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Hdf5 speedup#28

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jeremyleung521 wants to merge 29 commits intodevelopjeremyleung521/westpa:developfrom hdf5-speedupjeremyleung521/westpa:hdf5-speedupCopy head branch name to clipboard

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Commits on Nov 22, 2023

• modifications to allow template files + netcdf loader

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• Merge branch 'develop' of github.com:westpa/westpa into hdf5-speedup

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Commits on Nov 26, 2023

• Update load_netcdf to output WESTTrajectory class objects, which supports exporting unitcell dimensions & time.

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Commits on Nov 27, 2023

• fix declaration of valid_callbacks

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Commits on Nov 30, 2023

• Merge executable_mod into the main executable.py

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Commits on Dec 8, 2023

• Create trajectory/restart/log datasets regardless

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Commits on Dec 13, 2023

• lint and additional checks for h5repack

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• Fix tables import error in h5io

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Commits on Dec 15, 2023

• Units! Make sure everything is in nm.

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Commits on Jan 23, 2024

• Bug fixes for the units conversion thing.

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Commits on Jan 26, 2024

• A cleaner check for unit conversion

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Commits on Feb 13, 2024

• Merge branch 'develop' of github.com:westpa/westpa into hdf5-speedup

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Commits on Feb 19, 2024

• Merge branch 'develop' of github.com:westpa/westpa into hdf5-speedup

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Commits on Apr 11, 2024

• remove need for netCDF4, add in mda_trajectory_loader

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Commits on Apr 12, 2024

• new load_netcdf should now work properly

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Commits on Apr 15, 2024

• convert mda topology to mdtraj topology, tested on pdb, prmtop

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• better docstrings

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• remove a lengthy mdtraj.formats import

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Commits on May 13, 2024

• Merge branch 'develop' into hdf5-speedup

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• shoddy merge

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• fix loader specification

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Commits on May 24, 2024

• ignore NaturalNameWarning (westpa#416)

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• fix summary tables in westpa.analysis (westpa#418)

  jeremyleung521

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• fix w_states --replace reporting (westpa#421)

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• README update (westpa#420)

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Commits on Jun 10, 2024

• Merge branch 'develop' of github.com:jeremyleung521/westpa into hdf5-speedup

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Commits on Sep 4, 2024

• Merge branch 'develop' of github.com:westpa/westpa into hdf5-speedup

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Commits on Oct 30, 2024

• Merge branch 'develop' of ssh://github.com/westpa/westpa into hdf5-speedup

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Commits on Nov 12, 2024

• Merge branch 'develop' of ssh://github.com/westpa/westpa into hdf5-speedup

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