Add Pylint #55
Add Pylint #55
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Address pylint rules W0611, W0102, W1401, E1120, C0121, C0123, C0325, R0124, R1714.
Address pylint rules W0311, W1309.
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You can find a list of Pylint's rules here.
Due to the large number of changes, and the fact that some changes affect scripts that are not covered by the testsuite, I would recommend allocating more than 1 code reviewer to this PR.
Address Pylint rules W0123, R1722.
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I have been checking around, testing the parts that are not covered by the CI and I did not find any further issue with the PR. Still, it would be good if at least @paobtorres or @davidbbeyer checks as well before I merge this PR |
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| # Peptide parameters | |||
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| sequence = 'nEEEEEc' | |||
| sequence = 'EEEEDDDD' | |||
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What is the reason for getting rid of the termini here?
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@davidbbeyer the reason is that the termini were actually not parametrized in parameters/peptides/Lunkad2021.json. In earlier versions of this script, this was bypassed by adding a generic parametrization for the non-parametrized aminoacid particles. This was a convenient solution to allow to run any peptide sequence, but not really a good practice (since we were basically teaching people to mix parameters instead of thinking about what should be a good parametrization). With @mariusaarsten we have done a more complete parametrization of the amino acids which he will add in his master thesis and we will also provide in pyMBE so we can have a first complete set of parameters for all aminoacids.
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@davidbbeyer @paobtorres I think we are ready now for merging this PR. If you agree, please leave a review approving these changes (go to the files changes tab, review changes botton, and press approve). @paobtorres please open a dedicated PR to fix the issues that you spotted in the create_paper_data.py script.
Description of changes:
assign_molecule_id()and sample scriptspdocwarnings in CI