[bug#34882] [PATCH] Update to Pandas, enable Excel writer support

[Maxim Cournoyer <maxim.cournoyer@gmail.com>]

Hello Ricardo,

Ricardo Wurmus <rekado@elephly.net> writes:

> Maxim Cournoyer <maxim.cournoyer@gmail.com> writes:
>
>> From ad1f0efe4a5c3d28ee9d7e2e5da275721af9e172 Mon Sep 17 00:00:00 2001
>> From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
>> Date: Sat, 9 Feb 2019 00:25:51 -0500
>> Subject: [PATCH 5/5] gnu: python-pandas: Update to 0.24.2.
>>
>> * gnu/packages/python-xyz.scm (python-pandas): Update to 0.24.2.
>> [phases]{patch-which}: Add phase.
>> [inputs]: Add WHICH.
>
> I have no objections to updating Pandas, but please make sure that this
> version of Pandas works well with the other scientific Python packages
> like numpy, scipy, sklearn, numba, etc.
>
> These packages usually have rather strict interdependencies and need to
> be updated together to avoid breakage.

I've already went ahead and merged those changes,  but retested the
following (on master) to make sure:

--8<---------------cut here---------------start------------->8---
for o in $(./pre-inst-env guix refresh -l python-pandas | cut -d':' -f2); do ./pre-inst-env guix build --check --no-grafts "$o" && echo "$o OK" >> build.results || echo "$o NOK" >>  build.results; done
--8<---------------cut here---------------end--------------->8---

And then:
--8<---------------cut here---------------start------------->8---
$ cat build.results
cnvkit@0.9.5 OK
deeptools@3.1.3 NOK
nanopolish@0.10.2-1.50e8b5c NOK
pigx@0.0.3 NOK
python-biom-format@2.1.7 NOK
python-feather-format@0.4.0 NOK
python-hic2cool@0.4.2 OK
python-plastid@0.4.8 OK
python-pybedtools@0.8.0 OK
python-pygenometracks@2.0 OK
python-scanpy@1.2.2 OK
python-scikit-image@0.14.2 OK
python-velocyto@0.17.17 OK
--8<---------------cut here---------------end--------------->8---

So nanopolish, deeptools, python-feather-format, python-biom-format, and
pigx are currently broken, but...

When using master on commit g8c72f13fd4
# (and re-running the same script as earlier)

--8<---------------cut here---------------start------------->8---
cat build.results.g8c72f13fd4 
cnvkit@0.9.5 OK
deeptools@3.1.3 NOK
nanopolish@0.10.2-1.50e8b5c NOK
pigx@0.0.3 NOK
python-biom-format@2.1.7 NOK
python-feather-format@0.4.0 NOK
python-hic2cool@0.4.2 OK
python-plastid@0.4.8 OK
python-pybedtools@0.8.0 NOK
python-pygenometracks@2.0 OK
python-scanpy@1.2.2 OK
python-scikit-image@0.14.2 OK
python-velocyto@0.17.17 OK
--8<---------------cut here---------------end--------------->8---

they already were!

I've also found out while testing that Pandas was not reproducible (this
was true also before my changes).

I will create tickets for all of these problems.

Apart from that, I have run some script which uses Pandas successfully
(and the Pandas test suite passes).

Are these verifications sufficient? And why does 'guix refresh -l' seem
to miss some packages which depend on python-pandas, e.g. python-seaborn?

Thanks,

Maxim