Nuclinfo Major Pair and Minor Pair overhaul#3735

Merged

orbeckst merged 45 commits intoMDAnalysis:developfrom

ALescoulie:nuclinfo_dist_rebuild

Oct 10, 2023

Commits on Jun 17, 2022

Commits on Jun 26, 2022

Commits on Aug 19, 2023

Merge branch 'develop' into nuclinfo_dist_rebuild
Alia
committed

Commits on Aug 21, 2023

fix documentation formatting

ALescoulie
authored and
ALescoulie
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refactor to use select_strand_atoms staticmethod

ALescoulie
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ALescoulie
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fix major and minor pair selections

ALescoulie
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ALescoulie
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refactor tests to use pytest approx

ALescoulie
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ALescoulie
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remove dihedral import

ALescoulie
authored and
ALescoulie
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fix WCDist not passing all kwargs into selector

ALescoulie
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ALescoulie
committed
add test for empty AtomGroup error

ALescoulie
authored and
ALescoulie
committed
update atom names in pair distance classes
ALescoulie
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fix whitespace for pep8
ALescoulie
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use typealias for union[residue, reiduegroup]
ALescoulie
committed

Commits on Aug 28, 2023

revert kwargs names to preserve old api
ALescoulie
committed

Commits on Aug 29, 2023

update NucPairDist.select_strand_atoms add docs
ALescoulie
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refactor results dict and clarify result structure
ALescoulie
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include versionadded in major and minor pair dists
ALescoulie
committed

Commits on Aug 30, 2023

refactor WatsonCrickDist to raise
ALescoulie
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make error messages consistent
ALescoulie
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update CHANGELOG
ALescoulie
committed

Commits on Sep 2, 2023

Merge branch 'develop' into nuclinfo_dist_rebuild
orbeckst
authored

Commits on Sep 4, 2023

fix type alias import issue
ALescoulie
committed
Merge branch 'develop' into nuclinfo_dist_rebuild
ALescoulie
authored

Commits on Sep 5, 2023

Commits on Sep 11, 2023

update documentation with more detailed
ALescoulie
committed
fix DeprecationWarning in WCDist for case where
ALescoulie
committed

Commits on Sep 12, 2023

add verification helper method to WCDist init to
ALescoulie
committed

Commits on Sep 25, 2023

Add deprecation notice to docs and changelog for
ALescoulie
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fix deprecation_warn test and add test for strand
ALescoulie
committed

Commits on Sep 27, 2023

fix docs issues
ALescoulie
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fix formatting
ALescoulie
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simplify tests
ALescoulie
committed

Commits on Sep 29, 2023

Merge branch 'develop' into nuclinfo_dist_rebuild
IAlibay
authored

Commits on Oct 9, 2023

Update CHANGELOG
orbeckst
authored

Commits on Oct 10, 2023

Update docs in nucleicacids.py
orbeckst
authored
Apply suggestions from code review
orbeckst
authored
fix pep8
ALescoulie
committed
fix pep8 after rebase
ALescoulie
committed
fix pep8 after rebase
ALescoulie
committed