[med-svn] [Git][med-team/pyranges][master] 4 commits: Your message

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / pyranges


Commits:
77860006 by SpaciousCoder78 at 2026-01-31T08:03:07+05:30
Your message

- - - - -
1219ae2c by SpaciousCoder78 at 2026-02-01T09:06:29+05:30
Fix RC bug for python3-pkg-resources

- - - - -
a54fe273 by SpaciousCoder78 at 2026-02-01T09:08:49+05:30
Fix RC bug

- - - - -
cfe01569 by Andreas Tille at 2026-02-03T08:50:45+01:00
Merge branch 'fix-rc' into 'master'

Fix rc

See merge request med-team/pyranges!2
- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/remove-pkg-resources-dep.diff
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+pyranges (0.0.111+ds-11) unstable; urgency=medium
+
+  * Patched the usage of pkg-resources
+  * Add myself as uploader
+  * Bump Standards-Version to 4.7.3
+  * Remove dependency python3-pkg-resources (Closes: #1125824)
+  * Update d/copyright years
+
+ -- Aryan Karamtoth <spaciouscoder78 at disroot.org>  Fri, 30 Jan 2026 19:50:33 +0530
+
 pyranges (0.0.111+ds-10) unstable; urgency=medium
 
   * Team Upload


=====================================
debian/control
=====================================
@@ -3,9 +3,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders:
  Steffen Moeller <moeller at debian.org>,
  Étienne Mollier <emollier at debian.org>,
+ Aryan Karamtoth <spaciouscoder78 at disroot.org>
 Section: python
 Testsuite: autopkgtest-pkg-python
-Priority: optional
 Build-Depends:
  debhelper-compat (= 13),
  dh-sequence-python3,
@@ -19,7 +19,7 @@ Build-Depends:
  python3-setuptools,
  python3-sorted-nearest,
  samtools,
-Standards-Version: 4.7.2
+Standards-Version: 4.7.3
 Vcs-Browser: https://salsa.debian.org/med-team/pyranges
 Vcs-Git: https://salsa.debian.org/med-team/pyranges.git
 Homepage: https://github.com/biocore-ntnu/pyranges
@@ -27,7 +27,6 @@ Homepage: https://github.com/biocore-ntnu/pyranges
 Package: python3-pyranges
 Architecture: all
 Depends:
- python3-pkg-resources,
  ${misc:Depends},
  ${python3:Depends},
 Suggests:


=====================================
debian/patches/remove-pkg-resources-dep.diff
=====================================
@@ -0,0 +1,62 @@
+Description: Remove python3-pkg-resources dependency code
+ This is a temporary patch to remove the usage of
+ the deprecated python3-pkg-resources dependency
+ .
+ pyranges (0.0.111+ds-11) unstable; urgency=medium
+ .
+   * Patched the usage of pkg-resources
+   * Add myself as uploader
+   * Bump Standards-Version to 4.7.3
+   * Remove dependency python3-pkg-resources (Closes: #1125824)
+   * Update d/copyright years
+Author: Aryan Karamtoth <spaciouscoder78 at disroot.org>
+Applied-Upstream: https://github.com/pyranges/pyranges/commit/6c85a806989689af1ff69b4612e2d9f21b46ff2c
+Last-Update: 2026-01-30
+
+--- pyranges-0.0.111+ds.orig/pyranges/__init__.py
++++ pyranges-0.0.111+ds/pyranges/__init__.py
+@@ -1,5 +1,6 @@
+ from __future__ import print_function
+ 
++import importlib
+ import sys
+ 
+ from collections import defaultdict
+@@ -15,7 +16,6 @@ import numpy as np
+ 
+ import pyranges as pr
+ 
+-import pkg_resources
+ 
+ from pyranges.pyranges import PyRanges
+ from pyranges import data
+--- pyranges-0.0.111+ds.orig/pyranges/data.py
++++ pyranges-0.0.111+ds/pyranges/data.py
+@@ -21,7 +21,7 @@ Stranded PyRanges object has 3 rows and
+ For printing, the PyRanges was sorted on Chromosome and Strand.
+ """
+ 
+-import pkg_resources
++import importlib.resources
+ 
+ import pyranges as pr
+ import pandas as pd
+@@ -31,14 +31,12 @@ __all__ = ["f1", "f2", "chipseq", "chips
+ 
+ def get_example_path(basename):
+ 
+-    full_path = pkg_resources.resource_filename(
+-        "pyranges", "example_data/{}".format(basename))
++    full_path = importlib.resources.files("pyranges").joinpath("example_data/{}".format(basename))
+ 
+-    if full_path.endswith(".bam"):
+-        _hack_to_load_idx = pkg_resources.resource_filename(
+-            "pyranges", "example_data/{}.bai".format(basename))
++    if full_path.suffix == ".bam":
++        _hack_to_load_idx = importlib.resources.files("pyranges").joinpath("example_data/{}.bai".format(basename))
+ 
+-    return full_path
++    return str(full_path)
+ 
+ 
+ def aorta():


=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ healthcheck-all.patch
 no_install_depends_cython.patch
 pandas2.0.patch
 fix-test_unary.patch
+remove-pkg-resources-dep.diff



View it on GitLab: https://salsa.debian.org/med-team/pyranges/-/compare/a5e2a05c61adb5a74a9e461111e34dd3e862e0cf...cfe0156909ea226d2fe0a17497a9499cf4cc8e39

-- 
View it on GitLab: https://salsa.debian.org/med-team/pyranges/-/compare/a5e2a05c61adb5a74a9e461111e34dd3e862e0cf...cfe0156909ea226d2fe0a17497a9499cf4cc8e39
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