Étienne Mollier pushed to branch master at Debian Med / python-biopython
Commits:
4394f8e6 by Étienne Mollier at 2024-09-16T22:29:51+02:00
fix-type-cast-i386.patch: dep3 header.
Gbp-Dch: ignore
- - - - -
7ad9a4d9 by Étienne Mollier at 2024-09-16T22:33:36+02:00
d/TODO: build reproducibility needs fixing.
- - - - -
2b329888 by Étienne Mollier at 2024-09-16T22:36:54+02:00
Ready for upload to experimental.
- - - - -
3 changed files:
- + debian/TODO
- debian/changelog
- debian/patches/fix-type-cast-i386.patch
Changes:
=====================================
debian/TODO
=====================================
@@ -0,0 +1,11 @@
+python-biopython (1.84+dfsg-1~0exp1) experimental; urgency=medium
+
+ Starting with Biopython 1.84, the documentation moved from the
+ not-so-simple Tutorial.tex to Sphinx documentation. The latter
+ introduced a regression in package reproducibility discussed with
+ upstream developpers on github[1].
+
+ [1]: https://github.com/biopython/biopython/issues/4839
+
+ -- Étienne Mollier <emollier at debian.org> Mon, 16 Sep 2024 22:31:02 +0200
+
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-python-biopython (1.84+dfsg-1~0exp1) UNRELEASED; urgency=medium
+python-biopython (1.84+dfsg-1~0exp1) experimental; urgency=medium
* New upstream version 1.84+dfsg
* d/watch: fix debian version mangling.
@@ -23,8 +23,10 @@ python-biopython (1.84+dfsg-1~0exp1) UNRELEASED; urgency=medium
* d/python-biopython-doc.doc-base: update location of the Tutorial.
* d/python-biopython-doc.examples: new: install examples.
* d/python-biopython-doc.lintian-overrides: flag another empty test file.
+ * fix-type-cast-i386.patch: new: fix PDB test failure on 32-bit.
+ * d/TODO: build reproducibility needs fixing.
- -- Étienne Mollier <emollier at debian.org> Sat, 14 Sep 2024 22:34:46 +0200
+ -- Étienne Mollier <emollier at debian.org> Mon, 16 Sep 2024 22:34:06 +0200
python-biopython (1.83+dfsg1-5) unstable; urgency=medium
=====================================
debian/patches/fix-type-cast-i386.patch
=====================================
@@ -1,3 +1,25 @@
+Description: fix test failure on 32-bit platforms.
+ This fixes the following symptom while running the test suite of
+ Biopython on 32-bit processors:
+ .
+ File "/builds/med-team/python-biopython/debian/output/source_dir/.pybuild/cpython3_3.12/build/Bio/PDB/binary_cif.py", line 85, in _run_length_decoder
+ decoded_data = np.repeat(data[::2].astype(dtype), data[1::2])
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+ File "/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py", line 466, in repeat
+ return _wrapfunc(a, 'repeat', repeats, axis=axis)
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+ File "/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py", line 68, in _wrapfunc
+ return _wrapit(obj, method, *args, **kwds)
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+ File "/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py", line 45, in _wrapit
+ result = getattr(asarray(obj), method)(*args, **kwds)
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+ TypeError: Cannot cast array data from dtype('uint32') to dtype('int32') according to the rule 'safe'
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2024-09-16
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- python-biopython.orig/Bio/PDB/binary_cif.py
+++ python-biopython/Bio/PDB/binary_cif.py
@@ -3,6 +3,7 @@
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/b096ace064e13939b8bf960e3830a86872443178...2b3298889e8c8af9dfd04c92d509f0dfefdeb22c
--
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/b096ace064e13939b8bf960e3830a86872443178...2b3298889e8c8af9dfd04c92d509f0dfefdeb22c
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