Feat/ruff fix fmt by mikemhenry · Pull Request #120 · OpenFreeEnergy/kartograf

mikemhenry · 2026-01-13T20:25:47Z

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Developers certificate of origin

I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

codecov · 2026-01-13T20:28:35Z

Codecov Report

❌ Patch coverage is 97.93814% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 98.18%. Comparing base (1b58f03) to head (ae2e68a).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/kartograf/atom_mapper.py	97.82%	1 Missing ⚠️
...rtograf/mapping_metrics/metric_shape_difference.py	91.66%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #120      +/-   ##
==========================================
- Coverage   98.23%   98.18%   -0.05%     
==========================================
  Files          14       13       -1     
  Lines         678      661      -17     
==========================================
- Hits          666      649      -17     
  Misses         12       12

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atravitz

Just a couple things!

atravitz · 2026-01-14T18:36:06Z

src/kartograf/atom_mapping_scorer.py

Looks like this is causing the docs to fail - could you remove this in the docs as well? And add to the 2.0 changelog!

src/kartograf/filters/__init__.py

src/kartograf/filters/ring_changes.py

atravitz · 2026-01-14T18:42:14Z

src/kartograf/mapping_metrics/__init__.py

+from .metric_shape_difference import (
+    MappingShapeMismatchScorer as MappingShapeMismatchScorer,
 )
 from .metric_shape_difference import (


same as above, I (subjectively) prefer the prior formatting.

not sure if this changed or my opinion changed, but i'm fine with this now 😄

atravitz · 2026-01-14T18:42:45Z

src/kartograf/mapping_metrics/metric_mapping_rmsd.py

        beta = 1000 / (const.k * const.Avogadro * T)
        V = k_hook * (rmsd - accepted_distance_rmsd)
-        p = np.exp(-beta * V) if (np.exp(-beta * V) < 1) else 1
+        p = min(1, np.exp(-beta * V))


…OpenFreeEnergy/openfe-benchmarks@23f2c94

mikemhenry · 2026-02-06T15:51:15Z

Looks like changes in OpenFreeEnergy/openfe-benchmarks@23f2c94 are causing an issue, not sure why pinning the commit hash didn't fix it

…eems to be flaky

atravitz

lgtm!

src/kartograf/filters/ring_changes.py

atravitz · 2026-02-10T19:46:37Z

src/kartograf/mapping_metrics/__init__.py

+from .metric_shape_difference import (
+    MappingShapeMismatchScorer as MappingShapeMismatchScorer,
 )
 from .metric_shape_difference import (


not sure if this changed or my opinion changed, but i'm fine with this now 😄

atravitz · 2026-02-10T19:51:56Z

src/kartograf/utils/optional_imports.py

+
 import functools
-from typing import Callable
+from collections.abc import Callable


atravitz · 2026-02-10T19:55:52Z

pyproject.toml

+  "ANN",  # type annotations  https://pypi.org/project/flake8-annotations/
+  "E",    # pycodestyle errors
+  "ERA",  # find commented-out code https://pypi.org/project/eradicate/
+  "F",    # Pyflakes
+  "FURB", # A tool for refurbishing and modernizing Python codebases https://github.com/dosisod/refurb
+  "I",    # isort
+  # "C901",  # mccabe complexity  TODO: add this back in
+  "S",   # security related lint https://pypi.org/project/flake8-bandit/
+  "UP",  # pyupgrade 
+  "W",   # pycodestyle warnings
+  "YTT", # detect issues using sys to check python version https://pypi.org/project/flake8-2020/
 ]


excited about many of these - I'll add some to konnektor and gufe!

mikemhenry · 2026-02-10T22:56:16Z

we need openfe for testing the notebook, just need to make sure that CI uninstalls the kartograf that gets pulled in

mikemhenry · 2026-02-10T23:01:04Z

 Installing collected packages: kartograf
  Attempting uninstall: kartograf
    Found existing installation: kartograf 1.2.0
    Uninstalling kartograf-1.2.0:
      Successfully uninstalled kartograf-1.2.0
Successfully installed kartograf-0.0.1.dev1+g594abb341

Sweet that works

github-actions · 2026-02-10T23:02:46Z

No API break detected ✅

mikemhenry added 2 commits January 13, 2026 13:18

ruff fmt + check

ee9a8ea

setup ruff to use pyupgrade

74cdcb3

mikemhenry added 3 commits January 13, 2026 13:32

turn on pyupgrade

2c1ee89

pyupgrade --py311-plus

1208870

Format pyproject.toml

f0744eb

mikemhenry requested a review from atravitz January 13, 2026 21:36

mikemhenry added 10 commits January 13, 2026 15:36

more ruff fixes

8b45cf1

imoport fixes

dfae282

more linting rules

34e35f6

furby the codebase

8e497ce

fix import in notebooks

1eff717

skip unused import on bit of code it can't see is actually used

b8dfbc9

remove commented out code

0acd60b

add YTT

2993bb9

fix syntax error in pyproject.toml

8733e49

fix formatting and explain what is going on with the linters

d807ef9

atravitz requested changes Jan 14, 2026

View reviewed changes

mikemhenry added 12 commits January 14, 2026 13:04

add missing return types

8d58626

add missing return types

dadbc8d

format pyproject.toml and add security linter

580bb5b

added noqa, still need to fix #121

93fa908

make explcit where our src is

b69778a

force imports to be on one line (need to fix group)

6a60c0f

this is closer now to what we want

461e5ca

ruff fmt

31d0dd4

format imports

f39c2ef

testing isort

25bae5f

atom_mapping_scorer is now mapping_metrics

ddd5e19

pin openfe_benchmarks to hash since the package has changed a TON, see …

9e9f7e1

…OpenFreeEnergy/openfe-benchmarks@23f2c94

mikemhenry added 2 commits February 9, 2026 10:50

bump, is passing locally

8374b04

need to catch ImportError as well

13f0c7d

mikemhenry requested a review from atravitz February 9, 2026 19:47

each import on a new line tokeep diffs small and clean

6b4927e

mikemhenry mentioned this pull request Feb 10, 2026

Consider removing usage of openfe-benchmarks for docs #99

Closed

mikemhenry added 2 commits February 10, 2026 12:40

reformat imports

4270415

install openfe_benchmarks directly in env, installing from notebook s…

86104ec

…eems to be flaky

atravitz approved these changes Feb 10, 2026

View reviewed changes

mikemhenry added 3 commits February 10, 2026 15:26

need to install openfe for testing

d056379

bump, is passing locally

1c94027

make sure we install a newer version of openfe than 0.1

5831bdf

mikemhenry added 2 commits February 10, 2026 16:01

remove old cruft

c0150ed

pyproject-fmt

ae2e68a

mikemhenry merged commit e2c9a6a into main Feb 11, 2026
7 of 9 checks passed

This was referenced Feb 13, 2026

Review existence of atom_mapping_scorer for 2.0 #55

Closed

Add Linting #107

Closed

Add pre-commit and lint #79

Closed

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mikemhenry commented Jan 13, 2026

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