speed up tests

[AnthonyBogetti]

I (with help from Gemini) re-wrote the pfam tests to not query the server each time. I think this should significantly speed up the tests through GitHub CI. I narrowed it down to this test by looking at time per tests and some of these would randomly hang for like 10-20 mins. There could be other culprits, but maybe this is a good place to start.

Also includes fixes for intermittent test failure and speeds up other tests like test_bioexcel.py.

[AnthonyBogetti]

Thanks @jamesmkrieger. I will return the doc strings that AI removed. The checks were sporadically not starting before these changes (I saw yesterday from Isabelle's PR on the hinge finding code). I will look into that and fix. I also found the other tests taking too long and will fix those as well in a separate PR.

[AnthonyBogetti]

Hi @jamesmkrieger, I re-generated the "fixed" test with doc strings and keeping all original assert statements. I also modified main.yml to hopefully fix the intermittent CI testing failures.

[AnthonyBogetti]

Now it only takes 30 mins! And hopefully the intermittent crashes are fixed...

[AnthonyBogetti]

Now it's down to 15ish minutes.

[AnthonyBogetti]

OK it's under 10 mins now (Ubuntu ones are faster than the macos ones, but not a big deal). That might be the limit. The tests I changes were pfam, bioexcel, anmd, insty, prody_catdcd, prody_examples and prody_pca. Also, the main.yml was modified for faster env setup and stability. @jamesmkrieger I think I am done with this. I made sure original doc strings, formatting, comments and assert statements were preserved in each test.

[jamesmkrieger]

That’s wonderful! I’ll have a look over the next few days

[AnthonyBogetti]

Generally looks good. Please do make sure that there is still one query each to pfam and bioexcel to make sure we’re keeping in line with changes there

Great, thanks for the review! I'll work on addressing these tomorrow.