| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| remove_mathml-qname.patch | Remove non DFSG free DTD | Andreas Tille <tille@debian.org> | yes | 2014-04-30 | ||
| privacy_breach.patch | Do not use privacy-breach-logo | Andreas Tille <tille@debian.org> | not-needed | 2015-05-12 | ||
| privacy_breach_ie9.patch | fix privacy breach with html5shiv Actually the script called is commented out, except when reading the page with Internet Explorer 9. This patch makes sure the script is not called at all, even if it is very unlikely that HTML document installed in Debian will ever be read with this browser. |
=?utf-8?q?=C3=89tienne_Mollier?= <etienne.mollier@mailoo.org> | not-needed | 2020-09-11 | ||
| muscle3.patch | expect muscle3 as executable instead of muscle. When installed concurrently, muscle3 may be a preferable default over plain muscle because the latter would probably be muscle 5, which is not compatible with the biopython wrapper. Forwarding is not needed since wrappers are deprecated and due to be removed in an upcoming biopython version. |
=?utf-8?q?=C3=89tienne_Mollier?= <emollier@debian.org> | not-needed | debian | 2022-11-24 | |
| skip-scipy-in-codonalign.patch | skip scipy tests within test_Align_codonalign. Note that this patch may be related to #1086108. Chances are it will be removable once the bug is resolved. This patch is introduced to give some breath to Risc-V CI runners while the core of the problem is investigated. |
=?utf-8?q?=C3=89tienne_Mollier?= <emollier@debian.org> | not-needed | debian | 2024-08-25 | |
| 0010-Python-3.13-Replace-deprecated-PyEval_CallObject.patch | Python 3.13: Replace deprecated PyEval_CallObject() The function has been deprecated since Python 3.9 and will be removed from Python 3.13. |
Sandro <devel@penguinpee.nl> | no | 2024-04-19 | ||
| croak-on-muscle5.patch | raise runtime error when trying to use wrapper on muscle 5. The muscle wrapper only supports muscle 3, and the biopython project is aiming to remove wrapper support in an upcoming version. Port of the wrapping code to support both muscle versions will thus probably never happen. The affected code section is due to disappear in an upcoming biopython version and it thus not forwarded upstream. |
=?utf-8?q?=C3=89tienne_Mollier?= <emollier@debian.org> | yes | debian upstream | 2024-09-14 | |
| fix-type-cast-i386.patch | 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' |
Étienne Mollier <emollier@debian.org> | no | 2024-09-16 |