Skip to content

Commit

Permalink
Switch from using rubric in release notes (scverse#3172)
Browse files Browse the repository at this point in the history
  • Loading branch information
flying-sheep authored Jul 26, 2024
1 parent 62454de commit b78e9dc
Show file tree
Hide file tree
Showing 53 changed files with 174 additions and 216 deletions.
14 changes: 13 additions & 1 deletion docs/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,12 @@

import sys
from datetime import datetime
from functools import partial
from pathlib import Path
from typing import TYPE_CHECKING

import matplotlib # noqa
from docutils import nodes
from packaging.version import Version

# Don’t use tkinter agg when importing scanpy → … → matplotlib
Expand Down Expand Up @@ -50,7 +52,14 @@
templates_path = ["_templates"]
master_doc = "index"
default_role = "literal"
exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
exclude_patterns = [
"_build",
"Thumbs.db",
".DS_Store",
"**.ipynb_checkpoints",
# exclude all 0.x.y.md files, but not index.md
"release-notes/[!i]*.md",
]

extensions = [
"myst_nb",
Expand Down Expand Up @@ -96,6 +105,7 @@
"html_admonition",
]
myst_url_schemes = ("http", "https", "mailto", "ftp")
myst_heading_anchors = 3
nb_output_stderr = "remove"
nb_execution_mode = "off"
nb_merge_streams = True
Expand Down Expand Up @@ -151,6 +161,8 @@

def setup(app: Sphinx):
"""App setup hook."""
app.add_generic_role("small", partial(nodes.inline, classes=["small"]))
app.add_generic_role("smaller", partial(nodes.inline, classes=["smaller"]))
app.add_config_value(
"recommonmark_config",
{
Expand Down
8 changes: 0 additions & 8 deletions docs/ecosystem.md
Original file line number Diff line number Diff line change
@@ -1,13 +1,5 @@
# Ecosystem

```{eval-rst}
.. role:: small
```

```{eval-rst}
.. role:: smaller
```

```{warning}
We are no longer accepting new tools on this page.
Instead, please submit your tool to the [scverse ecosystem package listing](https://scverse.org/packages/#ecosystem).
Expand Down
8 changes: 0 additions & 8 deletions docs/index.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,14 +2,6 @@
:end-before: '## Citation'
```

```{eval-rst}
.. role:: small
```

```{eval-rst}
.. role:: smaller
```

::::{grid} 1 2 3 3
:gutter: 2

Expand Down
6 changes: 0 additions & 6 deletions docs/news.md
Original file line number Diff line number Diff line change
@@ -1,12 +1,6 @@
(News)=

## News

```{eval-rst}
.. role:: small
```

<!-- marker: after prelude -->

### `rapids-singlecell` brings scanpy to the GPU! {small}`2024-03-18`
Expand Down
1 change: 1 addition & 0 deletions docs/release-notes/0.1.0.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
(v0.1.0)=
### 0.1.0 {small}`2017-05-17`

Scanpy computationally outperforms and allows reproducing both the [Cell Ranger
Expand Down
1 change: 1 addition & 0 deletions docs/release-notes/0.2.1.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
(v0.2.1)=
### 0.2.1 {small}`2017-07-24`

Scanpy includes preprocessing, visualization, clustering, pseudotime and
Expand Down
4 changes: 2 additions & 2 deletions docs/release-notes/0.2.9.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
(v0.2.9)=
### 0.2.9 {small}`2017-10-25`

```{rubric} Initial release of the new trajectory inference method [PAGA](https://github.com/theislab/paga)
```
#### Initial release of the new trajectory inference method [PAGA](https://github.com/theislab/paga)

- {func}`~scanpy.tl.paga` computes an abstracted, coarse-grained (PAGA) graph of the neighborhood graph {smaller}`A Wolf`
- {func}`~scanpy.pl.paga_compare` plot this graph next an embedding {smaller}`A Wolf`
Expand Down
1 change: 1 addition & 0 deletions docs/release-notes/0.3.0.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
(v0.3.0)=
### 0.3.0 {small}`2017-11-16`

- {class}`~anndata.AnnData` gains method {meth}`~anndata.AnnData.concatenate` {smaller}`A Wolf`
Expand Down
1 change: 1 addition & 0 deletions docs/release-notes/0.3.2.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
(v0.3.2)=
### 0.3.2 {small}`2017-11-29`

- finding marker genes via {func}`~scanpy.pl.rank_genes_groups_violin` improved,
Expand Down
1 change: 1 addition & 0 deletions docs/release-notes/0.4.0.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
(v0.4.0)=
### 0.4.0 {small}`2017-12-23`

- export to [SPRING] {cite:p}`Weinreb2017` for interactive visualization of data:
Expand Down
1 change: 1 addition & 0 deletions docs/release-notes/0.4.2.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
(v0.4.2)=
### 0.4.2 {small}`2018-01-07`

- amendments in [PAGA](https://github.com/theislab/paga) and its plotting functions {smaller}`A Wolf`
1 change: 1 addition & 0 deletions docs/release-notes/0.4.3.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
(v0.4.3)=
### 0.4.3 {small}`2018-02-09`

- {func}`~scanpy.pl.clustermap`: heatmap from hierarchical clustering,
Expand Down
6 changes: 6 additions & 0 deletions docs/release-notes/0.4.4.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
(v0.4.4)=
### 0.4.4 {small}`2018-02-26`

- embed cells using {func}`~scanpy.tl.umap` {cite:p}`McInnes2018` {pr}`92` {smaller}`G Eraslan`
- score sets of genes, e.g. for cell cycle, using {func}`~scanpy.tl.score_genes` {cite:p}`Satija2015`:
[notebook](https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/180209_cell_cycle/cell_cycle.ipynb)
10 changes: 4 additions & 6 deletions docs/release-notes/1.0.0.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
(v1.0.0)=
### 1.0.0 {small}`2018-03-30`

```{rubric} Major updates
```
#### Major updates

- Scanpy is much faster and more memory efficient: preprocess, cluster and
visualize 1.3M cells in [6h], 130K cells in [14min], and 68K cells in [3min] {smaller}`A Wolf`
Expand All @@ -10,8 +10,7 @@
delegated {smaller}`A Wolf`

```{warning}
```{rubric} Upgrading to 1.0 isn’t fully backwards compatible in the following changes
```
#### Upgrading to 1.0 isn’t fully backwards compatible in the following changes
- the graph-based tools {func}`~scanpy.tl.louvain`
{func}`~scanpy.tl.dpt` {func}`~scanpy.tl.draw_graph`
Expand All @@ -35,8 +34,7 @@
some results might therefore look slightly different
```

```{rubric} Further updates
```
#### Further updates

- UMAP {cite:p}`McInnes2018` can serve as a first visualization of the data just as tSNE,
in contrast to tSNE, UMAP directly embeds the single-cell graph and is faster;
Expand Down
1 change: 1 addition & 0 deletions docs/release-notes/1.1.0.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
(v1.1.0)=
### 1.1.0 {small}`2018-06-01`

- {func}`~scanpy.set_figure_params` by default passes `vector_friendly=True` and allows you to produce reasonablly sized pdfs by rasterizing large scatter plots {smaller}`A Wolf`
Expand Down
16 changes: 6 additions & 10 deletions docs/release-notes/1.10.0.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
(v1.10.0)=
### 1.10.0 {small}`2024-03-26`

`scanpy` 1.10 brings a large amount of new features, performance improvements, and improved documentation.
Expand All @@ -10,8 +11,7 @@ Some highlights:
* Ability to `mask` observations or variables from a number of methods (see {doc}`/tutorials/plotting/advanced` for an example with plotting embeddings)
* A new function {func}`~scanpy.get.aggregate` for computing aggregations of your data, very useful for pseudo bulking!

```{rubric} Features
```
#### Features

* {func}`~scanpy.pp.scrublet` and {func}`~scanpy.pp.scrublet_simulate_doublets` were moved from {mod}`scanpy.external.pp` to {mod}`scanpy.pp`. The `scrublet` implementation is now maintained as part of scanpy {pr}`2703` {smaller}`P Angerer`
* {func}`scanpy.pp.pca`, {func}`scanpy.pp.scale`, {func}`scanpy.pl.embedding`, and {func}`scanpy.experimental.pp.normalize_pearson_residuals_pca` now support a `mask` parameter {pr}`2272` {smaller}`C Bright, T Marcella, & P Angerer`
Expand All @@ -32,8 +32,7 @@ Some highlights:
* {func}`scanpy.pp.scale` now clips `np.ndarray` also at `- max_value` for zero-centering {pr}`2913` {smaller}`S Dicks`
* Support sparse chunks in dask {func}`~scanpy.pp.scale`, {func}`~scanpy.pp.normalize_total` and {func}`~scanpy.pp.highly_variable_genes` (`seurat` and `cell-ranger` tested) {pr}`2856` {smaller}`ilan-gold`

```{rubric} Docs
```
#### Docs

* Doc style overhaul {pr}`2220` {smaller}`A Gayoso`
* Re-add search-as-you-type, this time via `readthedocs-sphinx-search` {pr}`2805` {smaller}`P Angerer`
Expand All @@ -44,8 +43,7 @@ Some highlights:
* Overhauled {doc}`/tutorials/index` page, and added new {doc}`/how-to/index` section to docs {pr}`2901` {smaller}`I Virshup`
* Added a new tutorial on working with dask ({doc}`/tutorials/experimental/dask`) {pr}`2901` {smaller}`I Gold` {smaller}`I Virshup`

```{rubric} Bug fixes
```
#### Bug fixes

* Updated {func}`~scanpy.read_visium` such that it can read spaceranger 2.0 files {smaller}`L Lehner`
* Fix {func}`~scanpy.pp.normalize_total` for dask {pr}`2466` {smaller}`P Angerer`
Expand All @@ -61,14 +59,12 @@ Some highlights:
* Fix pytest deprecation warning {pr}`2879` {smaller}`P Angerer`


```{rubric} Development
```
#### Development

* Scanpy is now tested against python 3.12 {pr}`2863` {smaller}`ivirshup`
* Fix testing package build {pr}`2468` {smaller}`P Angerer`

```{rubric} Deprecations
```
#### Deprecations

* Dropped support for Python 3.8. [More details here](https://numpy.org/neps/nep-0029-deprecation_policy.html). {pr}`2695` {smaller}`P Angerer`
* Deprecated specifying large numbers of function parameters by position as opposed to by name/keyword in all public APIs.
Expand Down
10 changes: 4 additions & 6 deletions docs/release-notes/1.10.1.md
Original file line number Diff line number Diff line change
@@ -1,16 +1,14 @@
(v1.10.1)=
### 1.10.1 {small}`2024-04-09`

```{rubric} Docs
```
#### Docs

* Added {doc}`how-to example </how-to/plotting-with-marsilea>` on plotting with [Marsilea](https://marsilea.readthedocs.io) {pr}`2974` {smaller}`Y Zheng`

```{rubric} Bug fixes
```
#### Bug fixes

* Fix `aggregate` when aggregating by more than two groups {pr}`2965` {smaller}`I Virshup`


```{rubric} Performance
```
#### Performance
* {func}`~scanpy.pp.scale` now uses numba kernels for `sparse.csr_matrix` and `sparse.csc_matrix` when `zero_center==False` and `mask_obs` is provided. This greatly speed up execution {pr}`2942` {smaller}`S Dicks`
13 changes: 5 additions & 8 deletions docs/release-notes/1.10.2.md
Original file line number Diff line number Diff line change
@@ -1,21 +1,19 @@
(v1.10.2)=
### 1.10.2 {small}`2024-06-25`

```{rubric} Development features
```
#### Development features

* Add performance benchmarking {pr}`2977` {smaller}`R Shrestha`, {smaller}`P Angerer`

```{rubric} Docs
```
#### Docs

* Document several missing parameters in docstring {pr}`2888` {smaller}`S Cheney`
* Fixed incorrect instructions in "testing" dev docs {pr}`2994` {smaller}`I Virshup`
* Update marsilea tutorial to use `group_` methods {pr}`3001` {smaller}`I Virshup`
* Fixed citations {pr}`3032` {smaller}`P Angerer`
* Improve dataset documentation {pr}`3060` {smaller}`P Angerer`

```{rubric} Bug fixes
```
#### Bug fixes

* Compatibility with `matplotlib` 3.9 {pr}`2999` {smaller}`I Virshup`
* Add clear errors where `backed` mode-like matrices (i.e., from `sparse_dataset`) are not supported {pr}`3048` {smaller}`I gold`
Expand All @@ -24,8 +22,7 @@
* Fix zappy support {pr}`3089` {smaller}`P Angerer`
* Fix dotplot group order with {mod}`pandas` 1.x {pr}`3101` {smaller}`P Angerer`

```{rubric} Performance
```
#### Performance

* `sparse_mean_variance_axis` now uses all cores for the calculations {pr}`3015` {smaller}`S Dicks`
* `pp.highly_variable_genes` with `flavor=seurat_v3` now uses a numba kernel {pr}`3017` {smaller}`S Dicks`
Expand Down
13 changes: 5 additions & 8 deletions docs/release-notes/1.10.3.md
Original file line number Diff line number Diff line change
@@ -1,18 +1,15 @@
(v1.10.3)=
### 1.10.3 {small}`the future`

```{rubric} Development features
```
#### Development features

```{rubric} Docs
```
#### Docs

```{rubric} Bug fixes
```
#### Bug fixes

* Prevent empty control gene set in {func}`~scanpy.tl.score_genes` {pr}`2875` {smaller}`M Müller`
* Fix `subset=True` of {func}`~scanpy.pp.highly_variable_genes` when `flavor` is `seurat` or `cell_ranger`, and `batch_key!=None` {pr}`3042` {smaller}`E Roellin`
* Add compatibility with {mod}`numpy` 2.0 {pr}`3065` and {pr}`3115` {smaller}`P Angerer`
* Fix `legend_loc` argument in {func}`scanpy.pl.embedding` not accepting matplotlib parameters {pr}`3163` {smaller}`P Angerer`

```{rubric} Performance
```
#### Performance
13 changes: 5 additions & 8 deletions docs/release-notes/1.11.0.md
Original file line number Diff line number Diff line change
@@ -1,16 +1,13 @@
(v1.11.0)=
### 1.11.0 {small}`the future`

```{rubric} Features
```
#### Features

* Add layer argument to {func}`scanpy.tl.score_genes` and {func}`scanpy.tl.score_genes_cell_cycle` {pr}`2921` {smaller}`L Zappia`
* Prevent `raw` conflict with `layer` in {func}`~scanpy.tl.score_genes` {pr}`3155` {smaller}`S Dicks`

```{rubric} Docs
```
#### Docs

```{rubric} Bug fixes
```
#### Bug fixes

```{rubric} Deprecations
```
#### Deprecations
1 change: 1 addition & 0 deletions docs/release-notes/1.2.0.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
(v1.2.0)=
### 1.2.0 {small}`2018-06-08`

- {func}`~scanpy.tl.paga` improved, see [PAGA](https://github.com/theislab/paga); the default model changed, restore the previous default model by passing `model='v1.0'`
4 changes: 2 additions & 2 deletions docs/release-notes/1.2.1.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
(v1.2.1)=
### 1.2.1 {small}`2018-06-08`

~~~{rubric} Plotting of {ref}`pl-generic` marker genes and quality control.
~~~
#### Plotting of {ref}`pl-generic` marker genes and quality control.

- {func}`~scanpy.pl.highest_expr_genes` for quality control; plot genes with highest mean fraction of cells, similar to `plotQC` of *Scater* {cite:p}`McCarthy2017` {pr}`169` {smaller}`F Ramirez`
10 changes: 4 additions & 6 deletions docs/release-notes/1.3.1.md
Original file line number Diff line number Diff line change
@@ -1,20 +1,18 @@
(v1.3.1)=
### 1.3.1 {small}`2018-09-03`

```{rubric} RNA velocity in single cells {cite:p}`LaManno2018`
```
#### RNA velocity in single cells {cite:p}`LaManno2018`

- Scanpy and AnnData support loom’s layers so that computations for single-cell RNA velocity {cite:p}`LaManno2018` become feasible {smaller}`S Rybakov and V Bergen`
- [scvelo] harmonizes with Scanpy and is able to process loom files with splicing information produced by Velocyto {cite:p}`LaManno2018`, it runs a lot faster than the count matrix analysis of Velocyto and provides several conceptual developments

~~~{rubric} Plotting ({ref}`pl-generic`)
~~~
#### Plotting ({ref}`pl-generic`)

- {func}`~scanpy.pl.dotplot` for visualizing genes across conditions and clusters, see [here](https://gist.github.com/fidelram/2289b7a8d6da055fb058ac9a79ed485c) {pr}`199` {smaller}`F Ramirez`
- {func}`~scanpy.pl.heatmap` for pretty heatmaps {pr}`175` {smaller}`F Ramirez`
- {func}`~scanpy.pl.violin` produces very compact overview figures with many panels {pr}`175` {smaller}`F Ramirez`

~~~{rubric} There now is a section on imputation in {doc}`external <../external/index>`:
~~~
#### There now is a section on imputation in {doc}`external <../external/index>`:

- {func}`~scanpy.external.pp.magic` for imputation using data diffusion {cite:p}`vanDijk2018` {pr}`187` {smaller}`S Gigante`
- {func}`~scanpy.external.pp.dca` for imputation and latent space construction using an autoencoder {cite:p}`Eraslan2019` {pr}`186` {smaller}`G Eraslan`
Expand Down
10 changes: 4 additions & 6 deletions docs/release-notes/1.3.3.md
Original file line number Diff line number Diff line change
@@ -1,18 +1,16 @@
(v1.3.3)=
### 1.3.3 {small}`2018-11-05`

```{rubric} Major updates
```
#### Major updates

- a fully distributed preprocessing backend {smaller}`T White and the Laserson Lab`

```{rubric} Code design
```
#### Code design

- {func}`~scanpy.read_10x_h5` and {func}`~scanpy.read_10x_mtx` read Cell Ranger 3.0 outputs {pr}`334` {smaller}`Q Gong`

```{note}
```{rubric} Also see changes in anndata 0.6.
```
#### Also see changes in anndata 0.6.
- changed default compression to `None` in {meth}`~anndata.AnnData.write_h5ad` to speed up read and write, disk space use is usually less critical
- performance gains in {meth}`~anndata.AnnData.write_h5ad` due to better handling of strings and categories {smaller}`S Rybakov`
Expand Down
1 change: 1 addition & 0 deletions docs/release-notes/1.3.4.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
(v1.3.4)=
### 1.3.4 {small}`2018-11-24`

- {func}`~scanpy.tl.leiden` wraps the recent graph clustering package by {cite:t}`Traag2019` {smaller}`K Polanski`
Expand Down
Loading

0 comments on commit b78e9dc

Please sign in to comment.