From 40a48781f268dc045001256f1943df2d3db009a2 Mon Sep 17 00:00:00 2001 From: Isaac Virshup Date: Sat, 9 Sep 2023 15:17:50 +0200 Subject: [PATCH] Doc preparation for 0.10.0rc1 (#1129) * Doc preparation for 0.10.0rc1 * Update release notes * Final touches --- anndata/experimental/merge.py | 1 + docs/api.md | 9 +++++++++ docs/index.md | 12 +++++++----- docs/release-notes/0.10.0.md | 28 ++++++++++++++++++++-------- docs/release-notes/index.md | 19 +++++++++++++++++++ docs/release-notes/release-latest.md | 19 ------------------- 6 files changed, 56 insertions(+), 32 deletions(-) diff --git a/anndata/experimental/merge.py b/anndata/experimental/merge.py index 87f986c7c..711bcd52d 100644 --- a/anndata/experimental/merge.py +++ b/anndata/experimental/merge.py @@ -427,6 +427,7 @@ def concat_on_disk( arrays use the max_loaded_elems argument; for dense arrays see the Dask documentation, as the Dask concatenation function is used to concatenate dense arrays in this function + Params ------ in_files diff --git a/docs/api.md b/docs/api.md index 3c14e3500..bf9761be1 100644 --- a/docs/api.md +++ b/docs/api.md @@ -103,6 +103,15 @@ Interface for accessing on-disk sparse data: experimental.CSCDataset ``` +Out of core concatenation + +```{eval-rst} +.. autosummary:: + :toctree: generated/ + + experimental.concat_on_disk +``` + Low level methods for reading and writing elements of an `` AnnData` `` object to a store: ```{eval-rst} diff --git a/docs/index.md b/docs/index.md index f9fc8b2d5..3a3324a6e 100644 --- a/docs/index.md +++ b/docs/index.md @@ -9,16 +9,13 @@ ```{include} ../README.md ``` -# News - -```{include} news.md -``` - # Latest additions ```{include} release-notes/release-latest.md ``` +See {doc}`/release-notes/index` for more. + ```{toctree} :hidden: true :maxdepth: 1 @@ -33,3 +30,8 @@ contributing release-notes/index references ``` + +# News + +```{include} news.md +``` diff --git a/docs/release-notes/0.10.0.md b/docs/release-notes/0.10.0.md index 77405a309..eba157b3d 100644 --- a/docs/release-notes/0.10.0.md +++ b/docs/release-notes/0.10.0.md @@ -1,24 +1,36 @@ -### 0.10.0 {small}`the future` +### 0.10.0rc1 {small}`2023-09-09` + +````{note} +anndata 0.10.0 is currently available as a release candidate for testing. You can install this version of anndata with: + +``` +pip install -U --pre anndata +``` + +We expect to make a full release by October. +```` ```{rubric} Features ``` **GPU Support** -* Support for dense and sparse cupy arrays {pr}`1066` {user}`ivirshup` +* Dense and sparse [`CuPy`](https://docs.cupy.dev/l) arrays are now supported {pr}`1066` {user}`ivirshup` + * Once you have `CuPy` arrays in your anndata, use it with: [`rapids-singlecell`](https://rapids-singlecell.readthedocs.io/en/latest/index.html) from v0.9+ * anndata now has GPU enabled CI. Made possibly by a grant from [CZI's EOSS program](https://chanzuckerberg.com/eoss/) and managed via [Cirun](https://Cirun.io) {pr}`1066` {pr}`1084` {user}`Zethson` {user}`ivirshup` +**Out of core** + +* Concatenate on-disk anndata objects with {func}`anndata.experimental.concat_on_disk` {pr}`955` {user}`selmanozleyen` +* AnnData can now hold dask arrays with `scipy.sparse.spmatrix` chunks {pr}`1114` {user}`ivirshup` +* Public API for interacting with on disk sparse arrays: {func}`~anndata.experimental.sparse_dataset`, {class}`~anndata.experimental.CSRDataset`, and {class}`~anndata.experimental.CSCDataset` {pr}`765` {user}`ilan-gold` {user}`ivirshup` + **Improved errors and warnings** * Improved error messages when combining dataframes with duplicated column names {pr}`1029` {user}`ivirshup` * Improved warnings when modifying views of `AlingedMappings` {pr}`1016` {user}`flying-sheep` {user}`ivirshup` * `AnnDataReadError`s have been removed. The original error is now thrown with additional information in a note {pr}`1055` {user}`ivirshup` -**Out of core** - -* AnnData can now hold dask arrays with `scipy.sparse.spmatrix` chunks {pr}`1114` {user}`ivirshup` -* Export {func}`~anndata.experimental.sparse_dataset`, {class}`~anndata.experimental.CSRDataset`, and {class}`~anndata.experimental.CSCDataset` from `experimental` to allow for use with `zarr` stores {pr}`765` {user}`ilan-gold` {user}`ivirshup` - ```{rubric} Documentation ``` @@ -32,7 +44,7 @@ ```{rubric} Other updates ``` -- Bump minimum python version to 3.9 {pr}`1117` {user}`flying-sheep` +* Bump minimum python version to 3.9 {pr}`1117` {user}`flying-sheep` ```{rubric} Deprecations ``` diff --git a/docs/release-notes/index.md b/docs/release-notes/index.md index 7a1832bca..b808c6167 100644 --- a/docs/release-notes/index.md +++ b/docs/release-notes/index.md @@ -3,6 +3,25 @@ ```{include} /release-notes/release-latest.md ``` +## Version 0.9 + +```{include} /release-notes/0.9.2.md +``` + +```{include} /release-notes/0.9.1.md +``` + +```{include} /release-notes/0.9.0.md +``` + +## Version 0.8 + +```{include} /release-notes/0.8.1.md +``` + +```{include} /release-notes/0.8.0.md +``` + ## Version 0.7 ```{include} /release-notes/0.7.8.md diff --git a/docs/release-notes/release-latest.md b/docs/release-notes/release-latest.md index 83902ff47..0a89b1582 100644 --- a/docs/release-notes/release-latest.md +++ b/docs/release-notes/release-latest.md @@ -2,22 +2,3 @@ ```{include} /release-notes/0.10.0.md ``` - -## Version 0.9 - -```{include} /release-notes/0.9.2.md -``` - -```{include} /release-notes/0.9.1.md -``` - -```{include} /release-notes/0.9.0.md -``` - -## Version 0.8 - -```{include} /release-notes/0.8.1.md -``` - -```{include} /release-notes/0.8.0.md -```