Remove autodoc_mock_imports to fix RTD build

.readthedocs.yaml

@@ -2,21 +2,22 @@
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
-# Required
 version: 2
 
-# Set the version of Python and other tools you might need
+# Configuration file for build in doc/ subdirectory
+sphinx:
+  configuration: doc/conf.py
+
+# Specify mambaforge such that we can install dependencies via mamba package manager
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
-
-# Build documentation in the docs/ directory with Sphinx
-sphinx:
-  configuration: doc/conf.py
+    python: "mambaforge-22.9"
+  jobs:
+    install:
+      - tar --exclude=./python -cvf ./python/s-dftd3.tar . && mkdir -p ./python/subprojects/s-dftd3 && tar xvf ./python/s-dftd3.tar -C ./python/subprojects/s-dftd3
+      - pip install ./python -v
 
-# We recommend specifying your dependencies to enable reproducible builds:
-# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-python:
-  install:
-  - requirements: doc/requirements.txt
+# Get dependencies for docs, package and build from conda-forge
+conda:
+  environment: doc/environment.yml

doc/_static/references.bib

@@ -351,3 +351,16 @@ @article{blum2009
   volume  = {180}
 }
 
+@article{jurecka2006,
+  title     = {Benchmark database of accurate ({MP2} and {CCSD(T)} complete basis set limit) interaction energies of small model complexes, {DNA} base pairs, and amino acid pairs},
+  author    = {Jure{\v{c}}ka, Petr and {\v{S}}poner, Ji{\v{r}}{\'{\i}} and {\v{C}}ern{\'y}, Ji{\v{r}}{\'{\i}} and Hobza, Pavel},
+  journal   = {Phys. Chem. Chem. Phys.},
+  volume    = {8},
+  number    = {17},
+  pages     = {1985--1993},
+  year      = {2006},
+  publisher = {Royal Society of Chemistry},
+  doi       = {10.1039/B600027D},
+  url       = {https://doi.org/10.1039/B600027D}
+}
+

doc/conf.py

@@ -13,6 +13,7 @@
 release = version
 
 extensions = [
+    "myst_nb",
     "sphinx_design",
     "sphinx_copybutton",
     "sphinx.ext.autosummary",
@@ -25,6 +26,9 @@
     "sphinxcontrib.bibtex",
 ]
 
+nb_execution_mode = "auto"
+myst_enable_extensions = ["dollarmath"]
+
 html_theme = "sphinx_book_theme"
 html_title = "Simple DFT-D3"
 
@@ -41,7 +45,6 @@
 html_static_path = ["_static"]
 templates_path = ["_templates"]
 locale_dirs = ["locales"]
-autodoc_mock_imports = ["dftd3.library", "numpy", "ase", "qcelemental", "pyscf"]
 bibtex_bibfiles = ["_static/references.bib"]
 
 master_doc = "index"

doc/environment.yml

@@ -0,0 +1,25 @@
+name: dftd3-docs
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  # documentation dependencies
+  - myst-nb
+  - sphinx-book-theme
+  - sphinx-copybutton
+  - sphinx-design
+  - sphinxcontrib-bibtex
+  # package dependencies
+  - ase
+  - cffi
+  - numpy
+  - qcelemental
+  # extra dependencies for notebooks
+  - pyscf
+  # build dependencies
+  - c-compiler
+  - fortran-compiler
+  - meson !=1.8.0
+  - ninja
+  - pkg-config
+  - pip

doc/requirements.txt

@@ -2,6 +2,7 @@ sphinx-book-theme
 sphinx-copybutton
 sphinx-design
 sphinxcontrib-bibtex
+myst-nb
 numpy
 ase
 cffi

doc/tutorial/index.rst

@@ -7,3 +7,4 @@ This section contains tutorials on using D3.
 
    first-steps-cli
    first-steps-fortran
+   using-3c-methods