From c2beff2cb74aa534ca4a273312548da3d49cacd3 Mon Sep 17 00:00:00 2001 From: Isaac Virshup Date: Fri, 26 Jan 2024 13:21:46 +0000 Subject: [PATCH] Switch from using rubric --- docs/release-notes/0.10.0.md | 18 ++++++------------ docs/release-notes/0.10.1.md | 3 +-- docs/release-notes/0.10.2.md | 6 ++---- docs/release-notes/0.10.3.md | 9 +++------ docs/release-notes/0.10.4.md | 6 ++---- docs/release-notes/0.10.5.md | 9 +++------ docs/release-notes/0.10.6.md | 9 +++------ docs/release-notes/0.11.0.md | 15 +++++---------- docs/release-notes/0.7.0.md | 3 +-- docs/release-notes/0.7.2.md | 6 ++---- docs/release-notes/0.7.3.md | 3 +-- docs/release-notes/0.7.4.md | 6 ++---- docs/release-notes/0.7.5.md | 6 ++---- docs/release-notes/0.7.6.md | 9 +++------ docs/release-notes/0.7.7.md | 6 ++---- docs/release-notes/0.7.8.md | 3 +-- docs/release-notes/0.8.0.md | 12 ++++-------- docs/release-notes/0.8.1.md | 6 ++---- docs/release-notes/0.9.0.md | 18 ++++++------------ docs/release-notes/0.9.1.md | 3 +-- docs/release-notes/0.9.2.md | 3 +-- 21 files changed, 53 insertions(+), 106 deletions(-) diff --git a/docs/release-notes/0.10.0.md b/docs/release-notes/0.10.0.md index 01520e33c..b63529544 100644 --- 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` {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 index 2b775c696..c078489ec 100644 --- 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 index 411d6a072..975aa450f 100644 --- 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 index 9b39925e8..64aad8f1f 100644 --- 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 index 5588f534a..eae0d9324 100644 --- a/docs/release-notes/0.10.4.md +++ b/docs/release-notes/0.10.4.md @@ -1,7 +1,6 @@ ### 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` @@ -9,6 +8,5 @@ * `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 index 8ffb759a6..5b0fba7df 100644 --- 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 index abdb08924..3702f4103 100644 --- 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 index 4e2e332db..f6e34f873 100644 --- 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 index c81970d2d..89028b61f 100644 --- 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 index bf9766cd7..06011fac3 100644 --- a/docs/release-notes/0.7.2.md +++ b/docs/release-notes/0.7.2.md @@ -8,8 +8,7 @@ - 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` @@ -17,8 +16,7 @@ - {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 index f03be2ab6..36c8d8aa8 100644 --- 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 index 16efc35db..9514a21da 100644 --- 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 index 9000c7847..3146e2226 100644 --- 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 index 8fc87257a..4529ed167 100644 --- 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 index 411f7f7f3..ecc7ba8ec 100644 --- 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 index 0ca52a092..a02a57892 100644 --- 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 index 6b9bec31b..facb3d1b8 100644 --- 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 index 8de88d195..888d1ba92 100644 --- 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 index 4e56178fb..e4b046344 100644 --- a/docs/release-notes/0.9.0.md +++ b/docs/release-notes/0.9.0.md @@ -1,7 +1,6 @@ ### 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` @@ -9,8 +8,7 @@ - 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() ` 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() ` 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 index 30c7ac7fb..3e0f01a0d 100644 --- 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` diff --git a/docs/release-notes/0.9.2.md b/docs/release-notes/0.9.2.md index fb798e3e4..eb67b13c3 100644 --- a/docs/release-notes/0.9.2.md +++ b/docs/release-notes/0.9.2.md @@ -1,7 +1,6 @@ ### 0.9.2 {small}`2023-07-25` -```{rubric} Bugfix -``` +#### Bugfix * Views of `awkward.Array`s now work with `awkward>=2.3` {pr}`1040` {user}`ivirshup` * Fix ufuncs of views like `adata.X[:10].cov(axis=0)` returning views {pr}`1043` {user}`flying-sheep`