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Add hierarchy scheme iterators to Topology #1661

Merged
merged 20 commits into from
Aug 22, 2023
Merged

Add hierarchy scheme iterators to Topology #1661

merged 20 commits into from
Aug 22, 2023

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mattwthompson
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@mattwthompson mattwthompson commented Jun 29, 2023 •
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Resolves #1601

Possibly blocked by #1660, would be convenient for a path forward with #1659 to also be decided.

  • Tag issue being addressed
  • Add tests
    • Error if any molecule is misses requested iterator
    • Order hierarchy elements by molecule, then whatever sorting is defined by the scheme itself
    • Make no effort to sort between molecules
    • Error out if a name conflict with existing attributes is found
  • Update docstrings/documentation, if applicable
  • Lint codebase
  • Update changelog

@mattwthompson mattwthompson changed the title Add topology iterators Add hierarchy scheme iterators to Topology Jun 29, 2023
@mattwthompson mattwthompson added this to the 0.14.1 milestone Jun 29, 2023
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codecov bot commented Jun 30, 2023 •
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Codecov Report

Merging #1661 (faab121) into main (615320f) will increase coverage by 0.00%.
The diff coverage is 100.00%.

Additional details and impacted files

@mattwthompson mattwthompson marked this pull request as ready for review June 30, 2023 18:06
j-wags
j-wags requested changes Jul 16, 2023
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Thanks for taking a stab at this - I hadn't appreciated how complex this would end up being. Left a few suggestions but overall this is on a good track.

openff/toolkit/_tests/test_topology.py Outdated Show resolved Hide resolved
openff/toolkit/topology/topology.py Outdated Show resolved Hide resolved
openff/toolkit/topology/topology.py Outdated Show resolved Hide resolved
openff/toolkit/topology/topology.py Outdated Show resolved Hide resolved
mattwthompson and others added 11 commits August 14, 2023 11:29
@mattwthompson
Merge remote-tracking branch 'upstream/main' into add-topology-iterators
36901ff
@mattwthompson @j-wags
Apply suggestions from code review
52052de 
Co-authored-by: Jeff Wagner <jeffrey.wagner+github@openforcefield.org>
@mattwthompson
Merge remote-tracking branch 'upstream/add-topology-iterators' into a…
e80134e 
…dd-topology-iterators
@mattwthompson @j-wags
Update openff/toolkit/_tests/test_topology.py
977ffba 
Co-authored-by: Jeff Wagner <jeffrey.wagner+github@openforcefield.org>
@mattwthompson
Merge remote-tracking branch 'upstream/add-topology-iterators' into a…
a2a77c6 
…dd-topology-iterators
@mattwthompson
Allow iterators with API clash
6109e74
@mattwthompson
Improve error message
82640ba
@mattwthompson
Catch KeyError
aaf92f3
@mattwthompson
Do not install NAGL rc
842ccdc
@mattwthompson
Merge branch 'no-nagl-rc' into add-topology-iterators
ee2c13e
@mattwthompson
Merge remote-tracking branch 'upstream/main' into add-topology-iterators
faab121
j-wags
j-wags approved these changes Aug 22, 2023
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Excellent! Thanks @mattwthompson.

@j-wags j-wags merged commit 9163ebd into main Aug 22, 2023
16 checks passed
@j-wags j-wags deleted the add-topology-iterators branch August 22, 2023 00:17
@mattwthompson mattwthompson mentioned this pull request Oct 6, 2023
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Add hierarchy iterators as attributes of Topology
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@mattwthompson @j-wags