Deeptime Ml Deeptime Versions Save

What's Changed

• remove print by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/257
• Remove deprecated CK Test validator by @clonker in https://github.com/deeptime-ml/deeptime/pull/258
• TV derivative and minor documentation fixes by @clonker in https://github.com/deeptime-ml/deeptime/pull/260
• Lorenz system, Thomas attractor, Improvements regarding documentation, TV Derivative improvements by @clonker in https://github.com/deeptime-ml/deeptime/pull/261
• Added an optional argument for specifying the tolerance in is_reversi… by @wehs7661 in https://github.com/deeptime-ml/deeptime/pull/262
• Enable python 3.11 in CI pipelines by @clonker in https://github.com/deeptime-ml/deeptime/pull/263
• pyproject.toml config by @clonker in https://github.com/deeptime-ml/deeptime/pull/264
• Update for scikit-learn 1.2 by @clonker in https://github.com/deeptime-ml/deeptime/pull/267
• cibuildwheel cleanup by @clonker in https://github.com/deeptime-ml/deeptime/pull/268

New Contributors

• @wehs7661 made their first contribution in https://github.com/deeptime-ml/deeptime/pull/262

Full Changelog: https://github.com/deeptime-ml/deeptime/compare/v0.4.3...v0.4.4

What's Changed

• CI: Update manifest to include npz data files, don't use editable install for nox make_docs by @clonker in https://github.com/deeptime-ml/deeptime/pull/233
• plot energy surfaces by @clonker in https://github.com/deeptime-ml/deeptime/pull/234
• Network plots by @clonker in https://github.com/deeptime-ml/deeptime/pull/236
• plot fluxes by @clonker in https://github.com/deeptime-ml/deeptime/pull/237
• Fix preprocess data call in SINDy by @clonker in https://github.com/deeptime-ml/deeptime/pull/240
• Fix shape of empty count models by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/239
• proper exception handling in trajectory-generating openmp block by @clonker in https://github.com/deeptime-ml/deeptime/pull/242
• better error handling for trajectories dataset by @clonker in https://github.com/deeptime-ml/deeptime/pull/243
• [ci] fix python 3.8 by @clonker in https://github.com/deeptime-ml/deeptime/pull/244
• Convergence warning bugfix by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/245
• Fix the bug by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/246
• Contour and density plot utility functions by @clonker in https://github.com/deeptime-ml/deeptime/pull/247
• py38 by @clonker in https://github.com/deeptime-ml/deeptime/pull/249
• [setup] exclude examples, docs, devtools when packaging by @clonker in https://github.com/deeptime-ml/deeptime/pull/250
• Var_cutoff can be disabled in covariance koopman models. Fixes #254. by @clonker in https://github.com/deeptime-ml/deeptime/pull/255

Full Changelog: https://github.com/deeptime-ml/deeptime/compare/v0.4.2...v0.4.3

What's Changed

• new tram notebook version by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/210
• add device option for TAE class by @philipyoung9561 in https://github.com/deeptime-ml/deeptime/pull/211
• Docs update by @clonker in https://github.com/deeptime-ml/deeptime/pull/213
• Use CMake as primary build system via scikit-build by @clonker in https://github.com/deeptime-ml/deeptime/pull/215
• Tram experiments by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/214
• use Agg backend in plotting tests by @clonker in https://github.com/deeptime-ml/deeptime/pull/216
• Fix bug in statdist caching for msms by @clonker in https://github.com/deeptime-ml/deeptime/pull/219
• Tram experiments by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/217
• typos in _koopman.py by @KirillShmilovich in https://github.com/deeptime-ml/deeptime/pull/221
• Disable TF-32 tensor cores for VAMPNET training by @yuxuanzhuang in https://github.com/deeptime-ml/deeptime/pull/222
• Small doc fixes and update testing dependencies by @clonker in https://github.com/deeptime-ml/deeptime/pull/223
• pyproject.toml: use dynamic version by @clonker in https://github.com/deeptime-ml/deeptime/pull/226
• Update versioneer and run cython from CMake by @clonker in https://github.com/deeptime-ml/deeptime/pull/228
• [datasets] correct 1D triple well docs by @thempel in https://github.com/deeptime-ml/deeptime/pull/229
• update project metadata by @clonker in https://github.com/deeptime-ml/deeptime/pull/230
• Fix in setup by @clonker in https://github.com/deeptime-ml/deeptime/pull/231
• update manifest to include cmakelists by @clonker in https://github.com/deeptime-ml/deeptime/pull/232

New Contributors

• @philipyoung9561 made their first contribution in https://github.com/deeptime-ml/deeptime/pull/211
• @KirillShmilovich made their first contribution in https://github.com/deeptime-ml/deeptime/pull/221
• @yuxuanzhuang made their first contribution in https://github.com/deeptime-ml/deeptime/pull/222

Full Changelog: https://github.com/deeptime-ml/deeptime/compare/v0.4.1...v0.4.2

What's Changed

• Update readme and use pyroject.toml in setup by @clonker in https://github.com/deeptime-ml/deeptime/pull/197
• Hotfix tramdataset by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/196
• Finish progress callbacks by @clonker in https://github.com/deeptime-ml/deeptime/pull/198
• Log space sample weights by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/199
• Implied timescales plot by @clonker in https://github.com/deeptime-ml/deeptime/pull/200
• Make sample weights normalized by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/201
• Fix numpy deprecated warning by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/204
• New Chapman-Kolmogorov test implementation by @clonker in https://github.com/deeptime-ml/deeptime/pull/202
• Update validation loss on TAE by @clarktemple03 in https://github.com/deeptime-ml/deeptime/pull/205
• Fix the calculation of the PMF. by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/206
• Mbar initialization for tram by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/207
• Minor changes by @clonker in https://github.com/deeptime-ml/deeptime/pull/208
• fix TRAM bug by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/209

New Contributors

• @clarktemple03 made their first contribution in https://github.com/deeptime-ml/deeptime/pull/205

Full Changelog: https://github.com/deeptime-ml/deeptime/compare/v0.4.0...v0.4.1

What's Changed

• Catch2 unit tests infrastructure by @clonker in https://github.com/deeptime-ml/deeptime/pull/170
• Compile time index and include dir hierarchy by @clonker in https://github.com/deeptime-ml/deeptime/pull/171
• Use mamba over conda for CI by @clonker in https://github.com/deeptime-ml/deeptime/pull/172
• Fix mapping states back to symbols by @clonker in https://github.com/deeptime-ml/deeptime/pull/174
• Minor docs updates by @clonker in https://github.com/deeptime-ml/deeptime/pull/176
• Some cleanup refactoring by @clonker in https://github.com/deeptime-ml/deeptime/pull/177
• Fix state assignments in HMM submodels by @thempel in https://github.com/deeptime-ml/deeptime/pull/178
• Flaky test support by @clonker in https://github.com/deeptime-ml/deeptime/pull/179
• TRAM by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/168
• Minor documentation fixes for TRAM by @clonker in https://github.com/deeptime-ml/deeptime/pull/181
• TOC and a bugfix by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/182
• Unify header location and fix gil scoped release issues by @clonker in https://github.com/deeptime-ml/deeptime/pull/184
• TRAM tests by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/183
• Update installation instructions by @clonker in https://github.com/deeptime-ml/deeptime/pull/186
• TRAM model by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/185
• Bump numpy from 1.19.3 to 1.21.0 in /tests by @dependabot in https://github.com/deeptime-ml/deeptime/pull/187
• Allow KMeans with no iterations by @thempel in https://github.com/deeptime-ml/deeptime/pull/189
• TRAM docs and a unit test by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/188
• TRAM docs - last little things by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/190
• TRAM Progress bar handling by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/191
• Fix submodel_disconnect and add test by @thempel in https://github.com/deeptime-ml/deeptime/pull/193
• Refactor by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/192
• Trajectory fragments: split on negative state indices by @MaaikeG in https://github.com/deeptime-ml/deeptime/pull/194
• Cluster progress by @clonker in https://github.com/deeptime-ml/deeptime/pull/195

New Contributors

• @MaaikeG made their first contribution in https://github.com/deeptime-ml/deeptime/pull/168
• @dependabot made their first contribution in https://github.com/deeptime-ml/deeptime/pull/187

Full Changelog: https://github.com/deeptime-ml/deeptime/compare/v0.3.1...v0.4.0

Makes deeptime Python 3.10 ready

What's Changed

• Nox by @clonker in https://github.com/deeptime-ml/deeptime/pull/164
• fix matmul import for old torch versions by @thempel in https://github.com/deeptime-ml/deeptime/pull/165
• make docs with nox by @clonker in https://github.com/deeptime-ml/deeptime/pull/166
• enable python 3.10 in build matrix by @clonker in https://github.com/deeptime-ml/deeptime/pull/167

Full Changelog: https://github.com/deeptime-ml/deeptime/compare/v0.3.0...v0.3.1

Patch release for custom metrics handling