Debian Patches

Status for python-biopython/1.80+dfsg-4

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

All known versions for source package 'python-biopython'

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