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Move scattered constants into constants.py - #119
stephaniewankowicz merged 1 commit into
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📝 WalkthroughWalkthroughThe change centralizes oxygen metadata, EDIA filtering defaults, graph cutoffs, and radial basis defaults in shared constants. Dataset, inference, confidence, utility, and script APIs now reference these constants. New tests verify values and references. ChangesShared default constants
Estimated code review effort: 2 (Simple) | ~10 minutes Merge Risk: 🟡 Moderate · up to The training command still uses a hardcoded graph cutoff instead of the shared default, so future updates could make training and graph construction behave differently. Update the CLI to use the centralized constant before merging. Suggested reviewers: 🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
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Pull request overview
This PR consolidates previously scattered literal “defaults” (edge cutoff, oxygen vdW radius, oxygen element index, and minimum EDIA threshold) into src/constants.py, then updates call sites to reference the shared constants and adds a unit test to prevent regressions/drift.
Changes:
- Added
OXYGEN_VDW_RADIUS,DEFAULT_MIN_EDIA, andOXYGEN_INDEXtosrc/constants.py. - Replaced hardcoded defaults (
8.0,0.4, oxygen index derivations) with shared constants acrosssrc/andscripts/. - Added
tests/test_constants.pyto assert constant values and ensure key APIs default to those constants (via signature inspection).
Reviewed changes
Copilot reviewed 10 out of 10 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| tests/test_constants.py | New unit tests asserting constant values and that key APIs reference them as defaults. |
| src/utils.py | Uses NUM_RBF/RBF_CUTOFF constants as compute_edge_features defaults. |
| src/inference_graph.py | Defaults inference graph cutoff to DEFAULT_EDGE_CUTOFF and imports it. |
| src/dataset.py | Defaults min_edia and cutoff parameters to shared constants. |
| src/constants.py | Adds consolidated constants for oxygen vdW radius, min EDIA threshold, and oxygen index. |
| src/confidence.py | Imports OXYGEN_VDW_RADIUS/DEFAULT_EDGE_CUTOFF and removes local constant redeclaration. |
| src/confidence_dataset.py | Replaces locally-derived oxygen index with OXYGEN_INDEX. |
| scripts/train.py | Uses DEFAULT_MIN_EDIA as CLI default. |
| scripts/predict_waters.py | Uses DEFAULT_EDGE_CUTOFF when reading flow config cutoff. |
| scripts/inference.py | Uses DEFAULT_MIN_EDIA in dataset filter config extraction. |
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Inline comments:
In `@scripts/train.py`:
- Line 45: Update the training CLI parser default near the argument definition
to use the imported DEFAULT_EDGE_CUTOFF constant instead of the literal 8.0, and
import that symbol from src.constants alongside DEFAULT_MIN_EDIA.
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📒 Files selected for processing (10)
scripts/inference.pyscripts/predict_waters.pyscripts/train.pysrc/confidence.pysrc/confidence_dataset.pysrc/constants.pysrc/dataset.pysrc/inference_graph.pysrc/utils.pytests/test_constants.py
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| @pytest.mark.unit | ||
| class TestConstantsAreReferencedNotRedeclared: | ||
| """Downstream defaults should reference the shared constants, not re-hardcode | ||
| the literal. Comparing the recorded default to the constant catches a regression | ||
| where someone reintroduces a bare ``0.4`` / ``1.52``.""" |
| type=float, | ||
| default=8.0, | ||
| default=DEFAULT_EDGE_CUTOFF, | ||
| help="Distance cutoff in Angstroms for radius edges (default: 8.0)", |
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Nice library! Wanted to start with sth. small to get familiar, so I picked up #104
Moved the constants that were defined locally or hardcoded in a few places into
constants.pyand import them from there. No behavioiur change, same values everywhere with a small test so they don't drift back.Summary by CodeRabbit
Improvements
Tests