GNU bug report logs - #48703
[PATCH 0/4] Update python-numpy

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Package: guix-patches;

Reported by: Greg Hogan <code <at> greghogan.com>

Date: Thu, 27 May 2021 15:12:02 UTC

Severity: normal

Tags: patch

Done: Greg Hogan <code <at> greghogan.com>

Bug is archived. No further changes may be made.

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Report forwarded to guix-patches <at> gnu.org:
bug#48703; Package guix-patches. (Thu, 27 May 2021 15:12:02 GMT) Full text and rfc822 format available.

Acknowledgement sent to Greg Hogan <code <at> greghogan.com>:
New bug report received and forwarded. Copy sent to guix-patches <at> gnu.org. (Thu, 27 May 2021 15:12:02 GMT) Full text and rfc822 format available.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Greg Hogan <code <at> greghogan.com>
To: guix-patches <at> gnu.org
Subject: [PATCH 0/4] Update python-numpy
Date: Thu, 27 May 2021 11:10:59 -0400
[Message part 1 (text/plain, inline)]
In March there were two attempts to update python-numpy (#45698 and #47183
/ #47184) which failed to build python-pandas and python-scipy.

The attached patches update and successfully build python-numpy,
python-pandas, python-matplotlib, and python-scipy.

In addition to modified dependencies, python-matplotlib expanded the regex
to silence image font differences and I was only able to successfully build
and test python-pandas when replacing python-openpyxl
with python-xlsxwriter.

Greg
[Message part 2 (text/html, inline)]
[0003-gnu-python-matplotlib-Update-to-3.4.2.patch (application/octet-stream, attachment)]
[0001-gnu-python-numpy-Update-to-1.20.3.patch (application/octet-stream, attachment)]
[0002-gnu-python-pandas-Update-to-1.2.4.patch (application/octet-stream, attachment)]
[0004-gnu-python-scipy-Update-to-1.6.3.patch (application/octet-stream, attachment)]

Information forwarded to guix-patches <at> gnu.org:
bug#48703; Package guix-patches. (Wed, 02 Jun 2021 19:15:02 GMT) Full text and rfc822 format available.

Message #8 received at 48703 <at> debbugs.gnu.org (full text, mbox):

From: Xinglu Chen <public <at> yoctocell.xyz>
To: Greg Hogan <code <at> greghogan.com>, 48703 <at> debbugs.gnu.org
Subject: Re: [bug#48703] [PATCH 0/4] Update python-numpy
Date: Wed, 02 Jun 2021 21:14:50 +0200
[Message part 1 (text/plain, inline)]
On Thu, May 27 2021, Greg Hogan wrote:

> In March there were two attempts to update python-numpy (#45698 and #47183
> / #47184) which failed to build python-pandas and python-scipy.
>
> The attached patches update and successfully build python-numpy,
> python-pandas, python-matplotlib, and python-scipy.
>
> In addition to modified dependencies, python-matplotlib expanded the regex
> to silence image font differences and I was only able to successfully build
> and test python-pandas when replacing python-openpyxl
> with python-xlsxwriter.

Thank you for working on this!

All the four packages you mentioned, ‘python-numpy’, ‘python-pandas’,
‘python-matplotlib’, and ‘python-scipy’ build for me.

[signature.asc (application/pgp-signature, inline)]

Information forwarded to guix-patches <at> gnu.org:
bug#48703; Package guix-patches. (Wed, 16 Jun 2021 09:12:02 GMT) Full text and rfc822 format available.

Message #11 received at 48703 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 48703 <at> debbugs.gnu.org
Subject: [PATCH 0/4] Update python-numpy
Date: Wed, 16 Jun 2021 09:10:52 +0000
Hello,

Since this is a mid to long term update (the packages have quite a few
[heavy] dependents), I'd like to suggest some refactoring. I will talk
about each package separately.

- python-numpy:

1. Why is it sourced from a tar.gz in the github releases page and not
from PyPI or a checkout? I had a look at the PyPI source file and the
tests are provided. If that source is required, a comment would help.

2.

> ;; Tests can only be run after the library has been installed and not
> ;; within the source directory.

I'm not sure if pytest was invoked manually or if the runtests.py
script was executed to reach that conclusion.

Numpy uses the tests under subdirectories structure. In that case,
tests should run with "python -m pytest --pyargs numpy" or "pytest --
pyargs numpy". I have this generic template that worked for all of my
packages so far:

> (replace 'check
>   (lambda* (#:key inputs outputs tests? #:allow-other-keys)
>     (when tests?
>       (add-installed-pythonpath inputs outputs)
>       (invoke "python" "-m" "pytest" "--pyargs" "numpy"))))

NumPy could be a special case, but a more detailed comment would help.

3. #:tests? is not respected.

4. Don't return #t in the phases.

- python-scipy

1. Same comment about tests from NumPy. Overriding the check would also
allow removing the 'disable-broken-tests phase.

2. #:tests? is not respected here either.

3. Don't return #t in the phases.

4. Since documentation is being built, it would be good to have the
sphinx theme for scipy ready. The current documentation doesn't have
any CSS. Not a big problem though.

- python-matplotlib

1. Respect #:tests?.

2. Don't return #t in the phases.

LGTM otherwise.

- python-pandas

1. I think the check phase could be simplified by using the same pytest
structure suggested in numpy and scipy.
2. Respect #:tests?
3. Don't return #t in the phases.





Reply sent to Greg Hogan <code <at> greghogan.com>:
You have taken responsibility. (Fri, 28 Jan 2022 11:50:01 GMT) Full text and rfc822 format available.

Notification sent to Greg Hogan <code <at> greghogan.com>:
bug acknowledged by developer. (Fri, 28 Jan 2022 11:50:01 GMT) Full text and rfc822 format available.

Message #16 received at 48703-done <at> debbugs.gnu.org (full text, mbox):

From: Greg Hogan <code <at> greghogan.com>
To: 48703-done <at> debbugs.gnu.org
Subject: Re: bug#48703: Acknowledgement ([PATCH 0/4] Update python-numpy)
Date: Fri, 28 Jan 2022 06:48:52 -0500
[Message part 1 (text/plain, inline)]
The same or newer package versions are in the main branch. Closing.

On Thu, May 27, 2021 at 11:12 AM GNU bug Tracking System <
help-debbugs <at> gnu.org> wrote:

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[Message part 2 (text/html, inline)]

bug archived. Request was from Debbugs Internal Request <help-debbugs <at> gnu.org> to internal_control <at> debbugs.gnu.org. (Fri, 25 Feb 2022 12:24:04 GMT) Full text and rfc822 format available.

This bug report was last modified 2 years and 31 days ago.

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