Your message dated Thu, 29 Dec 2022 14:37:28 +0000
with message-id <[email protected]>
and subject line Bug#1027253: fixed in python-biopython 1.80+dfsg-4
has caused the Debian Bug report #1027253,
regarding python-biopython: autopkgtest fail with numpy/1.24.1
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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1027253: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1027253
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: python-biopython
Severity: important
User: [email protected]
Usertags: numpy1.24
Hello,
recently numpy/1.24.1 has been uploaded to experimental, and this package
autopkgtest fail when running against it.
An overview of the upstream changes in the 1.24.x series is available at:
https://numpy.org/doc/stable/release/1.24.0-notes.html
Several of the errors are in the form of:
AttributeError: module 'numpy' has no attribute 'X'
with X in [float, int, bool, object, ...]. This is because, numpy upstream in
1.24.0, finally decided to expire
https://numpy.org/doc/stable/release/1.24.0-notes.html#:~:text=The%20deprecation%20for%20the%20aliases
some deprecations introduced in 1.20.0
https://numpy.org/doc/stable/release/1.20.0-notes.html#using-the-aliases-of-builtin-types-like-np-int-is-deprecated
(released almost 2 years ago).
All of those are quite straightforward to fix, since often it's just necessary
to stop importing them from numpy and use the python native types.
Other changes may requires a bit more rework to be addressed.
Currently numpy/1.24.x is in experimental, but given the possible longer support
that it'll receive from upstream, we're hopeful to include this in bookworm, so
your help is necessary to address this bug ASAP.
Regards,
Sandro
--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.80+dfsg-4
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-biopython, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <[email protected]> (supplier of updated python-biopython package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
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Hash: SHA256
Format: 1.8
Date: Thu, 29 Dec 2022 18:52:07 +0530
Source: python-biopython
Architecture: source
Version: 1.80+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 1027253
Changes:
python-biopython (1.80+dfsg-4) unstable; urgency=medium
.
* Team Upload.
* Cherry-pick upstream patch to fix problems with
numpy 1.24 (Closes: #1027253)
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