Debian Patches
Status for python-pbcore/2.1.2+dfsg-12
| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| doc-theme.patch | Use default Sphinx theme for documentation The upstream's original theme includes their corporate logo. To be safe, this patch ignores it and configures the documentation builder to use the default theme. |
Afif Elghraoui <afif@ghraoui.name> | no | 2015-06-21 | ||
| exclude_test_missing_data.patch | Missing data for this test | Andreas Tille <tille@debian.org> | no | 2018-10-31 | ||
| b24746790c7105212e45dc2f40115d231bd8baae.patch | [PATCH] [SL-5880] abandon pyxb, use xmlschema for validation if installed (and xsd is defined) Fixes #122 |
Nathaniel Echols <nechols@pacificbiosciences.com> | no | 2020-06-23 | ||
| seek-curdir-for-xml.patch | Try looking for mapping.xml in the current directory helps when package is not installed for generating docs etc | Nilesh Patra <nilesh@debian.org> | no | 2021-12-23 | ||
| numpy_1.24.patch | Fix AttributeError: module 'numpy' has no attribute 'float'. with numpy/1.24.1 | Andreas Tille <tille@debian.org> | no | debian | 2022-12-29 | |
| no-intersphinx.patch | remove intersphinx | Andreas Tille <tille@debian.org> | no | debian | 2024-12-16 | |
| remove-pkg-resources.patch | Remove usages of pkg_resources pkg_resources are no longer available in Python 3.12 due to setuptools removal from the default installation. This patch replaces the usages of pkg_resources with importlib.resources. |
Vladimir Petko <vladimir.petko@canonical.com> | yes | debian upstream | 2025-01-15 | |
| numpy2.patch | workaround overflow errors with numpy 2. These changes fix various overflow errors caught since numpy 2 by restoring the former behavior by emulating the situation when overflows weren't trapped. The -1 error code in unsigned types is handled by setting the value to the maximum unsigned integer instead, and large index values not fitting in 32-bit are guarded with modulo operation. . The change also includes a slight modification to account for weirder base 16 numbers caught by end user upstream, resolving the following error: . File "/home/shuaiw/miniconda3/envs/methy2/lib/python3.11/site-packages/pbcore/io/align/BamIO.py", line 218, in __init__ self._loadReadGroupInfo() File "/home/shuaiw/miniconda3/envs/methy2/lib/python3.11/site-packages/pbcore/io/align/BamIO.py", line 89, in _loadReadGroupInfo rgID = rgAsInt(rg["ID"]) ^^^^^^^^^^^^^^^^^ File "/home/shuaiw/miniconda3/envs/methy2/lib/python3.11/site-packages/pbcore/io/align/_BamSupport.py", line 70, in rgAsInt return np.int32(int(rgIdString.split("/")[0], 16)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: invalid literal for int() with base 16: 'cb4d472d-100C60F6' . I'm reluctant to formally send that patch upstream, as it feels like a workaround where the right answer would probably be to bump the type sizes to 64-bit. However, I do not know what is the actually correct approach. |
Étienne Mollier <emollier@debian.org> | yes | debian upstream | 2025-02-27 |
All known versions for source package 'python-pbcore'
- 2.1.2+dfsg-12 (sid)
- 2.1.2+dfsg-11 (forky, trixie)
- 2.1.2+dfsg-5 (bookworm)