Bug 1731583 (python-pingouin)
| Summary: | Review Request: python-pingouin - Statistical package for Python | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | Ankur Sinha (FranciscoD) <sanjay.ankur> |
| Component: | Package Review | Assignee: | Timothée Floure <timothee.floure> |
| Status: | CLOSED RAWHIDE | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
| Severity: | medium | Docs Contact: | |
| Priority: | medium | ||
| Version: | rawhide | CC: | package-review, timothee.floure |
| Target Milestone: | --- | Flags: | timothee.floure:
fedora-review+
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| Target Release: | --- | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Fixed In Version: | Doc Type: | If docs needed, set a value | |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2020-02-14 08:08:14 UTC | Type: | --- |
| Regression: | --- | Mount Type: | --- |
| Documentation: | --- | CRM: | |
| Verified Versions: | Category: | --- | |
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |
| Cloudforms Team: | --- | Target Upstream Version: | |
| Embargoed: | |||
| Bug Depends On: | 1674101, 1731568, 1770496 | ||
| Bug Blocks: | 1276941 | ||
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Description
Ankur Sinha (FranciscoD)
2019-07-19 20:39:17 UTC
Package Review ============== * Upstream is GPLv3, not BSD: https://github.com/raphaelvallat/pingouin/blob/master/LICENSE * The tests under the check section are not run by default and fail if enabled (do not seem related to missing pytest-sugar): https://paste.sr.ht/~fnux/9aa513ec18533e34f405da400ab027636306fb10 * The doc subpackage ships quite a lot of third-party web assets (such as bootstrap, which is MIT-licensed), which might be a licensing issue. See https://paste.sr.ht/~fnux/ba797c6e6a3ae7ca90835d9e9e7aa06c3fabaddb for details. I do not think we can do much, but I think we have to specify the licenses. * The `%{?python_enable_dependency_generator}` is no required for F30+, do you plan to backport this package to F29? (https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/#_automatically_generated_dependencies) * You might want to use the `%pypi_source` macro: https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated althoug ===== MUST items ===== Generic: [x]: Package is licensed with an open-source compatible license and meets other legal requirements as defined in the legal section of Packaging Guidelines. [!]: License field in the package spec file matches the actual license. [x]: License file installed when any subpackage combination is installed. [x]: Package contains no bundled libraries without FPC exception. [x]: Changelog in prescribed format. [x]: Sources contain only permissible code or content. [-]: Package contains desktop file if it is a GUI application. [-]: Development files must be in a -devel package [x]: Package uses nothing in %doc for runtime. [x]: Package consistently uses macros (instead of hard-coded directory names). [x]: Package is named according to the Package Naming Guidelines. [x]: Package does not generate any conflict. [x]: Package obeys FHS, except libexecdir and /usr/target. [-]: If the package is a rename of another package, proper Obsoletes and Provides are present. [x]: Requires correct, justified where necessary. [x]: Spec file is legible and written in American English. [-]: Package contains systemd file(s) if in need. [x]: Package is not known to require an ExcludeArch tag. [x]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. [x]: Package complies to the Packaging Guidelines [x]: Package successfully compiles and builds into binary rpms on at least one supported primary architecture. [x]: Package installs properly. [x]: Rpmlint is run on all rpms the build produces. [x]: If (and only if) the source package includes the text of the license(s) in its own file, then that file, containing the text of the license(s) for the package is included in %license. [x]: Package requires other packages for directories it uses. [x]: Package must own all directories that it creates. [x]: Package does not own files or directories owned by other packages. [x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT [x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the beginning of %install. [x]: Macros in Summary, %description expandable at SRPM build time. [x]: Dist tag is present. [x]: Package does not contain duplicates in %files. [x]: Permissions on files are set properly. [x]: Package must not depend on deprecated() packages. [x]: Package use %makeinstall only when make install DESTDIR=... doesn't work. [x]: Package is named using only allowed ASCII characters. [x]: Package does not use a name that already exists. [x]: Package is not relocatable. [x]: Sources used to build the package match the upstream source, as provided in the spec URL. [x]: Spec file name must match the spec package %{name}, in the format %{name}.spec. [x]: File names are valid UTF-8. [x]: Packages must not store files under /srv, /opt or /usr/local Python: [x]: Python eggs must not download any dependencies during the build process. [-]: A package which is used by another package via an egg interface should provide egg info. [x]: Package meets the Packaging Guidelines::Python [x]: Package contains BR: python2-devel or python3-devel [x]: Packages MUST NOT have dependencies (either build-time or runtime) on packages named with the unversioned python- prefix unless no properly versioned package exists. Dependencies on Python packages instead MUST use names beginning with python2- or python3- as appropriate. [x]: Python packages must not contain %{pythonX_site(lib|arch)}/* in %files [x]: Binary eggs must be removed in %prep ===== SHOULD items ===== Generic: [!]: Avoid bundling fonts in non-fonts packages. [-]: If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it. [x]: Final provides and requires are sane (see attachments). [-]: Fully versioned dependency in subpackages if applicable. [x]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [-]: Description and summary sections in the package spec file contains translations for supported Non-English languages, if available. [x]: Package should compile and build into binary rpms on all supported architectures. [!]: %check is present and all tests pass. [-]: Packages should try to preserve timestamps of original installed files. [x]: Reviewer should test that the package builds in mock. [x]: Buildroot is not present [x]: Package has no %clean section with rm -rf %{buildroot} (or $RPM_BUILD_ROOT) [x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin. [x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file [x]: Sources can be downloaded from URI in Source: tag [x]: SourceX is a working URL. [x]: Spec use %global instead of %define unless justified. ===== EXTRA items ===== Rpmlint ------- Checking: python3-pingouin-0.2.7-1.fc31.noarch.rpm python-pingouin-doc-0.2.7-1.fc31.noarch.rpm python-pingouin-0.2.7-1.fc31.src.rpm python3-pingouin.noarch: W: spelling-error %description -l en_US ancova -> cordovan python3-pingouin.noarch: W: spelling-error %description -l en_US hocs -> hos, chocs, hocks python3-pingouin.noarch: W: spelling-error %description -l en_US intraclass -> intramuscular python3-pingouin.noarch: W: spelling-error %description -l en_US sphericity -> spherical python3-pingouin.noarch: W: spelling-error %description -l en_US homoscedasticity -> homosexuality python-pingouin.src: W: spelling-error %description -l en_US ancova -> cordovan python-pingouin.src: W: spelling-error %description -l en_US hocs -> hos, chocs, hocks python-pingouin.src: W: spelling-error %description -l en_US intraclass -> intramuscular python-pingouin.src: W: spelling-error %description -l en_US sphericity -> spherical python-pingouin.src: W: spelling-error %description -l en_US homoscedasticity -> homosexuality 3 packages and 0 specfiles checked; 0 errors, 10 warnings. Thanks for the quick review, Timothée. Please let me know if I can review something for you in return. :) (In reply to Timothée Floure from comment #1) > Package Review > ============== > > * Upstream is GPLv3, not BSD: > https://github.com/raphaelvallat/pingouin/blob/master/LICENSE Gah. Sorry---updated. > * The tests under the check section are not run by default and fail if > enabled (do not seem related to missing pytest-sugar): > https://paste.sr.ht/~fnux/9aa513ec18533e34f405da400ab027636306fb10 A missing BR: pytest-cov. Added it now. I verified in a virtual environment that all tests pass. I'll enable them as soon as pytest-sugar is approved. > * The doc subpackage ships quite a lot of third-party web assets (such as > bootstrap, which is MIT-licensed), which might be a licensing issue. See > https://paste.sr.ht/~fnux/ba797c6e6a3ae7ca90835d9e9e7aa06c3fabaddb for > details. I do not think we can do much, but I think we have to specify the > licenses. I added MIT to the license list and included a comment explaining it too. > * The `%{?python_enable_dependency_generator}` is no required for F30+, do > you plan to backport this package to F29? > (https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ > #_automatically_generated_dependencies) Yes. We want to support F29 too. > * You might want to use the `%pypi_source` macro: > https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ Unfortunately, the PyPi tar does not contain tests or docs so I must use the github release. Updated spec/srpm: Spec URL: https://ankursinha.fedorapeople.org/python-pingouin/python-pingouin.spec SRPM URL: https://ankursinha.fedorapeople.org/python-pingouin/python-pingouin-0.2.7-1.fc30.src.rpm > Thanks for the quick review, Timothée. Please let me know if I can review something for you in return. :) Not right now but I'll keep it in mind. Thanks! > Yes. We want to support F29 too. A conditional and/or a comment would be nice so that an useless macro is not forgotten for the next ten Fedora releases ;-) > A missing BR: pytest-cov. Added it now. I verified in a virtual environment that all tests pass. I'll enable them as soon as pytest-sugar is approved. The pytest-cov issue is fixed but there is a failing test on my side, using your python3-pytest-sugar package: https://paste.sr.ht/~fnux/620bae68a1983798babcc943a726fc0f0d1c64aa I believe you should remove `Documentation is available at https://raphaelvallat.github.io/pingouin/build/html/index.html.` from the description field: it is not relevant and the link is broken anyway. (In reply to Timothée Floure from comment #3) > > Thanks for the quick review, Timothée. Please let me know if I can review something for you in return. :) > > Not right now but I'll keep it in mind. Thanks! > > > Yes. We want to support F29 too. > > A conditional and/or a comment would be nice so that an useless macro is not > forgotten for the next ten Fedora releases ;-) I've added a comment. It won't be forgotten, it already doesn't do anything in F30 and I'm sure it'll be mass-removed when it's not needed :) > > > A missing BR: pytest-cov. Added it now. I verified in a virtual environment > that all tests pass. I'll enable them as soon as pytest-sugar is approved. > > The pytest-cov issue is fixed but there is a failing test on my side, using > your python3-pytest-sugar package: > https://paste.sr.ht/~fnux/620bae68a1983798babcc943a726fc0f0d1c64aa Odd. I'm not getting it here in the virtual environment . Your error seems to be related to pandas but the version in Fedora is fine. I guess we can wait for python-pytest-sugar to be approved and then test it out with that. Testing it on local machines won't tell us the issue. $ pytest . Test session starts (platform: linux, Python 3.7.4, pytest 5.0.1, pytest-sugar 0.9.2) rootdir: /home/asinha/rpmbuild/SOURCES/pingouin-0.2.7, inifile: setup.cfg plugins: remotedata-0.3.1, travis-fold-1.3.0, sugar-0.9.2, cov-2.7.1 collecting ... pingouin/tests/test_bayesian.py ✓✓✓ 4% ▍ pingouin/tests/test_circular.py ✓✓✓✓✓✓✓ 13% █▍ pingouin/tests/test_contingency.py ✓✓✓✓ 18% █▊ pingouin/tests/test_correlation.py ✓✓✓✓ 23% ██▍ pingouin/tests/test_distribution.py ✓✓✓✓✓✓ 30% ███▏ pingouin/tests/test_effsize.py ✓✓✓✓✓ 37% ███▋ pingouin/tests/test_multicomp.py ✓✓✓✓ 42% ████▎ pingouin/tests/test_multivariate.py ✓✓ 44% ████▌ pingouin/tests/test_nonparametric.py ✓✓✓✓✓✓✓ 53% █████▍ pingouin/tests/test_pairwise.py ✓✓✓✓ 58% █████▉ pingouin/tests/test_pandas.py ✓ 59% █████▉ pingouin/tests/test_parametric.py ✓✓✓✓✓✓✓ 68% ██████▉ pingouin/tests/test_plotting.py ✓✓✓✓✓✓ 76% ███████▋ pingouin/tests/test_power.py ✓✓✓✓✓✓ 84% ████████▍ pingouin/tests/test_regression.py ✓✓✓ 87% ████████▊ pingouin/tests/test_reliability.py ✓✓ 90% █████████ pingouin/tests/test_utils.py ✓✓✓✓✓✓✓✓ 100% ██████████ ============================================================================================================== warnings summary ============================================================================================================== pingouin/tests/test_correlation.py::TestCorrelation::test_partial_corr /home/asinha/rpmbuild/SOURCES/pingouin-0.2.7/pingouin/utils.py:297: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working x_is_iter = isinstance(x, collections.Iterable) pingouin/tests/test_parametric.py::TestParametric::test_ancova /home/asinha/.local/share/virtualenvs/pingouin/lib/python3.7/site-packages/patsy/constraint.py:13: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Mapping pingouin/tests/test_parametric.py::TestParametric::test_ancova /home/asinha/.local/share/virtualenvs/pingouin/lib64/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject return f(*args, **kwds) -- Docs: https://docs.pytest.org/en/latest/warnings.html ----------- coverage: platform linux, python 3.7.4-final-0 ----------- Name Stmts Miss Branch BrPart Cover Missing ----------------------------------------------------------------------- pingouin/__init__.py 19 0 0 0 100% pingouin/bayesian.py 67 0 16 0 100% pingouin/circular.py 86 0 20 0 100% pingouin/contingency.py 80 0 40 1 99% 351->354 pingouin/correlation.py 222 0 64 1 99% 80->79 pingouin/distribution.py 170 0 56 0 100% pingouin/effsize.py 174 0 82 1 99% 537->exit pingouin/multicomp.py 67 0 14 0 100% pingouin/multivariate.py 76 0 14 2 98% 87->93, 204->212 pingouin/nonparametric.py 121 1 20 1 99% 499, 498->499 pingouin/pairwise.py 276 0 140 0 100% pingouin/pandas.py 47 0 0 0 100% pingouin/parametric.py 419 0 101 2 99% 446->450, 892->896 pingouin/plotting.py 244 0 54 2 99% 466->470, 627->631 pingouin/power.py 240 0 112 0 100% pingouin/regression.py 205 0 76 0 100% pingouin/reliability.py 41 0 12 0 100% pingouin/utils.py 135 0 61 1 99% 162->174 ----------------------------------------------------------------------- TOTAL 2689 1 882 11 99% ========================================================================================================= slowest 10 test durations ========================================================================================================== 5.96s call pingouin/tests/test_regression.py::TestRegression::test_mediation_analysis 3.80s call pingouin/tests/test_pairwise.py::TestPairwise::test_pairwise_corr 3.34s call pingouin/tests/test_plotting.py::TestPlotting::test_plot_skipped_corr 1.42s call pingouin/tests/test_pairwise.py::TestPairwise::test_pairwise_ttests 1.08s call pingouin/tests/test_plotting.py::TestPlotting::test_plot_paired 1.00s call pingouin/tests/test_effsize.py::TestEffsize::test_compute_boot_esci 0.63s call pingouin/tests/test_parametric.py::TestParametric::test_ancova 0.59s call pingouin/tests/test_pandas.py::TestParametric::test_pandas 0.43s call pingouin/tests/test_correlation.py::TestCorrelation::test_corr 0.39s call pingouin/tests/test_plotting.py::TestPlotting::test_plot_shift Results (24.24s): 79 passed > > I believe you should remove `Documentation is available at > https://raphaelvallat.github.io/pingouin/build/html/index.html.` from the > description field: it is not relevant and the link is broken anyway. Removed too. Updated spec/srpm: Spec URL: https://ankursinha.fedorapeople.org/python-pingouin/python-pingouin.spec SRPM URL: https://ankursinha.fedorapeople.org/python-pingouin/python-pingouin-0.2.7-1.fc30.src.rpm The latest 0.28 version depends on scipy 1.3.0 so we'll have to wait for the fedora package to be updated. Yes. We also have to understand the failing test but the package looks good to me :-) I will approve once those last issues have been fixed. The new version requires a package that's not in Fedora now: pandas-flavor :( Working on that now. Finally ready now, all deps packaged and all tests pass: Successful scratch build: https://koji.fedoraproject.org/koji/taskinfo?taskID=39453904 Updated spec/srpm: - spec: https://ankursinha.fedorapeople.org/python-pingouin/python-pingouin.spec - srpm: https://ankursinha.fedorapeople.org/python-pingouin/python-pingouin-0.3.1-1.fc32.src.rpm Thanks for being patient :) Ankur All good :-) (fedscm-admin): The Pagure repository was created at https://src.fedoraproject.org/rpms/python-pingouin |