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MAINT: mkdtemp 3.12 support - #4309

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IAlibay merged 1 commit into
MDAnalysis:developfrom
tylerjereddy:treddy_312_support_pt3
Oct 12, 2023
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MAINT: mkdtemp 3.12 support#4309
IAlibay merged 1 commit into
MDAnalysis:developfrom
tylerjereddy:treddy_312_support_pt3

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@tylerjereddy

@tylerjereddy tylerjereddy commented Oct 2, 2023

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  • force the use of a relative path for mkdtemp in our source code because, from the Python 3.12 release notes:

tempfile.mkdtemp() now always returns an absolute path, even if the
argument provided to the dir parameter is a relative path.

  • with this patch, the full testsuite now passes on (x86_64 Linux) Python 3.12.0 (which is now out) when combined with MAINT: Python 3.12 cleanups part 2 #4301 and MAINT: Python 3.12 support improve #4300 (though see my cautions about thread safety/concurrency for the latter)

  • this fixes the 1 remaining failure with 3.12: MDAnalysisTests/analysis/test_hole2.py::TestCheckAndFixLongFilename::test_symlink_dir

[skip cirrus]


📚 Documentation preview 📚: https://mdanalysis--4309.org.readthedocs.build/en/4309/

* force the use of a relative path for `mkdtemp` in our source code
because, from the Python `3.12` release notes:

> `tempfile.mkdtemp() now always returns an absolute path, even if the
argument provided to the dir parameter is a relative path.`

* with this patch, the full testsuite now passes on Python `3.12.0`
(which is now out) when combined with MDAnalysisgh-4301 and MDAnalysisgh-4300 (though
see my cautions about thread safety/concurrency for the latter)

* this fixes the 1 remaining failure with 3.12:
`MDAnalysisTests/analysis/test_hole2.py::TestCheckAndFixLongFilename::test_symlink_dir`

[skip cirrus]
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Linter Bot Results:

Hi @tylerjereddy! Thanks for making this PR. We linted your code and found the following:

There are currently no issues detected! 🎉

@codecov

codecov Bot commented Oct 2, 2023

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Codecov Report

All modified lines are covered by tests ✅

Comparison is base (427f1a7) 93.40% compared to head (6a7f2f2) 93.40%.

Additional details and impacted files
@@            Coverage Diff             @@
##           develop    #4309     +/-   ##
==========================================
  Coverage    93.40%   93.40%             
==========================================
  Files          170      184     +14     
  Lines        22257    23365   +1108     
  Branches      4071     4071             
==========================================
+ Hits         20790    21825   +1035     
- Misses         951     1024     +73     
  Partials       516      516             
Files Coverage Δ
package/MDAnalysis/analysis/hole2/utils.py 74.84% <100.00%> (ø)

... and 14 files with indirect coverage changes

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@IAlibay

IAlibay commented Oct 2, 2023

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Thanks @tylerjereddy !

I'll try to get the py3.12 CI PR updated tomorrow and we can start merging in all your PRs.

@IAlibay
IAlibay merged commit a522325 into MDAnalysis:develop Oct 12, 2023
@tylerjereddy
tylerjereddy deleted the treddy_312_support_pt3 branch October 15, 2023 16:28
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3 participants