Removes output files from results if they should not exist

[hannahbaumann]

Description

If the user decides to e.g. not run an energy minimization, the ProtocolResults would still return the filenames to the energy minimization outputs, even though they would not exist. This PR only stores files if the output files would be expected. This does NOT check if the files indeed exist, I'm not sure yet if that would be better or not.

This PR addresses following issues:
#27 : Remove filepaths from outputs if the files are not expected to be created
#34 : Remove stub files

[pep8speaks]

Hello @hannahbaumann! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file openfe_gromacs/protocols/gromacs_md/md_methods.py:

Line 170:80: E501 line too long (86 > 79 characters)
Line 1131:80: E501 line too long (81 > 79 characters)
Line 1132:80: E501 line too long (81 > 79 characters)
Line 1133:80: E501 line too long (81 > 79 characters)
Line 1134:80: E501 line too long (81 > 79 characters)
Line 1135:80: E501 line too long (81 > 79 characters)
Line 1136:80: E501 line too long (81 > 79 characters)
Line 1137:80: E501 line too long (81 > 79 characters)
Line 1166:80: E501 line too long (83 > 79 characters)
Line 1167:80: E501 line too long (83 > 79 characters)
Line 1168:80: E501 line too long (83 > 79 characters)
Line 1169:80: E501 line too long (83 > 79 characters)
Line 1170:80: E501 line too long (83 > 79 characters)
Line 1171:80: E501 line too long (83 > 79 characters)
Line 1172:80: E501 line too long (83 > 79 characters)
Line 1204:80: E501 line too long (83 > 79 characters)
Line 1205:80: E501 line too long (83 > 79 characters)
Line 1206:80: E501 line too long (83 > 79 characters)
Line 1207:80: E501 line too long (83 > 79 characters)
Line 1208:80: E501 line too long (83 > 79 characters)
Line 1209:80: E501 line too long (83 > 79 characters)
Line 1210:80: E501 line too long (83 > 79 characters)

• In the file openfe_gromacs/tests/protocols/conftest.py:

Line 176:80: E501 line too long (81 > 79 characters)

• In the file openfe_gromacs/tests/protocols/test_gromacs_md.py:

Line 310:80: E501 line too long (81 > 79 characters)
Line 317:80: E501 line too long (81 > 79 characters)

Comment last updated at 2024-09-26 14:43:29 UTC

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.42%. Comparing base (f3b85ee) to head (45c6ccb).
Report is 80 commits behind head on main.

Additional details and impacted files

[IAlibay]

Couple of things, otherwise it looks good.

[IAlibay]

Two small things, otherwise lgtm!

[IAlibay]

Are these singular / you take the first element because the expectation is that the input gro file should be the same for all repeat?

If so:

1. Could you write a comment about it somewhere?
2. Could you update the docstring to not say "llist of paths" for here and I think also get_top_filename?

[hannahbaumann]

Yes, only a single filepath will be returned as the SetupUnit is only run once, even with multiple repeats. I updated the docstring to clarify this.

[IAlibay]

the SetupUnit is only run once

Not to be fixed here, and I'll have to think about this one a bit more, I'm not sure that this doesn't break the model for gufe generations (i.e. extensions). Something to keep in mind in the future.

[IAlibay]

Just a couple of typos otherwise lgtm!