| Message ID | ecd331465d03183053f8f9597253c81f9079aa14.camel@planete-kraus.eu |
|---|---|
| State | New |
| Headers | show |
| Series | [bug#53402] Rebase it for the new python packages | expand |
| Context | Check | Description |
|---|---|---|
| cbaines/applying patch | fail | View Laminar job |
| cbaines/issue | success | View issue |
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
From f1deca828dddb258791c98ef52be14a8cf6c6c22 Mon Sep 17 00:00:00 2001 From: Vivien Kraus <vivien@planete-kraus.eu> Date: Thu, 20 Jan 2022 23:21:25 +0100 Subject: [PATCH v4 18/18] gnu: Add python-mne. * gnu/packages/python-science.scm (python-mne): New variable. --- gnu/packages/python-science.scm | 45 +++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 66c79b2e69..61ab831457 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -39,6 +39,7 @@ (define-module (gnu packages python-science) #:use-module (gnu packages databases) #:use-module (gnu packages gcc) #:use-module (gnu packages image-processing) + #:use-module (gnu packages jupyter) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -1194,3 +1195,47 @@ (define-public python-nitime level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code.") (license license:bsd-3))) + +(define-public python-mne + (package + (name "python-mne") + (version "0.24.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "mne" version)) + (sha256 + (base32 + "039h0pwcvl4ywfa4ij7w6x61czd322csqr59yhzfil3a7b8gzjrq")))) + (build-system python-build-system) + (arguments + ;; The test data is distributed in a separate repository without a + ;; license, https://github.com/mne-tools/mne-testing-data + `(#:tests? #f)) + (propagated-inputs (list python-numpy python-scipy)) + (native-inputs (list python-check-manifest + python-codespell + python-edflib + python-eeglabio + python-flake8 + python-flake8-array-spacing + python-imageio-ffmpeg + python-nbclient + python-nitime + python-numpydoc + python-pooch + python-pydocstyle + python-pytest + python-pytest-cov + python-pytest-harvest + python-pytest-timeout + python-sphinx-gallery + python-twine + python-wheel)) + (home-page "https://mne.tools/dev/") + (synopsis "MNE-Python project for MEG and EEG data analysis") + (description + "Open-source Python package for exploring, visualizing, and +analyzing human neurophysiological data: MEG, EEG, sEEG, ECoG, NIRS, and +more.") + (license license:bsd-3))) -- 2.34.0