diff --git a/docs/conf.py b/docs/conf.py index f9c9fee35..ec253fc68 100644 --- a/docs/conf.py +++ b/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( diff --git a/docs/index.md b/docs/index.md index 3a3324a6e..b868fa134 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,20 +1,10 @@ -```{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. ```{toctree} :hidden: true diff --git a/docs/news.md b/docs/news.md index fae034f1e..f75e68d2c 100644 --- a/docs/news.md +++ b/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]. diff --git a/docs/release-notes/0.10.0.md b/docs/release-notes/0.10.0.md index 01520e33c..a4ed8a826 100644 --- a/docs/release-notes/0.10.0.md +++ b/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` {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..dae8af856 100644 --- a/docs/release-notes/0.10.1.md +++ b/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` diff --git a/docs/release-notes/0.10.2.md b/docs/release-notes/0.10.2.md index 411d6a072..ea878abcf 100644 --- a/docs/release-notes/0.10.2.md +++ b/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` diff --git a/docs/release-notes/0.10.3.md b/docs/release-notes/0.10.3.md index 9b39925e8..4e5918d40 100644 --- a/docs/release-notes/0.10.3.md +++ b/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` diff --git a/docs/release-notes/0.10.4.md b/docs/release-notes/0.10.4.md index 5588f534a..46ec222a9 100644 --- a/docs/release-notes/0.10.4.md +++ b/docs/release-notes/0.10.4.md @@ -1,7 +1,7 @@ +(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` @@ -9,6 +9,5 @@ * `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..edb7db10b 100644 --- a/docs/release-notes/0.10.5.md +++ b/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` diff --git a/docs/release-notes/0.10.6.md b/docs/release-notes/0.10.6.md index 781bcd6f6..4bef8f562 100644 --- a/docs/release-notes/0.10.6.md +++ b/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` diff --git a/docs/release-notes/0.10.7.md b/docs/release-notes/0.10.7.md index 94b591207..f3ea34cd0 100644 --- a/docs/release-notes/0.10.7.md +++ b/docs/release-notes/0.10.7.md @@ -1,15 +1,11 @@ +(v0.10.7)= ### 0.10.7 {small}`2024-04-09` -```{rubric} Bugfix -``` +#### Bugfix * Handle upstream `numcodecs` bug where read-only string arrays cannot be encoded {user}`ivirshup` {pr}`1421` * Use in-memory sparse matrix directly to fix compatibility with `scipy` `1.13` {user}`ilan-gold` {pr}`1435` -```{rubric} Documentation -``` - -```{rubric} Performance -``` +#### Performance * Remove `vindex` for subsetting `dask.array.Array` because of its slowness and memory consumption {user}`ilan-gold` {pr}`1432` diff --git a/docs/release-notes/0.10.8.md b/docs/release-notes/0.10.8.md index 65fd3889d..1093d2288 100644 --- a/docs/release-notes/0.10.8.md +++ b/docs/release-notes/0.10.8.md @@ -1,13 +1,12 @@ +(0.10.8)= ### 0.10.8 {small}`2024-06-20` -```{rubric} Bugfix -``` +#### Bugfix * Write out `64bit` indptr when appropriate for {func}`~anndata.experimental.concat_on_disk` {pr}`1493` {user}`ilan-gold` * Support for Numpy 2 {pr}`1499` {user}`flying-sheep` * Fix {func}`~anndata.experimental.sparse_dataset` docstring test on account of new {mod}`scipy` version {pr}`1514` {user}`ilan-gold` -```{rubric} Documentation -``` +#### Documentation * Improved example for {func}`~anndata.experimental.sparse_dataset` {pr}`1468` {user}`ivirshup` diff --git a/docs/release-notes/0.10.9.md b/docs/release-notes/0.10.9.md index 72dc6513a..ddfb0274d 100644 --- a/docs/release-notes/0.10.9.md +++ b/docs/release-notes/0.10.9.md @@ -1,14 +1,12 @@ +(0.10.9)= ### 0.10.9 {small}`the future` -```{rubric} Bugfix -``` +#### Bugfix * Coerce {class}`numpy.matrix` classes to arrays when trying to store them in `AnnData` {pr}`1516` {user}`flying-sheep` * Fix for setting a dense `X` view with a sparse matrix {pr}`1532` {user}`ilan-gold` * Upper bound {mod}`numpy` for `gpu` installation on account of https://github.com/cupy/cupy/issues/8391 {pr}`1540` {user}`ilan-gold` -```{rubric} Documentation -``` +#### Documentation -```{rubric} Performance -``` +#### Performance diff --git a/docs/release-notes/0.4.0.md b/docs/release-notes/0.4.0.md index 7aefa55be..06266aa84 100644 --- a/docs/release-notes/0.4.0.md +++ b/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 diff --git a/docs/release-notes/0.5.0.md b/docs/release-notes/0.5.0.md index 476f7574c..554a7e5f7 100644 --- a/docs/release-notes/0.5.0.md +++ b/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` diff --git a/docs/release-notes/0.6.0.md b/docs/release-notes/0.6.0.md index ab4316f64..dc9f2e981 100644 --- a/docs/release-notes/0.6.0.md +++ b/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 diff --git a/docs/release-notes/0.6.x.md b/docs/release-notes/0.6.x.md new file mode 100644 index 000000000..a16984372 --- /dev/null +++ b/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` diff --git a/docs/release-notes/0.7.0.md b/docs/release-notes/0.7.0.md index c81970d2d..5374a096e 100644 --- a/docs/release-notes/0.7.0.md +++ b/docs/release-notes/0.7.0.md @@ -1,3 +1,4 @@ +(v0.7.0)= ### 0.7.0 {small}`22 January, 2020` ```{warning} @@ -9,8 +10,7 @@ Breaking changes introduced between `0.6.22.post1` and `0.7`: - The old deprecated attributes `.smp*`. `.add` and `.data` have been removed. ``` -~~~{rubric} View overhaul {pr}`164` -~~~ +#### View overhaul {pr}`164` - Indexing into a view no longer keeps a reference to intermediate view, see {issue}`62`. - Views are now lazy. Elements of view of AnnData are not indexed until they’re accessed. @@ -18,8 +18,7 @@ Breaking changes introduced between `0.6.22.post1` and `0.7`: - All elements of AnnData should now follow the same rules about how they’re subset, see {issue}`145`. - Can now index by observations and variables at the same time. -~~~{rubric} IO overhaul {pr}`167` -~~~ +#### IO overhaul {pr}`167` - Reading and writing has been overhauled for simplification and speed. - Time and memory usage can be half of previous in typical use cases @@ -27,8 +26,7 @@ Breaking changes introduced between `0.6.22.post1` and `0.7`: - Backed mode should see significant speed and memory improvements for access along compressed dimensions and IO. PR {pr}`241`. - {class}`~pandas.Categorical`s can now be ordered (PR {pr}`230`) and written to disk with a large number of categories (PR {pr}`217`). -~~~{rubric} Mapping attributes overhaul {smaller}`(obsm, varm, layers, ...)` -~~~ +#### Mapping attributes overhaul {smaller}`(obsm, varm, layers, ...)` - New attributes {attr}`~anndata.AnnData.obsp` and {attr}`~anndata.AnnData.varp` have been added for two dimensional arrays where each axis corresponds to a single axis of the AnnData object. PR {pr}`207`. - These are intended to store values like cell-by-cell graphs, which are currently stored in {attr}`~anndata.AnnData.uns`. @@ -36,8 +34,7 @@ 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..24cdb09b3 100644 --- a/docs/release-notes/0.7.2.md +++ b/docs/release-notes/0.7.2.md @@ -1,15 +1,14 @@ +(v0.7.2)= ### 0.7.2 {small}`15 May, 2020` -~~~{rubric} Concatenation overhaul {smaller}`I Virshup` -~~~ +#### Concatenation overhaul {smaller}`I Virshup` - Elements of `uns` can now be merged, see {pr}`350` - Outer joins now work for `layers` and `obsm`, see {pr}`352` - 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..6123b12b2 100644 --- a/docs/release-notes/0.7.3.md +++ b/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` diff --git a/docs/release-notes/0.7.4.md b/docs/release-notes/0.7.4.md index 16efc35db..fc3f710b0 100644 --- a/docs/release-notes/0.7.4.md +++ b/docs/release-notes/0.7.4.md @@ -1,18 +1,16 @@ +(v0.7.4)= ### 0.7.4 {small}`10 July, 2020` -~~~{rubric} Concatenation overhaul {pr}`378` {smaller}`I Virshup` -~~~ +#### Concatenation overhaul {pr}`378` {smaller}`I Virshup` - 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..140c058e7 100644 --- a/docs/release-notes/0.7.5.md +++ b/docs/release-notes/0.7.5.md @@ -1,12 +1,11 @@ +(v0.7.5)= ### 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..5bd2779ab 100644 --- a/docs/release-notes/0.7.6.md +++ b/docs/release-notes/0.7.6.md @@ -1,13 +1,12 @@ +(v0.7.6)= ### 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 +16,7 @@ - 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..dac5feb55 100644 --- a/docs/release-notes/0.7.7.md +++ b/docs/release-notes/0.7.7.md @@ -1,14 +1,13 @@ +(v0.7.7)= ### 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..1bc33742d 100644 --- a/docs/release-notes/0.7.8.md +++ b/docs/release-notes/0.7.8.md @@ -1,6 +1,6 @@ +(v0.7.8)= ### 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..0bda4382d 100644 --- a/docs/release-notes/0.8.0.md +++ b/docs/release-notes/0.8.0.md @@ -1,7 +1,7 @@ +(v0.8.0)= ### 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 +17,7 @@ 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 +28,13 @@ 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 deleted file mode 100644 index 8de88d195..000000000 --- a/docs/release-notes/0.8.1.md +++ /dev/null @@ -1,11 +0,0 @@ -### 0.8.1 {small}`the future` - -```{rubric} 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 -``` diff --git a/docs/release-notes/0.9.0.md b/docs/release-notes/0.9.0.md index 4e56178fb..d38c7f78c 100644 --- a/docs/release-notes/0.9.0.md +++ b/docs/release-notes/0.9.0.md @@ -1,7 +1,7 @@ +(v0.9.0)= ### 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 +9,7 @@ - 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 @@ -28,26 +27,25 @@ - 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 +- 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` - 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` diff --git a/docs/release-notes/0.9.1.md b/docs/release-notes/0.9.1.md index 30c7ac7fb..f90672d60 100644 --- a/docs/release-notes/0.9.1.md +++ b/docs/release-notes/0.9.1.md @@ -1,6 +1,6 @@ +(v0.9.1)= ### 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..286f43b3d 100644 --- a/docs/release-notes/0.9.2.md +++ b/docs/release-notes/0.9.2.md @@ -1,7 +1,7 @@ +(v0.9.2)= ### 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` diff --git a/docs/release-notes/index.md b/docs/release-notes/index.md index b808c6167..264a096cd 100644 --- a/docs/release-notes/index.md +++ b/docs/release-notes/index.md @@ -1,8 +1,39 @@ # Release notes -```{include} /release-notes/release-latest.md +(v0.10)= +## Version 0.10 + +```{include} /release-notes/0.10.9.md +``` + +```{include} /release-notes/0.10.8.md +``` + +```{include} /release-notes/0.10.7.md +``` + +```{include} /release-notes/0.10.6.md +``` + +```{include} /release-notes/0.10.5.md ``` +```{include} /release-notes/0.10.4.md +``` + +```{include} /release-notes/0.10.3.md +``` + +```{include} /release-notes/0.10.2.md +``` + +```{include} /release-notes/0.10.1.md +``` + +```{include} /release-notes/0.10.0.md +``` + +(v0.9)= ## Version 0.9 ```{include} /release-notes/0.9.2.md @@ -14,14 +45,13 @@ ```{include} /release-notes/0.9.0.md ``` +(v0.8)= ## Version 0.8 -```{include} /release-notes/0.8.1.md -``` - ```{include} /release-notes/0.8.0.md ``` +(v0.7)= ## Version 0.7 ```{include} /release-notes/0.7.8.md @@ -48,16 +78,22 @@ ```{include} /release-notes/0.7.0.md ``` +(v0.6)= ## Version 0.6 +```{include} /release-notes/0.6.x.md +``` + ```{include} /release-notes/0.6.0.md ``` +(v0.5)= ## Version 0.5 ```{include} /release-notes/0.5.0.md ``` +(v0.4)= ## Version 0.4 ```{include} /release-notes/0.4.0.md diff --git a/docs/release-notes/release-latest.md b/docs/release-notes/release-latest.md deleted file mode 100644 index 34f8b35d6..000000000 --- a/docs/release-notes/release-latest.md +++ /dev/null @@ -1,31 +0,0 @@ -## Version 0.10 - -```{include} /release-notes/0.10.9.md -``` - -```{include} /release-notes/0.10.8.md -``` - -```{include} /release-notes/0.10.7.md -``` - -```{include} /release-notes/0.10.6.md -``` - -```{include} /release-notes/0.10.5.md -``` - -```{include} /release-notes/0.10.4.md -``` - -```{include} /release-notes/0.10.3.md -``` - -```{include} /release-notes/0.10.2.md -``` - -```{include} /release-notes/0.10.1.md -``` - -```{include} /release-notes/0.10.0.md -```