Change from jupyter-book to sphinx, update docs and add some more logging

Author: finsberg

.pre-commit-config.yaml

@@ -21,7 +21,7 @@ repos:
         args: [ --fix ]
       # Run the formatter.
       - id: ruff-format
-        exclude: 'demos/.*.py$'
+        exclude: 'demo/.*.py$'
 
 
   - repo: https://github.com/asottile/add-trailing-comma

_config.yml

@@ -4,6 +4,7 @@ root: README
 parts:
   - caption: Demos
     chapters:
+    - file: "demo/maths.py"
     - file: "demo/unit_cube"
     - file: "demo/lv_ellipsoid"
     - file: "demo/biv_ellipsoid"

_toc.yml

@@ -0,0 +1,104 @@
+###############################################################################
+# 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"
+bibtex_bibfiles = ["docs/refs.bib"]
+codeautolink_concat_default = True
+comments_config = {"hypothesis": False, "utterances": False}
+copyright = "2025"
+exclude_patterns = [
+    "**.ipynb_checkpoints",
+    ".DS_Store",
+    ".github/*",
+    ".pytest_cache/*",
+    ".tox/*",
+    "Thumbs.db",
+    "_build",
+    "third_party/*",
+    "jupyter_execute/",
+    "**.jupyter_cache",
+]
+extensions = [
+    "sphinx_togglebutton",
+    "sphinx_copybutton",
+    "myst_nb",
+    "sphinx_comments",
+    "sphinx_external_toc",
+    "sphinx.ext.intersphinx",
+    "sphinx_design",
+    "sphinx_book_theme",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinxcontrib.bibtex",
+    "sphinx_codeautolink",
+    "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_static_path = ["_static"]
+html_theme = "sphinx_book_theme"
+html_theme_options = {
+    "search_bar_text": "Search this book...",
+    "launch_buttons": {
+        "notebook_interface": "classic",
+        "binderhub_url": "",
+        "jupyterhub_url": "",
+        "thebe": False,
+        "colab_url": "",
+        "deepnote_url": "",
+    },
+    "path_to_docs": "",
+    "repository_url": "https://github.com/finsberg/fenicsx-pulse",
+    "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 = "fenicsx-pulse"
+intersphinx_mapping = {
+    "basix": ["https://docs.fenicsproject.org/basix/main/python/", None],
+    "ffcx": ["https://docs.fenicsproject.org/ffcx/main/", None],
+    "ufl": ["https://docs.fenicsproject.org/ufl/main/", None],
+    "dolfinx": ["https://docs.fenicsproject.org/dolfinx/main/python", None],
+    "petsc4py": ["https://petsc.org/release/petsc4py", None],
+    "mpi4py": ["https://mpi4py.readthedocs.io/en/stable", None],
+    "numpy": ["https://numpy.org/doc/stable/", None],
+    "matplotlib": ["https://matplotlib.org/stable/", None],
+    "pyvista": ["https://docs.pyvista.org/", None],
+    "packaging": ["https://packaging.pypa.io/en/stable/", None],
+    "gotranx": ["https://finsberg.github.io/gotranx/", None],
+    "cardiac_geometries": ["https://computationalphysiology.github.io/cardiac-geometriesx/", None],
+}
+latex_engine = "pdflatex"
+myst_enable_extensions = ["amsmath", "dollarmath", "linkify"]
+myst_url_schemes = ["mailto", "http", "https"]
+nb_custom_formats = {".py": ["jupytext.reads", {"fmt": "py"}]}
+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_show_tb = True
+nb_execution_timeout = 3000
+nb_output_stderr = "show"
+numfig = True
+pygments_style = "sphinx"
+suppress_warnings = ["mystnb.unknown_mime_type", "bibtex.duplicate_citation"]
+use_jupyterbook_latex = True
+use_multitoc_numbering = True