| Message ID | df09d62f7aa0e6a21362f9b7df5a88ff0ddd0a41.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 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
From 08ad35d954b27d697688d10e04a0244091b50614 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 18/18] gnu: Add python-mne. * gnu/packages/python-science.scm (python-mne): New variable. --- gnu/packages/python-science.scm | 53 +++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 6c0915e927..33e48b1be0 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) @@ -1193,3 +1194,55 @@ (define-public python-nitime 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 + (list #:tests? #f ;The test data are not distributed + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'set-home + (lambda _ + (setenv "HOME" + (getcwd)))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "mne"))))))) + (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