Switch from using rubric in release notes

docs/conf.py

@@ -2,10 +2,13 @@
 
 import sys
 from datetime import datetime
+from functools import partial
 from importlib import metadata
 from pathlib import Path
 from typing import TYPE_CHECKING
 
+from docutils import nodes
+
 if TYPE_CHECKING:
     from sphinx.application import Sphinx
 
@@ -33,6 +36,8 @@
     ".DS_Store",
     "**.ipynb_checkpoints",
     "tutorials/notebooks/*.rst",
+    # exclude all 0.x.y.md files, but not index.md
+    "release-notes/[!i]*.md",
 ]
 pygments_style = "sphinx"
 
@@ -59,6 +64,7 @@
 myst_enable_extensions = [
     "html_image",  # So README.md can be used on github and sphinx docs
 ]
+myst_heading_anchors = 3
 
 # Generate the API documentation when building
 autosummary_generate = True
@@ -96,8 +102,8 @@
 
 
 def setup(app: Sphinx):
-    # Don’t allow broken links. DO NOT CHANGE THIS LINE, fix problems instead.
-    app.warningiserror = True
+    app.add_generic_role("small", partial(nodes.inline, classes=["small"]))
+    app.add_generic_role("smaller", partial(nodes.inline, classes=["smaller"]))
 
 
 intersphinx_mapping = dict(

docs/index.md

@@ -1,20 +1,11 @@
-```{eval-rst}
-.. role:: small
-```
-
-```{eval-rst}
-.. role:: smaller
-```
-
 ```{include} ../README.md
 ```
 
 # Latest additions
 
-```{include} release-notes/release-latest.md
-```
-
-See {doc}`/release-notes/index` for more.
+See {doc}`/release-notes/index`,
+particularly {ref}`v0.10` for the current release,
+and {ref}`v0.11` for the upcoming release,
 
 ```{toctree}
 :hidden: true

docs/news.md

@@ -1,7 +1,3 @@
-```{eval-rst}
-.. role:: small
-```
-
 # Muon paper published {small}`2022-02-02`
 
 Muon has been published in Genome Biology [^cite_bredikhin22].

docs/release-notes/0.10.0.md

@@ -1,7 +1,7 @@
+(v0.10.0)=
 ### 0.10.0 {small}`2023-10-06`
 
-```{rubric} Features
-```
+#### Features
 
 **GPU Support**
 
@@ -23,28 +23,23 @@
 * `AnnDataReadError`s have been removed. The original error is now thrown with additional information in a note {pr}`1055` {user}`ivirshup`
 
 
-```{rubric} Documentation
-```
+#### Documentation
 
 * Added zarr examples to {doc}`file format docs</fileformat-prose>` {pr}`1162` {user}`ivirshup`
 
-```{rubric} Breaking changes
-```
+#### Breaking changes
 
 * {meth}`anndata.AnnData.transpose` no longer copies unnecessarily. If you rely on the copying behavior, call `.copy` on the resulting object. {pr}`1114` {user}`ivirshup`
 
-```{rubric} Other updates
-```
+#### Other updates
 
 * Bump minimum python version to 3.9 {pr}`1117` {user}`flying-sheep`
 
-```{rubric} Deprecations
-```
+#### Deprecations
 
 * Deprecate `anndata.read`, which was just an alias for {func}`anndata.read_h5ad` {pr}`1108` {user}`ivirshup`.
 * `dtype` argument to `AnnData` constructor is now deprecated {pr}`1153` {user}`ivirshup`
 
-```{rubric} Bug fixes
-```
+#### Bug fixes
 
 * Fix shape inference on initialization when `X=None` is specified {pr}`1121` {user}`flying-sheep`

docs/release-notes/0.10.1.md

@@ -1,6 +1,6 @@
+(v0.10.1)=
 ### 0.10.1 {small}`2023-10-08`
 
-```{rubric} Bugfix
-```
+#### Bugfix
 
 * Fix `ad.concat` erroring when concatenating a categorical and object column {pr}`1171` {user}`ivirshup`

docs/release-notes/0.10.2.md

@@ -1,7 +1,7 @@
+(v0.10.2)=
 ### 0.10.2 {small}`2023-10-11`
 
-```{rubric} Bugfix
-```
+#### Bugfix
 
 * Added compatibility layer for packages relying on `anndata._core.sparse_dataset.SparseDataset`.
   Note that this API is *deprecated* and new code should use {class}`~anndata.experimental.CSRDataset`, {class}`~anndata.experimental.CSCDataset`, and {func}`~anndata.experimental.sparse_dataset` instead.
@@ -11,7 +11,6 @@
 * `as_dense` argument of `write_h5ad` no longer writes an array without encoding metadata {pr}`1193` {user}`flying-sheep`
 
 
-```{rubric} Performance
-```
+#### Performance
 
 * Improved performance of `concat_on_disk` with dense arrays in some cases {pr}`1169` {user}`selmanozleyen`

docs/release-notes/0.10.3.md

@@ -1,14 +1,12 @@
+(v0.10.3)=
 ### 0.10.3 {small}`2023-10-31`
 
-```{rubric} Bugfix
-```
+#### Bugfix
 * Prevent pandas from causing infinite recursion when setting a slice of a categorical column {pr}`1211` {user}`flying-sheep`
 
-```{rubric} Documentation
-```
+#### Documentation
 * Stop showing “Support for Awkward Arrays is currently experimental” warnings when
   reading, concatenating, slicing, or transposing AnnData objects {pr}`1182` {user}`flying-sheep`
 
-```{rubric} Other updates
-```
+#### Other updates
 * Fail canary CI job when tests raise unexpected warnings. {pr}`1182` {user}`flying-sheep`

docs/release-notes/0.10.4.md

@@ -1,14 +1,13 @@
+(v0.10.4)=
 ### 0.10.4 {small}`2024-01-04`
 
-```{rubric} Bugfix
-```
+#### Bugfix
 * Only try to use `Categorical.map(na_action=…)` in actually supported Pandas ≥2.1 {pr}`1226` {user}`flying-sheep`
 * `AnnData.__sizeof__()` support for backed datasets {pr}`1230` {user}`Neah-Ko`
 * `adata[:, []]` now returns an `AnnData` object empty on the appropriate dimensions instead of erroring {pr}`1243` {user}`ilan-gold`
 * `adata.X[mask]` works in newer `numpy` versions when `X` is `backed` {pr}`1255` {user}`ilan-gold`
 * `adata.X[...]` fixed for `X` as a `BaseCompressedSparseDataset` with `zarr` backend {pr}`1265` {user}`ilan-gold`
 * Improve read/write error reporting {pr}`1273` {user}`flying-sheep`
 
-```{rubric} Documentation
-```
+#### Documentation
 * Improve aligned mapping error messages {pr}`1252` {user}`flying-sheep`

docs/release-notes/0.10.5.md

@@ -1,19 +1,17 @@
+(v0.10.5)=
 ### 0.10.5 {small}`2024-01-25`
 
-```{rubric} Bugfix
-```
+#### Bugfix
 
 * Fix outer concatenation along variables when only a subset of objects had an entry in layers {pr}`1291` {user}`ivirshup`
 * Fix comparison of >2d arrays in `uns` during concatenation {pr}`1300` {user}`ivirshup`
 * Fix IO with awkward array version 2.5.2 {pr}`1328` {user}`ivirshup`
 * Fix bug (introduced in 0.10.4) where indexing an AnnData with `list[bool]` would return the wrong result {pr}`1332` {user}`ivirshup`
 
-```{rubric} Documentation
-```
+#### Documentation
 * Re-add search-as-you-type, this time via `readthedocs-sphinx-search` {pr}`1311` {user}`flying-sheep`
 
-```{rubric} Performance
-```
+#### Performance
 
 * `BaseCompressedSparseDataset`'s `indptr` is cached {pr}`1266` {user}`ilan-gold`
 * Improved performance when indexing backed sparse matrices with boolean masks along their major axis {pr}`1233` {user}`ilan-gold`

docs/release-notes/0.10.6.md

@@ -1,7 +1,7 @@
+(v0.10.6)=
 ### 0.10.6 {small}`2024-03-11`
 
-```{rubric} Bugfix
-```
+#### Bugfix
 
 * Defer import of zarr in test helpers, as scanpy CI job relies on them {pr}`1343` {user}`ilan-gold`
 * Writing a dataframe with non-unique column names now throws an error, instead of silently overwriting {pr}`1335` {user}`ivirshup`
@@ -11,13 +11,11 @@
 * Modified `ValueError` message for invalid `.X` during construction to show more helpful list instead of ambiguous `__name__` {pr}`1395` {user}`eroell`
 * Pin `array-api-compat!=1.5` to avoid incorrect implementation of `asarray` {pr}`1411` {user}`ivirshup`
 
-```{rubric} Documentation
-```
+#### Documentation
 
 * Type hints and docstrings for `.to_df` method are updated and fixed {pr}`1402` {user}`WeilerP`
 
-```{rubric} Development
-```
+#### Development
 
 * `anndata`'s CI now tests against minimum versions of it's dependencies. As a result, several dependencies had their minimum required version bumped. See diff for details {pr}`1314` {user}`ivirshup`
 * `anndata` now tests against Python 3.12 {pr}`1373` {user}`ivirshup`

docs/release-notes/0.10.7.md

@@ -1,3 +1,4 @@
+(v0.10.7)=
 ### 0.10.7 {small}`2024-04-09`
 
 ```{rubric} Bugfix

docs/release-notes/0.10.8.md

@@ -1,3 +1,4 @@
+(0.10.8)=
 ### 0.10.8 {small}`2024-06-20`
 
 ```{rubric} Bugfix

docs/release-notes/0.10.9.md

@@ -1,3 +1,4 @@
+(0.10.9)=
 ### 0.10.9 {small}`the future`
 
 ```{rubric} Bugfix

docs/release-notes/0.11.0.md

@@ -1,23 +1,20 @@
+(v0.11.0)=
 ### 0.11.0 {small}`the future`
 
-```{rubric} Features
-```
+#### Features
+
 * Allow `axis` parameter of e.g. :func:`anndata.concat` to accept `'obs'` and `'var` {pr}`1244` {user}`flying-sheep`
 * Add `settings` object with methods for altering internally-used options, like checking for uniqueness on `obs`' index {pr}`1270` {user}`ilan-gold`
 * Add `should_remove_unused_categories` option to `anndata.settings` to override current behavior.  Default is `True` (i.e., previous behavior).  Please refer to the [documentation](https://anndata.readthedocs.io/en/latest/generated/anndata.settings.html) for usage.  {pr}`1340` {user}`ilan-gold`
 * `scipy.sparse.csr_array` and `scipy.sparse.csc_array` are now supported when constructing `AnnData` objects {pr}`1028` {user}`ilan-gold` {user}`isaac-virshup`
 * Add `should_check_uniqueness` option to `anndata.settings` to override current behavior.  Default is `True` (i.e., previous behavior).  Please refer to the [documentation](https://anndata.readthedocs.io/en/latest/generated/anndata.settings.html) for usage.  {pr}`1507` {user}`ilan-gold`
 
-```{rubric} Bugfix
-```
+#### Bugfix
 
-```{rubric} Documentation
-```
+#### Documentation
 
-```{rubric} Performance
-```
+#### Performance
 
-```{rubric} Breaking
-```
+#### Breaking
 
 * Removed deprecated modules `anndata.core` and `anndata.readwrite` {pr}`1197` {user}`ivirshup`

docs/release-notes/0.4.0.md

@@ -1,3 +1,4 @@
+(v0.4.0)=
 ### 0.4.0 {small}`23 December, 2017`
 
 - read/write [.loom](https://loompy.org) files

docs/release-notes/0.5.0.md

@@ -1,3 +1,4 @@
+(v0.5.0)=
 ### 0.5.0 {small}`9 February, 2018`
 
 - inform about duplicates in {class}`~anndata.AnnData.var_names` and resolve them using {func}`~anndata.AnnData.var_names_make_unique`

docs/release-notes/0.6.0.md

@@ -1,28 +1,4 @@
-### 0.6.\* {small}`2019-*-*`
-
-- better support for aligned mappings (obsm, varm, layers)
-  `0.6.22` {pr}`155` {smaller}`I Virshup`
-- convenience accessors {func}`~anndata.AnnData.obs_vector`, {func}`~anndata.AnnData.var_vector` for 1d arrays.
-  `0.6.21` {pr}`144` {smaller}`I Virshup`
-- compatibility with Scipy >=1.3 by removing `IndexMixin` dependency.
-  `0.6.20` {pr}`151` {smaller}`P Angerer`
-- bug fix for second-indexing into views.
-  `0.6.19` {smaller}`P Angerer`
-- bug fix for reading excel files.
-  `0.6.19` {smaller}`A Wolf`
-- changed default compression to `None` in {func}`~anndata.AnnData.write_h5ad` to speed up read and write, disk space use is usually less critical.
-  `0.6.16` {smaller}`A Wolf`
-- maintain dtype upon copy.
-  `0.6.13` {smaller}`A Wolf`
-- {attr}`~anndata.AnnData.layers` inspired by [.loom](https://loompy.org) files allows their information lossless reading via {func}`~anndata.read_loom`.
-  `0.6.7`–`0.6.9` {pr}`46` & {pr}`48` {smaller}`S Rybakov`
-- support for reading zarr files: {func}`~anndata.read_zarr`
-  `0.6.7` {pr}`38` {smaller}`T White`
-- initialization from pandas DataFrames
-  `0.6.` {smaller}`A Wolf`
-- iteration over chunks {func}`~anndata.AnnData.chunked_X` and {func}`~anndata.AnnData.chunk_X`
-  `0.6.1` {pr}`20` {smaller}`S Rybakov`
-
+(v0.6.0)=
 ### 0.6.0 {small}`1 May, 2018`
 
 - compatibility with Seurat converter

docs/release-notes/0.6.x.md

@@ -0,0 +1,25 @@
+(v0.6.x)=
+### 0.6.\* {small}`2019-*-*`
+
+- better support for aligned mappings (obsm, varm, layers)
+  `0.6.22` {pr}`155` {smaller}`I Virshup`
+- convenience accessors {func}`~anndata.AnnData.obs_vector`, {func}`~anndata.AnnData.var_vector` for 1d arrays.
+  `0.6.21` {pr}`144` {smaller}`I Virshup`
+- compatibility with Scipy >=1.3 by removing `IndexMixin` dependency.
+  `0.6.20` {pr}`151` {smaller}`P Angerer`
+- bug fix for second-indexing into views.
+  `0.6.19` {smaller}`P Angerer`
+- bug fix for reading excel files.
+  `0.6.19` {smaller}`A Wolf`
+- changed default compression to `None` in {func}`~anndata.AnnData.write_h5ad` to speed up read and write, disk space use is usually less critical.
+  `0.6.16` {smaller}`A Wolf`
+- maintain dtype upon copy.
+  `0.6.13` {smaller}`A Wolf`
+- {attr}`~anndata.AnnData.layers` inspired by [.loom](https://loompy.org) files allows their information lossless reading via {func}`~anndata.read_loom`.
+  `0.6.7`–`0.6.9` {pr}`46` & {pr}`48` {smaller}`S Rybakov`
+- support for reading zarr files: {func}`~anndata.read_zarr`
+  `0.6.7` {pr}`38` {smaller}`T White`
+- initialization from pandas DataFrames
+  `0.6.` {smaller}`A Wolf`
+- iteration over chunks {func}`~anndata.AnnData.chunked_X` and {func}`~anndata.AnnData.chunk_X`
+  `0.6.1` {pr}`20` {smaller}`S Rybakov`

docs/release-notes/0.7.0.md

@@ -1,3 +1,4 @@
+(v0.7.0)=
 ### 0.7.0 {small}`22 January, 2020`
 
 ```{warning}
@@ -36,8 +37,7 @@ Breaking changes introduced between `0.6.22.post1` and `0.7`:
 - DataFrames are now allowed as values in {attr}`~anndata.AnnData.obsm` and {attr}`~anndata.AnnData.varm`.
 - All mapping attributes now share an implementation and will have the same behaviour. PR {pr}`164`.
 
-```{rubric} Miscellaneous improvements
-```
+#### Miscellaneous improvements
 
 - Mapping attributes now have ipython tab completion (e.g. `adata.obsm["\\t` can provide suggestions) PR {pr}`183`.
 - {class}`~anndata.AnnData` attributes are now delete-able (e.g. `del adata.raw`) PR {pr}`242`.

docs/release-notes/0.7.2.md

@@ -1,3 +1,4 @@
+(v0.7.2)=
 ### 0.7.2 {small}`15 May, 2020`
 
 ~~~{rubric} Concatenation overhaul {smaller}`I Virshup`
@@ -8,17 +9,15 @@
 - Fill value for outer joins can now be specified
 - Expect improvements in performance, see {issue}`303`
 
-```{rubric} Functionality
-```
+#### Functionality
 
 - {attr}`~anndata.AnnData.obsp` and {attr}`~anndata.AnnData.varp` can now be transposed {pr}`370` {smaller}`A Wolf`
 - {meth}`~anndata.AnnData.obs_names_make_unique` is now better at making values unique, and will warn if ambiguities arise {pr}`345` {smaller}`M Weiden`
 - {attr}`~anndata.AnnData.obsp` is now preferred for storing pairwise relationships between observations. In practice, this means there will be deprecation warnings and reformatting applied to objects which stored connectivities under `uns["neighbors"]`. Square matrices in {attr}`~anndata.AnnData.uns` will no longer be sliced (use `.{obs,var}p` instead). {pr}`337` {smaller}`I Virshup`
 - {class}`~anndata.ImplicitModificationWarning` is now exported {pr}`315` {smaller}`P Angerer`
 - Better support for {class}`~numpy.ndarray` subclasses stored in `AnnData` objects {pr}`335` {smaller}`michalk8`
 
-```{rubric} Bug fixes
-```
+#### Bug fixes
 
 - Fixed inplace modification of {class}`~pandas.Index` objects by the make unique function {pr}`348` {smaller}`I Virshup`
 - Passing ambiguous keys to {meth}`~anndata.AnnData.obs_vector` and {meth}`~anndata.AnnData.var_vector` now throws errors {pr}`340` {smaller}`I Virshup`

docs/release-notes/0.7.3.md

@@ -1,6 +1,6 @@
+(v0.7.3)=
 ### 0.7.3 {small}`20 May, 2020`
 
-```{rubric} Bug fixes
-```
+#### Bug fixes
 
 - Fixed bug where graphs used too much memory when copying {pr}`381` {smaller}`I Virshup`