[med-svn] [Git][med-team/pyranges][master] 4 commits: No runtime dependency from cython

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / pyranges


Commits:
4f78e86f by Andreas Tille at 2023-12-11T21:34:48+01:00
No runtime dependency from cython

- - - - -
b6bf28d5 by Andreas Tille at 2023-12-11T21:35:25+01:00
routine-update: Build-Depends: s/dh-python/dh-sequence-python3/

- - - - -
b94e7777 by Andreas Tille at 2023-12-11T21:35:34+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse.

Changes-By: lintian-brush

- - - - -
59681612 by Andreas Tille at 2023-12-11T22:11:22+01:00
Upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/control
- + debian/patches/no_install_depends_cython.patch
- debian/patches/series
- debian/rules
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+pyranges (0.0.111+ds-6) unstable; urgency=medium
+
+  * Team upload.
+  * No runtime dependency from cython
+    Closes: #1058012
+  * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+  Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse.
+
+ -- Andreas Tille <tille at debian.org>  Mon, 11 Dec 2023 21:36:05 +0100
+
 pyranges (0.0.111+ds-5) unstable; urgency=medium
 
   * healthcheck-all.patch: new: fix test failure.


=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Section: python
 Testsuite: autopkgtest-pkg-python
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
-               dh-python,
+               dh-sequence-python3,
                python3-setuptools,
                python3-all,
                python3-ncls <!nocheck>,


=====================================
debian/patches/no_install_depends_cython.patch
=====================================
@@ -0,0 +1,16 @@
+Description: No runtime dependency from cython
+Bug-Debian: https://bugs.debian.org/1058012
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 11 Dec 2023 10:10:25 +0100
+
+--- a/setup.py
++++ b/setup.py
+@@ -6,7 +6,7 @@ __version__ = open("pyranges/version.py"
+     '"', '').strip()
+ 
+ install_requires = [
+-    "cython", "pandas", "ncls>=0.0.62", "tabulate", "sorted_nearest>=0.0.33", "pyrle",
++    "pandas", "ncls>=0.0.62", "tabulate", "sorted_nearest>=0.0.33", "pyrle",
+     "natsort"] #,
+ 
+ # optional_requires = ["bamread", "pybigwig", "ray"]


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ fix_dtype.patch
 reorder.patch
 numpy_1.24.patch
 healthcheck-all.patch
+no_install_depends_cython.patch


=====================================
debian/rules
=====================================
@@ -11,7 +11,7 @@ export PYBUILD_BEFORE_TEST=cp -av {dir}/tests/*.bed {build_dir}/tests && \
 export PYBUILD_TEST_ARGS=-n $(shell nproc)
 
 %:
-	dh $@ --with python3 --buildsystem=pybuild
+	dh $@ --buildsystem=pybuild
 
 execute_after_dh_auto_build:
 	echo 'Generating corresponding files ...'


=====================================
debian/upstream/metadata
=====================================
@@ -1,7 +1,7 @@
 ---
 Archive: GitHub
-Bug-Database: https://github.com/biocore-ntnu/pyranges/issues
-Bug-Submit: https://github.com/biocore-ntnu/pyranges/issues/new
+Bug-Database: https://github.com/pyranges/pyranges/issues
+Bug-Submit: https://github.com/pyranges/pyranges/issues/new
 Changelog: https://github.com/biocore-ntnu/pyranges/tags
 Reference:
  - Author: Endre Bakken Stovner and Pål Sætrom
@@ -24,4 +24,4 @@ Registry:
  - Name: conda:bioconda
    Entry: pyranges
 Repository: https://github.com/biocore-ntnu/pyranges.git
-Repository-Browse: https://github.com/biocore-ntnu/pyranges
+Repository-Browse: https://github.com/pyranges/pyranges



View it on GitLab: https://salsa.debian.org/med-team/pyranges/-/compare/e47fd1e3b19c858115e54a5a56f9e6193cb36bed...59681612db1acf7f772ae721a371e3891e5517b8

-- 
View it on GitLab: https://salsa.debian.org/med-team/pyranges/-/compare/e47fd1e3b19c858115e54a5a56f9e6193cb36bed...59681612db1acf7f772ae721a371e3891e5517b8
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