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feat: add noncovalent-interactions#18

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leonwehrhan merged 22 commits intomainfrom
noncovalent-interactions
Sep 2, 2025
Merged

feat: add noncovalent-interactions#18
leonwehrhan merged 22 commits intomainfrom
noncovalent-interactions

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@leonwehrhan
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@leonwehrhan leonwehrhan commented Aug 4, 2025

Benchmark addition

Description

NCI benchmark is added.

Checklist

  • Benchmark class is fully implemented, including
    all abstract method implementations.
  • Benchmark is fully tested following our standard
    testing pattern.
  • Input data uploaded to HF is validated and correct.
  • The corresponding documentation is added and up to date.
  • The ui code is added and up-to-date and has been tested.
  • Our license has been added to any Python file.

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github-actions bot commented Aug 4, 2025

Coverage

Coverage Report
FileStmtsMissCoverMissing
src/mlipaudit
   __init__.py20100% 
   benchmark.py37975%93, 97, 103–105, 111–112, 122, 135
   io.py270100% 
src/mlipaudit/bond_length_distribution
   __init__.py10100% 
   bond_length_distribution.py700100% 
src/mlipaudit/conformer_selection
   __init__.py10100% 
   conformer_selection.py780100% 
src/mlipaudit/dihedral_scan
   __init__.py10100% 
   dihedral_scan.py930100% 
src/mlipaudit/folding_stability
   __init__.py10100% 
   folding_stability.py720100% 
   helpers.py350100% 
src/mlipaudit/noncovalent_interactions
   __init__.py10100% 
   noncovalent_interactions.py142497%200, 203, 306, 320
src/mlipaudit/reactivity
   __init__.py10100% 
   reactivity.py930100% 
src/mlipaudit/ring_planarity
   __init__.py10100% 
   ring_planarity.py750100% 
src/mlipaudit/small_molecule_minimization
   __init__.py10100% 
   small_molecule_minimization.py1090100% 
src/mlipaudit/solvent_radial_distribution
   __init__.py10100% 
   solvent_radial_distribution.py76198%243
src/mlipaudit/tautomers
   __init__.py10100% 
   tautomers.py710100% 
src/mlipaudit/utils
   __init__.py20100% 
   trajectory_helpers.py340100% 
   unallowed_elements.py100100% 
src/mlipaudit/water_radial_distribution
   __init__.py10100% 
   water_radial_distribution.py590100% 
TOTAL10961498% 

Tests Skipped Failures Errors Time
66 0 💤 0 ❌ 0 🔥 5.597s ⏱️

@leonwehrhan leonwehrhan marked this pull request as ready for review August 12, 2025 16:07
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@lwalew lwalew left a comment

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Lots of small nitpicks here, feel free to resolve them yourself. Just a number of small issues including:

  • Some missing docs for the classes.
  • Potentially an issue with units. If this is the case, I think it might be worth adding a test case that would catch this (indeed when I fix the units the output looks more reasonable - see image below)
  • Number of minor code improvements. I think on the whole, I would rather break up some of the post-processing in the ui and add it to the benchmark page and include what is necessary in the results.
Screenshot 2025-08-13 at 15 25 42

@lwalew lwalew requested a review from chrbrunk August 13, 2025 13:27
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@leonwehrhan. Looks really nice, I added my comments as well. Regarding the tests, please let me or @lwalew know if you want to quickly discuss in a call if details are unclear, I think all other things are really minor, but the unit tests we need to add a few I think.

@leonwehrhan leonwehrhan requested a review from lwalew August 27, 2025 12:40
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Very nice!

@leonwehrhan leonwehrhan merged commit d2e87a1 into main Sep 2, 2025
3 checks passed
lwalew pushed a commit that referenced this pull request Sep 4, 2025
* feat: benchmark class

* feat: unit test run model

* feat: unit test for analyze

* docs: add noncovalent interactions

* fix: add license to conftest

* feat: update main

* feat: number of skipped structures as attribute

* feat: refactor nci output

* feat: refactor benchmark output

* feat: ui

* feat: ui skipped structures

* chore: smaller test data

* chore: unit tests for unallowed elements

* chore: update tests

* chore: update benchmark class

* chore: update docs

* chore: update ui

* chore: linters
lwalew pushed a commit that referenced this pull request Sep 4, 2025
* feat: benchmark class

* feat: unit test run model

* feat: unit test for analyze

* docs: add noncovalent interactions

* fix: add license to conftest

* feat: update main

* feat: number of skipped structures as attribute

* feat: refactor nci output

* feat: refactor benchmark output

* feat: ui

* feat: ui skipped structures

* chore: smaller test data

* chore: unit tests for unallowed elements

* chore: update tests

* chore: update benchmark class

* chore: update docs

* chore: update ui

* chore: linters
lwalew pushed a commit that referenced this pull request Sep 17, 2025
* feat: benchmark class

* feat: unit test run model

* feat: unit test for analyze

* docs: add noncovalent interactions

* fix: add license to conftest

* feat: update main

* feat: number of skipped structures as attribute

* feat: refactor nci output

* feat: refactor benchmark output

* feat: ui

* feat: ui skipped structures

* chore: smaller test data

* chore: unit tests for unallowed elements

* chore: update tests

* chore: update benchmark class

* chore: update docs

* chore: update ui

* chore: linters
lwalew pushed a commit that referenced this pull request Sep 17, 2025
* feat: benchmark class

* feat: unit test run model

* feat: unit test for analyze

* docs: add noncovalent interactions

* fix: add license to conftest

* feat: update main

* feat: number of skipped structures as attribute

* feat: refactor nci output

* feat: refactor benchmark output

* feat: ui

* feat: ui skipped structures

* chore: smaller test data

* chore: unit tests for unallowed elements

* chore: update tests

* chore: update benchmark class

* chore: update docs

* chore: update ui

* chore: linters
@chrbrunk chrbrunk deleted the noncovalent-interactions branch November 21, 2025 14:15
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3 participants