GNU bug report logs - #50813
[PATCH] gnu: python-pandas: Update to 1.3.3.

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From: Greg Hogan <code <at> greghogan.com>
To: Felix Gruber <felgru <at> posteo.net>
Cc: Ludovic Courtès <ludo <at> gnu.org>, 50813 <at> debbugs.gnu.org
Subject: [bug#50813] [PATCH v2 0/6] gnu: python-pandas: Update to 1.3.3.
Date: Tue, 12 Oct 2021 09:28:18 -0400

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#48703 was an attempt in May to update numpy, scipy, and pandas. If and
when this patchset is accepted first I can then update #48703 for the more
recent numpy and scipy releases.

On Sun, Oct 10, 2021 at 11:06 AM Felix Gruber <felgru <at> posteo.net> wrote:

> Hi Ludo’,
>
> On 10/7/21 11:07 AM, Ludovic Courtès wrote:
> >
> > Felix Gruber <felgru <at> posteo.net> skribis:
> >
> >> * gnu/packages/python-science.scm (python-pandas): Update to 1.3.3.
> >
> > The upgrade appears to cause build failures for python-dask and
> > pigx-rnaseq (via snakemake) among other things.
> >
> > Could you take a look?
>
> I could not reproduce the build failure in pigx-rnaseq. For python-dask
> the build failure could be fixed by upgrading it to 2021.9.1, whose
> changelog mentioned that they've deactivated a failing test when
> building against Pandas >= 1.3.3. After updating dask, its dependent
> packages python-distributed and python-eliot failed to build.  I've
> fixed both by updating them to their latest releases and disabling
> failing tests.
> I've also took the oppurtunity to update the synapse package which was
> the only package depending on python-eliot.
>
> > For the record, I tried to build everything reported by ‘guix refresh -l
> > python-pandas’ though some of them (ocaml4.07-re, etc.) would already
> > fail to build before the upgrade.
>
> Of the remaining packages reported by `guix refresh -l python-pandas`,
> I've identified the following packages with build failures:
>
> * clipper <at> 2.0
>   sometimes fails due to nondeterministic test
>   `test_get_FDR_cutoff_mean`.  The docstring of this test already says
>   "Difficult to test because of random sampling" followed by a TODO.
>   I've thus deactivated this test, to make it build deterministically.
> * pplacer <at> 1.1.alpha19
>   already failed on master due to unbuildable ocaml4.07-re <at> 1.10.3.
> * python-scikit-rebate <at> 0.6
>   Already failed on master in test `skrebate`:
>   ModuleNotFoundError: No module named 'sklearn.externals.joblib'
>   (A guix refresh -u python-scikit-rebate would update it to 0.62 which
>    was buildable, but this version seemed to come without any tests, so
>    I'm not sure if this is the right solution.)
> * orange <at> 3.28.0
>   Already failed to build on mater, because its dependency
>   python-orange-canvas-core.
>   I've looked into updating both to their latest version, but that
>   would require updating python-pygments to >= 2.8.0 which would entail
>   rebuilding 561 dependent packages.
> * imp <at> 2.13.0
>   I was running out of memory while building imp, which in the end
>   killed the build process. It seems that my 8GB of RAM are not
>   sufficient to build imp, so I cannot tell if the update of
>   python-pandas might break imp.
> * tadbit <at> 1.0.1
>   depends on imp, so I couldn't build it either.
>
> I've prepared patches for those packages that I was able to fix.
>
> Best,
> Felix
>
> Felix Gruber (6):
>   gnu: python-pandas: Update to 1.3.3.
>   gnu: python-dask: Update to 2021.9.1.
>   gnu: python-distributed: Update to 2021.09.1.
>   gnu: python-eliot: Update to 1.13.0.
>   gnu: synapse: Update to 1.44.0.
>   gnu: clipper: Disable non-deterministic test.
>
>  gnu/packages/bioinformatics.scm |  9 ++++++++-
>  gnu/packages/matrix.scm         |  5 +++--
>  gnu/packages/python-science.scm | 15 +++++++++------
>  gnu/packages/python-xyz.scm     | 19 +++++++++++++++----
>  4 files changed, 35 insertions(+), 13 deletions(-)
>
> --
> 2.30.2
>
>
>
>
>

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