From 5a008cf3fb4337fdeaff7629989d088f61353fff Mon Sep 17 00:00:00 2001 From: Isaac Virshup Date: Tue, 21 Feb 2023 17:26:05 +0100 Subject: [PATCH] Prep 0.9rc1 (#919) * Release notes clean up * Format fixes + bug fixes * Add dummy awkward-array-view class --- anndata/_core/views.py | 4 ++- docs/release-notes/0.9.0.rst | 47 ++++++++++++++++++++++-------------- 2 files changed, 32 insertions(+), 19 deletions(-) diff --git a/anndata/_core/views.py b/anndata/_core/views.py index 514337f83..4604a6a37 100644 --- a/anndata/_core/views.py +++ b/anndata/_core/views.py @@ -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): diff --git a/docs/release-notes/0.9.0.rst b/docs/release-notes/0.9.0.rst index b3fb2c755..2413fe594 100644 --- a/docs/release-notes/0.9.0.rst +++ b/docs/release-notes/0.9.0.rst @@ -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 `__ :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 `__ :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 ` 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() ` :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 ` 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() ` :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() ` 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() ` is now deprecated in favour of :func:`anndata.concat` :pr:`845` :user:`ivirshup` -* Previously deprecated `force_dense` arugment :meth:`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() ` 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` \ No newline at end of file