Modernise package: Python 3.10+ compatibility, pytest, bug fixes, updated tests#25
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New pynb with Schutte potential
- traj.py: fix typo _read_dtraj -> _read_distraj (broke discrete traj loading) - msm.py: fix wrong loop variable self.keys[k] -> self.keys[i] in do_lbrate - msm.py: replace deprecated np.float() with float() (removed in NumPy>=1.24) - msm_lib.py: replace deprecated np.matrix() with plain ndarray in do_boots_worker - traj_lib.py: remove unconditional top-level hdbscan import (optional dependency) - traj.py: make hdbscan a lazy import with a clear ImportError message - test/download_data.py: use __file__-relative paths instead of os.getcwd() - test/test_trajectory.py: fix import paths and hardcoded 'test/data/' paths - test/test_msm.py: fix import path for download_data All 14 tests now pass. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Runs pytest on push/PR to master and develop across: - OS: ubuntu-latest, macos-latest - Python: 3.10, 3.11, 3.12 Uses miniforge/conda to install mdtraj and scientific stack reliably. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Same broken 'from test.download_data import ...' path that was causing pytest collection to fail across all CI matrix jobs. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Travis CI no longer supports open source projects. Replaced with the new GitHub Actions CI badge pointing to BioKT/MasterMSM. Removed the Codacy badge which referenced the old repo and is not configured. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- msm_lib.py: fix two remaining np.float() calls in calc_mlrate - ci.yml: print package versions before tests and use --tb=long to diagnose the Python 3.10-specific failure Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Fix TimeSeries(dtraj=) → TimeSeries(distraj=) kwarg typo in test setUp - Fix SuperMSM.__init__ missing self.keys (AttributeError in do_lbrate) - Fix MSM.calc_count using x.keys instead of self.keys - Fix calc_eigsK eigenvector arrays: float → complex to avoid ComplexWarning - Re-enable TestMSMLib (19 methods) and add fresh TestSuperMSM (3 methods); fix deprecated np.float/np.complex in test_calc_eigsK; fix tau_averages call signature; 1 active test → 37 active tests, all passing - Update setup.py: version 0.1dev → 0.2.0, Python 3.10/3.11/3.12 classifiers, python_requires>=3.10, install_requires list - Add mdtraj and scikit-learn to requirements.txt - Add TODO.md Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
SuperMSM.self.keysAttributeError,MSM.calc_countwrongx.keysreference,TimeSeries(dtraj=)kwarg typo,calc_eigsKcomplex eigenvector array typemsm.pyandtraj.pysignificantly simplified and modernised;traj_lib.pytrimmed;np.float/np.matrixdeprecations removedTestMSMLib(19 methods), added freshTestSuperMSM(3 methods)0.1dev→0.2.0, Python 3.10/3.11/3.12 classifiers,python_requires>=3.10,install_requireslist,scikit-learnadded to requirementsTest plan
pytest mastermsm/test/ -v→ 37 passed locallypip install -e .succeeds cleanly🤖 Generated with Claude Code