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Prep 0.9rc1 (#919)
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* Release notes clean up
* Format fixes + bug fixes
* Add dummy awkward-array-view class
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ivirshup authored Feb 21, 2023
1 parent e102113 commit 5a008cf
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4 changes: 3 additions & 1 deletion anndata/_core/views.py
Original file line number Diff line number Diff line change
Expand Up @@ -257,7 +257,9 @@ def as_view_awkarray(array, view_args):
ak.behavior["AwkwardArrayView"] = AwkwardArrayView

except ImportError:
pass

class AwkwardArrayView:
pass


def _resolve_idxs(old, new, adata):
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47 changes: 29 additions & 18 deletions docs/release-notes/0.9.0.rst
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@@ -1,33 +1,44 @@
0.9.0 :small:`the future`
~~~~~~~~~~~~~~~~~~~~~~~~~
0.9.0.rc1 :small:`2023-02-21`
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. rubric:: Features


* Unordered categorical columns are no longer cast to object during :func:`anndata.concat` :pr:`763` :user:`ivirshup`
* Added support for dask arrays :pr:`813` :user:`syelman` :user:`rahulbshrestha`
* `obsm`, `varm` and `uns` can now hold `AwkwardArrays <https://awkward-array.org/quickstart.html>`__ :pr:`647` :user:`giovp`, :user:`grst`, :user:`ivirshup`
* Better error messages during IO :pr:`734` :user:`flying-sheep`, :user:`ivirshup`
- Added experimental support for dask arrays :pr:`813` :user:`syelman` :user:`rahulbshrestha`
- `obsm`, `varm` and `uns` can now hold `AwkwardArrays <https://awkward-array.org/quickstart.html>`__ :pr:`647` :user:`giovp`, :user:`grst`, :user:`ivirshup`
- Added experimental functions :func:`anndata.experimental.read_dispatched` and :func:`anndata.experimental.write_dispatched` which allow customizing IO with a callback :pr:`873` :user:`ilan-gold` :user:`ivirshup`
- Better error messages during IO :pr:`734` :user:`flying-sheep`, :user:`ivirshup`
- Unordered categorical columns are no longer cast to object during :func:`anndata.concat` :pr:`763` :user:`ivirshup`

.. rubric:: Documentation

* :doc:`New tutorial <../tutorials/notebooks/anndata_dask_array>` on using `dask.array` with `AnnData` :pr:`886` :user:`syelman`
* :doc:`File format description </fileformat-prose>` now includes a more formal specification :pr:`882` :user:`ivirshup`
* Expanded docstring more documentation for ``backed`` argument of :func:`anndata.read_h5ad` :pr:`812` :user:`jeskowagner`
* Documented how to use alternative compression methods for the `h5ad` file format, see :meth:`AnnData.write_h5ad() <anndata.AnnData.write_h5ad>` :pr:`857` :user:`nigeil`
- New tutorials for experimental features

.. rubric:: Breaking changes
- :doc:`/tutorials/notebooks/anndata_dask_array` – :pr:`886` :user:`syelman`
- :doc:`/tutorials/notebooks/{read,write}_dispatched` – :pr:`scverse/anndata-tutorials#17` :user:`ilan-gold`
- :doc:`/tutorials/notebooks/awkward-arrays` – :pr:`scverse/anndata-tutorials#15` :user:`grst`
- :doc:`File format description </fileformat-prose>` now includes a more formal specification :pr:`882` :user:`ivirshup`
- :doc:`/interoperability`: new page on interoperability with other packages :pr:`831` :user:`ivirshup`
- Expanded docstring more documentation for ``backed`` argument of :func:`anndata.read_h5ad` :pr:`812` :user:`jeskowagner`
- Documented how to use alternative compression methods for the `h5ad` file format, see :meth:`AnnData.write_h5ad() <anndata.AnnData.write_h5ad>` :pr:`857` :user:`nigeil`
- General typo corrections 😅 :pr:`870` :user:`folded`

* The `AnnData` `dtype` argument no longer defaults to `float32` :pr:`854` :user:`ivirshup`
.. rubric:: Breaking changes

.. rubric:: Bug fixes
- The `AnnData` `dtype` argument no longer defaults to `float32` :pr:`854` :user:`ivirshup`
- Previously deprecated `force_dense` arugment :meth:`AnnData.write_h5ad() <anndata.AnnData.write_h5ad>` has been removed. :pr:`855` :user:`ivirshup`
- Previously deprecated behaviour around storing adjacency matrices in `uns` has been removed :pr:`866` :user:`ivirshup`

.. rubric:: Updates
.. rubric:: Other updates

* Bump minimum python version to 3.8 :pr:`820` :user:`ivirshup`
- Bump minimum python version to 3.8 :pr:`820` :user:`ivirshup`

.. rubric:: Deprecations

* :meth:`AnnData.concatenate() <anndata.AnnData.concatenate>` is now deprecated in favour of :func:`anndata.concat` :pr:`845` :user:`ivirshup`
* Previously deprecated `force_dense` arugment :meth:`AnnData.write_h5ad() <anndata.AnnData.write_h5ad>` has been removed. :pr:`855` :user:`ivirshup`
* Previously deprecate behaviour around storing adjacency matrices in `uns` has been removed :pr:`866` :user:`ivirshup`
- :meth:`AnnData.concatenate() <anndata.AnnData.concatenate>` is now deprecated in favour of :func:`anndata.concat` :pr:`845` :user:`ivirshup`

.. rubric:: Bug fixes

- Fixed order dependent outer concatenation bug :pr:`904` :user:`ivirshup`, reported by :user:`szalata`
- Fixed bug in renaming categories :pr:`790` :user:`ivirshup`, reported by :user:`perrin-isir`
- Fixed IO bug when keys in `uns` ended in `_categories` :pr:`806` :user:`ivirshup`, reported by :user:`Hrovatin`

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