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Pull request overview
This PR introduces a new resolution-guessing implementation that returns a structured resolution object (value + reason), migrates the codebase away from the old toputils.guess_resolution, and updates settings/schema and regression expectations accordingly.
Changes:
- Added
grodecoder.guesser.guess_resolution()returning aMolecularResolutionmodel with{value, reason}, plus new unit tests. - Removed the legacy
guess_resolutionfromtoputilsand updated core/CLI/settings to use the new resolution model and renameddistance_cutoff→cutoff_distance. - Updated regression expected JSON outputs to the new resolution schema, removed
streamlitfrom dev deps, and refreshed lockfile versions.
Reviewed changes
Copilot reviewed 28 out of 29 changed files in this pull request and generated 7 comments.
Show a summary per file
| File | Description |
|---|---|
| uv.lock | Updates locked dependency versions and artifacts. |
| pyproject.toml | Removes streamlit from dev dependencies. |
| src/grodecoder/toputils.py | Removes legacy guess_resolution implementation. |
| src/grodecoder/guesser.py | Adds new resolution guessing logic and resolution/reason models. |
| src/grodecoder/core.py | Switches decode flow to new guesser + renamed cutoff settings. |
| src/grodecoder/settings.py | Renames cutoff fields and updates cutoff-guessing plumbing. |
| src/grodecoder/models.py | Replaces old MolecularResolution enum with guesser model type. |
| src/grodecoder/main.py | Updates CLI → settings assignment to cutoff_distance. |
| src/grodecoder/identifier.py | Minor typing/selection string adjustments. |
| src/grodecoder/databases/api.py | Expands ModelType TypeVar to include MAD/CSML residue models. |
| tests/test_toputils/test_toputils_integration.py | Removes integration tests tied to old toputils.guess_resolution. |
| tests/test_toputils/test_toputils.py | Removes unit tests tied to old toputils.guess_resolution. |
| tests/test_guesser.py | Adds unit tests for new resolution guesser behavior. |
| tests/data/regression_data/expected_results/noriega_CG_CRD_3CAL.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/noriega_AA_CRD_3CAL.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/barstar.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/RNA_start.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/DNA_start.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/DMPC_PI.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/5ZOA.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/5MBA.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/4ZRY.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/4MQJ_ABCD.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/2MAT.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/1QJ8_solution.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/1QJ8_membrane.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/1QJ8_ETH_ACN_MET_URE_SOL.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/1QJ8.json | Updates expected output (resolution now structured, plus key ordering). |
| tests/data/regression_data/expected_results/1BRS.json | Updates expected output (resolution now structured, plus key ordering). |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
…rResolution class
…decoder into feature/new-guess-resolution
- settings.DistanceCutoff.guess: update to account for new MolecularResolution class - various minor fixes
…decoder into feature/new-guess-resolution
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