| 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. |
Étienne Mollier <etienne.mollier@mailoo.org> | not-needed | 2020-09-11 | ||
| fix-use-of-unversioned-python.patch | fix use of unversioned 'python' interpreter The Doc/Makefile uses python to evaluate the current version of the library in order to build the documentation, but the unversioned "python" interpreter is not available anymore, at least not in the build context. |
Étienne Mollier <etienne.mollier@mailoo.org> | not-needed | 2020-09-09 | ||
| reproduciblebuild.patch | make the build reproducible This patch removes the last update date, which would correspond to the moment when the package was build, and wouldn't be too relevant in the document. Focusing on the version number would be a better approach here. This patch is not needed upstream, as it would interfere with development releases, marked only with the version "dev", so would benefit of the date here. |
Étienne Mollier <etienne.mollier@mailoo.org> | not-needed | 2020-09-12 | ||
| 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. |
Étienne Mollier <emollier@debian.org> | yes | debian upstream | 2022-11-24 | |
| muscle3.patch | expect muscle3 as executable instead of muscle. When installed concurrently, muscle3 may be a preferrable 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. |
Étienne Mollier <emollier@debian.org> | not-needed | debian | 2022-11-24 | |
| port_tutorial_to_muscle3.patch | adjust tutorial to document muscle3 usage. In addition to being up to date with the way of doing things for the upcoming Debian version, this fixes the doctest failures. |
Étienne Mollier <emollier@debian.org> | no | 2022-12-04 | ||
| numpy-1.24.patch | [PATCH] fixing numpy type issues - replaced `np.int` with `np.int64` - replaced `np.bool` with `bool` | Adam Vandergriff <adam.vandergriff@gmail.com> | no | 2022-12-20 |