Code

OpenBabelParser and Tests#12

Code

Merged

lunamorrow merged 29 commits intoMDAnalysis:mainMDAnalysis/mda-openbabel-converter:mainfrom lunamorrow:parser_and_testslunamorrow/mda-openbabel-converter:parser_and_testsCopy head branch name to clipboardJul 31, 2024

+316-23

Commits

Commits on Jul 24, 2024

• Start of the parser and associated tests

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  c1865e6

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• for help with using pytest

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  fca21ac

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• fix a few bits of cruft

  

  hmacdope

  authored and

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• OpenBabelParser and tests work 29 June

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• rough functionality sorted, can now parse all attributes and test the basic ones (atoms, bonds, segments and residues)

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• cleaned up tests and parser a bit more, and added aromaticity test

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• mostly functional parser and tests, ready for review please

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• updates after pair-coding session with Hugo and fix CI

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• CI fix take 5

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• trying again

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• I'm getting closer...

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• Fixing for pep8

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• Install appropriate/specific OpenBabel version for imports

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• Specified less specific openbabel version

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• Fixing new error

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• Fixing new error take 2

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• Fixing new error take 3

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• Fixing new error take 7

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• push to stash changes before switching over to CI fix branch

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• Rebase done

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• updates after rebase and applying Cedric's review

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• Getting things straightened up

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• remove dependency for pylint to work

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• update ob imports to work for openbabel>=3.0.0

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Commits on Jul 31, 2024

• Support updated to OpenBabel 3.x instead of 2.x

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• Added MDAnalysisTests to environment for CI imports

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• Fixing silly typo

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• Cleaned up the last bits of chirality to remove CI env errors

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• Final fixes for PEP8

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