GNU bug report logs - #53402
Add python-mne

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From: Vivien <vivien <at> planete-kraus.eu>
To: Vinicius Monego <monego <at> posteo.net>, 53402 <at> debbugs.gnu.org
Subject: [bug#53402] Rebase it for the new python packages
Date: Fri, 11 Feb 2022 04:03:14 +0100

[Message part 1 (text/plain, inline)]

Hello, and thank you for your new review!

Le dimanche 06 février 2022 à 20:06 +0000, Vinicius Monego a écrit :
> 
> I noticed that some of the tests aren't running, like in flake8-array-
> spacing. If the check phase ends with "Ran 0 tests" then the tests are
> not being collected.


> If there are no tests to be collected, the package should have a
> #:tests? #f along with a comment saying that there are no tests. If
> there are tests to run, the check phase will have to be overriden to
> run them.

I tried to make sure that this situation didn’t happen again.

> > For MNE, the test data set is a separate repository without a
> > license,
> > so I disabled the tests.
> > 
> 
> OK. I tried to download the test dataset from within the mne module
> and
> they don't have a license agreement or anything, while to download
> individiual datasets the user has to agree to the (non-free) terms. I
> wonder if that's acceptable for merging in Guix?

I think it’s not, plus these are medical data (anonymized but still) so
maybe we shouldn’t take the risk.

> In [1] I found that there are more base dependencies that aren't
> listed
> in the pypi importer. They should be added to propagated-inputs. If
> tests can't run, then native-inputs can be removed.

I had nervous laughter when I read that page. I managed to package
everything except for the JS widgets (I don’t know how to tackle that
and I fear it would be a lot of work for very little benefit, since
there are other visualization platforms from what I understand) and
mne-qt-browser, because it depends on MNE.

> Usually, pytest modules should go into python-check.scm, not python-
> xyz.scm.

I tried to separate them, but they depend on a lot of stuff which is
not easy to organize into acyclic module imports.

> > > Could you style it as
> > > 
> > >     (source
> > >      (origin
> > >        (method url-fetch)
> > >        (uri (pypi-uri "imageio-ffmpeg" version))
> > >        (sha256
> > >         (base32
> > > "0ff14079izsyxwf6ki68k9a7w5krjlal7lwqvzg2bbddl92l5spj"))))
> > > 
> > > and the other packages too?
> > 
> > OK.
> > 
> 
> The base32 line was truncated in the mail, the hash should be in the
> same line of 'base32'. But I can fix that.

I fixed that occurence, but as a general rule I’m not very confident in
my indentation taste.

> 
> [...]
> 
> > 
> > > 
> > > Some of the descriptions are not full sentences (e.g. in python-
> > > pytest-
> > > harvest-minimal). Please check that descriptions are full
> > > sentences.
> > 
> > I’m not sure I understand. I reworked some descriptions, but didn’t
> > find non-full sentences. Could you explain what you mean?
> > 
> 
> Full sentences are made of a subject + predicate. This one:
> 
> +    (description "I/O support for EEGLAB files in Python.")
> 
> doesn't have a subject.
> 
> Usually the subject in the description is the package's name itself
> or
> "This package...". e.g. "EEGLABIO is a library..." or "This package
> provides I/O support..."

I think I got it.

> 
> Something else to avoid in descriptions is marketing talk, such as
> 'simple and reliable' in python-imageio-ffmpeg.

There were some more occurences that I neutralized.

> 
> [...]
> 
> The package modules you changed are also missing your copyright line.

OK.

As you see in the new series, vtk doesn’t install an egg-info, which
breaks the sanity-check phase of dependent python packages. There was
an option to let setuptools build the whole project, so the egg-info
would be installed too, but the installation plan with setup.py is
dysfunctional. So I made a terrible hack to "install" an egg-info.
There’s surely a better way to do it with python or pip, but I have no
clue as to what it would be and I can’t do much trial and error since I
have to wait for everything to build again (and vtk is quite a long
thing to compile).

Here is the v5!

I’m not used to managing such a large patch series; I hope I didn’t
make too many errors.

Best regards,

Vivien

> 
> [1]
> https://github.com/mne-tools/mne-python/blob/main/requirements_base.txt

[v5-0001-gnu-Add-python-imageio-ffmpeg.patch (text/x-patch, attachment)]

[v5-0002-gnu-Add-python-edflib.patch (text/x-patch, attachment)]

[v5-0003-gnu-Add-python-eeglabio.patch (text/x-patch, attachment)]

[v5-0004-gnu-Add-python-nibabel.patch (text/x-patch, attachment)]

[v5-0005-gnu-Add-python-nitime.patch (text/x-patch, attachment)]

[v5-0006-gnu-Add-python-flake8-array-spacing.patch (text/x-patch, attachment)]

[v5-0007-gnu-Add-python-makefun.patch (text/x-patch, attachment)]

[v5-0008-gnu-Add-python-pytest-logging.patch (text/x-patch, attachment)]

[v5-0009-gnu-Add-a-test-less-python-decopatch.patch (text/x-patch, attachment)]

[v5-0010-gnu-Add-a-test-less-python-pytest-harvest.patch (text/x-patch, attachment)]

[v5-0011-gnu-Add-a-test-less-python-pytest-steps.patch (text/x-patch, attachment)]

[v5-0012-gnu-Add-a-test-less-python-pytest-cases.patch (text/x-patch, attachment)]

[v5-0013-gnu-Add-python-decopatch.patch (text/x-patch, attachment)]

[v5-0014-gnu-Add-python-pytest-cases.patch (text/x-patch, attachment)]

[v5-0015-gnu-Add-python-pytest-harvest.patch (text/x-patch, attachment)]

[v5-0016-gnu-Add-python-pytest-steps.patch (text/x-patch, attachment)]

[v5-0017-gnu-python-pooch-Update-to-1.6.0.patch (text/x-patch, attachment)]

[v5-0018-gnu-Add-python-h5io.patch (text/x-patch, attachment)]

[v5-0019-gnu-Add-python-pymatreader.patch (text/x-patch, attachment)]

[v5-0020-gnu-Add-python-picard.patch (text/x-patch, attachment)]

[v5-0021-gnu-Add-python-dipy.patch (text/x-patch, attachment)]

[v5-0022-gnu-Add-python-no-version.patch (text/x-patch, attachment)]

[v5-0023-gnu-Add-python-pyperf.patch (text/x-patch, attachment)]

[v5-0024-gnu-Add-python-pyvips.patch (text/x-patch, attachment)]

[v5-0025-gnu-Add-python-scooby.patch (text/x-patch, attachment)]

[v5-0026-gnu-Add-python-nilearn.patch (text/x-patch, attachment)]

[v5-0027-gnu-vtk-Also-install-a-.egg-info.patch (text/x-patch, attachment)]

[v5-0028-gnu-Add-python-pyvista.patch (text/x-patch, attachment)]

[v5-0029-gnu-Add-python-pytest-memprof.patch (text/x-patch, attachment)]

[v5-0030-gnu-Add-python-pyvistaqt.patch (text/x-patch, attachment)]

[v5-0031-gnu-Add-python-mffpy.patch (text/x-patch, attachment)]

[v5-0032-gnu-Add-python-mne.patch (text/x-patch, attachment)]

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