https://bugzilla.redhat.com/show_bug.cgi?id=1288870
Bug ID: 1288870 Summary: Review Request: python-pymc3 - Bayesian statistical modeling and model fitting Product: Fedora Version: rawhide Component: Package Review Severity: medium Priority: medium Assignee: nobody@fedoraproject.org Reporter: i.gnatenko.brain@gmail.com QA Contact: extras-qa@fedoraproject.org CC: package-review@lists.fedoraproject.org
Spec URL: https://ignatenkobrain.fedorapeople.org/neurofedora/python-pymc3.spec SRPM URL: https://ignatenkobrain.fedorapeople.org/neurofedora/python-pymc3-3.0-0.1.git... Description: PyMC3 is a python module for Bayesian statistical modeling and model fitting which focuses on advanced Markov chain Monte Carlo fitting algorithms. Its flexibility and extensibility make it applicable to a large suite of problems. Fedora Account System Username: ignatenkobrain
https://bugzilla.redhat.com/show_bug.cgi?id=1288870
Igor Gnatenko i.gnatenko.brain@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |1276941 (fedora-neuro) Alias| |python-pymc3
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1276941 [Bug 1276941] Fedora NeuroImaging and NeuroScience tracking bug
https://bugzilla.redhat.com/show_bug.cgi?id=1288870
Zbigniew Jędrzejewski-Szmek zbyszek@in.waw.pl changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED CC| |zbyszek@in.waw.pl Assignee|nobody@fedoraproject.org |zbyszek@in.waw.pl
--- Comment #1 from Zbigniew Jędrzejewski-Szmek zbyszek@in.waw.pl --- + license is OK (ASL 2.0) + license file is present, %license is used + latest version (git snapshot) + new python template is used - provides and requires look fine Some tests are skipped with because statsmodels is missing. We have statsmodels packaged, consider adding it to BR and Recommends.
+ no scriptlets + check is present and tests pass - the tests run unparallized. It would be nice to make them parallel, because the tests are the slowest thing when building.
Tests fail with: ====================================================================== FAIL: pymc3.tests.test_stats.test_dic_warns_on_transformed_rv Test that deviance information criterion calculation warns when an RV is transformed ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/builddir/build/BUILD/pymc3-7427adb98c3fc6a7617415e9309c2bf0dc80d8bb/pymc3/tests/test_stats.py", line 62, in test_dic_warns_on_transformed_rv assert(len(w) == 1) AssertionError: -------------------- >> begin captured stdout << --------------------- [-----------------100%-----------------] 100 of 100 complete in 0.0 sec
--------------------- >> end captured stdout << ----------------------
---------------------------------------------------------------------- Ran 594 tests in 2785.901s
FAILED (failures=1, skipped=12)
https://bugzilla.redhat.com/show_bug.cgi?id=1288870
--- Comment #2 from Igor Gnatenko i.gnatenko.brain@gmail.com ---
the tests run unparallized
have no idea how to do this...
Tests fail with:
If I will add some sleep between py2 and py3 tests it will work, dont know why.
https://bugzilla.redhat.com/show_bug.cgi?id=1288870
--- Comment #3 from Zbigniew Jędrzejewski-Szmek zbyszek@in.waw.pl --- (In reply to Igor Gnatenko from comment #2)
the tests run unparallized
have no idea how to do this...
I tried experimenting with nosetests --processes=<n> parameter, but it doesn't seem to work. Running tests in parallel requires some support, so it would probably be best handled upstream.
Filed https://github.com/pymc-devs/pymc3/issues/889.
Tests fail with:
If I will add some sleep between py2 and py3 tests it will work, dont know why.
Let's see what happens in koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=12168920.
https://bugzilla.redhat.com/show_bug.cgi?id=1288870
--- Comment #4 from Upstream Release Monitoring upstream-release-monitoring@fedoraproject.org --- zbyszek's scratch build of python-pymc3-3.0-0.1.git7427adb.fc24.src.rpm for rawhide failed http://koji.fedoraproject.org/koji/taskinfo?taskID=12168920
https://bugzilla.redhat.com/show_bug.cgi?id=1288870
Yanis Guenane yguenane@redhat.com changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |yguenane@redhat.com
--- Comment #5 from Yanis Guenane yguenane@redhat.com --- My review is yet unofficial as I am not part of the packager group.
I have three remarks one the spec file.
1. Can you condition the py3 related actions (subpackages, build, install, %files) ? This way we can use the same spec file on Fedora with python3 support, and EL7 with no python3 support.
Using something like the following :
%if 0%{?fedora} %global with_python3 1 %endif
%if 0%{?with_python3} %py3_build %endif
2. Upstream provides several files that should go in a %doc in the %files section but they are not currently listed. I am thinking about
* changelog.md * readme.md * release-notes.md
3. Upstream provides a way to generate a complete documentation[1], a -doc subpackage might be a good idea to provide it for the end user.
[1] https://github.com/pymc-devs/pymc3/blob/master/howto_docs.md
https://bugzilla.redhat.com/show_bug.cgi?id=1288870
--- Comment #6 from Zbigniew Jędrzejewski-Szmek zbyszek@in.waw.pl --- (In reply to Yanis Guenane from comment #5)
- Can you condition the py3 related actions (subpackages, build, install,
%files) ? This way we can use the same spec file on Fedora with python3 support, and EL7 with no python3 support.
Using something like the following :
%if 0%{?fedora} %global with_python3 1 %endif
%if 0%{?with_python3} %py3_build %endif
What you propose is useful, but OTOH, there is little reason to introduce this until the EPEL package actually happens. It is quite likely that this package will never be built for EPEL, and then this is wasted effort. If the need ever arises to add this, those conditionals can be added in the exact same way.
- Upstream provides several files that should go in a %doc in the %files
section but they are not currently listed. I am thinking about
- changelog.md
- readme.md
- release-notes.md
- Upstream provides a way to generate a complete documentation[1], a -doc
subpackage might be a good idea to provide it for the end user.
[1] https://github.com/pymc-devs/pymc3/blob/master/howto_docs.md
Agreed with the other two comments.
https://bugzilla.redhat.com/show_bug.cgi?id=1288870
--- Comment #7 from Zbigniew Jędrzejewski-Szmek zbyszek@in.waw.pl --- ... so, what's the plan here? I guess that parallelized tests are not possible now. There are a few issues raised in comments #1 and #5. Can you fix/reject those and make a new version?
https://bugzilla.redhat.com/show_bug.cgi?id=1288870
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |sanjay.ankur@gmail.com Flags| |needinfo?(i.gnatenko.brain@ | |gmail.com)
https://bugzilla.redhat.com/show_bug.cgi?id=1288870
Igor Gnatenko i.gnatenko.brain@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |CLOSED Resolution|--- |WONTFIX Flags|needinfo?(i.gnatenko.brain@ | |gmail.com) | Last Closed| |2018-08-22 03:30:26
--- Comment #8 from Igor Gnatenko i.gnatenko.brain@gmail.com --- Unfortunately I don't have time to work on these review requests anymore, sorry.
https://bugzilla.redhat.com/show_bug.cgi?id=1288870
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Depends On| |201449 (FE-DEADREVIEW)
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=201449 [Bug 201449] FE-DEADREVIEW -- Reviews stalled due to lack of submitter response should be blocking this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=1288870
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |201449 (FE-DEADREVIEW) Depends On|201449 (FE-DEADREVIEW) |
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=201449 [Bug 201449] FE-DEADREVIEW -- Reviews stalled due to lack of submitter response should be blocking this bug.
package-review@lists.fedoraproject.org