GNU bug report logs - #53402
Add python-mne

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

From: Vivien <vivien <at> planete-kraus.eu>
To: guix-patches <guix-patches <at> gnu.org>
Subject: Add python-mne
Date: Thu, 20 Jan 2022 23:46:54 +0100

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

Dear guix,

I am trying to get python-mne package [1]. So far I’ve managed to get
all the advertised dependencies, but I can’t get the tests to pass.

For python-nitime, I get IndexError: tuple index out of range

For python-mne, I get TypeError: annotate_nan() missing 1 required
positional argument: 'raw'

Both errors seem to occur because a function with optional or keyword
arguments is called without enough arguments. However, I can disable
all tests that call the function, but the error stays there.

Can someone help me?

Best regards,

Vivien


[1]: https://mne.tools/stable/index.html

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

[0017-gnu-python-pooch-Update-to-1.5.2.patch (text/x-patch, attachment)]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Message #8 received at 53402 <at> debbugs.gnu.org (full text, mbox):

From: Vivien Kraus <vivien <at> planete-kraus.eu>
To: 53402 <at> debbugs.gnu.org
Subject: Add python-mne: fix or disable tests
Date: Fri, 21 Jan 2022 09:17:38 +0100

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

Dear guix,

I could fix one test suite, but as luis-felipe told me on #guix, the
test data isn’t fully distributed by pypi for mne, so I had to disable
it.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[0017-gnu-python-pooch-Update-to-1.5.2.patch (text/x-patch, attachment)]

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

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Message #11 received at 53402 <at> debbugs.gnu.org (full text, mbox):

From: Vivien <vivien <at> planete-kraus.eu>
To: 53402 <at> debbugs.gnu.org
Subject: Rebase it for the new python packages
Date: Thu, 03 Feb 2022 20:29:03 +0100

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

Dear guix,

We have 2 new python packages, so my patch series creates a trivial
conflict. Here is a new version that you can apply directly.

Best regards,

Vivien

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[0017-gnu-python-pooch-Update-to-1.5.2.patch (text/x-patch, attachment)]

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

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

Message #14 received at 53402 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: Vivien <vivien <at> planete-kraus.eu>, 53402 <at> debbugs.gnu.org
Subject: Re: Rebase it for the new python packages
Date: Thu, 03 Feb 2022 20:49:08 +0000

Em qui, 2022-02-03 às 20:29 +0100, Vivien escreveu:
> Dear guix,
> 
> We have 2 new python packages, so my patch series creates a trivial
> conflict. Here is a new version that you can apply directly.
> 
> Best regards,
> 
> Vivien

Hi,

To avoid future merge conflicts, please move the packages somewhere in
the middle of the files instead of the bottom.

As a rule of thumb for Python packages with tests in Pytest, the check
phase is overriden and Pytest is called manually. When the tests are in
a subfolder inside the module, add a --pyargs <package> parameter to
the pytest command, see e.g. the python-cartopy package. I could run
the python-nibabel tests with this change without having to delete
anything.

If the tests still can't run because of missing data, it's fine to
source from the upstream repository instead of PyPI, or skip the few
tests that need them or at all if the repository doesn't ship a
setup.py. If tests are to be disabled, they should also have a comment
with the reason.

The 'test-less' packages shouldn't be needed AFAICS. Tests should run
by overriding the check phase as stated above (untested).

I also have a few comments about the patches in general:

> +    (source (origin
> +              (method url-fetch)
> +              (uri (pypi-uri "imageio-ffmpeg" version))
> +              (sha256
> +               (base32
> +               
> "0ff14079izsyxwf6ki68k9a7w5krjlal7lwqvzg2bbddl92l5spj"))))

Could you style it as

    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "imageio-ffmpeg" version))
       (sha256
        (base32
"0ff14079izsyxwf6ki68k9a7w5krjlal7lwqvzg2bbddl92l5spj"))))

and the other packages too?

Gexps should only be used when ungexp (#$) is used. On many patches
(e.g. python-nitime) ungexp is not being used.

When using gexp, it's better to style the arguments as:

+    (arguments
+     (list
+       #:phases
+       #~(modify-phases %standard-phases

to save columns (some of the packages exceeded the 78 columns limit),
instead of

> +    (arguments
> +     (list #:phases
> +           #~(modify-phases %standard-phases
> 

.

Some of the descriptions are not full sentences (e.g. in python-pytest-
harvest-minimal). Please check that descriptions are full sentences.

When sending an updated series, use patch versions with --reroll-
count=4 or -v4.

Could you send a v4 with the requested changes?

Vinicius

Message #17 received at 53402 <at> debbugs.gnu.org (full text, mbox):

From: Vivien <vivien <at> planete-kraus.eu>
To: Vinicius Monego <monego <at> posteo.net>, 53402 <at> debbugs.gnu.org
Subject: Re: Rebase it for the new python packages
Date: Sun, 06 Feb 2022 15:49:44 +0100

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

Hello, thank you for your review!

Le jeudi 03 février 2022 à 20:49 +0000, Vinicius Monego a écrit :
> To avoid future merge conflicts, please move the packages somewhere
> in
> the middle of the files instead of the bottom.

OK.

> As a rule of thumb for Python packages with tests in Pytest, the
> check
> phase is overriden and Pytest is called manually. When the tests are
> in
> a subfolder inside the module, add a --pyargs <package> parameter to
> the pytest command, see e.g. the python-cartopy package. I could run
> the python-nibabel tests with this change without having to delete
> anything.

OK.

> If the tests still can't run because of missing data, it's fine to
> source from the upstream repository instead of PyPI, or skip the few
> tests that need them or at all if the repository doesn't ship a
> setup.py. If tests are to be disabled, they should also have a
> comment
> with the reason.

For MNE, the test data set is a separate repository without a license,
so I disabled the tests.

> The 'test-less' packages shouldn't be needed AFAICS. Tests should run
> by overriding the check phase as stated above (untested).

The test-less packages are part of a dependency cycle; decopatch
requires them for the tests to run, and they require decopatch or each
other too. If I disable all tests (pytest-* and decopatch) it would
work, but I’m not sure I should do that.

> I also have a few comments about the patches in general:
> 
> > +    (source (origin
> > +              (method url-fetch)
> > +              (uri (pypi-uri "imageio-ffmpeg" version))
> > +              (sha256
> > +               (base32
> > +               
> > "0ff14079izsyxwf6ki68k9a7w5krjlal7lwqvzg2bbddl92l5spj"))))
> 
> 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.

> Gexps should only be used when ungexp (#$) is used. On many patches
> (e.g. python-nitime) ungexp is not being used.

OK, I upgraded python-pooch again and it needs gexps too now.

> 
> When using gexp, it's better to style the arguments as:
> 
> +    (arguments
> +     (list
> +       #:phases
> +       #~(modify-phases %standard-phases
> 
> to save columns (some of the packages exceeded the 78 columns limit),
> instead of
> 
> > +    (arguments
> > +     (list #:phases
> > +           #~(modify-phases %standard-phases
> > 

OK.

> .
> 
> 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?

> When sending an updated series, use patch versions with --reroll-
> count=4 or -v4.

I didn’t know that option.

> Could you send a v4 with the requested changes?

Sure!

Best regards,

Vivien

[v4-0001-gnu-Add-python-imageio-ffmpeg.patch (text/x-patch, attachment)]

[v4-0002-gnu-Add-python-edflib.patch (text/x-patch, attachment)]

[v4-0003-gnu-Add-python-eeglabio.patch (text/x-patch, attachment)]

[v4-0004-gnu-Add-python-nibabel.patch (text/x-patch, attachment)]

[v4-0005-gnu-Add-python-nitime.patch (text/x-patch, attachment)]

[v4-0006-gnu-Add-python-flake8-array-spacing.patch (text/x-patch, attachment)]

[v4-0007-gnu-Add-python-makefun.patch (text/x-patch, attachment)]

[v4-0008-gnu-Add-python-pytest-logging.patch (text/x-patch, attachment)]

[v4-0009-gnu-Add-a-test-less-python-decopatch.patch (text/x-patch, attachment)]

[v4-0010-gnu-Add-a-test-less-python-pytest-harvest.patch (text/x-patch, attachment)]

[v4-0011-gnu-Add-a-test-less-python-pytest-steps.patch (text/x-patch, attachment)]

[v4-0012-gnu-Add-a-test-less-python-pytest-cases.patch (text/x-patch, attachment)]

[v4-0013-gnu-Add-python-decopatch.patch (text/x-patch, attachment)]

[v4-0014-gnu-Add-python-pytest-cases.patch (text/x-patch, attachment)]

[v4-0015-gnu-Add-python-pytest-harvest.patch (text/x-patch, attachment)]

[v4-0016-gnu-Add-python-pytest-steps.patch (text/x-patch, attachment)]

[v4-0017-gnu-python-pooch-Update-to-1.6.0.patch (text/x-patch, attachment)]

[v4-0018-gnu-Add-python-mne.patch (text/x-patch, attachment)]

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Message #20 received at 53402 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: Vivien <vivien <at> planete-kraus.eu>, 53402 <at> debbugs.gnu.org
Subject: Re: Rebase it for the new python packages
Date: Sun, 06 Feb 2022 20:06:38 +0000

Em dom, 2022-02-06 às 15:49 +0100, Vivien escreveu:
> Hello, thank you for your review!
> 

Thanks for the v4.

[...]

> 
> > As a rule of thumb for Python packages with tests in Pytest, the
> > check
> > phase is overriden and Pytest is called manually. When the tests
> > are
> > in
> > a subfolder inside the module, add a --pyargs <package> parameter
> > to
> > the pytest command, see e.g. the python-cartopy package. I could
> > run
> > the python-nibabel tests with this change without having to delete
> > anything.
> 
> OK.

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.

For imageio-ffmpeg there are tests in github but not PyPI. I tried to
source from github but most tests require online data. In that case
#:tests? #f should be added with an explanation.

> 
> > If the tests still can't run because of missing data, it's fine to
> > source from the upstream repository instead of PyPI, or skip the
> > few
> > tests that need them or at all if the repository doesn't ship a
> > setup.py. If tests are to be disabled, they should also have a
> > comment
> > with the reason.
> 
> 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?

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.

> > The 'test-less' packages shouldn't be needed AFAICS. Tests should
> > run
> > by overriding the check phase as stated above (untested).
> 
> The test-less packages are part of a dependency cycle; decopatch
> requires them for the tests to run, and they require decopatch or
> each
> other too. If I disable all tests (pytest-* and decopatch) it would
> work, but I’m not sure I should do that.
> 

OK, it seems that they have a web of dependencies on each other. This
is the first time I see such a case.

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

> > I also have a few comments about the patches in general:
> > 
> > > +    (source (origin
> > > +              (method url-fetch)
> > > +              (uri (pypi-uri "imageio-ffmpeg" version))
> > > +              (sha256
> > > +               (base32
> > > +               
> > > "0ff14079izsyxwf6ki68k9a7w5krjlal7lwqvzg2bbddl92l5spj"))))
> > 
> > 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.

[...]

> 
> > 
> > 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..."

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

[...]

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

Vinicius

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

> 
> 
> Sure!
> 
> Best regards,
> 
> Vivien

Message #23 received at 53402 <at> debbugs.gnu.org (full text, mbox):

From: Vivien <vivien <at> planete-kraus.eu>
To: Vinicius Monego <monego <at> posteo.net>, 53402 <at> debbugs.gnu.org
Subject: Re: 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)]

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

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

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

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

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Message #26 received at 53402 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Vinicius Monego <monego <at> posteo.net>
Cc: Vivien <vivien <at> planete-kraus.eu>, 53402 <at> debbugs.gnu.org
Subject: Re: bug#53402: Add python-mne
Date: Sun, 06 Mar 2022 22:48:45 +0100

Hello!

Vinicius, could you take a look at v5 of this patch series?

Thanks for reviewing!

Ludo’.

Message #29 received at 53402 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: Ludovic Courtès <ludo <at> gnu.org>
Cc: Vivien <vivien <at> planete-kraus.eu>, 53402 <at> debbugs.gnu.org
Subject: Re: bug#53402: Add python-mne
Date: Wed,  9 Mar 2022 23:28:00 +0000

On 06/03/2022 6:48 PM, Ludovic Courtès wrote:

> Hello!
>
> Vinicius, could you take a look at v5 of this patch series?
>
> Thanks for reviewing!
>
> Ludo’.

Hi Ludo, Vivien.

Sorry for the long wait. I will be busy until mid-April. I did review
the patches earlier and LGTM apart from minor style/lint and description
issues, but I could fix that before committing. I saw that someone
pushed a wip-python-mne branch and thought they were taking care of this.

I have some questions for other maintainers, like

1. Is it OK to have that many bootstrap packages for pytest modules
(patches 8 to 16) and in files different than where they are supposed to
be (e.g. decopatch-minimal in python-check to bootstrap pytest-harvest)?
It seems that there are no other options in this case though.

2. Should python-no-verison (patch 22) be a public variable? It is an
example package, doesn't seem to be useful to expose it.

If it's OK I could push the series up to patch 26. I haven't reviewed 27
and on in v5.

3. Not a question but it would be good to review FSDG status of
python-mne, since it contains code to download non-free data.

Message #34 received at 53402 <at> debbugs.gnu.org (full text, mbox):

From: Vivien Kraus <vivien <at> planete-kraus.eu>
To: 53402 <at> debbugs.gnu.org
Subject: Update dependencies and rebase on newer work
Date: Thu, 26 May 2022 23:24:27 +0200

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

Dear guix,

Since I made the last update to this series, someone did work in the
python science packages and I had to publish a new rebase of my work,
discarding duplicate packaging efforts. I also used that opportunity to
update my dependencies.

Could you publish the new rebase in a new branch? Previously, nckx did
it to wip-python-mne. It was of great help to me because I can use the
branch in gitlab CI without having to patch and rebuild guix in the
pipeline. It would be wiser to use a new branch, based on master.

Thank you for the time you already spent helping me.

Best regards,

Vivien

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[v6-0009-gnu-Add-a-test-less-python-decopatch.patch (text/x-patch, attachment)]

[v6-0010-gnu-Add-a-test-less-python-pytest-harvest.patch (text/x-patch, attachment)]

[v6-0011-gnu-Add-a-test-less-python-pytest-steps.patch (text/x-patch, attachment)]

[v6-0012-gnu-Add-a-test-less-python-pytest-cases.patch (text/x-patch, attachment)]

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[v6-0014-gnu-Add-python-pytest-cases.patch (text/x-patch, attachment)]

[v6-0015-gnu-Add-python-pytest-harvest.patch (text/x-patch, attachment)]

[v6-0016-gnu-Add-python-pytest-steps.patch (text/x-patch, attachment)]

[v6-0017-gnu-python-pooch-Update-to-1.6.0.patch (text/x-patch, attachment)]

[v6-0018-gnu-Add-python-h5io.patch (text/x-patch, attachment)]

[v6-0019-gnu-Add-python-pymatreader.patch (text/x-patch, attachment)]

[v6-0020-gnu-Add-python-picard.patch (text/x-patch, attachment)]

[v6-0021-gnu-Add-python-dipy.patch (text/x-patch, attachment)]

[v6-0022-gnu-Add-python-no-version.patch (text/x-patch, attachment)]

[v6-0023-gnu-Add-python-nilearn.patch (text/x-patch, attachment)]

[v6-0024-gnu-vtk-Also-install-a-.egg-info.patch (text/x-patch, attachment)]

[v6-0025-gnu-Add-python-pytest-memprof.patch (text/x-patch, attachment)]

[v6-0026-gnu-Add-python-pyvistaqt.patch (text/x-patch, attachment)]

[v6-0027-gnu-Add-python-mffpy.patch (text/x-patch, attachment)]

[v6-0028-gnu-Add-python-mne.patch (text/x-patch, attachment)]

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