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- Refactored `tests/conftest.py` to conditionally mock heavy dependencies (`torch`, `ase`, `fairchem`, `rdkit`, `morfeus`, `torch_sim`) using `sys.modules` injection. This allows tests to run in lightweight environments while supporting real dependencies if available.
- Updated `mock_atoms_factory` to dynamically return atomic coordinates and symbols matching the requested size, resolving issues with `zip` length mismatch in IO tests.
- Improved `MockConformerEnsemble` to correctly handle `from_rdkit` and return appropriate conformers (e.g., handling SMILES like "CCCC" to match test expectations).
- Expanded test coverage:
- Added `tests/test_decorators.py`.
- Added tests for `HF_TOKEN` configuration handling in `tests/test_models.py`.
- Added tests for optimizer convergence warnings in `tests/test_optimizer.py`.
- Verified and fixed existing tests in `tests/test_api.py`, `tests/test_cli.py`, `tests/test_config.py`, `tests/test_io.py`, `tests/test_models.py`, `tests/test_optimizer.py`.
- Addressed all code review feedback, including cleaner environment variable handling with `monkeypatch` and better mocking strategies.
Co-authored-by: niklashoelter <83964137+niklashoelter@users.noreply.github.com>
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This PR introduces a comprehensive test suite for the GPUMA repository. It addresses the lack of testing by enabling tests to run in environments without heavy dependencies installed (via robust, conditional mocking in
conftest.py). The suite covers the full API, CLI, configuration, IO handling, and optimizer logic. Special care was taken to mock Fairchem and Torch-Sim models securely, handlingHF_TOKENrequirements as requested.PR created automatically by Jules for task 6643312877358509178 started by @niklashoelter