Switch from using rubric

scverse · Jan 26, 2024 · c2beff2 · c2beff2
1 parent e07477d
commit c2beff2
Show file tree

Hide file tree

Showing 21 changed files with 53 additions and 106 deletions.
diff --git a/docs/release-notes/0.10.0.md b/docs/release-notes/0.10.0.md
@@ -1,7 +1,6 @@
 ### 0.10.0 {small}`2023-10-06`
 
-```{rubric} Features
-```
+#### Features
 
 **GPU Support**
 
@@ -23,28 +22,23 @@
 * `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`
diff --git a/docs/release-notes/0.10.1.md b/docs/release-notes/0.10.1.md
@@ -1,6 +1,5 @@
 ### 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`
diff --git a/docs/release-notes/0.10.2.md b/docs/release-notes/0.10.2.md
@@ -1,7 +1,6 @@
 ### 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 +10,6 @@
 * `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`
diff --git a/docs/release-notes/0.10.3.md b/docs/release-notes/0.10.3.md
@@ -1,14 +1,11 @@
 ### 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`
diff --git a/docs/release-notes/0.10.4.md b/docs/release-notes/0.10.4.md
@@ -1,14 +1,12 @@
 ### 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`
diff --git a/docs/release-notes/0.10.5.md b/docs/release-notes/0.10.5.md
@@ -1,19 +1,16 @@
 ### 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`
diff --git a/docs/release-notes/0.10.6.md b/docs/release-notes/0.10.6.md
@@ -1,10 +1,7 @@
 ### 0.10.6 {small}`the future`
 
-```{rubric} Bugfix
-```
+#### Bugfix
 
-```{rubric} Documentation
-```
+#### Documentation
 
-```{rubric} Performance
-```
+#### Performance
diff --git a/docs/release-notes/0.11.0.md b/docs/release-notes/0.11.0.md
@@ -1,18 +1,13 @@
 ### 0.11.0 {small}`the future`
 
-```{rubric} Features
-```
+#### Features
 
-```{rubric} Bugfix
-```
+#### Bugfix
 
-```{rubric} Documentation
-```
+#### Documentation
 
-```{rubric} Performance
-```
+#### Performance
 
-```{rubric} Breaking
-```
+#### Breaking
 
 * Removed deprecated modules `anndata.core` and `anndata.readwrite` {pr}`1197` {user}`ivirshup`
diff --git a/docs/release-notes/0.7.0.md b/docs/release-notes/0.7.0.md
@@ -36,8 +36,7 @@ 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`.

diff --git a/docs/release-notes/0.7.2.md b/docs/release-notes/0.7.2.md
@@ -8,17 +8,15 @@
 - 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`

diff --git a/docs/release-notes/0.7.3.md b/docs/release-notes/0.7.3.md
@@ -1,6 +1,5 @@
 ### 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`
diff --git a/docs/release-notes/0.7.4.md b/docs/release-notes/0.7.4.md
@@ -6,13 +6,11 @@
 - New function {func}`anndata.concat` for concatenating `AnnData` objects along either observations or variables
 - New documentation section: {doc}`/concatenation`
 
-```{rubric} Functionality
-```
+#### Functionality
 
 - AnnData object created from dataframes with sparse values will have sparse `.X` {pr}`395` {smaller}`I Virshup`
 
-```{rubric} Bug fixes
-```
+#### Bug fixes
 
 - Fixed error from `AnnData.concatenate` by bumping minimum versions of numpy and pandas {issue}`385`
 - Fixed colors being incorrectly changed when `AnnData` object was subset {pr}`388`
diff --git a/docs/release-notes/0.7.5.md b/docs/release-notes/0.7.5.md
@@ -1,12 +1,10 @@
 ### 0.7.5 {small}`12 November, 2020`
 
-```{rubric} Functionality
-```
+#### Functionality
 
 - Added ipython tab completion and a useful return from `.keys` to `adata.uns` {pr}`415` {smaller}`I Virshup`
 
-```{rubric} Bug fixes
-```
+#### Bug fixes
 
 - Compatibility with `h5py>=3` strings {pr}`444` {smaller}`I Virshup`
 - Allow `adata.raw = None`, as is documented {pr}`447` {smaller}`I Virshup`

diff --git a/docs/release-notes/0.7.6.md b/docs/release-notes/0.7.6.md
@@ -1,13 +1,11 @@
 ### 0.7.6 {small}`11 April, 2021`
 
-```{rubric} New features
-```
+#### New features
 
 - Added {meth}`anndata.AnnData.to_memory` for returning an in memory object from a backed one {pr}`470` {pr}`542` {smaller}`V Bergen` {smaller}`I Virshup`
 - {meth}`anndata.AnnData.write_loom` now writes `obs_names` and `var_names` using the `Index`'s `.name` attribute, if set {pr}`538` {smaller}`I Virshup`
 
-```{rubric} Bug fixes
-```
+#### Bug fixes
 
 - Fixed bug where `np.str_` column names errored at write time {pr}`457` {smaller}`I Virshup`
 - Fixed "value.index does not match parent’s axis 0/1 names" error triggered when a data frame is stored in obsm/varm after obs_names/var_names is updated {pr}`461` {smaller}`G Eraslan`
@@ -17,8 +15,7 @@
 - Fixed copying a backed `AnnData` from changing which file the original object points at {pr}`533` {smaller}`ilia-kats`
 - Fixed a bug where calling `AnnData.concatenate` an `AnnData` with no variables would error {pr}`537` {smaller}`I Virshup`
 
-```{rubric} Deprecations
-```
+#### Deprecations
 
 - Passing positional arguments to {func}`anndata.read_loom` besides the path is now deprecated {pr}`538` {smaller}`I Virshup`
 - {func}`anndata.read_loom` arguments `obsm_names` and `varm_names` are now deprecated in favour of `obsm_mapping` and `varm_mapping` {pr}`538` {smaller}`I Virshup`
diff --git a/docs/release-notes/0.7.7.md b/docs/release-notes/0.7.7.md
@@ -1,14 +1,12 @@
 ### 0.7.7 {small}`9 November, 2021`
 
-```{rubric} Bug fixes
-```
+#### Bug fixes
 
 - Fixed propagation of import error when importing `write_zarr` but not all dependencies are installed {pr}`579` {smaller}`R Hillje`
 - Fixed issue with `.uns` sub-dictionaries being referenced by copies {pr}`576` {smaller}`I Virshup`
 - Fixed out-of-bounds integer indices not raising {class}`IndexError` {pr}`630` {smaller}`M Klein`
 - Fixed backed `SparseDataset` indexing with scipy 1.7.2 {pr}`638` {smaller}`I Virshup`
 
-```{rubric} Development processes
-```
+#### Development processes
 
 - Use PEPs 621 (standardized project metadata), 631 (standardized dependencies), and 660 (standardized editable installs) {pr}`639` {smaller}`I Virshup`
diff --git a/docs/release-notes/0.7.8.md b/docs/release-notes/0.7.8.md
@@ -1,6 +1,5 @@
 ### 0.7.8 {small}`9 November, 2021`
 
-```{rubric} Bug fixes
-```
+#### Bug fixes
 
 - Re-include test helpers {pr}`641` {smaller}`I Virshup`
diff --git a/docs/release-notes/0.8.0.md b/docs/release-notes/0.8.0.md
@@ -1,7 +1,6 @@
 ### 0.8.0 {small}`14th March, 2022`
 
-```{rubric} IO Specification
-```
+#### IO Specification
 
 ```{warning}
 The on disk format of AnnData objects has been updated with this release.
@@ -17,8 +16,7 @@ This should make it much easier to support new datatypes, use partial access, an
 - Support for nullable integer and boolean data arrays. More data types to come!
 - Experimental support for low level access to the IO API via {func}`~anndata.experimental.read_elem` and {func}`~anndata.experimental.write_elem`
 
-```{rubric} Features
-```
+#### Features
 
 - Added PyTorch dataloader {class}`~anndata.experimental.AnnLoader` and lazy concatenation object {class}`~anndata.experimental.AnnCollection`. See the [tutorials] {pr}`416` {smaller}`S Rybakov`
 - Compatibility with `h5ad` files written from Julia {pr}`569` {smaller}`I Kats`
@@ -29,15 +27,13 @@ This should make it much easier to support new datatypes, use partial access, an
 - Removed hard `xlrd` dependency {smaller}`I Virshup`
 - `obs` and `var` dataframes are no longer copied by default on `AnnData` instantiation {issue}`371` {smaller}`I Virshup`
 
-```{rubric} Bug fixes
-```
+#### Bug fixes
 
 - Fixed issue where `.copy` was creating sparse matrices views when copying {pr}`670` {smaller}`michalk8`
 - Fixed issue where `.X` matrix read in from `zarr` would always have `float32` values {pr}`701` {smaller}`I Virshup`
 - `` Raw.to_adata` `` now includes `obsp` in the output {pr}`404` {smaller}`G Eraslan`
 
-```{rubric} Dependencies
-```
+#### Dependencies
 
 - `xlrd` dropped as a hard dependency
 - Now requires `h5py` `v3.0.0` or newer

diff --git a/docs/release-notes/0.8.1.md b/docs/release-notes/0.8.1.md
@@ -1,11 +1,9 @@
 ### 0.8.1 {small}`the future`
 
-```{rubric} Bug fixes
-```
+#### Bug fixes
 
 - Fix warning from `rename_categories` {pr}`790` {smaller}`I Virshup`
 - Remove backwards compat checks for categories in `uns` when we can tell the file is new enough {pr}`790` {smaller}`I Virshup`
 - Categorical arrays are now created with a python `bool` instead of a `numpy.bool_` {pr}`856`
 
-```{rubric} Documentation
-```
+#### Documentation
diff --git a/docs/release-notes/0.9.0.md b/docs/release-notes/0.9.0.md
@@ -1,16 +1,14 @@
 ### 0.9.0 {small}`2023-04-11`
 
-```{rubric} Features
-```
+#### Features
 
 - 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
-```
+#### Documentation
 
 - New tutorials for experimental features
 
@@ -28,25 +26,21 @@
 
 - General typo corrections 😅 {pr}`870` {user}`folded`
 
-```{rubric} Breaking changes
-```
+#### Breaking changes
 
 - The `AnnData` `dtype` argument no longer defaults to `float32` {pr}`854` {user}`ivirshup`
 - Previously deprecated `force_dense` argument {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} Other updates
-```
+#### Other updates
 
 - Bump minimum python version to 3.8 {pr}`820` {user}`ivirshup`
 
-```{rubric} Deprecations
-```
+#### Deprecations
 
 - {meth}`AnnData.concatenate() <anndata.AnnData.concatenate>` is now deprecated in favour of {func}`anndata.concat` {pr}`845` {user}`ivirshup`
 
-```{rubric} Bug fixes
-```
+#### 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`

diff --git a/docs/release-notes/0.9.1.md b/docs/release-notes/0.9.1.md
@@ -1,6 +1,5 @@
 ### 0.9.1 {small}`2023-04-11`
 
-```{rubric} Bugfix
-```
+#### Bugfix
 
 * Fixing windows support {pr}`958` {user}`Koncopd`