -
7fadeead by Emmanuel Arias at 2025-01-22T19:47:40-03:00
d/t/control: disable cram autopkgtests. detection_bam* tests are already disabled due to the missing data, version.t test fails due to the different usage formatting in python 3.13 (Closes: #1092749).

* d/t/control: disable cram autopkgtests. detection_bam* tests are already
  disabled due to the missing data, version.t test fails due to the
  different usage formatting in python 3.13 (Closes: #1092749).
  - Thanks Vladimir Petko for the patch.

- - - - -
6f9b2e0c by Emmanuel Arias at 2025-01-22T19:47:56-03:00
prepare for upload

- - - - -


4 changed files:

- debian/changelog
- + debian/patches/remove-pkg-resources.patch
- debian/patches/series
- debian/tests/control


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+kineticstools (0.6.1+git20220223.1326a4d+dfsg-5) unstable; urgency=medium
+
+  * Team upload.
+  * d/patches/remove-pkg-resources.patch: Add patch to replace the usages of
+    pkg_resources with importlib.resources.
+    - Thanks Vladimir Petko for the patch.
+  * d/t/control: disable cram autopkgtests. detection_bam* tests are already
+    disabled due to the missing data, version.t test fails due to the
+    different usage formatting in python 3.13 (Closes: #1092749).
+    - Thanks Vladimir Petko for the patch.
+
+ -- Emmanuel Arias <eamanu at debian.org>  Wed, 22 Jan 2025 18:39:57 -0300
+
 kineticstools (0.6.1+git20220223.1326a4d+dfsg-4) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/remove-pkg-resources.patch
=====================================
@@ -0,0 +1,58 @@
+Description: Remove usages of pkg_resources
+ pkg_resources are no longer available in Python 3.12 due to setuptools
+ removal from the default installation. This patch replaces the usages of
+ pkg_resources with importlib.resources.
+Author: Vladimir Petko <vladimir.petko at canonical.com>
+Bug: https://github.com/PacificBiosciences/kineticsTools/pull/105
+Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/kineticstools/+bug/2095050
+Last-Update: 2025-01-16
+
+--- a/kineticsTools/ipdModel.py
++++ b/kineticsTools/ipdModel.py
+@@ -1,4 +1,4 @@
+-from pkg_resources import Requirement, resource_filename
++from importlib import resources
+ import logging
+ import gzip
+ import os.path as op
+@@ -47,9 +47,11 @@
+
+
+ def _getAbsPath(fname):
+-    return resource_filename(Requirement.parse(
+-        'kineticsTools'), 'kineticsTools/%s' % fname)
+-
++    try:
++        with resources.as_file(resources.files('kineticsTools') / fname) as path:
++            return str(path)
++    except:
++        return os.path.join(os.path.dirname(__file__), path)
+
+ class GbmContextModel(object):
+
+--- a/kineticsTools/ipdSummary.py
++++ b/kineticsTools/ipdSummary.py
+@@ -20,7 +20,7 @@
+ import numpy as np
+ import queue
+ import traceback
+-from pkg_resources import Requirement, resource_filename
++from importlib import resources
+
+ from pbcommand.common_options import add_debug_option
+ from pbcommand.cli import get_default_argparser_with_base_opts, pacbio_args_runner
+@@ -43,9 +43,11 @@
+
+
+ def _getResourcePathSpec():
+-    default_dir = resource_filename(Requirement.parse(
+-        'kineticsTools'), 'kineticsTools/resources')
+-    return loader.getResourcePathSpec(default_dir)
++    try:
++        with resources.as_file(resources.files('kineticTools') / 'resources') as path:
++            return loader.getResourcePathSpec(path)
++    except:
++        return loader.getResourcePathSpec(os.path.join(os.path.dirname(__file__), 'resources'))
+
+
+ def _validateResource(func, p):


=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ spelling.patch
 #ignore_h5py_deprecation_warnings_in_test.patch
 tests2to3.patch
 man-align-cols.patch
+remove-pkg-resources.patch


=====================================
debian/tests/control
=====================================
@@ -2,11 +2,12 @@ Test-Command:
 	cp -r Makefile test $AUTOPKGTEST_TMP/
 	&& cd $AUTOPKGTEST_TMP
 	&& ln -s /usr/share/kineticstools kineticsTools
-	&& make -k py-tests cram-tests
-Depends:
-	make,
-	@,
-	python3-cram,
-	python3-pytest,
-	hdf5-tools,
+	&& make -k py-tests
+Depends: hdf5-tools,
+         make,
+         python3-cram,
+         python3-pytest,
+         python3-pytest-cov,
+         python3-pytest-xdist,
+         @,
 Restrictions: allow-stderr,



View it on GitLab: https://salsa.debian.org/med-team/kineticstools/-/compare/8153139da559c0748d8815aff8ad44b255a469cd...6f9b2e0c8f4b78455451cf33c2cd4b6e82fb8f37

-- 
View it on GitLab: https://salsa.debian.org/med-team/kineticstools/-/compare/8153139da559c0748d8815aff8ad44b255a469cd...6f9b2e0c8f4b78455451cf33c2cd4b6e82fb8f37
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