[med-svn] [Git][med-team/python-pybedtools][master] 7 commits: skip-tests-in-autopkgtest-context.patch: new.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Oct 17 18:34:16 BST 2026
Étienne Mollier pushed to branch master at Debian Med / python-pybedtools
Commits:
bfab7011 by Étienne Mollier at 2026-10-17T19:22:43+02:00
skip-tests-in-autopkgtest-context.patch: new.
Skip some tests in autopkgtest context, because otherwise they attempt
to write into the test data directory provided by the package, which
is read-only.
Closes: #1149833
- - - - -
94badb49 by Étienne Mollier at 2026-10-17T19:23:40+02:00
d/copyright: remove the unused paragraph about plain GPL-2.
- - - - -
141cf11f by Étienne Mollier at 2026-10-17T19:24:11+02:00
d/control: provide an extended description to python-pybedtools-doc.
- - - - -
b82e5bc4 by Étienne Mollier at 2026-10-17T19:26:09+02:00
fix-privacy-breaches.patch: new: remove linked images.
- - - - -
9fc41083 by Étienne Mollier at 2026-10-17T19:33:34+02:00
d/python3-pybedtools.lintian-overrides: flag false positives.
- - - - -
c5d70b7d by Étienne Mollier at 2026-10-17T19:33:34+02:00
define_filenotfounderror_python2.patch: normalise the timestamp.
- - - - -
d0fd43b4 by Étienne Mollier at 2026-10-17T19:33:34+02:00
d/changelog: ready for upload to unstable.
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/define_filenotfounderror_python2.patch
- + debian/patches/fix-privacy-breaches.patch
- debian/patches/series
- + debian/patches/skip-tests-in-autopkgtest-context.patch
- + debian/python3-pybedtools.lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+python-pybedtools (0.12.1-2) unstable; urgency=medium
+
+ * Team upload.
+ * skip-tests-in-autopkgtest-context.patch: new.
+ Skip some tests in autopkgtest context, because otherwise they attempt
+ to write into the test data directory provided by the package, which
+ is read-only. (Closes: #1149833)
+ * d/copyright: remove the unused paragraph about plain GPL-2.
+ * d/control: provide an extended description to python-pybedtools-doc.
+ * fix-privacy-breaches.patch: new: remove linked images.
+ * d/python3-pybedtools.lintian-overrides: flag false positives.
+ * define_filenotfounderror_python2.patch: normalise the timestamp.
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 17 Oct 2026 19:28:36 +0200
+
python-pybedtools (0.12.1-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -71,4 +71,8 @@ Suggests:
Built-Using:
${sphinxdoc:Built-Using},
Description: Documentation for pybedtools library
- Sphinx-generated documentation.
+ The BEDTools suite of programs is widely used for genomic interval
+ manipulation or “genome algebra”. pybedtools wraps and extends BEDTools and
+ offers feature-level manipulations from within Python.
+ .
+ This package provides the Sphinx-generated documentation.
=====================================
debian/copyright
=====================================
@@ -34,26 +34,6 @@ License: MIT
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
-License: GPL-2
- This program is free software; you can redistribute it
- and/or modify it under the terms of the GNU General Public
- License as published by the Free Software Foundation at
- version 2 of the License.
- .
- This program is distributed in the hope that it will be
- useful, but WITHOUT ANY WARRANTY; without even the implied
- warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- PURPOSE. See the GNU General Public License for more
- details.
- .
- You should have received a copy of the GNU General Public License
- along with this package; if not, see <https://www.gnu.org/licenses/>.
- .
- On Debian systems, the full text of the GNU General Public
- License version 2 can be found in the file
- `/usr/share/common-licenses/GPL-2'.
-
-
Files: pybedtools/include/gzstream.cpp
pybedtools/include/gzstream.h
Copyright: 2001, Deepak Bandyopadhyay, Lutz Kettner
=====================================
debian/patches/define_filenotfounderror_python2.patch
=====================================
@@ -1,5 +1,5 @@
Author: Liubov Chuprikova <chuprikovalv at gmail.com>
-Last-Update: Wed, 13 July 2018 11:36:44 +0300
+Last-Update: 2018-07-13
Description: Define FileNotFoundError as OSError for python 2
=====================================
debian/patches/fix-privacy-breaches.patch
=====================================
@@ -0,0 +1,23 @@
+Description: fix privacy breaches.
+ This patch removes a couple of links to on-line images from the offline
+ documentation shipped by the package.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: not-needed
+Last-Update: 2026-10-17
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pybedtools.orig/README.rst
++++ python-pybedtools/README.rst
+@@ -2,12 +2,6 @@
+ Overview
+ --------
+
+-.. image:: https://badge.fury.io/py/pybedtools.svg?style=flat
+- :target: https://badge.fury.io/py/pybedtools
+-
+-.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg
+- :target: https://bioconda.github.io
+-
+ The `BEDTools suite of programs <http://bedtools.readthedocs.org/>`_ is widely
+ used for genomic interval manipulation or "genome algebra". `pybedtools` wraps
+ and extends BEDTools and offers feature-level manipulations from within
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,5 @@ define_filenotfounderror_python2.patch
add_missing_shebang.patch
yaml_safe_load.patch
doc-build-no-special-path
+skip-tests-in-autopkgtest-context.patch
+fix-privacy-breaches.patch
=====================================
debian/patches/skip-tests-in-autopkgtest-context.patch
=====================================
@@ -0,0 +1,36 @@
+Description: workaround autopkgtest failures.
+ This patch skips a couple of tests in autopkgtest context, as
+ otherwise, they attempt to write into the read-only system directory
+ holding the dataset, which fails with:
+ .
+ E PermissionError: [Errno 13] Could not open output: Permission denied: '/usr/lib/python3/dist-packages/pybedtools/test/data/a.bed.gz'
+ .
+ Further errors ensue. A proper approache might be to fetch the data
+ set from some place else or adjust the test suite to output
+ intermediate data in a suitable directory.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/1149833
+Forwarded: not-needed
+Last-Update: 2026-10-17
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pybedtools.orig/pybedtools/test/test_1.py
++++ python-pybedtools/pybedtools/test/test_1.py
+@@ -128,6 +128,8 @@
+ assert x[0]["ID"] == "gene1"
+
+
++ at pytest.mark.skipif(os.getenv("AUTOPKGTEST_TMP") != None,
++ reason="Tries to write into system directories")
+ def test_tabix_csi():
+ for idx_type in ("tbi", "csi"):
+ try:
+@@ -192,6 +194,8 @@
+ assert len(a.tabix_intervals("chr1")) == 1
+
+
++ at pytest.mark.skipif(os.getenv("AUTOPKGTEST_TMP") != None,
++ reason="Tries to write into system directories")
+ def test_tabix_contigs_csi():
+ a = pybedtools.example_bedtool("a.bed")
+ a = a.tabix(force=True, use_csi=True)
=====================================
debian/python3-pybedtools.lintian-overrides
=====================================
@@ -0,0 +1,7 @@
+# This is not documentation, but the test data of the python3 module.
+package-contains-documentation-outside-usr-share-doc [usr/lib/python3*/dist-packages/pybedtools/test/data/a.links.html]
+image-file-in-usr-lib [usr/lib/python3*/dist-packages/pybedtools/test/gchart-expected.png]
+image-file-in-usr-lib [usr/lib/python3*/dist-packages/pybedtools/test/mpl-expected.png]
+compressed-duplicate [usr/lib/python3*/dist-packages/pybedtools/test/data/a.bed.gz]
+compressed-duplicate [usr/lib/python3*/dist-packages/pybedtools/test/data/gdc.gff.gz]
+compressed-duplicate [usr/lib/python3*/dist-packages/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz]
View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/compare/708eea9819bba400df823fe3c039b0e853f3de31...d0fd43b4fcb3c567e2b1a7a95da9544e3c542a1f
--
View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/compare/708eea9819bba400df823fe3c039b0e853f3de31...d0fd43b4fcb3c567e2b1a7a95da9544e3c542a1f
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