Created attachment 234730 [details] Upgrade MDAnalysis to 2.2.0 Version 0.19.2 is too old and does not support Python-3.9. Releases notes at <https://github.com/MDAnalysis/mdanalysis/releases>.
The latest versions of MDAnalysis require py-threadpoolctl which I didn't commit yet because it is broken due to https://github.com/python/cpython/issues/92828 being unresolved.
Created attachment 234731 [details] Full log of py39-MDAnalysis-2.2.0 With the attached patch it builds fine without that. Full log attached.
(In reply to Thierry Thomas from comment #2) 2.2.0 requires py-threadpoolctl that fails due to a python issue linked above. Yuri
Created attachment 234753 [details] New patch to upgrade science/py-MDAnalysis and science/py-MDAnalysisTests disabling threadpoolctl OK, I see the problem. I have just submitted a review in Phabricator to get some more eyes on this problem: https://reviews.freebsd.org/D35513 But meanwhile, I think that we can disable threadpoolctl (see my new proposed patch). Of course, this could impact performance in some cases, but according to my tests the port is usable. When running `make test' in py-MDAnalysisTests, it produces the following result on my workstation: 12 failed, 17600 passed, 159 skipped, 2 xfailed, 2 xpassed, 31881 warnings, 3 errors and the errors do not seem related with this issue. Note: many tests are skipped because sklearn (from science/py-scikit-learn) also requires threadpoolctl which is missing; some other are skipped because some ports are not yet available in the tree, e.g. - py-chemfiles is missing (see https://pypi.org/project/chemfiles/) - py-hole is missing (see https://pypi.org/project/hole/) - py-tidynamics is missing (see https://pypi.org/project/tidynamics/).
(In reply to Thierry Thomas from comment #4) In MDAnalysis/transformations/base.py they have 'from threadpoolctl import threadpool_limits' which would fail at some point which would make this package broken.
(In reply to Yuri Victorovich from comment #5) Ooops, I missed this one! Will try to fix it…
(In reply to Yuri Victorovich from comment #5) Sorry Yuri, but I don't find it: MDAnalysis/transformations/base.py is patched by science/py-MDAnalysis/files/patch-MDAnalysis_transformations_base.py. Could you please check again the submitted patch?
(In reply to Thierry Thomas from comment #7) Hi Thierry, You patched away threadpoolctl from setup.py, but the project still installs Python file that import threadpoolctl. For me this command finds it: > $ grep -r import work-py*/stage/ | grep thread > work-py38/stage/usr/local/lib/python3.8/site-packages/MDAnalysis/transformations/base.py:from threadpoolctl import threadpool_limits This means that the updated py-MDAnalysis package would be broken, while the current one isn't broken. py-threadpoolctl should be fixed and added first before the update.
(In reply to Yuri Victorovich from comment #8) You cannot use a simple grep like this, you need -A and -B, because the import line belongs to commented lines. But it you prefer, just delete it, no problem for me.
(In reply to Thierry Thomas from comment #9) Thierry, I am sorry, I misunderstood what you said. The patch is fine, please go ahead and commit it. Thank you!
Committed, thanks!
A commit in branch main references this bug: URL: https://cgit.FreeBSD.org/ports/commit/?id=40568cac8e3e1931ca48becdfd18e2bf0aab1061 commit 40568cac8e3e1931ca48becdfd18e2bf0aab1061 Author: Thierry Thomas <thierry@FreeBSD.org> AuthorDate: 2022-06-16 16:10:38 +0000 Commit: Thierry Thomas <thierry@FreeBSD.org> CommitDate: 2022-06-21 17:26:21 +0000 science/py-MDAnalysis*: upgrade to 2.2.0 Version 0.19.2 is too old and does not support Python-3.9. Remark: threadpoolctl is disabled in this port. See <https://github.com/MDAnalysis/mdanalysis/pull/2950> for the impacts on performance. Releases notes at <https://github.com/MDAnalysis/mdanalysis/releases>. PR: 264716 Approved by: yuri (maintainer) science/py-MDAnalysis/Makefile | 27 +++++++---- science/py-MDAnalysis/distinfo | 6 +-- .../patch-MDAnalysis.egg-info_requires.txt (new) | 10 ++++ .../patch-MDAnalysis_transformations_base.py (new) | 23 +++++++++ science/py-MDAnalysis/files/patch-setup.py | 20 +++++--- science/py-MDAnalysisTests/Makefile | 7 ++- science/py-MDAnalysisTests/distinfo | 6 +-- ...alysisTests_transformations_test__base.py (new) | 54 ++++++++++++++++++++++ 8 files changed, 129 insertions(+), 24 deletions(-)