Refresh Docs (#1171)

* WIP refresh WK docs structure; update Python deps

* Replace pdocs with mkdocstrings

* remove pdoc templates

* only create api docs for classes in wk-libs submodules

* fix generate.sh script

* added some comments

* formatting

* update CI for building docs

* fix markdown links, changed due mkdocs

* Update docs/generate.sh

Co-authored-by: Mark Bader <[email protected]>

* fix API overview page

* restructure navigation menu

* Revert "restructure navigation menu"

This reverts commit d8e039d.

* restructure nav

* fix issues with mkdocs-videos and empty pages

* added index pages to all sections

* update mkdocs-glightbox

* remove unused styles; add custom page footer

* enable dark/light mode

* update nav index

* updates to navigation

* more nav

* fix API nav links

* more spacing for the content page footer

* apply albane's changes

* stuff

* fix webknossos-libs build

* update cluster_tools build

---------

Co-authored-by: markbader <[email protected]>

Author: hotzenklotz

.github/workflows/ci.yml

@@ -47,7 +47,7 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v3
         with:
-          version: "0.4.19"
+          version: "0.4.22"
 
       - name: Set up Python ${{ matrix.python-version }}
         run: uv python install ${{ matrix.python-version }}
@@ -165,7 +165,7 @@ jobs:
         uses: astral-sh/setup-uv@v3
         with:
           # Install a specific version of uv.
-          version: "0.4.19"
+          version: "0.4.22"
 
       - name: Set up Python ${{ matrix.python-version }}
         run: uv python install ${{ matrix.python-version }}
@@ -207,7 +207,7 @@ jobs:
         uses: astral-sh/setup-uv@v3
         with:
           # Install a specific version of uv.
-          version: "0.4.19"
+          version: "0.4.22"
       - name: Write version file
         run: |
           pushd webknossos
@@ -284,7 +284,7 @@ jobs:
         uses: astral-sh/setup-uv@v3
         with:
           # Install a specific version of uv.
-          version: "0.4.19"
+          version: "0.4.22"
       - name: Build Docs
         run: |
           cd docs
@@ -336,7 +336,7 @@ jobs:
         uses: astral-sh/setup-uv@v3
         with:
           # Install a specific version of uv.
-          version: "0.4.19"
+          version: "0.4.22"
       - name: Publish python packages
         env:
           UV_PUBLISH_TOKEN: ${{ secrets.PYPI_PASSWORD }}

CONTRIBUTING.md

@@ -1,6 +1,6 @@
 # Contributing Guide
 
-**Welcome to the WEBKNOSSOS-libs contributing guide :sparkles: **
+**Welcome to the WEBKNOSSOS-libs contributing guide :sparkles:**
 
 Thank you for taking the time to contribute to this project! The following is a set of guidelines for contributing to the different WEBKNOSSOS related Python libraries, which are part of the [WEBKNOSSOS-libs repository on GitHub](https://github.com/scalableminds/webknossos-libs). These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request.
 

cluster_tools/pyproject.toml

@@ -30,8 +30,11 @@ dev-dependencies = [
 requires = ["setuptools>=70.0", "wheel; python_version>='3.12'"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools]
-packages = ["cluster_tools"]
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["cluster_tools*"]
+exclude = ["cluster_tools.tests"]
+
 
 [tool.ruff]
 # Exclude a variety of commonly ignored directories.

docs/generate.sh

@@ -12,7 +12,7 @@ rm -rf src/api/webknossos
 uv run --frozen generate_api_doc_pages.py 
 
 if [ $# -eq 1 ] && [ "$1" = "--persist" ]; then
-    uv run mkdocs build
+    uv run --with black mkdocs build
 else
-    uv run mkdocs serve -a localhost:8197 --watch-theme
+    uv run --with black mkdocs serve -a localhost:8197 --watch-theme
 fi