Updating CI/CD (#981)

* Modernised setup

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* added excludes

* removed redundant action

* fixed linting

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* added pre-commit exclude for .pyi

* added arg

* added arg

* added arg

* added arg

* added arg

* Removed .pyi files

* added exports

* removed unused typehints

* Removed lintconfig from tox

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: timtreis

.github/release.yml

@@ -25,4 +25,4 @@ changelog:
               - "release-security"
         - title: Other Changes
           labels:
-              - "*"
+              - "*"

.github/workflows/lint.yml

@@ -11,7 +11,7 @@ jobs:
         steps:
             - uses: actions/checkout@v3
             - name: Set up Python 3.12
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: "3.12"
                   cache: pip

.github/workflows/release.yml

@@ -35,7 +35,7 @@ jobs:
         steps:
             - uses: actions/checkout@v3
             - name: Set up Python ${{ matrix.python }}
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: ${{ matrix.python }}
 

.github/workflows/test.yml

@@ -1,11 +1,17 @@
 fail_fast: false
+default_language_version:
+    python: python3
 default_stages:
     - pre-commit
     - pre-push
-minimum_pre_commit_version: 2.9.3
+minimum_pre_commit_version: 2.16.0
 repos:
+    - repo: https://github.com/rbubley/mirrors-prettier
+      rev: v3.5.1
+      hooks:
+          - id: prettier
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.9.10
+      rev: v0.11.2
       hooks:
           - id: ruff
             types_or: [python, pyi, jupyter]
@@ -16,6 +22,5 @@ repos:
       rev: v1.15.0
       hooks:
           - id: mypy
-            additional_dependencies: [numpy, pandas, types-requests]
-            exclude: .scripts/ci/download_data.py|squidpy/datasets/_(dataset|image).py # See https://github.com/
-  
+            additional_dependencies: [numpy, types-requests]
+            exclude: tests/|docs/

.pre-commit-config.yaml

@@ -1,21 +1,22 @@
 version: 2
 
 build:
-    os: ubuntu-22.04
+    os: ubuntu-24.04
     tools:
-        python: "3.10"
+        python: "3.12"
+    commands:
+        - asdf plugin add uv
+        - asdf install uv latest
+        - asdf global uv latest
+        - uv venv
+        - uv pip install .[docs,pre]
+        - .venv/bin/python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
 
 sphinx:
     builder: html
     configuration: docs/conf.py
     fail_on_warning: false
 
-python:
-    install:
-        - method: pip
-          path: .
-          extra_requirements: [docs]
-
 submodules:
     include: [docs/notebooks]
     recursive: true

.readthedocs.yml

@@ -3,7 +3,7 @@
 }
 
 div.version {
-    color: #FFD92C!important;
+    color: #ffd92c !important;
 }
 
 .wy-nav-side {
@@ -15,7 +15,7 @@ div.version {
 }
 
 .wy-side-nav-search input[type="text"] {
-    border-radius: 6px!important;
+    border-radius: 6px !important;
 }
 
 .wy-nav-content {
@@ -51,41 +51,52 @@ div.version {
 }
 
 a {
-    color: #5B64B1;
+    color: #5b64b1;
 }
 
 .rst-content .viewcode-link {
     color: #7013e1d9;
 }
 
 .highlight {
-    background: #f1f5fb!important;
+    background: #f1f5fb !important;
 }
 
 .rst-content div[class^="highlight"] {
     border: 1px solid #e4eaf2;
 }
 
 .wy-menu-vertical p.caption {
-    color: #FFD92C;
+    color: #ffd92c;
 }
 
-div.output_subarea.output_html.rendered_html.output_result{
+div.output_subarea.output_html.rendered_html.output_result {
     overflow: auto;
 }
 
 /* function/class top bar */
-html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple) > dt {
+html.writer-html5
+    .rst-content
+    dl[class]:not(.option-list):not(.field-list):not(.footnote):not(
+        .glossary
+    ):not(.simple)
+    > dt {
     color: #404040;
     border-top: solid 4px #7013e1d9;
-    background: #FFD833A8;
+    background: #ffd833a8;
 }
 
 /* class params */
-html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple) dl:not(.field-list) > dt {
+html.writer-html5
+    .rst-content
+    dl[class]:not(.option-list):not(.field-list):not(.footnote):not(
+        .glossary
+    ):not(.simple)
+    dl:not(.field-list)
+    > dt {
     color: #404040;
     border-left: solid 4px #7013e1d9;
-    background: #FFD8338F;
+    background: #ffd8338f;
 }
 
 /* the other elements, but more specific - leave them be */
@@ -104,9 +115,9 @@ code.docutils.literal.notranslate > span[class="pre"] {
 }
 
 .rst-content .seealso {
-    background: #fafae2!important;
+    background: #fafae2 !important;
 }
 
 .rst-content .seealso .admonition-title {
-    background: #7013e1d9!important;
+    background: #7013e1d9 !important;
 }

docs/_static/css/custom.css

@@ -3,41 +3,41 @@
 /* modified margin-left */
 
 table.dataframe {
-  border: none !important;
-  border-collapse: collapse;
-  border-spacing: 0;
-  border-color: transparent;
-  color: black;
-  font-size: 12px;
-  table-layout: fixed;
-  margin-left: 0!important;
+    border: none !important;
+    border-collapse: collapse;
+    border-spacing: 0;
+    border-color: transparent;
+    color: black;
+    font-size: 12px;
+    table-layout: fixed;
+    margin-left: 0 !important;
 }
 
 table.dataframe thead {
-  border-bottom: 1px solid black;
-  vertical-align: bottom;
+    border-bottom: 1px solid black;
+    vertical-align: bottom;
 }
 
 table.dataframe tr,
 table.dataframe th,
 table.dataframe td {
-  text-align: right;
-  vertical-align: middle;
-  padding: 0.5em 0.5em;
-  line-height: normal;
-  white-space: normal;
-  max-width: none;
-  border: none;
+    text-align: right;
+    vertical-align: middle;
+    padding: 0.5em 0.5em;
+    line-height: normal;
+    white-space: normal;
+    max-width: none;
+    border: none;
 }
 
 table.dataframe th {
-  font-weight: bold;
+    font-weight: bold;
 }
 
 table.dataframe tbody tr:nth-child(odd) {
-  background: #f5f5f5;
+    background: #f5f5f5;
 }
 
 table.dataframe tbody tr:hover {
-  background: rgba(66, 165, 245, 0.2);
+    background: rgba(66, 165, 245, 0.2);
 }

docs/_static/css/dataframe.css

@@ -10,11 +10,11 @@ div.nboutput.container div.prompt > div.highlight {
 
 div.nbinput.container div.input_area div[class*="highlight"] > pre,
 div.nboutput.container div.output_area div[class*="highlight"] > pre {
-    padding: 8px!important;
+    padding: 8px !important;
 }
 
 div.nboutput.container div.output_area > div[class^="highlight"] {
-    background-color: #fafae2!important;
+    background-color: #fafae2 !important;
 }
 
 .rst-content .output_area img {