Your message dated Sun, 01 Jan 2023 12:53:29 +0000
with message-id <[email protected]>
and subject line Bug#1027232: fixed in pairtools 1.0.2-1
has caused the Debian Bug report #1027232,
regarding pairtools: 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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1027232: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1027232
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: pairtools
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: pairtools
Source-Version: 1.0.2-1
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
pairtools, 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 pairtools 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])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sun, 01 Jan 2023 17:51:23 +0530
Source: pairtools
Architecture: source
Version: 1.0.2-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 1027232 1027335
Changes:
pairtools (1.0.2-1) unstable; urgency=medium
.
[ Nilesh Patra ]
* Team Upload.
* Add patch to fix FTBFS with numpy 1.24 (Closes: #1027232)
* Bump Standards-Version to 4.6.2 (no changes needed)
* New upstream version 1.0.2
* Add patch for missing bam_dup1 declaration (Closes: #1027335)
* Versioned Build dep against pysam
* Build depend on python3-bioframe
* Skip building docs, as manpages are not rendered the same
way anymore
* Get rid of B-D on sphinx-click
* Move doc/examples/* installation to dedicated examples package
* Add patch to not run coverage tests. It makes no sense to
run them downstream.
* Add patch to take python3 interpreter as different during
testing, if CURPY var is set at runtime; helps run build time
tests for all supported pyvers
.
[ Andreas Tille]
* Fix clean target
* Build-Depends: python3-pandas, python3-pysam, python3-scipy, libhts-dev,
python3-yaml <!nocheck>
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