docs: add sphinx docs and rtd site config (#74)

Close #56

- move examples folder from the root to docs/examples/...
- setup sphinx configuration with nbsphinx for notebooks
- convert notebooks to jupytext light format python scripts
- setup readthedocs site configuration

Author: wpbonelli

.gitignore

@@ -140,4 +140,19 @@ dmypy.json
 uv.lock
 
 # temporary test folders
-autotest/temp/**
+autotest/temp/**
+
+# notebooks
+docs/examples/notebooks/*.ipynb
+
+# autosummary
+docs/_autosummary/
+
+# mf6 output files
+**/*.lst
+**/*.stdout
+**/*.cbc
+**/*.cbb
+**/*.hds
+**/*.hed
+**/*.grb

.readthedocs.yml

@@ -0,0 +1,15 @@
+version: 2
+build:
+  os: "ubuntu-24.04"
+  tools:
+    python: "3.13"
+sphinx:
+  configuration: docs/conf.py
+formats:
+  - pdf
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

README.md

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/Makefile

@@ -0,0 +1,36 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../'))
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+project = 'modflowapi'
+copyright = '2025, modflowapi developers'
+author = 'modflowapi developers'
+release = '0.3.0.dev0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "myst_parser",
+    "nbsphinx"
+]
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**/Extensions.py']
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']
+
+# -- nbsphinx configuration -------------------------------------------------
+nbsphinx_custom_formats = {
+    '.py': ['jupytext.reads', {'fmt': 'py:light'}],
+}