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New conftest for dask #6

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New conftest for dask #6

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Commits on Jun 9, 2023

  1. Add scheduler to wbridge tests

    Egor Marin committed Jun 9, 2023
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Commits on Jun 14, 2023

  1. Fix protocol with running _compute instead of run

    Egor Marin committed Jun 14, 2023
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Commits on Jun 15, 2023

  1. Add implementation of _setup_bslices with handling of frames parameter

    Egor Marin committed Jun 15, 2023
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  2. Fix implementation for frames parameter in _setup_bslices

    Egor Marin committed Jun 15, 2023
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  3. Remove _scheduler attribute and make dask-based tests run properly

    Egor Marin committed Jun 15, 2023
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Commits on Jun 20, 2023

  1. Refactor scheduler usage

    Egor Marin committed Jun 20, 2023
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  2. Add multiple workers in dask for testing

    Egor Marin committed Jun 20, 2023
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Commits on Jun 21, 2023

  1. Refactor _setup_bslices and add processes to dask scheduler kwargs

    Egor Marin committed Jun 21, 2023
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Commits on Jun 22, 2023

  1. Create frame_indices and trajectory for each bslice during _setup_bsl… 

    …ices
    Egor Marin committed Jun 22, 2023
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  2. Use explicit initialisation of timeseries wiith zeros

    Egor Marin committed Jun 22, 2023
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  3. Add non-trivial _parallel_conclude function

    Egor Marin committed Jun 22, 2023
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  4. Fix tests for new dask fixture

    Egor Marin committed Jun 22, 2023
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Commits on Jun 23, 2023

  1. Add type-matching _parallel_conclude

    Egor Marin committed Jun 23, 2023
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Commits on Jun 25, 2023

  1. Add fixtures to test combinations of dask and multiprocessing

    Egor Marin committed Jun 25, 2023
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  2. dask and multiprocessing works in test_atomicdistances.py

    Egor Marin committed Jun 25, 2023
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  3. Fix bug in results is np.ndarray codepath

    Egor Marin committed Jun 25, 2023
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  4. Add _setup_scheduler raising NotImplemented error in align.py::Averag… 

    …eStructure
    Egor Marin committed Jun 25, 2023
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  5. dask and multiprocessing schedulers to test_align.py

    Egor Marin committed Jun 25, 2023
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  6. dask scheduler for test_contacts.py and test for incompatibility with… 

    … multiprocessing
    Egor Marin committed Jun 25, 2023
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  7. dask and multiprocessing scheduler for test_density.py

    Egor Marin committed Jun 25, 2023
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  8. Add _parallel_conclude implementation for dielectric

    Egor Marin committed Jun 25, 2023
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  9. dask and multiprocessing schedulers for test_dielectric.py

    Egor Marin committed Jun 25, 2023
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  10. dask and multiprocessing schedulers for test_diffusionmap.py

    Egor Marin committed Jun 25, 2023
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  11. Add NotImplementedError for parallel schedulers in dihedrals.py

    Egor Marin committed Jun 25, 2023
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  12. only current scheduler for test_dihedrals.py

    Egor Marin committed Jun 25, 2023
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  13. dask and multiprocessing tests for test_encore.py -- but some fail be… 

    …cause of RMSF module
    Egor Marin committed Jun 25, 2023
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  14. Add NotImplementedError for _setup_scheduler in gnm.py

    Egor Marin committed Jun 25, 2023
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  15. Add NotImplementedError for _setup_scheduler in helix_analysis.py

    Egor Marin committed Jun 25, 2023
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  16. current process scheduler for test_helix_analysis.py

    Egor Marin committed Jun 25, 2023
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  17. dask and multiprocessing schedulers for test_hole2.py

    Egor Marin committed Jun 25, 2023
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  18. Add NotImplementedError in for not-None schedulers

    Egor Marin committed Jun 25, 2023
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  19. current process scheduler and test for failing non-current ones in te… 

    …st_hydrogendbonds_analysis.py
    Egor Marin committed Jun 25, 2023
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  20. current process only scheduler and failing test for others in test_li… 

    …neardensity.py
    Egor Marin committed Jun 25, 2023
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  21. Add NotImplementedError for non-current process schedulers

    Egor Marin committed Jun 25, 2023
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  22. current process scheduler only and failing tests for non-current ones… 

    … in test_msd.py
    Egor Marin committed Jun 25, 2023
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  23. Add NotImplementedError for non-current process schedulers

    Egor Marin committed Jun 25, 2023
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  24. Fix scope of fixtures

    Egor Marin committed Jun 25, 2023
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  25. Add NotImplemented error for all non-current process schedulers

    Egor Marin committed Jun 25, 2023
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  26. only current process scheduler and failing tests for test_nucleicacid… 

    …s.py
    Egor Marin committed Jun 25, 2023
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  27. dask and multiprocessing schedulers for test_persistentlength.py

    Egor Marin committed Jun 25, 2023
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  28. Add _parallel_conclude implementation

    Egor Marin committed Jun 25, 2023
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  29. dask and multiprocessing schedulers for test_psa.py

    Egor Marin committed Jun 25, 2023
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  30. Add _parallel_conclude implementation for RDF and RDF_S

    Egor Marin committed Jun 25, 2023
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  31. dask and multiprocessing schedulers for test_rdf_s.py

    Egor Marin committed Jun 25, 2023
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  32. dask and multiprocessing schedulers for test_rdf.py

    Egor Marin committed Jun 25, 2023
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  33. Add NotImplementedError for RMSD and RMSF classes

    Egor Marin committed Jun 25, 2023
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  34. only local process scheduler and failing tests for others for test_rm… 

    …s.py
    Egor Marin committed Jun 25, 2023
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  35. current process scheduler only and failing test for others for test_w… 

    …bridge.py
    Egor Marin committed Jun 25, 2023
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  36. Add NotImplementedError in _setup_scheduler

    Egor Marin committed Jun 25, 2023
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  37. Add more clear message during exception

    Egor Marin committed Jun 25, 2023
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Commits on Jun 29, 2023

  1. Add timeseries aggregation function

    Egor Marin committed Jun 29, 2023
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  2. dask and multiprocessing scheduler for most of the test_base.py testc… 

    …ases
    Egor Marin committed Jun 29, 2023
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  3. dask and multiprocessing schedulers for test_rms.py::TestRMSD

    Egor Marin committed Jun 29, 2023
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  4. Add NotImplementedError for pca and rms

    Egor Marin committed Jun 29, 2023
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  5. dask and multiprocessing schedulers for test_bat

    Egor Marin committed Jun 29, 2023
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  6. dcurrent process scheduler for test_gnm.py

    Egor Marin committed Jun 29, 2023
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  7. dcurrent process scheduler for test_pca.py

    Egor Marin committed Jun 29, 2023
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  8. Fix rmsf-related scheduler usage to only current process scheduler

    Egor Marin committed Jun 29, 2023
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  9. remove fixme marks

    Egor Marin committed Jun 29, 2023
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Commits on Jun 30, 2023

  1. Switch to enumerate in _compute main loop and fix code review comments

    Egor Marin committed Jun 30, 2023
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Commits on Jul 2, 2023

  1. Add dask to CI setup actions

    Egor Marin committed Jul 2, 2023
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  2. Remove local scheduler for progressbar test

    Egor Marin committed Jul 2, 2023
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  3. Add installation with dask as asetup option

    Egor Marin committed Jul 2, 2023
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  4. fix hole2 tests for -- implement only current scheduler and add faili… 

    …ng test
    Egor Marin committed Jul 2, 2023
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Commits on Jul 3, 2023

  1. fix progressbar test by changing order of ProgressBar and enumerate

    Egor Marin committed Jul 3, 2023
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Commits on Jul 4, 2023

  1. use only frame indices and frames in _setup_bslices after writing a b… 

    …logpost
    Egor Marin committed Jul 4, 2023
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  2. Refactor _setup_bslices: move enumerate to numpy and fuse logic in de… 

    …fining type of input
    Egor Marin committed Jul 4, 2023
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  3. Add documentation to AnalysisBase._parallel_conclude()

    Egor Marin committed Jul 4, 2023
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Commits on Jul 20, 2023

  1. add functional-like interface draft

    Egor Marin committed Jul 20, 2023
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Commits on Jul 23, 2023

  1. Implement proper Client class, separating computations from AnalysisBase

    Egor Marin committed Jul 23, 2023
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  2. FINALLY implement working one-time dask cluster setup in kwargs of a … 

    …client
    Egor Marin committed Jul 23, 2023
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  3. Correct tests accordingly

    Egor Marin committed Jul 23, 2023
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Commits on Jul 24, 2023

  1. Separately process case of only one remote worker

    Egor Marin committed Jul 24, 2023
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  2. Add available_schedulers to AverageStructure

    Egor Marin committed Jul 24, 2023
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  3. Use automatic fixture for AverageStructure

    Egor Marin committed Jul 24, 2023
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  4. Add fixture for AverageStructure

    Egor Marin committed Jul 24, 2023
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  5. Add fixture for AtomicDistances

    Egor Marin committed Jul 24, 2023
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  6. Change default available_backends to all implemented in Client

    Egor Marin committed Jul 24, 2023
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  7. Limit available backends for AverageStructure

    Egor Marin committed Jul 24, 2023
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  8. Add fixture for BAT

    Egor Marin committed Jul 24, 2023
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  9. Add fixture tests to Contacts

    Egor Marin committed Jul 24, 2023
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  10. Fix n_workers check and boolean frames handling

    Egor Marin committed Jul 24, 2023
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Commits on Jul 27, 2023

  1. Fix performance of backend="dask"

    Egor Marin committed Jul 27, 2023
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  2. Add available_backends for Contacts

    Egor Marin committed Jul 27, 2023
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  3. Remove _setup_scheduler

    Egor Marin committed Jul 27, 2023
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  4. Use client fixture for Contacts

    Egor Marin committed Jul 27, 2023
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  5. Use client fixture for RMSD/RMSF

    Egor Marin committed Jul 27, 2023
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  6. Revert files to their state in develop

    Egor Marin committed Jul 27, 2023
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  7. Delete files_for_undoing_changes.txt

    Egor Marin authored Jul 27, 2023
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  8. Delete conftest.py

    Egor Marin authored Jul 27, 2023
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  9. Delete parallel_analysis_demo.ipynb

    Egor Marin authored Jul 27, 2023
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  10. Clean up notebook

    Egor Marin committed Jul 27, 2023
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  11. remove notebook

    Egor Marin committed Jul 27, 2023
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  12. Limit available schedulers in RMSF

    Egor Marin committed Jul 27, 2023
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  13. Split test in two due to failing with "expectation" parametrization

    Egor Marin committed Jul 27, 2023
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  14. Add fixture generator and fixtures for test_base and test_rms

    Egor Marin committed Jul 27, 2023
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  15. Add dask to pyproject.toml

    Egor Marin committed Jul 27, 2023
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  16. Return computation groups explicitly

    Egor Marin committed Jul 27, 2023
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Commits on Aug 1, 2023

  1. Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis in… 

    …to feature/parallel_backend
    Egor Marin committed Aug 1, 2023
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Commits on Aug 2, 2023

  1. Fix dask position in setup-deps/action.yaml

    Egor Marin committed Aug 2, 2023
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  2. Add dask[distributed] to mdanalysis[parallel] installation

    Egor Marin committed Aug 2, 2023
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  3. Undo autoformatter

    Egor Marin committed Aug 2, 2023
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Commits on Aug 6, 2023

  1. Manually define available_backends for RMSD class

    Egor Marin committed Aug 6, 2023
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  2. Create separate "parallel" entry

    Egor Marin committed Aug 6, 2023
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  3. Add is_installed function to utils

    Egor Marin committed Aug 6, 2023
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  4. Add dict-based validatdion and computation logic for ParallelExecutor

    Egor Marin committed Aug 6, 2023
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  5. Add tests for ParallelExecutor

    Egor Marin committed Aug 6, 2023
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  6. Add documentation for "apply" method of ParallelExecutor

    Egor Marin committed Aug 6, 2023
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  7. Correct dask.distributed name

    Egor Marin committed Aug 6, 2023
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  8. Use chunksize=1 instead of explicit Pool in _compute_with_dask

    Egor Marin committed Aug 6, 2023
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  9. Remove unnecessary function in conftest

    Egor Marin committed Aug 6, 2023
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  10. Fix function to retrieve dask client if dask is not installed

    Egor Marin committed Aug 6, 2023
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  11. Fix base tests when dask is not installed

    Egor Marin committed Aug 6, 2023
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Commits on Aug 8, 2023

  1. Use new LocalCluster every time

    Egor Marin committed Aug 8, 2023
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  2. Fix client/backend logic

    Egor Marin committed Aug 8, 2023
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  3. Add documentation to a silly square function

    Egor Marin committed Aug 8, 2023
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  4. Switch to package-wise autouse fixture for dask.distributed.Client

    Egor Marin committed Aug 8, 2023
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  5. Add explicit result() when computing with cluster

    Egor Marin committed Aug 8, 2023
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Commits on Aug 17, 2023

  1. Fix codereview

    Egor Marin committed Aug 17, 2023
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  2. Replace list with tuple in available_backends for RMSD

    Egor Marin committed Aug 17, 2023
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  3. Remove unnecessary get_running_dask_client

    Egor Marin committed Aug 17, 2023
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  4. Implement fixture injection for subclasses testing

    Egor Marin committed Aug 17, 2023
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  5. Add warnings filters

    Egor Marin committed Aug 17, 2023
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  6. Fix backend check when client is present

    Egor Marin committed Aug 17, 2023
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  7. Return get_runnning_dask_client function

    Egor Marin committed Aug 17, 2023
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Commits on Aug 18, 2023

  1. Change dask fixture scope

    Egor Marin committed Aug 18, 2023
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  2. Close LocalCluster to avoid trillions of logs

    Egor Marin committed Aug 18, 2023
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  3. Implement ResultsGroup based aggregation instead of type matching

    Egor Marin committed Aug 18, 2023
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  4. Add non-default _get_aggregator() to RMS and Base classes

    Egor Marin committed Aug 18, 2023
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Commits on Aug 19, 2023

  1. Mark test_multiprocessing.py::test_creating_multiple_universe_without… 

    …_offset as skipped
    Egor Marin committed Aug 19, 2023
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  2. Restore failing test

    Egor Marin committed Aug 19, 2023
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Commits on Aug 21, 2023

  1. Make aggregation functions static methods of ResultsGroup

    Egor Marin committed Aug 21, 2023
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  2. Merge branch 'feature/dask-0' of github.com:marinegor/mdanalysis into… 

    … feature/parallel_backend
    Egor Marin committed Aug 21, 2023
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  3. Remove test skip

    Egor Marin committed Aug 21, 2023
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Commits on Aug 24, 2023

  1. Move parallel part into a separate file

    Egor Marin committed Aug 24, 2023
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Commits on Aug 31, 2023

  1. Fix imports

    Egor Marin committed Aug 31, 2023
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Commits on Sep 5, 2023

  1. Proof of concept for duck-typed backends

    Egor Marin committed Sep 5, 2023
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  2. Remove unused code

    Egor Marin committed Sep 5, 2023
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Commits on Sep 12, 2023

  1. Replace ParallelExecutor with multiple backend classes and add duck-t… 

    …yping backend in AnalysisBase.run()
    Egor Marin committed Sep 12, 2023
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  2. Add all tests for analysis/parallel.py and fix bug in ResultsGroup.nd… 

    …array_mean
    Egor Marin committed Sep 12, 2023
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Commits on Sep 13, 2023

  1. Change typing to py3.9 compatible syntax

    Egor Marin committed Sep 13, 2023
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  2. Add _is_parallelizable to AnalysisFromFunction

    Egor Marin committed Sep 13, 2023
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  3. Remove dask[distributed] even as an optional dependency

    Egor Marin committed Sep 13, 2023
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  4. Update documentation

    Egor Marin committed Sep 13, 2023
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  5. Remove function to get running dask client

    Egor Marin committed Sep 13, 2023
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  6. Remove unused code from analysis/conftest.py

    Egor Marin committed Sep 13, 2023
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  7. Fix documentation and minor issues from codereview

    Egor Marin committed Sep 13, 2023
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  8. Update package/MDAnalysis/analysis/rms.py 

    Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
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    Egor Marin and IAlibay authored Sep 13, 2023
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  9. Merge branch 'feature/dask-0' of github.com:marinegor/mdanalysis into… 

    … feature/dask-0
    Egor Marin committed Sep 13, 2023
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  10. Add more backend validation tests and fix autoformatter issues

    Egor Marin committed Sep 13, 2023
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Commits on Sep 15, 2023

  1. Start implementing correct result sizes in separate computation groups

    Egor Marin committed Sep 15, 2023
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  2. Continue working: diffusionmap and PCA tests fail

    Egor Marin committed Sep 15, 2023
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Commits on Jan 10, 2024

  1. Merge remote-tracking branch 'upstream/develop' into feature/appropri… 

    …ate-sized-results-in-parallel
    @marinegor
    marinegor committed Jan 10, 2024
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Commits on Jan 12, 2024

  1. Fix bug in PCA trajectory iteration -- avoid explicit usage of self.s… 

    …tart
    @marinegor
    marinegor committed Jan 12, 2024
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  2. update changelog and tests for PCA fix

    @marinegor
    marinegor committed Jan 12, 2024
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  3. Merge branch 'bugfix/pca-frames-iteration' into feature/appropriate-s… 

    …ized-results-in-parallel
    @marinegor
    marinegor committed Jan 12, 2024
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  4. Fix diffusionmap and pca

    @marinegor
    marinegor committed Jan 12, 2024
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  5. Make sure not to reset self.{start,stop,step} during self._compute

    @marinegor
    marinegor committed Jan 12, 2024
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  6. Change iteration pattern to sliced trajectory

    @marinegor
    marinegor committed Jan 12, 2024
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  7. Change iteration pattern to sliced trajectory

    @marinegor
    marinegor committed Jan 12, 2024
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  8. Update package/MDAnalysis/analysis/parallel.py 

    Co-authored-by: Yuxuan Zhuang <yuzhuang@stanford.edu>
    @yuxuanzhuang
    Egor Marin and yuxuanzhuang authored Jan 12, 2024
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  9. Apply suggestions from code review 

    Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
Co-authored-by: Yuxuan Zhuang <yuzhuang@stanford.edu>
    @RMeli @yuxuanzhuang
    3 people authored Jan 12, 2024
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  10. Split _setup_frames into two separate functions

    @marinegor
    marinegor committed Jan 12, 2024
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  11. Merge branch 'feature/appropriate-sized-results-in-parallel' into fea… 

    …ture/parallelization
    @marinegor
    marinegor committed Jan 12, 2024
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  12. Merge branch 'feature/analysisbase-code-deduplication' into feature/p… 

    …arallelization
    @marinegor
    marinegor committed Jan 12, 2024
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  13. Add docstrings for _prepare_sliced_trajectory and _define_run_frames

    @marinegor
    marinegor committed Jan 12, 2024
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  14. Remove dask-distributed from dependencies

    @marinegor
    marinegor committed Jan 12, 2024
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  15. Test only 2 processors with parallelizable backends

    @marinegor
    marinegor committed Jan 12, 2024
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  16. Rename available_backends and safe

    @marinegor
    marinegor committed Jan 12, 2024
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  17. Apply codereview changes

    @marinegor
    marinegor committed Jan 12, 2024
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Commits on Jan 13, 2024

  1. Make tests for AnalysisBase subclasses explicit

    @marinegor
    marinegor committed Jan 13, 2024
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  2. Exclude "multiprocessing" from analysis_class function available back… 

    …ends
    @marinegor
    marinegor committed Jan 13, 2024
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  3. Split parallel.py into results.py and parallel.py

    @marinegor
    marinegor committed Jan 13, 2024
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  4. Finalize separation of results and backends

    @marinegor
    marinegor committed Jan 13, 2024
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Commits on Jan 14, 2024

  1. Rename parallel.py to backends.py

    @marinegor
    marinegor committed Jan 14, 2024
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  2. Add results and backends to analysis/__init__.py

    @marinegor
    marinegor committed Jan 14, 2024
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  3. Fix pep8 errors in docstrings and code

    @marinegor
    marinegor committed Jan 14, 2024
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  4. Add versionadded to documentation

    @marinegor
    marinegor committed Jan 14, 2024
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Commits on Jan 17, 2024

  1. Merge branch 'feature/pep8-parallelization' into feature/parallelization

    @marinegor
    marinegor committed Jan 17, 2024
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  2. Update sphinx documentation with backends and results

    @marinegor
    marinegor committed Jan 17, 2024
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  3. Add parallelization reference to base.py

    @marinegor
    marinegor committed Jan 17, 2024
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  4. Switch to relative imports

    @marinegor
    marinegor committed Jan 17, 2024
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  5. Update documentation, adding introduced changes

    @marinegor
    marinegor committed Jan 17, 2024
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  6. Update documentation adding parallelization support for rms

    @marinegor
    marinegor committed Jan 17, 2024
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  7. Add module documentation to results and backends

    @marinegor
    marinegor committed Jan 17, 2024
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Commits on Jan 21, 2024

  1. Fix merge conflicts

    @marinegor
    marinegor committed Jan 21, 2024
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Commits on Jan 22, 2024

  1. Fix BackendSerial validation and add its tests

    @marinegor
    marinegor committed Jan 22, 2024
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  2. Fix calling of self._is_paralellizable()

    @marinegor
    marinegor committed Jan 22, 2024
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  3. Add tests on is_parallelizable and get_supported_backends

    @marinegor
    marinegor committed Jan 22, 2024
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Commits on Jan 24, 2024

  1. Fix bug with default progressbar_kwargs being dict

    @marinegor
    marinegor committed Jan 24, 2024
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Commits on Jan 30, 2024

  1. Merge branch 'develop' into feature/dask-0

    @RMeli
    RMeli authored Jan 30, 2024
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Commits on Jan 31, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
Co-authored-by: Yuxuan Zhuang <yuzhuang@stanford.edu>
    @RMeli @yuxuanzhuang
    3 people authored Jan 31, 2024
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Commits on Feb 7, 2024

  1. Add docstrings to apply() in backends

    @marinegor
    marinegor committed Feb 7, 2024
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  2. Add double n_worker check

    @marinegor
    marinegor committed Feb 7, 2024
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  3. Apply suggestions from code review 

    Co-authored-by: Paul Smith <paul.j.smith@ucl.ac.uk>
    @p-j-smith
    Egor Marin and p-j-smith authored Feb 7, 2024
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  4. Merge with develop

    @marinegor
    marinegor committed Feb 7, 2024
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  5. Merge remote-tracking branch 'origin/feature/dask-0' into feature/par… 

    …allelization
    @marinegor
    marinegor committed Feb 7, 2024
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  6. Fix hasattr in double n_worker check

    @marinegor
    marinegor committed Feb 7, 2024
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  7. Revert test with expectation in test_align

    @marinegor
    marinegor committed Feb 7, 2024
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Commits on Feb 21, 2024

  1. Merge remote-tracking branch 'upstream/develop' into feature/parallel… 

    …ization
    @marinegor
    marinegor committed Feb 21, 2024
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  2. Update testsuite/MDAnalysisTests/analysis/test_pca.py 

    Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
    @IAlibay
    Egor Marin and IAlibay authored Feb 21, 2024
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  3. Update package/MDAnalysis/lib/util.py 

    Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
    @IAlibay
    Egor Marin and IAlibay authored Feb 21, 2024
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  4. Update changelog

    @marinegor
    marinegor committed Feb 21, 2024
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  5. Merge remote-tracking branch 'origin/feature/dask-0' into feature/par… 

    …allelization
    @marinegor
    marinegor committed Feb 21, 2024
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  6. Apply suggestions from code review

    @marinegor
    marinegor committed Feb 21, 2024
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Commits on Feb 23, 2024

  1. Add parallelization section to the documentation

    @marinegor
    marinegor committed Feb 23, 2024
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  2. Fix versionadded in new classes

    @marinegor
    marinegor committed Feb 23, 2024
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  3. Finish parallelization section for documentation

    @marinegor
    marinegor committed Feb 23, 2024
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  4. Sync with develop

    @marinegor
    marinegor committed Feb 23, 2024
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  5. Fix typos

    @marinegor
    marinegor committed Feb 23, 2024
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Commits on Mar 4, 2024

  1. Merge branch 'develop' into feature/dask-0

    @RMeli
    RMeli authored Mar 4, 2024
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Commits on Mar 6, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
    @RMeli
    Egor Marin and RMeli authored Mar 6, 2024
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  2. Apply suggestions from code review 

    Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
    @RMeli
    Egor Marin and RMeli authored Mar 6, 2024
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Commits on Apr 8, 2024

  1. Refactor TreadsBackend example and add a warning

    @marinegor
    marinegor committed Apr 8, 2024
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  2. Add n_workers instantiation from backend argument

    @marinegor
    marinegor committed Apr 8, 2024
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  3. Update package/MDAnalysis/analysis/backends.py 

    Co-authored-by: Yuxuan Zhuang <yuzhuang@stanford.edu>
    @yuxuanzhuang
    Egor Marin and yuxuanzhuang authored Apr 8, 2024
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  4. Update package/doc/sphinx/source/documentation_pages/analysis/paralle… 

    …lization.rst

Co-authored-by: Yuxuan Zhuang <yuzhuang@stanford.edu>
    @yuxuanzhuang
    Egor Marin and yuxuanzhuang authored Apr 8, 2024
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  5. Add remark about RMSF parallelization

    @marinegor
    marinegor committed Apr 8, 2024
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  6. Merge remote-tracking branch 'origin/feature/dask-0' into feature/par… 

    …allelization
    @marinegor
    marinegor committed Apr 8, 2024
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  7. Merge develop and fix merge conflicts

    @marinegor
    marinegor committed Apr 8, 2024
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Commits on Apr 19, 2024

  1. Apply suggestions from codereview

    @marinegor
    marinegor committed Apr 19, 2024
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  2. Apply suggestions from code review

    @marinegor
    marinegor committed Apr 19, 2024
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  3. Fix documentation typo

    @marinegor
    marinegor committed Apr 19, 2024
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Commits on Apr 21, 2024

  1. Update dask installation test after exception text changed

    @marinegor
    marinegor committed Apr 21, 2024
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Commits on Apr 28, 2024

  1. Merge branch 'develop' into feature/dask-0

    @yuxuanzhuang
    yuxuanzhuang authored Apr 28, 2024
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Commits on May 1, 2024

  1. disable encore test

    @yuxuanzhuang
    yuxuanzhuang committed May 1, 2024
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  2. enable test

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    yuxuanzhuang committed May 1, 2024
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  3. disable all test

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    yuxuanzhuang committed May 1, 2024
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  4. enable some test

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    yuxuanzhuang committed May 1, 2024
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  5. enable pc test

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    yuxuanzhuang committed May 1, 2024
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  6. Update test_encore.py

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    yuxuanzhuang authored May 1, 2024
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  7. Update gh-ci.yaml

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    yuxuanzhuang authored May 1, 2024
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  8. Update utils.py

    @yuxuanzhuang
    yuxuanzhuang authored May 1, 2024
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  9. use manager context manager

    @yuxuanzhuang
    yuxuanzhuang committed May 1, 2024
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Commits on May 2, 2024

  1. reduce computation in encore

    @yuxuanzhuang
    yuxuanzhuang committed May 2, 2024
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Commits on May 3, 2024

  1. try self-hosted

    @yuxuanzhuang
    yuxuanzhuang committed May 3, 2024
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  2. reduce one worker

    @yuxuanzhuang
    yuxuanzhuang committed May 3, 2024
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  3. print conda

    @yuxuanzhuang
    yuxuanzhuang committed May 3, 2024
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  4. print nworkers

    @yuxuanzhuang
    yuxuanzhuang committed May 3, 2024
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  5. use 2 nworkers

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    yuxuanzhuang committed May 3, 2024
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  6. use self

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    yuxuanzhuang committed May 3, 2024
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  7. use self worker

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    yuxuanzhuang committed May 3, 2024
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  8. use self worker

    @yuxuanzhuang
    yuxuanzhuang committed May 3, 2024
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  9. use self worker

    @yuxuanzhuang
    yuxuanzhuang committed May 3, 2024
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  10. remove micromamba

    @yuxuanzhuang
    yuxuanzhuang committed May 3, 2024
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  11. print env

    @yuxuanzhuang
    yuxuanzhuang committed May 3, 2024
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Commits on May 4, 2024

  1. remove cuda channel

    @yuxuanzhuang
    yuxuanzhuang committed May 4, 2024
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  2. add cuda > 12

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    yuxuanzhuang committed May 4, 2024
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  3. use mac os 13

    @yuxuanzhuang
    yuxuanzhuang committed May 4, 2024
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  4. print more

    @yuxuanzhuang
    yuxuanzhuang committed May 4, 2024
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