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 <[email protected]> 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 <[email protected]> Sat, 14 Sep 2024 22:34:46 +0200 + -- Étienne Mollier <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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