Add docs for manual stats calculations outside of plots

devtools/conda-envs/env.yaml

@@ -25,6 +25,6 @@ dependencies:
 
   # docs
   - sphinx
-  - nbsphinx
+  - myst-nb
   - pip:
     - git+https://github.com/OpenFreeEnergy/ofe-sphinx-theme@main

docs/conf.py

@@ -50,7 +50,7 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.intersphinx",
     "sphinx.ext.extlinks",
-    "nbsphinx",
+    "myst_nb",
 ]
 
 autosummary_generate = True
@@ -80,7 +80,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path .
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "README.md"]
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "default"
@@ -174,4 +174,14 @@
 ]
 
 
+# -- myst-nb configuration ---------------------------------------------------
+
+# Do not re-execute notebooks during the build; use the pre-saved cell outputs
+nb_execution_mode = "off"
+
+# Generate HTML anchors for headings up to depth 3 so that plain #slug fragment
+# links inside notebooks resolve as HTML anchors rather than Sphinx cross-refs.
+# This restores the nbsphinx behavior for within-page heading links.
+myst_heading_anchors = 3
+
 # -- Extension configuration -------------------------------------------------

docs/tutorials/calculating-metrics.ipynb

@@ -0,0 +1 @@
+../../examples/calculating-metrics.ipynb

docs/tutorials/index.rst

@@ -14,4 +14,5 @@ API Tutorials
     :maxdepth: 1
 
     cinnabar-api
+    calculating-metrics
     ecdf-plots