Code

Cythonized Timestep [Core]#3683

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Merged

richardjgowers merged 73 commits intoMDAnalysis:developMDAnalysis/mdanalysis:developfrom hmacdope:CythonTimestephmacdope/mdanalysis:CythonTimestepCopy head branch name to clipboardJun 13, 2022

+1,196-961

Commits

Commits on May 24, 2022

• add start of timestep class

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• finalize copy over

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• add to init dunder and change tested class

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• passes api tests

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Commits on May 25, 2022

• partially working

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• fix hasattr calls

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• imporve error message

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• remove frame get set method

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• add _frame attr

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• make sure to cinit numpy arrays

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• working

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• make changes to base

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Commits on May 26, 2022

• partially fix pickling

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• move docs around

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• change dlpoly test to has_ rather than AttributeError

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• change dms test to has_velocities rather than hasattr

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• fix import in TRJ / TRZ

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• fix attributeError

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Commits on May 27, 2022

• improve setter API

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• remove requirement for c-style contiguity

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• add start of NPY API calls

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• work on correct casting and pathing for ndarray creation

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• move to helper method

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• improve casting etc, but whole new class of errors

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• stash

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Commits on May 28, 2022

• add in docs changes

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• remove doc subclasses of Timestep in TRJ and memory readers

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• add docs to build

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• tidy up a fraction in timestep.pyx

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  1f225e0

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• add cast

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• improve casts

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• okay I know this works

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• add options

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• promising improvememnt

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Commits on May 29, 2022

• move memory reader to Timestep

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• update forces and vels to use PyArray interface

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Commits on May 30, 2022

• clean up unsued snippets and make array innit smaller

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• add in some explanatory notes

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• Merge remote-tracking branch 'upstream/develop' into CythonTimestep

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Commits on May 31, 2022

• improve for docs

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• tidy docstrings

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• change to 0 size init

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• autopep8

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• add __all__ and change docs in init

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• fix docs build

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Commits on Jun 1, 2022

• fix bug on setting pos

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• change import

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• change refs in docs to base.Timestep to timestep.Timestep

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• fix imports in readers that specifically import timestep

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• change from attribute error in TRZwriter so that velocities can be correctly detected

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• add explicit import for NoDataError

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• move to copy api

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• iron out _frame attribute hanging around in TRZ reader

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• remove useless imports

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• add pxd and libmda imports

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• move decls of C level vars to pxd file

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Commits on Jun 5, 2022

• remove header junk

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• add and improve comments

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• change BUG to NOTE for dtype

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• add header int64_t

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• remove __ne__

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• change isinstance __eq__ check to return NotImplemented

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• add dtype tests

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• add timestep API test for setting box to None

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Commits on Jun 6, 2022

• remove try except block for repr

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• add test for __repr__ with and without a box

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• Merge remote-tracking branch 'upstream/develop' into CythonTimestep

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  93d63d6

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• add alloc flags

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• remove dtype kwarg

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• remove __getattr__ special method

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• add __getattr__ dunder back in

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• CHANGELOG

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Commits on Jun 13, 2022

• Merge branch 'develop' into CythonTimestep

  richardjgowers

  authored
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