removed support for Python <= 3.7 #265

orbeckst · 2023-11-08T04:13:15Z

close drop support for very old Python versions #259
removed six and replaced with Python 3.x constructs
updated package meta data
update installation docs (sphinx and README)
updated CHANGES

- removed six and replaced with Python 3.x constructs - updated package meta data - update installation docs (sphinx and README) - updated CHANGES

codecov · 2023-11-08T04:15:39Z

Codecov Report

Merging #265 (87509d5) into main (1001a09) will increase coverage by 2.39%.
The diff coverage is 87.50%.

@@            Coverage Diff             @@
##             main     #265      +/-   ##
==========================================
+ Coverage   66.50%   68.89%   +2.39%     
==========================================
  Files          23       22       -1     
  Lines        4356     3945     -411     
  Branches      758      708      -50     
==========================================
- Hits         2897     2718     -179     
+ Misses       1261     1047     -214     
+ Partials      198      180      -18

Files	Coverage Δ
gromacs/__init__.py	`72.30% <ø> (-0.42%)`	⬇️
gromacs/cbook.py	`27.40% <ø> (-0.21%)`	⬇️
gromacs/collections.py	`84.09% <100.00%> (ø)`
gromacs/config.py	`74.68% <100.00%> (-2.20%)`	⬇️
gromacs/core.py	`70.99% <100.00%> (-0.50%)`	⬇️
gromacs/environment.py	`70.76% <100.00%> (-0.45%)`	⬇️
gromacs/fileformats/__init__.py	`100.00% <ø> (ø)`
gromacs/fileformats/convert.py	`58.62% <100.00%> (-0.48%)`	⬇️
gromacs/fileformats/mdp.py	`96.92% <100.00%> (-0.10%)`	⬇️
gromacs/fileformats/ndx.py	`87.95% <ø> (-0.29%)`	⬇️
... and 10 more

... and 1 file with indirect coverage changes

📣 Codecov offers a browser extension for seamless coverage viewing on GitHub. Try it in Chrome or Firefox today!

Only use other GROMACS versions for spot testing at highest supported Python. Note that we had spurious failures of GROMACS 2021.1 with macOS Python 3.11 in the XFAIL TestAmber03star.test_mdrun and XFAIL TestAmber03w.test_mdrun. ;

orbeckst · 2023-11-08T04:41:44Z

The macOS 3.11 GROMACS 2023.1 tests fail

tests/test_setup.py::test_energy_minimize_custom_mdp
tests/fileformats/top/test_charmm22.py::TestCharmm22st::test_mdru
tests/test_setup.py::test_energy_minimize

                :-) GROMACS - gmx mdrun, 2023.1-conda_forge (-:

Executable:   /Users/runner/micromamba/envs/test/bin.AVX2_256/gmx
Data prefix:  /Users/runner/micromamba/envs/test
Working dir:  /private/var/folders/3s/vfzpb5r51gs6y328rmlgzm7c0000gn/T/pytest-of-runner/pytest-0/1ake0/em
Command line:
  gmx mdrun -nt 2 -v -stepout 10 -deffnm em -c em.pdb


Back Off! I just backed up em.log to ./#em.log.1#

-------------------------------------------------------
Program:     gmx mdrun, version 2023.1-conda_forge
Source file: src/gromacs/hardware/printhardware.cpp (line 108)

Fatal error:
The gmx mdrun executable was compiled to use the rdtscp CPU instruction.
However, this is not supported by the current hardware and continuing would
lead to a crash. Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake
option.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

It looks as if the conda-forge GROMACS package is incompatible with the run environment of GitHub. Not sure what to do...

- only explicitly include macOS runner - downgrade GROMACS to 2022.4 to avoid failing tests because conda-forge GROMACS 2023.1 was compiled to use rdtscp CPU instruction but these are not available on GitHub runners and lead to failing tests)

orbeckst · 2023-11-08T05:01:42Z

Let's see if downgrading to conda-forge GROMACS 2022.4 for macOS helps.

orbeckst · 2023-11-08T05:40:48Z

After reading https://manual.gromacs.org/2021.3/release-notes/2021/major/portability.html#rdtscp-usage-and-reporting

GROMACS now defaults always on x86 to use the RDTSCP machine instruction for lower latency timing. Very old machines might need to configure with GMX_USE_RDTSCP=off. Non-x86 platforms are unaffected, except that they will no longer report that RDTSCP is disabled (because that is self-evident).

I am just trying out the bioconda gromacs packages, maybe they are compiled differently??

orbeckst · 2023-11-08T05:45:09Z

didn't work

orbeckst · 2023-11-08T05:46:49Z

Previous successful macOS runners used

  + gromacs                        2021.1  nompi_h2eb4de6_102  bioconda        Cached

so I should try to get this version installed.

orbeckst · 2023-11-08T05:52:57Z

How the **** is this failing now when

  + gromacs                        2021.1  nompi_h2eb4de6_102  bioconda        Cached

is being installed in the macOS 3.11 runner?

The same set up passed the tests previously https://github.com/Becksteinlab/GromacsWrapper/actions/runs/6211029287/job/16859829487 .

orbeckst · 2023-11-08T06:09:55Z

There are a few very minor Python package version changes (e.g. numpy 1.24 to 1.25). The image is different 20230901.1 (mac OS 12.6.8) vs 20230921.1 (mac OS 12.6.9). I just don't understand why any of this should matter for GROMACS.

Failed test

2023-11-08, this PR

2023-11-08T05:49:34.5156160Z Current runner version: '2.311.0'
2023-11-08T05:49:34.5185150Z ##[group]Operating System
2023-11-08T05:49:34.5185780Z macOS
2023-11-08T05:49:34.5186100Z 12.6.9
2023-11-08T05:49:34.5186410Z 21G726
2023-11-08T05:49:34.5186730Z ##[endgroup]
2023-11-08T05:49:34.5187100Z ##[group]Runner Image
2023-11-08T05:49:34.5187530Z Image: macos-12
2023-11-08T05:49:34.5187900Z Version: 20230921.1
2023-11-08T05:49:34.5189060Z Included Software: https://github.com/actions/runner-images/blob/macOS-12/20230921.1/images/macos/macos-12-Readme.md
2023-11-08T05:49:34.5190870Z Image Release: https://github.com/actions/runner-images/releases/tag/macOS-12%2F20230921.1
2023-11-08T05:49:34.5191930Z ##[endgroup]
2023-11-08T05:49:34.5192320Z ##[group]Runner Image Provisioner
2023-11-08T05:49:34.5192830Z 2.0.312.1
2023-11-08T05:49:34.5193160Z ##[endgroup]

passed test

2023-09-17 , https://github.com/Becksteinlab/GromacsWrapper/actions/runs/6211029287/job/16859829487

2023-09-17T02:16:35.8965190Z Current runner version: '2.309.0'
2023-09-17T02:16:35.9006190Z ##[group]Operating System
2023-09-17T02:16:35.9006970Z macOS
2023-09-17T02:16:35.9007340Z 12.6.8
2023-09-17T02:16:35.9007660Z 21G725
2023-09-17T02:16:35.9008010Z ##[endgroup]
2023-09-17T02:16:35.9008330Z ##[group]Runner Image
2023-09-17T02:16:35.9008820Z Image: macos-12
2023-09-17T02:16:35.9009180Z Version: 20230901.1
2023-09-17T02:16:35.9009740Z Included Software: https://github.com/actions/runner-images/blob/macOS-12/20230901.1/images/macos/macos-12-Readme.md
2023-09-17T02:16:35.9010370Z Image Release: https://github.com/actions/runner-images/releases/tag/macOS-12%2F20230901.1
2023-09-17T02:16:35.9010930Z ##[endgroup]
2023-09-17T02:16:35.9011340Z ##[group]Runner Image Provisioner
2023-09-17T02:16:35.9011720Z 2.0.299.1
2023-09-17T02:16:35.9012010Z ##[endgroup]

orbeckst · 2023-11-08T06:13:47Z

I am reduced to trying out random GROMACS packages in the hope that one works... :-(

…l -a

orbeckst · 2023-11-08T06:46:53Z

Hooray 🎉 , the old GROMACS 2018.6 works on the macOS runners. I don't know why, but I'll take it...

jandom

Bye-bye legacy ware! Also nice adventure ripping this out – i enjoyed reading your mishaps above!

- remove six from all environments (should have been in PR #265, part of #259) - add sphinx_rtd_theme to the RTD CI as it is apparently no longer installed automatically by RTD. (fix #267)

removed support for Python <= 3.7

90128a7

- removed six and replaced with Python 3.x constructs - updated package meta data - update installation docs (sphinx and README) - updated CHANGES

orbeckst requested review from jandom and VOD555 November 8, 2023 04:13

orbeckst mentioned this pull request Nov 8, 2023

fix #216: angle parameters are not being read from topology file #264

Merged

switch to testing GROMACS 2023.1 for all Python

68269f6

Only use other GROMACS versions for spot testing at highest supported Python. Note that we had spurious failures of GROMACS 2021.1 with macOS Python 3.11 in the XFAIL TestAmber03star.test_mdrun and XFAIL TestAmber03w.test_mdrun. ;

changed macOS CI runner

6aecf8c

- only explicitly include macOS runner - downgrade GROMACS to 2022.4 to avoid failing tests because conda-forge GROMACS 2023.1 was compiled to use rdtscp CPU instruction but these are not available on GitHub runners and lead to failing tests)

downgrade GROMACS for macOS to 2020.6

e88edad

upgrade GROMACS for macOS to 2021.3-bioconda

faf5041

orbeckst force-pushed the remove-legacy-python branch from 167e6a8 to faf5041 Compare November 8, 2023 05:41

downgrade GROMACS for macOS to 2021.1 from bioconda (worked previously)

e615ec5

orbeckst force-pushed the remove-legacy-python branch from adcb81d to e615ec5 Compare November 8, 2023 05:49

downgrade macOS to 2020.5 bioconda

dd8a08b

orbeckst added 2 commits November 8, 2023 01:23

downgrade macOS to 2019.5 bioconda

398fabb

downgrade macOS to 2018.6 bioconda and look at /proc/cpuinfo or sysct…

87509d5

…l -a

orbeckst self-assigned this Nov 8, 2023

jandom approved these changes Nov 8, 2023

View reviewed changes

orbeckst merged commit 51e1a03 into main Nov 8, 2023
15 checks passed

orbeckst deleted the remove-legacy-python branch November 8, 2023 15:22

orbeckst added a commit that referenced this pull request Nov 9, 2023

updated CI environments

49d51a0

- remove six from all environments (should have been in PR #265, part of #259) - add sphinx_rtd_theme to the RTD CI as it is apparently no longer installed automatically by RTD. (fix #267)

orbeckst mentioned this pull request Nov 9, 2023

updated CI environments #268

Merged

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removed support for Python <= 3.7 #265

removed support for Python <= 3.7 #265

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removed support for Python <= 3.7 #265

removed support for Python <= 3.7 #265

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Failed test

passed test

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