[nomenclature._sort_all_consensus_labels] API CHANGE return also sort…#52

Merged

gph82 merged 84 commits intomasterfrom interface_selection

Sep 4, 2024

Commits on Aug 13, 2024

Commits on Aug 15, 2024

[contacts.ContactGroup.frequency_sum_per_residue_names] API BREAK refactor shorten_AAs -> AA_format to allow consensus labels, tests
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[contacts.ContactGroup.select_by_residues] Allow selection via consensus labels, tests
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[test_contacts] refactor ._contacts -> contact_pairs (don't test using private attributes)
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[nomeclature._lexsort_consensus_ctc_labels] fix
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[siteIO.sites_to_res_pairs] don't fail if conlab is missing (return none), assert consensus_maps are len=top.n_residues, kwargs documented, tests
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[residue_and_atom] typos
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[plots._sorter_by_key_or_val] new option 'consensus' for 'sort_by' argument, using _lexsort_consensus_ctc_labels
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[plots.compare_groups_of_contacts] adapt to refactor shorten_AAs -> AA_format in frequency_sum_per_residue_names
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[nomenclature] make tuples instead of lists for the consensus fragments sets
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[fragments.get_fragments] minor docs
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[fragments.check_if_fragment_clashes] correct typo in input prompt
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[fragments._fragments_strings_to_fragments] pass "method" directly to get_fragments
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[fragments.frag_list_2_frag_groups] can expand ranges, prompting expressions are now more informative, tests
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[cli._parse_consensus_option] minor
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[cli.residue_neighborhoods] don't store user_wants_consensus
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[cli.residue_selection] minor
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[fragments.frag_dict_2_frag_groups] new optarg fail_on_empty, tests
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[ContactGroup.plot_frequency_sums_as_bars] use AA_format when calling frequency_sum_per_residue_names
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[nomenclature.conlabs2confrags] refactor from _map2defs, simplify using DataFrame.groubpy, expose in the AP, expose in the APII
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[nomenclature.conlabs2confrags] new optarg replace_GPCR_frags
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[nomenclature.LabelerConsensus.top2labels] top arg can be a path to a filename, tests added
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[contacts.ContactGroup.plot_freqs_as_flareplot] minor docs
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[cli._parse_consensus_option] minor
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[cli._parse_consensus_options_and_return_fragment_defs] Return consensus fragments even if no ConsensusLabelers were passed but label lists were passed
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[cli.interface] When calling plot_freqs_as_flareplot include consensus_maps (lists)
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[cli.interface] new optarg AA_selection, tests
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[fragments._fragments_strings_to_fragments] sort the output of unsorted ranges, e.g. "30-40,20-25" -> [20,...,25,30,...,40]
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[cli.interface] better fragment handling
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[cli.interface] API BREAK frag_idxs_group_1, frag_idxs_group_2 becomes interface_selection_1, interface_selection_2
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[examples and parsers] refactor frag_idxs_group_1 -> interface_selection_1
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[examples.notebook] update to the refactor frag_idxs_group_1 -> interface_selection_1
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[examples.notebook.Missing_Contacts] add a cell showcasing AA_selection
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[cli._parse_fragdefs_fragnames_consensus] don't use consensus_labelers to get potential keys for the consensus maps
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[examples.fetch_example_data] new dataset ghrelin@ghsr
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Commits on Aug 16, 2024

Commits on Aug 17, 2024

[nomenclature.LabelerConsensus.top2frags] docs: also mention that the fragments parameter helps with the alignment, not only the clashes
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Commits on Aug 25, 2024

Commits on Aug 26, 2024

Commits on Aug 27, 2024

Commits on Aug 28, 2024

Commits on Aug 30, 2024

Commits on Sep 1, 2024

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Commits on Sep 3, 2024