Code

Specs for all elements#554

Code

Merged

ivirshup merged 44 commits intoscverse:masterscverse/anndata:masterfrom ivirshup:specs-basicivirshup/anndata:specs-basicCopy head branch name to clipboardDec 25, 2021

+1,457-660

Commits

Commits on Apr 15, 2021

• Initial replacement

  Show description for 56f4fc8
  ivirshup

  committed
  56f4fc8

  Copy full SHA for 56f4fc8

• Fixed most backed tests

  ivirshup

  committed
  0c7b1f1

  Copy full SHA for 0c7b1f1

• Fix for masked arrays

  ivirshup

  committed
  473efb8

  Copy full SHA for 473efb8

• Fix sparse dataset indexing return type (needs test)

  ivirshup

  committed
  d1246a4

  Copy full SHA for d1246a4

Commits on Nov 17, 2021

• Merge branch 'master' into specs-basic

  ivirshup

  committed
  9099e58

  Copy full SHA for 9099e58

• Remove old io interface for h5ad

  ivirshup

  committed
  00f7065

  Copy full SHA for 00f7065

• Update spec readers to use permissive hdf5 attribute reader

  ivirshup

  committed
  206cad7

  Copy full SHA for 206cad7

• Rename _read_hdf5_attribute to _read_attr

  ivirshup

  committed
  d20cd5c

  Copy full SHA for d20cd5c

• Add OldFormatWarning, and make sure new files don't throw one

  Show description for 38c12b5
  ivirshup

  committed
  38c12b5

  Copy full SHA for 38c12b5

• Merge branch 'master' into specs-basic

  ivirshup

  committed
  8938d36

  Copy full SHA for 8938d36

• Fix some typing warnings

  ivirshup

  committed
  5437858

  Copy full SHA for 5437858

• Add scanpy requirement for test

  ivirshup

  committed
  665f124

  Copy full SHA for 665f124

• Reorganize warning imports to have short paths

  ivirshup

  committed
  c874776

  Copy full SHA for c874776

• Support AnnData's in .uns

  ivirshup

  committed
  a4259f7

  Copy full SHA for a4259f7

Commits on Nov 18, 2021

• Minor spec cleanup

  ivirshup

  committed
  c95d5fe

  Copy full SHA for c95d5fe

• Hide some warnings at test time

  ivirshup

  committed
  c0112fc

  Copy full SHA for c0112fc

Commits on Nov 23, 2021

• Merge branch 'master' into specs-basic

  ivirshup

  committed
  2b6d7d1

  Copy full SHA for 2b6d7d1

• Make test collection work

  ivirshup

  committed
  b6f3dfe

  Copy full SHA for b6f3dfe

• Remove copies of warning definitions

  ivirshup

  committed
  c05e025

  Copy full SHA for c05e025

• Fix pre-commit check

  ivirshup

  committed
  d497ad4

  Copy full SHA for d497ad4

• Remove copies of warning definitions

  ivirshup

  committed
  a055494

  Copy full SHA for a055494

• Add support for zarr recarrays

  ivirshup

  committed
  cce53c5

  Copy full SHA for cce53c5

• Fix some small zarr compatability issues

  Show description for b0d0d08
  ivirshup

  committed
  b0d0d08

  Copy full SHA for b0d0d08

Commits on Dec 14, 2021

• Deprecations for read_attribute and write_attribute

  ivirshup

  committed
  5712bf9

  Copy full SHA for 5712bf9

• Added support for categorical arrays to test helpers

  ivirshup

  committed
  ce29ab2

  Copy full SHA for ce29ab2

• Add basic tests for per spec writing

  ivirshup

  committed
  e8b0f34

  Copy full SHA for e8b0f34

• Add tests for writing raw

  ivirshup

  committed
  b8612f3

  Copy full SHA for b8612f3

• More doc-string for write_elem

  ivirshup

  committed
  f22e17b

  Copy full SHA for f22e17b

• Basic zarr backwards compat (needs cleanup)

  ivirshup

  committed
  ffc09a6

  Copy full SHA for ffc09a6

Commits on Dec 20, 2021

• Write encoding type information with .write_* methods

  ivirshup

  committed
  704f6f6

  Copy full SHA for 704f6f6

• Cleanup _io/zarr.py and remove EncodingVersions type

  ivirshup

  committed
  bc917c7

  Copy full SHA for bc917c7

• Remove some unused imports from h5ad.py

  ivirshup

  committed
  5e7a072

  Copy full SHA for 5e7a072

• Also test zarr backend for anndatas in uns

  ivirshup

  committed
  2a52fd1

  Copy full SHA for 2a52fd1

• Fix read_dataframe reading strings as bytes for v0.1.0 dataframe encoding

  ivirshup

  committed
  c7d63ca

  Copy full SHA for c7d63ca

• Start updating docs for fileformat

  ivirshup

  committed
  6e73262

  Copy full SHA for 6e73262

Commits on Dec 21, 2021

• Allow calling write_elem(f, '/', v)

  ivirshup

  committed
  ffb7add

  Copy full SHA for ffb7add

• Start backwards compat tests

  ivirshup

  committed
  c6cbac9

  Copy full SHA for c6cbac9

• Reorganize specs module

  ivirshup

  committed
  2c9a54e

  Copy full SHA for 2c9a54e

• Slightly more useful OldFormatWarnings

  ivirshup

  committed
  4b4553d

  Copy full SHA for 4b4553d

• Ignore OldFormatWarnings on case by case basis. Will be loud until scverse/scanpy#2090 is fixed

  ivirshup

  committed
  49ea48f

  Copy full SHA for 49ea48f

Commits on Dec 25, 2021

• Use read_elem when possible

  ivirshup

  committed
  19e2b38

  Copy full SHA for 19e2b38

• Remove redundant dataframe reading code

  ivirshup

  committed
  d4481cf

  Copy full SHA for d4481cf

• Remove unused functions

  ivirshup

  committed
  f8573a0

  Copy full SHA for f8573a0

• Improve formating of write errors

  ivirshup

  committed
  ee1e3df

  Copy full SHA for ee1e3df