Update documentation build process to use pixi and adjust dependencies

Author: LouisFaure

.github/workflows/doc.yml

@@ -15,17 +15,11 @@ jobs:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v5
+    - name: Set up pixi
+      uses: prefix-dev/setup-pixi@v0.8.1
       with:
-        python-version: 3.11
-    - name: Prepare dependencies
-      run: |
-        sudo apt update && sudo apt install -y pandoc
-        pip install -r docs/requirements.txt
-        pip install mock pandoc
-        pip uninstall rpy2 -y
-        pip install --no-deps .
+        pixi-version: latest
+        cache: true
     - name: Build documentation
       run: |
-        sphinx-build docs/ docs/out/
+        pixi run -e docs docs

.gitignore

@@ -137,4 +137,6 @@ _build
 _templates
 # pixi environments
 .pixi/*
+.venv*
 !.pixi/config.toml
+scFates.*.rst

.readthedocs.yml

@@ -8,17 +8,18 @@ version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.11"
-
-# Build documentation in the docs/ directory with Sphinx
-sphinx:
-  configuration: docs/conf.py
+    python: "latest"
+  jobs:
+    create_environment:
+      - asdf plugin add pixi
+      - asdf install pixi latest
+      - asdf global pixi latest
+    install:
+      # Install the docs environment
+      - pixi install -e docs
+    build:
+      html:
+        - pixi run -e docs sphinx-build -T -b html docs $READTHEDOCS_OUTPUT/html
 
 formats:
   - pdf
-
-python:
-  install:
-  - method: pip
-    path: .
-  - requirements: docs/requirements.txt

pyproject.toml

@@ -27,10 +27,12 @@ platforms = ["linux-64"]
 scFates = { path = ".", editable = true }
 
 [tool.pixi.tasks]
+docs = "cd docs && make html"
 
 [tool.pixi.environments]
 default = { solve-group = "default" }
 test = { features = ["test"], solve-group = "default" }
+docs = { features = ["docs"], solve-group = "docs", no-default-feature = true }
 
 [tool.pixi.dependencies]
 python = "3.13.*"
@@ -42,3 +44,32 @@ pytest = "*"
 
 [tool.pixi.feature.test.tasks]
 test = "pytest scFates/tests"
+
+[tool.pixi.feature.docs.dependencies]
+python = "3.9.*"
+sphinx = ">=4.5.0"
+sphinx-rtd-theme = "*"
+sphinx-book-theme = "*"
+sphinxext-opengraph = "*"
+sphinx-copybutton = "*"
+matplotlib = "*"
+nbsphinx = "*"
+ipython = "*"
+anndata = "*"
+numpy = "*"
+pandas = "*"
+cycler = "*"
+docutils = "*"
+typing_extensions = "*"
+importlib_metadata = "*"
+mock = "*"
+
+[tool.pixi.feature.docs.pypi-dependencies]
+scFates = { path = ".", editable = true }
+scanpydoc = { version = ">=0.7.4", extras = ["typehints"] }
+readthedocs-sphinx-ext = "*"
+Jinja2 = ">=3.1.6"
+
+[tool.pixi.feature.docs.tasks]
+docs = "cd docs && make html"
+docs-build = "sphinx-build -T -b html docs"