Use furo for docs theme

.github/workflows/deploy.yml

@@ -33,7 +33,7 @@ jobs:
           pip install .[strict,docs]
 
       - name: Build
-        run: jupyter-book build docs --path-output docs_build
+        run: sphinx-build docs docs_build
 
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v3

.github/workflows/docs_manual.yml

@@ -29,7 +29,7 @@ jobs:
           pip install .[strict,docs]
 
       - name: Build
-        run: jupyter-book build docs --path-output docs_build
+        run: sphinx-build docs docs_build
 
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v3

.github/workflows/testing.yml

@@ -75,7 +75,7 @@ jobs:
           pip install .[strict,docs]
 
       - name: Build
-        run: jupyter-book build docs --path-output docs_build
+        run: sphinx-build docs docs_build
 
   automerge:
     needs: [lint, test, docs]

CONTRIBUTING.md

@@ -53,7 +53,7 @@ The basic procedure for making a PR is:
 
 We have a few tips for writing good PRs that are accepted into the main repo:
 
-- Use the Numpy Code style for all of your code. Find an example [here](hhttps://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html#example-numpy).
+- Use the Numpy Code style for all of your code. Find an example [here](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html#example-numpy).
 - Your code should have (4) spaces instead of tabs.
 - If needed, update the documentation.
 - **Write tests** for new features! Good tests are 100%, absolutely necessary

docs/_static/custom.css

@@ -1,70 +1,70 @@
-/* Override some aspects of the pydata-sphinx-theme */
-@import url('https://fonts.googleapis.com/css2?family=Lato:ital,wght@0,400;0,700;0,900;1,400;1,700;1,900&family=Open+Sans:ital,wght@0,400;0,600;1,400;1,600&display=swap');
+/*!* Override some aspects of the pydata-sphinx-theme *!*/
+/*@import url('https://fonts.googleapis.com/css2?family=Lato:ital,wght@0,400;0,700;0,900;1,400;1,700;1,900&family=Open+Sans:ital,wght@0,400;0,600;1,400;1,600&display=swap');*/
 
-:root {
-  /* Use softer blue from bootstrap's default info color */
-  --pst-color-info: 23, 162, 184;
-}
+/*:root {*/
+/*  !* Use softer blue from bootstrap's default info color *!*/
+/*  --pst-color-info: 23, 162, 184;*/
+/*}*/
 
-/* Main index page overview cards */
+/*!* Main index page overview cards *!*/
 
-.intro-card {
-  background: #fff;
-  border-radius: 0;
-  padding: 30px 10px 20px 10px;
-  margin: 10px 0px;
-}
+/*.intro-card {*/
+/*  background: #fff;*/
+/*  border-radius: 0;*/
+/*  padding: 30px 10px 20px 10px;*/
+/*  margin: 10px 0px;*/
+/*}*/
 
-.intro-card p.card-text {
-  margin: 0px;
-}
+/*.intro-card p.card-text {*/
+/*  margin: 0px;*/
+/*}*/
 
-.intro-card .card-img-top {
-  margin: 10px;
-  height: 52px;
-}
+/*.intro-card .card-img-top {*/
+/*  margin: 10px;*/
+/*  height: 52px;*/
+/*}*/
 
-.intro-card .card-header {
-  border: none;
-  background-color:white;
-  color: #150458 !important;
-  font-size: var(--pst-font-size-h5);
-  font-weight: bold;
-  padding: 2.5rem 0rem 0.5rem 0rem;
-}
+/*.intro-card .card-header {*/
+/*  border: none;*/
+/*  background-color:white;*/
+/*  color: #150458 !important;*/
+/*  font-size: var(--pst-font-size-h5);*/
+/*  font-weight: bold;*/
+/*  padding: 2.5rem 0rem 0.5rem 0rem;*/
+/*}*/
 
-.intro-card .card-footer {
-  border: none;
-  background-color:white;
-}
+/*.intro-card .card-footer {*/
+/*  border: none;*/
+/*  background-color:white;*/
+/*}*/
 
-.intro-card .card-footer p.card-text{
-  max-width: 220px;
-  margin-left: auto;
-  margin-right: auto;
-}
+/*.intro-card .card-footer p.card-text{*/
+/*  max-width: 220px;*/
+/*  margin-left: auto;*/
+/*  margin-right: auto;*/
+/*}*/
 
 
-body {
-  font-family: 'Open Sans', sans-serif;
-  color:#4A4A4A; /* numpy.org body color */
-}
+/*body {*/
+/*  font-family: 'Open Sans', sans-serif;*/
+/*  color:#4A4A4A; !* numpy.org body color *!*/
+/*}*/
 
-pre, code {
-  /*font-size: 100%;*/
-  /*line-height: 155%;*/
-}
+/*pre, code {*/
+/*  !*font-size: 100%;*!*/
+/*  !*line-height: 155%;*!*/
+/*}*/
 
-h1 {
-  font-family: "Lato", sans-serif;
-}
+/*h1 {*/
+/*  font-family: "Lato", sans-serif;*/
+/*}*/
 
 
-h2 {
-  letter-spacing: -.03em;
-}
+/*h2 {*/
+/*  letter-spacing: -.03em;*/
+/*}*/
 
-h3 {
-  /*color: #013243; !* warm black *!*/
-  letter-spacing: -.03em;
-}
+/*h3 {*/
+/*  !*color: #013243; !* warm black *!*!*/
+/*  letter-spacing: -.03em;*/
+/*}*/

docs/conf.py

@@ -0,0 +1,179 @@
+# ruff: noqa: E501
+
+"""Sphinx configuration file."""
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
+import os
+import sys
+
+# import typing
+# typing.TYPE_CHECKING = True
+from atomate2 import __version__
+
+sys.path.insert(0, os.path.abspath("../../"))
+
+# -- Project information -----------------------------------------------------
+
+project = "atomate2"
+copyright = "2023, materialsproject"
+author = "Alex Ganose"
+
+# The short X.Y version
+version = __version__
+# The full version, including alpha/beta/rc tags
+release = __version__
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.autosummary",
+    "myst_parser",
+    "sphinxcontrib.autodoc_pydantic",
+    "numpydoc",
+    "sphinx_design",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# 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 = ["Thumbs.db", ".DS_Store", "test*.py"]
+
+myst_heading_anchors = 2  # enable headings as link targets
+myst_enable_extensions = [
+    "amsmath",
+    "colon_fence",
+    "dollarmath",
+    "html_admonition",
+    "html_image",
+]
+
+# use type hints
+autodoc_typehints = "description"
+# autoclass_content = "both"
+# autodoc_member_order = "bysource"
+
+# better napoleon support
+napoleon_use_param = True
+napoleon_use_rtype = True
+napoleon_use_ivar = True
+
+# The suffix(es) of source filenames.
+source_suffix = [".rst", ".md"]
+
+mathjax3_config = {
+    "tex": {
+        "macros": {
+            "N": "\\mathbb{N}",
+            "floor": ["\\lfloor#1\\rfloor", 1],
+            "bmat": ["\\left[\\begin{array}"],
+            "emat": ["\\end{array}\\right]"],
+        }
+    }
+}
+latex_elements = {
+    "preamble": r"""\newcommand\N{\mathbb{N}}
+\newcommand\floor[1]{\lfloor#1\rfloor}
+\newcommand{\bmat}{\left[\begin{array}}
+\newcommand{\emat}{\end{array}\right]}
+"""
+}
+language = "en"
+html_extra_path = ["images/ badge.svg"]
+html_static_path = ["_static"]
+html_css_files = ["custom.css", "github.css"]
+suppress_warnings = "etoc.toctree"
+
+# autodoc options
+autosummary_imported_members = False
+autodoc_preserve_defaults = True
+autoclass_content = "class"
+autodoc_member_order = "bysource"
+
+python_use_unqualified_type_names = True
+
+# don't overwrite summary but generate them if they don't exist
+autosummary_generate = True
+autosummary_generate_overwrite = True
+
+# numpydoc options
+numpydoc_class_members_toctree = False
+numpydoc_show_class_members = False
+numpydoc_show_inherited_class_members = False
+numpydoc_attributes_as_param_list = False
+numpydoc_xref_param_type = True
+
+# sphinx-panels shouldn't add bootstrap css as the pydata-sphinx-theme already loads it
+panels_add_bootstrap_css = False
+
+# control pydantic model docs
+autodoc_pydantic_model_show_json = False
+autodoc_pydantic_model_show_field_summary = False
+autodoc_pydantic_model_show_config = False
+autodoc_pydantic_model_show_config_summary = False
+autodoc_pydantic_model_show_validator_members = False
+autodoc_pydantic_model_member_order = "bysource"
+autodoc_pydantic_settings_show_json = False
+autodoc_pydantic_settings_show_field_summary = False
+autodoc_pydantic_settings_show_config = False
+autodoc_pydantic_settings_show_config_summary = False
+autodoc_pydantic_settings_show_validator_members = False
+autodoc_pydantic_settings_member_order = "bysource"
+autodoc_pydantic_field_list_validators = False
+autodoc_pydantic_field_show_constraints = False
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "furo"
+html_theme_options = {
+    "footer_icons": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/materialsproject/atomate2",
+            "html": """
+<svg stroke="currentColor" fill="currentColor" stroke-width="0" viewBox="0 0 16 16">
+    <path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"></path>
+</svg>
+            """,
+            "class": "",
+        },
+    ],
+    "source_repository": "https://github.com/materialsproject/atomate2/",
+    "source_branch": "main",
+    "source_directory": "docs/",
+}
+
+
+# hide sphinx footer
+html_show_sphinx = False
+html_show_sourcelink = False
+html_title = "atomate2"
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3.8", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
+    "networkx": ("https://networkx.org/documentation/stable/", None),
+    "monty": ("https://materialsvirtuallab.github.io/monty/", None),
+    "jobflow": ("https://materialsproject.github.io/jobflow", None),
+}

docs/index.md

@@ -1,3 +1,35 @@
+```{toctree}
+:caption: User Guide
+:hidden:
+user/index
+user/install
+user/running-workflows
+user/fireworks
+user/codes/index
+```
+
+```{toctree}
+:caption: Reference
+:hidden:
+reference/index
+```
+
+```{toctree}
+:caption: Developer Guide
+:hidden:
+dev/dev_install
+dev/vasp_tests
+```
+
+```{toctree}
+:caption: About
+:hidden:
+about/changelog
+about/contributors
+about/contributing
+about/license
+```
+
 # atomate2 documentation
 
 **Date**: {sub-ref}`today`

docs/user/codes/index.md

@@ -3,3 +3,7 @@
 # Codes
 
 The section gives the instructions for codes supported by atomate2.
+
+```{toctree}
+vasp
+```

docs/user/codes/vasp.md

@@ -10,7 +10,6 @@ differences are:
 
 - Use of the PBEsol exchange–correlation functional instead of PBE.
 - Use of up-to-date pseudopotentials (PBE_54 instead of PBE_52).
-- Use of KSPACING for most calculations.
 
 ```{warning}
 The different input sets used in atomate2 mean total energies cannot be compared