Code

[WIP] IO refactor#167

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flying-sheep merged 60 commits intoscverse:masterscverse/anndata:masterfrom ivirshup:io_refactorivirshup/anndata:io_refactorCopy head branch name to clipboardSep 5, 2019

+1,573-716

Commits

Commits on Jul 29, 2019

• First take io_refactor

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• Writing working for h5ad

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• Made anndata.h5py.Group a Mapping

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• Got h5ad reading passing most tests

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• Rearange how h5ad write methods are dispatched

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• Docs + minor reorganization

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• Begin zarr refactor (squash into me!)

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• Most backed h5ad tests are passing

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• General cleanup, checkpoint, and vlen strings

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• All backed and h5ad tests passing!

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• Make df to hdf5 recarray more elegant

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• Make df to hdf5 recarray more elegant

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• Clean up read_h5ad

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• Simplify h5ad read_attribute dispatch

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• Fix and test writing with compression

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• Better h5ad support for nulls in categoricals

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Commits on Aug 5, 2019

• In progress zarr support

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• Actually this time

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Commits on Aug 6, 2019

• Cleanup zarr.py

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Commits on Aug 7, 2019

• Improved errors for reading zarr, added support for Raw

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Commits on Aug 8, 2019

• Address scverse#188, and test it a bunch

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• Docstring for key reporting decorator

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• Make sure better-error decorator gets used

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• Gave h5ad files better read errors as well

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Commits on Aug 9, 2019

• Added helper to test AnnData equivolence

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Commits on Aug 10, 2019

• Added test for utils

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• Improve readwrite tests for raw

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• Fix scverse#192

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• Switched h5ad dataframe rep to columnar format

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• Mark test I disagree with as xfail

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• Remove warning about adding dataframes to obsm, varm, layers

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Commits on Aug 11, 2019

• Minor cleanup of h5ad.py

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• Add tests for index name IO

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• Add support for reading legacy zarr files

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• Fix backed h5ad when raw present

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• Minor test updates

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Commits on Aug 14, 2019

• Support and test np int scalars

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• Improve string support in uns

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Commits on Aug 16, 2019

• Remove old code

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• Remove _to_dict_fixed_width_arrays

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• Simple zarr chunks

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Commits on Aug 19, 2019

• Formatting pass

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Commits on Aug 23, 2019

• Typing and easier naming for h5pys.

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• Minor typing fix, added todo for raw rep, probably squash

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• Merge branch 'master' into io_refactor

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• Whoops, 4 spaces, GitHub…

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• And don’t revert obsm_names/varm_names

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• OK, this is embarrassing

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• Merge branch 'master' into io_refactor

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Commits on Aug 24, 2019

• Merge branch 'io_refactor' of https://github.com/ivirshup/anndata into local io_refactor

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• Make raw a group for hdf5 backend

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• Big update focusing on backed Raw

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• Finish cleaning up checking backed raw.X

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• Remove df_to_records_fixed_width

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Commits on Sep 3, 2019

• Merge branch 'master' into io_refactor

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Commits on Sep 5, 2019

• Fix reading backed if raw/varm not present

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• Add Group.create_group to patched h5py

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• Remove dead code for categoricals in recarrays

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• Represent categoricals the same way in hdf5 as in zarr

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• Merge branch 'io_refactor' of https://github.com/ivirshup/anndata into io_refactor

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