Merge pull request #161 from ComputationalPhysiology/sphinx-docs

Use sphinx instead of jupyter-book

Author: finsberg

.github/workflows/build_docs.yml

@@ -12,7 +12,7 @@ jobs:
   build:
     runs-on: ubuntu-22.04
     env:
-      PUBLISH_DIR: ./_build/html
+      PUBLISH_DIR: ./_build
 
 
     steps:
@@ -22,13 +22,13 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v6
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: python3 -m pip install ".[docs]"
 
       - name: Build docs
-        run: jupyter-book build -W --keep-going .
+        run: python3 -m sphinx -b html . ${{ env.PUBLISH_DIR }}
 
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v4

_config.yml

@@ -0,0 +1,83 @@
+###############################################################################
+# Auto-generated by `jupyter-book config`
+# If you wish to continue using _config.yml, make edits to that file and
+# re-generate this one.
+###############################################################################
+author = "Henrik Finsberg og Kristian Hustad"
+comments_config = {"hypothesis": False, "utterances": False}
+copyright = "2025"
+exclude_patterns = [
+    "**.ipynb_checkpoints",
+    ".DS_Store",
+    ".github/*",
+    ".pytest_cache/*",
+    "Thumbs.db",
+    "_build",
+    "**.jupyter_cache",
+]
+extensions = [
+    "sphinx_togglebutton",
+    "sphinx_copybutton",
+    "myst_nb",
+    "jupyter_book",
+    "sphinx_thebe",
+    "sphinx_comments",
+    "sphinx_external_toc",
+    "sphinx.ext.intersphinx",
+    "sphinx_design",
+    "sphinx_book_theme",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx_jupyterbook_latex",
+    "sphinx_multitoc_numbering",
+]
+external_toc_exclude_missing = True
+external_toc_path = "_toc.yml"
+html_baseurl = ""
+html_favicon = ""
+html_last_updated_fmt = "%b %d, %Y"
+html_logo = "docs/logo.png"
+html_sourcelink_suffix = ""
+html_theme = "sphinx_book_theme"
+html_theme_options = {
+    "search_bar_text": "Search this book...",
+    "launch_buttons": {
+        "notebook_interface": "classic",
+        "binderhub_url": "",
+        "jupyterhub_url": "",
+        "thebe": True,
+        "colab_url": "",
+        "deepnote_url": "",
+    },
+    "path_to_docs": "docs",
+    "repository_url": "https://github.com/ComputationalPhysiology/ap_features",
+    "repository_branch": "main",
+    "extra_footer": "",
+    "home_page_in_toc": True,
+    "announcement": "",
+    "analytics": {
+        "google_analytics_id": "",
+        "plausible_analytics_domain": "",
+        "plausible_analytics_url": "https://plausible.io/js/script.js",
+    },
+    "use_repository_button": True,
+    "use_edit_page_button": False,
+    "use_issues_button": True,
+}
+html_title = "Action potential features"
+latex_engine = "pdflatex"
+myst_enable_extensions = ["amsmath", "dollarmath", "linkify"]
+myst_url_schemes = ["mailto", "http", "https"]
+nb_execution_allow_errors = False
+nb_execution_cache_path = ""
+nb_execution_excludepatterns: list[str] = []
+nb_execution_in_temp = False
+nb_execution_mode = "cache"
+nb_execution_timeout = 30
+nb_output_stderr = "show"
+numfig = True
+pygments_style = "sphinx"
+suppress_warnings = ["myst.domains"]
+use_jupyterbook_latex = True
+use_multitoc_numbering = True

conf.py

@@ -49,7 +49,14 @@ pypi = [
     "build"
 ]
 docs = [
-   "jupyter-book",
+   "jupyter-book<2.0",
+   "sphinx",
+   "sphinx-togglebutton",
+   "myst-nb",
+   "sphinx-copybutton",
+   "sphinx-comments",
+   "sphinx-external-toc",
+   "sphinx-thebe",
    "ap_features[plot]",
 ]
 test = [