[med-svn] [Git][med-team/pyensembl][master] 4 commits: Rediff patches
Alexandre Detiste (@detiste-guest)
gitlab at salsa.debian.org
Sun Apr 12 22:02:47 BST 2026
Alexandre Detiste pushed to branch master at Debian Med / pyensembl
Commits:
c02822af by Karsten Schöke at 2026-04-12T11:45:24+02:00
Rediff patches
- - - - -
6b6cbf63 by Karsten Schöke at 2026-04-12T12:37:40+02:00
insert patches for py14 compatiblity.
- - - - -
3e2759cf by Karsten Schöke at 2026-04-12T12:48:59+02:00
prepare 2.6.0-1 release
- - - - -
189f35ad by Alexandre Detiste at 2026-04-12T22:15:59+02:00
Merge branch 'karso' into 'master'
py13/14 compatiblity
See merge request med-team/pyensembl!1
- - - - -
6 changed files:
- debian/changelog
- + debian/patches/change-expected_deps-for-tests.patch
- + debian/patches/fix-argparse-nested-group.patch
- debian/patches/no_tinytimer_in_requirements.txt
- debian/patches/series
- debian/patches/skip-benchmark.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -11,7 +11,10 @@ pyensembl (2.6.0-1) UNRELEASED; urgency=medium
* d/copyright: Separated copyright for included fragments of
public databases.
- -- Alexandre Detiste <tchet at debian.org> Sun, 05 Apr 2026 00:19:45 +0200
+ [ Karsten Schöke ]
+ * insert patches for py14 compatiblity. (Closes: #1123067)
+
+ -- Karsten Schöke <karsten.schoeke at geobasis-bb.de> Sun, 12 Apr 2026 12:38:19 +0200
pyensembl (2.3.13-3) unstable; urgency=medium
=====================================
debian/patches/change-expected_deps-for-tests.patch
=====================================
@@ -0,0 +1,24 @@
+From: =?utf-8?q?Karsten_Sch=C3=B6ke?= <karsten.schoeke at geobasis-bb.de>
+Date: Sun, 12 Apr 2026 12:01:21 +0200
+Subject: change expected_deps for tests
+
+---
+ tests/test_build_system.py | 3 +--
+ 1 file changed, 1 insertion(+), 2 deletions(-)
+
+diff --git a/tests/test_build_system.py b/tests/test_build_system.py
+index 8b758e2..4488419 100644
+--- a/tests/test_build_system.py
++++ b/tests/test_build_system.py
+@@ -69,10 +69,9 @@ def test_dependencies_correct():
+ "typechecks>=0.0.2,<1.0.0",
+ "datacache>=1.4.0,<2.0.0",
+ "memoized-property>=1.0.2",
+- "tinytimer>=0.0.0,<1.0.0",
+ "gtfparse>=2.5.0,<3.0.0",
+ "serializable>=0.2.1,<1.0.0",
+- "numpy<2",
++ "numpy>=2.0.0,<3.0.0",
+ }
+
+ actual_deps = set(config["project"]["dependencies"])
=====================================
debian/patches/fix-argparse-nested-group.patch
=====================================
@@ -0,0 +1,24 @@
+From: =?utf-8?q?Karsten_Sch=C3=B6ke?= <karsten.schoeke at geobasis-bb.de>
+Date: Sun, 12 Apr 2026 12:32:43 +0200
+Subject: fix argparse nested group
+
+---
+ pyensembl/shell.py | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/pyensembl/shell.py b/pyensembl/shell.py
+index f446afa..f0bebfa 100755
+--- a/pyensembl/shell.py
++++ b/pyensembl/shell.py
+@@ -69,9 +69,9 @@ parser.add_argument(
+ )
+
+
+-root_group = parser.add_mutually_exclusive_group()
++root_group = parser # flatten group structure for Python 3.14 compatibility
+
+-release_group = root_group.add_argument_group()
++release_group = parser.add_argument_group()
+ release_group.add_argument(
+ "--release",
+ type=int,
=====================================
debian/patches/no_tinytimer_in_requirements.txt
=====================================
@@ -1,6 +1,17 @@
+From: Debian Med Packaging Team
+ <debian-med-packaging at lists.alioth.debian.org>
+Date: Sun, 12 Apr 2026 11:44:03 +0200
+Subject: no_tinytimer_in_requirements.txt
+
+---
+ pyproject.toml | 1 -
+ 1 file changed, 1 deletion(-)
+
+diff --git a/pyproject.toml b/pyproject.toml
+index 59739d1..8ac6dfc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
-@@ -24,7 +24,6 @@
+@@ -24,7 +24,6 @@ dependencies = [
"typechecks>=0.0.2,<1.0.0",
"datacache>=1.4.0,<2.0.0",
"memoized-property>=1.0.2",
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,4 @@
skip-benchmark.patch
no_tinytimer_in_requirements.txt
+change-expected_deps-for-tests.patch
+fix-argparse-nested-group.patch
=====================================
debian/patches/skip-benchmark.patch
=====================================
@@ -1,16 +1,26 @@
-Description: skip benchmark.
- By essence, benchmarks are flaky, as the success depends on the run time of
- the test item, which will be bound to be too tight for slow platforms.
- .
- Also this avoids having to prepare a side module for tinytimer. (:
+From: Debian Med Packaging Team
+ <debian-med-packaging at lists.alioth.debian.org>
+Date: Sun, 12 Apr 2026 11:44:03 +0200
+Subject: skip benchmark.
+MIME-Version: 1.0
+Content-Type: text/plain; charset="utf-8"
+Content-Transfer-Encoding: 8bit
+By essence, benchmarks are flaky, as the success depends on the run time of
+the test item, which will be bound to be too tight for slow platforms.
+
+Also this avoids having to prepare a side module for tinytimer. (:
Author: Étienne Mollier <emollier at debian.org>
Forwarded: not-needed
Last-Update: 2024-02-28
---
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- pyensembl.orig/tests/test_timings.py
-+++ pyensembl/tests/test_timings.py
+ tests/test_timings.py | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/tests/test_timings.py b/tests/test_timings.py
+index b0fd8e1..4cefa9e 100644
+--- a/tests/test_timings.py
++++ b/tests/test_timings.py
@@ -1,6 +1,5 @@
from pyensembl import genome_for_reference_name
-
@@ -19,7 +29,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
ensembl = genome_for_reference_name("GRCh38")
contigs = [str(i + 1) for i in range(22)] + ["X", "Y"]
-@@ -20,6 +19,7 @@
+@@ -20,6 +19,7 @@ def make_repeat_lookup_fn(lookup_fn, n_positions):
return repeat_lookup_fn
View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/compare/7277a088051546b311f1048236627c80935c354a...189f35ad55ba8348144a838eb855972ce34a7072
--
View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/compare/7277a088051546b311f1048236627c80935c354a...189f35ad55ba8348144a838eb855972ce34a7072
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