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Support Python 3.12#1325

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swails merged 11 commits into
ParmEd:masterfrom
mattwthompson:py312
Oct 23, 2023
Merged

Support Python 3.12#1325
swails merged 11 commits into
ParmEd:masterfrom
mattwthompson:py312

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@mattwthompson

@mattwthompson mattwthompson commented Oct 21, 2023

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@mattwthompson mattwthompson mentioned this pull request Oct 21, 2023
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@mattwthompson

mattwthompson commented Oct 23, 2023

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Well, this package's CI needing AmberTools and AmberTools builds needing this package is a bit of a quagmire

@swails

swails commented Oct 23, 2023

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AmberTools is an optional dependency, so tweaking the CI to add an option to exclude AmberTools would probably help get this over the finish line.

swails
swails reviewed Oct 23, 2023
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@mattwthompson

mattwthompson commented Oct 23, 2023

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I have to run for a now, but it looks like the first encountered failure is a false negative:

2023-10-23T15:04:31.2817006Z FAILED test_parmedtools_actions.py::TestAmoebaParmActions::test_summary - AssertionError: 'Amin[172 chars]     -0.0000\nTotal mass (amu):      14809.365[209 chars]51\n' != 'Amin[172 chars]     0.0000\nTotal mass (amu):      14809.3650[208 chars]51\n'
2023-10-23T15:04:31.2818452Z   Amino Acid Residues:   0
2023-10-23T15:04:31.2818837Z   Nucleic Acid Residues: 0
2023-10-23T15:04:31.2819197Z   Number of cations:     0
2023-10-23T15:04:31.2819564Z   Number of anions:      0
2023-10-23T15:04:31.2820048Z   Num. of solvent mols:  818
2023-10-23T15:04:31.2820419Z   Num. of unknown res:   2
2023-10-23T15:04:31.2820839Z - Total charge (e-):     -0.0000
2023-10-23T15:04:31.2821227Z ?                        -
2023-10-23T15:04:31.2821600Z + Total charge (e-):     0.0000
2023-10-23T15:04:31.2822006Z   Total mass (amu):      14809.3650
2023-10-23T15:04:31.2822425Z   Number of atoms:       2466
2023-10-23T15:04:31.2822793Z   Number of residues:    820
2023-10-23T15:04:31.2823193Z   Residue set:           ACE, NME, WAT
2023-10-23T15:04:31.2823681Z   Residue count:         ACE: 1, NME: 1, WAT: 818
2023-10-23T15:04:31.2824160Z   System volume (ang^3): 27031.52
2023-10-23T15:04:31.2824573Z   System density (g/mL): 0.909751
2023-10-23T15:04:31.2825191Z = 1 failed, 877 passed, 37 skipped, 1 xfailed, 9 warnings in 406.43s (0:06:46) =

@swails

swails commented Oct 23, 2023

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I think that test can be marked xfail. There are plenty of others that exercise the formatting of that action.

@mattwthompson mattwthompson marked this pull request as ready for review October 23, 2023 16:55
@mattwthompson mattwthompson requested a review from swails October 23, 2023 16:55
@mattwthompson

mattwthompson commented Oct 23, 2023

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My only objective was getting a CI run on 3.12 running, so this is good to go from my perspective. I searched warnings in the log of that run and nothing looked out of line.

Let me know if there's anything else you'd like included here!

@swails swails merged commit e283425 into ParmEd:master Oct 23, 2023
@swails

swails commented Oct 23, 2023

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I figured that was the case, so I made the tweak to xfail that test (I figured you wouldn't mind as you checked the box to allow maintainers to update) so I could get it in.

I'll cut a bugfix release once I get #1326 merged.

@mattwthompson

mattwthompson commented Oct 23, 2023

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No complaints here - thanks for accepting the patch!

@mattwthompson mattwthompson deleted the py312 branch October 23, 2023 18:12
timpalpant pushed a commit to timpalpant/ParmEd that referenced this pull request Nov 21, 2025
Cherry-pick ParmEd#1325
239839b
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