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test_rms.py::TestRMSD\r\n\r\n* Add NotImplementedError for pca and rms\r\n\r\n* dask and multiprocessing schedulers for test_bat\r\n\r\n* dcurrent process scheduler for test_gnm.py\r\n\r\n* dcurrent process scheduler for test_pca.py\r\n\r\n* Fix rmsf-related scheduler usage to only current process scheduler\r\n\r\n* remove fixme marks\r\n\r\n* Switch to enumerate in _compute main loop and fix code review comments\r\n\r\n* Add dask to CI setup actions\r\n\r\n* Remove local scheduler for progressbar test\r\n\r\n* Add installation with dask as  asetup option\r\n\r\n* fix hole2 tests for -- implement only current scheduler and add failing test\r\n\r\n* fix progressbar test by changing order of ProgressBar and enumerate\r\n\r\n* use only frame indices and frames in _setup_bslices after writing a blogpost\r\n\r\n* Refactor _setup_bslices: move enumerate to numpy and fuse logic in defining type of input\r\n\r\n* Add documentation to AnalysisBase._parallel_conclude()\r\n\r\n* add functional-like interface draft\r\n\r\n* Implement proper Client class, separating computations from AnalysisBase\r\n\r\n* FINALLY implement working one-time dask cluster setup in kwargs of a client\r\n\r\n* Correct tests accordingly\r\n\r\n* Separately process case of only one remote worker\r\n\r\n* Add available_schedulers to AverageStructure\r\n\r\n* Use automatic fixture for AverageStructure\r\n\r\n* Add fixture for AverageStructure\r\n\r\n* Add fixture for AtomicDistances\r\n\r\n* Change default available_backends to all implemented in Client\r\n\r\n* Limit available backends for AverageStructure\r\n\r\n* Add fixture for BAT\r\n\r\n* Add fixture tests to Contacts\r\n\r\n* Fix n_workers check and boolean frames handling\r\n\r\n* Fix performance of backend=\"dask\"\r\n\r\n* Add available_backends for Contacts\r\n\r\n* Remove _setup_scheduler\r\n\r\n* Use client fixture for Contacts\r\n\r\n* Use client fixture for RMSD/RMSF\r\n\r\n* Revert files to their state in develop\r\n\r\n* Delete files_for_undoing_changes.txt\r\n\r\n* Delete conftest.py\r\n\r\n* Delete parallel_analysis_demo.ipynb\r\n\r\n* Clean up notebook\r\n\r\n* Limit available schedulers in RMSF\r\n\r\n* Split test in two due to failing with \"expectation\" parametrization\r\n\r\n* Add fixture generator and fixtures for test_base and test_rms\r\n\r\n* Add dask to pyproject.toml\r\n\r\n* Return computation groups explicitly\r\n\r\n* Fix dask position in setup-deps/action.yaml\r\n\r\n* Add dask[distributed] to mdanalysis[parallel] installation\r\n\r\n* Undo autoformatter\r\n\r\n* Manually define available_backends for RMSD class\r\n\r\n* Create separate \"parallel\" entry\r\n\r\n* Add is_installed function to utils\r\n\r\n* Add dict-based validatdion and computation logic for ParallelExecutor\r\n\r\n* Add tests for ParallelExecutor\r\n\r\n* Add documentation for \"apply\" method of ParallelExecutor\r\n\r\n* Correct dask.distributed name\r\n\r\n* Use chunksize=1 instead of explicit Pool in _compute_with_dask\r\n\r\n* Remove unnecessary function in conftest\r\n\r\n* Fix function to retrieve dask client if dask is not installed\r\n\r\n* Fix base tests when dask is not installed\r\n\r\n* Use new LocalCluster every time\r\n\r\n* Fix client/backend logic\r\n\r\n* Add documentation to a silly square function\r\n\r\n* Switch to package-wise autouse fixture for dask.distributed.Client\r\n\r\n* Add explicit result() when computing with cluster\r\n\r\n* Fix codereview\r\n\r\n* Replace list with tuple in available_backends for RMSD\r\n\r\n* Remove unnecessary get_running_dask_client\r\n\r\n* Implement fixture injection for subclasses testing\r\n\r\n* Add warnings filters\r\n\r\n* Fix backend check when client is present\r\n\r\n* Return get_runnning_dask_client function\r\n\r\n* Change dask fixture scope\r\n\r\n* Close LocalCluster to avoid trillions of logs\r\n\r\n* Implement ResultsGroup based aggregation instead of type matching\r\n\r\n* Add non-default _get_aggregator() to RMS and Base classes\r\n\r\n* Mark test_multiprocessing.py::test_creating_multiple_universe_without_offset as skipped\r\n\r\n* Restore failing test\r\n\r\n* Make aggregation functions static methods of ResultsGroup\r\n\r\n* Remove test skip\r\n\r\n* Move parallel part into a separate file\r\n\r\n* Fix imports\r\n\r\n* Proof of concept for duck-typed backends\r\n\r\n* Remove unused code\r\n\r\n* Replace ParallelExecutor with multiple backend classes and add duck-typing backend in AnalysisBase.run()\r\n\r\n* Add all tests for analysis/parallel.py and fix bug in ResultsGroup.ndarray_mean\r\n\r\n* Change typing to py3.9 compatible syntax\r\n\r\n* Add _is_parallelizable to AnalysisFromFunction\r\n\r\n* Remove dask[distributed] even as an optional dependency\r\n\r\n* Update documentation\r\n\r\n* Remove function to get running dask client\r\n\r\n* Remove unused code from analysis/conftest.py\r\n\r\n* Fix documentation and minor issues from codereview\r\n\r\n* Update package/MDAnalysis/analysis/rms.py\r\n\r\nCo-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>\r\n\r\n* Add more backend validation tests and fix autoformatter issues\r\n\r\n* Start implementing correct result sizes in separate computation groups\r\n\r\n* Continue working: diffusionmap and PCA tests fail\r\n\r\n* Fix bug in PCA trajectory iteration -- avoid explicit usage of self.start\r\n\r\n* update changelog and tests for PCA fix\r\n\r\n* Fix diffusionmap and pca\r\n\r\n* Make sure not to reset self.{start,stop,step} during self._compute\r\n\r\n* Change iteration pattern to sliced trajectory\r\n\r\n* Change iteration pattern to sliced trajectory\r\n\r\n* Update package/MDAnalysis/analysis/parallel.py\r\n\r\nCo-authored-by: Yuxuan Zhuang <yuzhuang@stanford.edu>\r\n\r\n* Apply suggestions from code review\r\n\r\nCo-authored-by: Rocco Meli <r.meli@bluemail.ch>\r\nCo-authored-by: Yuxuan Zhuang <yuzhuang@stanford.edu>\r\n\r\n* Split _setup_frames into two separate 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Update changelog\r\n\r\n* Apply suggestions from code review\r\n\r\n* Add parallelization section to the documentation\r\n\r\n* Fix versionadded in new classes\r\n\r\n* Finish parallelization section for documentation\r\n\r\n* Fix typos\r\n\r\n* Apply suggestions from code review\r\n\r\nCo-authored-by: Rocco Meli <r.meli@bluemail.ch>\r\n\r\n* Apply suggestions from code review\r\n\r\nCo-authored-by: Rocco Meli <r.meli@bluemail.ch>\r\n\r\n* Refactor TreadsBackend example and add a warning\r\n\r\n* Add n_workers instantiation from backend argument\r\n\r\n* Update package/MDAnalysis/analysis/backends.py\r\n\r\nCo-authored-by: Yuxuan Zhuang <yuzhuang@stanford.edu>\r\n\r\n* Update package/doc/sphinx/source/documentation_pages/analysis/parallelization.rst\r\n\r\nCo-authored-by: Yuxuan Zhuang <yuzhuang@stanford.edu>\r\n\r\n* Add remark about RMSF parallelization\r\n\r\n* Apply suggestions from codereview\r\n\r\n* Apply suggestions from code review\r\n\r\n* Fix documentation typo\r\n\r\n* 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