From a08f3c68553cbf5fc28617bfec90210996682ee2 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Thu, 29 Jan 2026 11:24:47 +0100
Subject: [PATCH 1/7] add api docs

---
 docs/.DS_Store                                | Bin 0 -> 6148 bytes
 docs/ExampleNotebooks                         |   1 +
 docs/Makefile                                 |  20 +
 docs/_ext/.sass.py.swp                        | Bin 0 -> 12288 bytes
 docs/_ext/sass.py                             |  86 ++++
 docs/_sass/deflist-flowchart.scss             | 397 ++++++++++++++++++
 docs/_static/API.svg                          |   1 +
 docs/_static/CLI.svg                          |   1 +
 docs/_static/Cookbook.svg                     |   1 +
 docs/_static/Download.svg                     |   1 +
 docs/_static/OFE-color-icon.svg               |  12 +
 docs/_static/Rocket.svg                       |   1 +
 docs/_static/Showcase.svg                     |  75 ++++
 docs/_static/Tutorial.svg                     |   1 +
 docs/_static/UserGuide.svg                    |   1 +
 docs/_templates/autosummary/base.rst          |   5 +
 docs/_templates/autosummary/class.rst         |   5 +
 docs/conf.py                                  | 254 +++++++++++
 docs/environment.yaml                         |  36 ++
 docs/index.rst                                |  26 ++
 .../api/generated/openfe_analysis.rst         |  37 ++
 .../api/generated/openfe_analysis.utils.rst   |  29 ++
 docs/reference/api/index.rst                  |  10 +
 docs/reference/index.rst                      |   9 +
 src/openfe_analysis/rmsd.py                   |  38 +-
 25 files changed, 1039 insertions(+), 8 deletions(-)
 create mode 100644 docs/.DS_Store
 create mode 160000 docs/ExampleNotebooks
 create mode 100644 docs/Makefile
 create mode 100644 docs/_ext/.sass.py.swp
 create mode 100644 docs/_ext/sass.py
 create mode 100644 docs/_sass/deflist-flowchart.scss
 create mode 100644 docs/_static/API.svg
 create mode 100644 docs/_static/CLI.svg
 create mode 100644 docs/_static/Cookbook.svg
 create mode 100644 docs/_static/Download.svg
 create mode 100644 docs/_static/OFE-color-icon.svg
 create mode 100644 docs/_static/Rocket.svg
 create mode 100644 docs/_static/Showcase.svg
 create mode 100644 docs/_static/Tutorial.svg
 create mode 100644 docs/_static/UserGuide.svg
 create mode 100644 docs/_templates/autosummary/base.rst
 create mode 100644 docs/_templates/autosummary/class.rst
 create mode 100644 docs/conf.py
 create mode 100644 docs/environment.yaml
 create mode 100644 docs/index.rst
 create mode 100644 docs/reference/api/generated/openfe_analysis.rst
 create mode 100644 docs/reference/api/generated/openfe_analysis.utils.rst
 create mode 100644 docs/reference/api/index.rst
 create mode 100644 docs/reference/index.rst

diff --git a/docs/.DS_Store b/docs/.DS_Store
new file mode 100644
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diff --git a/docs/ExampleNotebooks b/docs/ExampleNotebooks
new file mode 160000
index 0000000..cef0451
--- /dev/null
+++ b/docs/ExampleNotebooks
@@ -0,0 +1 @@
+Subproject commit cef0451003a732a3014d00a4f2f25869ac40ce85
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000..eae0d86
--- /dev/null
+++ b/docs/Makefile
@@ -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    ?= -v -W --keep-going
+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)
diff --git a/docs/_ext/.sass.py.swp b/docs/_ext/.sass.py.swp
new file mode 100644
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diff --git a/docs/_ext/sass.py b/docs/_ext/sass.py
new file mode 100644
index 0000000..4ec4b35
--- /dev/null
+++ b/docs/_ext/sass.py
@@ -0,0 +1,86 @@
+"""
+sphinxcontrib-sass
+https://github.com/attakei-lab/sphinxcontrib-sass
+Kayuza Takei
+Apache 2.0
+
+Modified to:
+- Write directly to Sphinx output directory
+- Infer targets if not given
+- Ensure ``target: Path`` in ``configure_path()``
+- Return version number and thread safety from ``setup()``
+- Use compressed style by default
+- More complete type checking
+"""
+
+from os import PathLike
+from pathlib import Path
+from typing import Optional, Union
+
+import sass
+from sphinx.application import Sphinx
+from sphinx.environment import BuildEnvironment
+from sphinx.util import logging
+
+logger = logging.getLogger(__name__)
+
+
+def configure_path(conf_dir: str, src: Optional[Union[PathLike, Path]]) -> Path:
+    if src is None:
+        target = Path(conf_dir)
+    else:
+        target = Path(src)
+    if not target.is_absolute():
+        target = Path(conf_dir) / target
+    return target
+
+
+def get_targets(app: Sphinx) -> dict[Path, Path]:
+    src_dir = configure_path(app.confdir, app.config.sass_src_dir)
+    dst_dir = configure_path(app.outdir, app.config.sass_out_dir)
+
+    if isinstance(app.config.sass_targets, dict):
+        targets = app.config.sass_targets
+    else:
+        targets = {
+            path: path.relative_to(src_dir).with_suffix(".css")
+            for path in src_dir.glob("**/[!_]*.s[ca]ss")
+        }
+
+    return {src_dir / src: dst_dir / dst for src, dst in targets.items()}
+
+
+def build_sass_sources(app: Sphinx, env: BuildEnvironment):
+    logger.debug("Building stylesheet files")
+    include_paths = [str(p) for p in app.config.sass_include_paths]
+    targets = get_targets(app)
+    output_style = app.config.sass_output_style
+    # Build css files
+    for src, dst in targets.items():
+        content = src.read_text()
+        css = sass.compile(
+            string=content,
+            output_style=output_style,
+            include_paths=[str(src.parent)] + include_paths,
+        )
+        dst.parent.mkdir(exist_ok=True, parents=True)
+        dst.write_text(css)
+
+
+def setup(app: Sphinx):
+    """
+    Setup function for this extension.
+    """
+    logger.debug(f"Using {__name__}")
+    app.add_config_value("sass_include_paths", [], "html")
+    app.add_config_value("sass_src_dir", None, "html")
+    app.add_config_value("sass_out_dir", None, "html")
+    app.add_config_value("sass_targets", None, "html")
+    app.add_config_value("sass_output_style", "compressed", "html")
+    app.connect("env-updated", build_sass_sources)
+
+    return {
+        "version": "0.3.4ofe",
+        "parallel_read_safe": True,
+        "parallel_write_safe": True,
+    }
diff --git a/docs/_sass/deflist-flowchart.scss b/docs/_sass/deflist-flowchart.scss
new file mode 100644
index 0000000..b65f54b
--- /dev/null
+++ b/docs/_sass/deflist-flowchart.scss
@@ -0,0 +1,397 @@
+:root {
+    --arrow-thickness: 4px;
+    --arrow-head-size: 7px;
+    --arrow-length: 2em;
+    --arrow-multiple-gap: 20px;
+    --arrow-color: var(--pst-color-text-muted);
+    --arrow-fade-dist: 0px;
+    --flowchart-def-bg-color: var(--pst-color-surface);
+    --flowchart-bg-color: var(--pst-color-background);
+    --flowchart-def-border-color: var(--pst-color-border);
+    --flowchart-unit-width: 45px;
+    --flowchart-spacing: 0.5rem;
+    --flowchart-column-gap: calc(1.5 * var(--flowchart-spacing));
+    --flowchart-top-label-space: 26px;
+}
+.arrow.thick {
+    --arrow-thickness: 6px;
+    --arrow-head-size: 10px;
+}
+
+.deflist-flowchart ul,
+ul.deflist-flowchart {
+  display: flex;
+  flex-direction: column;
+  justify-content: space-between;
+  height: 100%;
+  grid-column-gap: var(--flowchart-column-gap);
+  margin: 0;
+  padding: 0;
+}
+
+.deflist-flowchart {
+  margin: 1em 0;
+
+  p:first-child {
+    margin-top: 0;
+  }
+
+  p:last-child {
+    margin-bottom: 0;
+  }
+
+  li,
+  li ul
+  {
+    margin: 0;
+    padding: 0;
+  }
+
+  li:empty:not([class])
+  {
+    display: None;
+  }
+
+  li {
+    list-style: none;
+  }
+
+  .arrow-down::after,
+  .arrow-up::after,
+  .arrow-multiple.arrow-down::before,
+  .arrow-multiple.arrow-up::before,
+  .arrow-cycle::after,
+  .arrow-cycle::before {
+    content: "";
+  }
+
+  .arrow-down,
+  .arrow-up,
+  .arrow-cycle
+  {
+    --arrow-head-size-clamped: calc(min(var(--arrow-head-size), var(--arrow-length) / 2));
+
+    display: flex;
+    justify-content: center;
+    align-items: center;
+    flex-grow: 1;
+    min-height: var(--arrow-length);
+    width: 100%;
+    margin: calc(2 * var(--flowchart-spacing)) auto;
+    position: relative;
+    z-index: 1;
+    padding: calc(var(--arrow-length) / 4) 0;
+
+    &::before, &::after {
+      --actual-arrow-length: max(var(--arrow-length), 100%);
+      --arrow-tail-gradient:
+        linear-gradient(
+          45deg,
+          transparent calc(50% - var(--arrow-thickness)/2),
+          var(--arrow-color) calc(50% - var(--arrow-thickness)/2),
+          var(--arrow-color) calc(50% + var(--arrow-thickness)/2),
+          transparent calc(50% + var(--arrow-thickness)/2)
+        );
+      --arrow-head-gradient:
+        linear-gradient(
+          -45deg,
+          var(--arrow-color) var(--arrow-head-size-clamped),
+          transparent var(--arrow-head-size-clamped)
+        );
+      height: calc(var(--actual-arrow-length)/1.4142);
+      width: auto;
+      aspect-ratio: 1;
+      padding: 0;
+      display: inline-block;
+      transform: rotate(45deg);
+      background-image:
+        var(--arrow-tail-gradient),
+        var(--arrow-head-gradient);
+      position: absolute;
+      top: 0;
+      left: 50%;
+      transform-origin: 0 0;
+      z-index: -1;
+    }
+
+    &.arrow-tail {
+      &::before, &::after {
+        background-image:
+          var(--arrow-tail-gradient);
+      }
+    }
+
+    > p {
+      background: linear-gradient(
+        transparent,
+        var(--flowchart-bg-color) var(--arrow-fade-dist),
+        var(--flowchart-bg-color) calc(100% - var(--arrow-fade-dist)),
+        transparent,
+      );
+      line-height: 1.5;
+      z-index: 10;
+    }
+  }
+
+  .arrow-down:not(.arrow-tail),
+  .arrow-cycle {
+    padding-bottom: calc(var(--arrow-head-size-clamped) + var(--arrow-length) / 4);
+  }
+
+  .arrow-up:not(.arrow-tail),
+  .arrow-cycle {
+    padding-top: calc(var(--arrow-head-size-clamped) + var(--arrow-length) / 4);
+  }
+
+  .arrow-cycle, .arrow-multiple {
+    &::after {
+      translate: calc(0.5 * var(--arrow-multiple-gap)) 0;
+    }
+    &::before {
+      translate: calc(-0.5 * var(--arrow-multiple-gap)) 0;
+    }
+  }
+
+  .arrow-up::after,
+  .arrow-multiple.arrow-up::before,
+  .arrow-cycle::before
+  {
+    transform: rotate(-135deg);
+    translate: 0 calc(var(--actual-arrow-length) + 2 * var(--flowchart-spacing) + var(--arrow-head-size-clamped) / 2);
+  }
+
+  .arrow-cycle::before {
+    translate:
+      calc(-0.5 * var(--arrow-multiple-gap))
+      140%;
+  }
+
+  .arrow-aside {
+    margin-left: calc(8 * var(--arrow-head-size-clamped));
+    &::after {
+      left: calc(-4 * var(--arrow-head-size-clamped));
+    }
+  }
+
+  .arrow-multiple-combine {
+    &::before {
+      content: "";
+      width: var(--arrow-multiple-gap);
+      border: var(--arrow-thickness) solid var(--arrow-color);
+      height: calc(var(--arrow-length) / 2);
+      background: var(--flowchart-bg-color);
+      transform: none;
+      left: auto;
+      z-index: 2;
+    }
+
+    &.arrow-down {
+      padding-top: calc(0.75 * var(--arrow-length) - var(--arrow-head-size-clamped) / 2);
+      padding-bottom: calc(0.5 * var(--arrow-head-size-clamped) + 0.25 * var(--arrow-length));
+      &::before {
+        border-top: 1px solid var(--flowchart-bg-color);
+      }
+    }
+
+    &.arrow-up {
+      &::before {
+        border-bottom: 1px solid var(--flowchart-bg-color);
+        top: auto;
+        bottom: -1px;
+      }
+    }
+  }
+
+  .arrow-tail {
+    &.arrow-down {
+      margin-bottom: 0;
+    }
+    &.arrow-up {
+      margin-top: 0;
+    }
+  }
+
+  .arrow-head {
+    &.arrow-up {
+      margin-bottom: 0;
+    }
+    &.arrow-down {
+      margin-top: 0;
+    }
+  }
+
+  .arrow-combine, .arrow-combine-left, .arrow-combine-right {
+    &.arrow-down.arrow-tail, &.arrow-up.arrow-head {
+      --arrow-combine-gradient-angle: 0deg;
+      padding-bottom: calc(0.5 * var(--arrow-thickness));
+      margin-bottom: calc(-0.5 * var(--arrow-thickness));
+    }
+    &.arrow-up.arrow-tail, &.arrow-down.arrow-head {
+      --arrow-combine-gradient-angle: 180deg;
+      padding-top: calc(0.5 * var(--arrow-thickness));
+      margin-top: calc(-0.5 * var(--arrow-thickness));
+    }
+    background-image:
+      linear-gradient(
+        var(--arrow-combine-gradient-angle),
+        var(--arrow-color) var(--arrow-thickness),
+        transparent var(--arrow-thickness)
+      );
+    background-repeat: no-repeat;
+
+    width: calc(max(100% + 2 * var(--flowchart-column-gap), var(--flowchart-unit-width)));
+    margin-left: calc(-1 * var(--flowchart-column-gap));
+
+    &.arrow-combine-left, &.arrow-combine-right {
+      background-size: 50%;
+
+      &.arrow-multiple {
+        background-size: calc(50% + 0.5 * var(--arrow-multiple-gap));
+      }
+    }
+
+    &.arrow-combine-right {
+      background-position-x: 100%;
+    }
+  }
+
+  > ul > li {
+    &.arrow-down,
+    &.arrow-up,
+    &.arrow-cycle {
+      width: calc(100% - var(--flowchart-top-label-space));
+      margin-left: 0;
+    }
+  }
+
+  dl {
+    display: flex;
+    flex-direction: row-reverse;
+    margin: 0;
+    padding: 0 var(--flowchart-spacing);
+  }
+  dt {
+    display: inline-block;
+    writing-mode: vertical-rl;
+    margin-top: .25rem;
+    flex-grow: 0;
+    width: var(--flowchart-top-label-space);
+    font-size: 1.1em;
+  }
+  dd {
+    text-align: center;
+    position: relative;
+    border: 1px solid var(--flowchart-def-border-color);
+    border-radius: .25rem;
+    margin: 0;
+    display: inline-block;
+    flex-grow: 1;
+    container-type: inline-size;
+    container-name: flowchart;
+    overflow-x: auto;
+  }
+
+  dd dl {
+    background-color: var(--flowchart-def-bg-color);
+    border-radius: 4px;
+    box-shadow: 0 6px 10px 0 rgba(0,0,0,0.14),
+                0 1px 18px 0 rgba(0,0,0,0.12),
+                0 3px 5px -1px rgba(0,0,0,0.4);
+    display: block;
+    margin: 0 auto;
+    padding: calc(var(--flowchart-spacing) / 2);
+    max-width: calc(100cqw - 2 * var(--flowchart-spacing));
+    min-width: calc(2 * var(--flowchart-unit-width) + var(--flowchart-column-gap));
+  }
+  dd dt {
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+<svg width="480" height="480" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xml:space="preserve" overflow="hidden"><defs><clipPath id="clip0"><rect x="395" y="100" width="480" height="480"/></clipPath></defs><g clip-path="url(#clip0)" transform="translate(-395 -100)"><path d="M825 210 825 455 445 455 445 210 415 210 415 490 590 490C590 498.5 596.5 505 605 505L665 505C673.5 505 680 498.5 680 490L855 490 855 210 825 210Z"/><path d="M805 180 465 180 465 435 805 435 805 180ZM495 210 625 210 625 405 495 405 495 210ZM775 405 645 405 645 210 775 210 775 405Z"/><path d="M675 260 745 260 745 275 675 275Z"/><path d="M675 290 745 290 745 305 675 305Z"/><path d="M675 320 723.5 320 723.5 335 675 335Z"/></g></svg>
diff --git a/docs/_templates/autosummary/base.rst b/docs/_templates/autosummary/base.rst
new file mode 100644
index 0000000..cdb86a6
--- /dev/null
+++ b/docs/_templates/autosummary/base.rst
@@ -0,0 +1,5 @@
+.. title:: {{ objname }}
+
+.. currentmodule:: {{ module }}
+
+.. auto{{ objtype }}:: {{ objname }}
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
new file mode 100644
index 0000000..cdb86a6
--- /dev/null
+++ b/docs/_templates/autosummary/class.rst
@@ -0,0 +1,5 @@
+.. title:: {{ objname }}
+
+.. currentmodule:: {{ module }}
+
+.. auto{{ objtype }}:: {{ objname }}
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000..d3f9db6
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,254 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- 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
+from importlib.metadata import version
+from inspect import cleandoc
+from pathlib import Path
+
+import git
+import nbformat
+import nbsphinx
+from packaging.version import parse
+
+sys.path.insert(0, os.path.abspath("../"))
+
+
+os.environ["SPHINX"] = "True"
+
+# -- Project information -----------------------------------------------------
+
+project = "OpenFE Analysis"
+copyright = "2022, The OpenFE Development Team"
+author = "The OpenFE Development Team"
+version = f"{parse(version('openfe_analysis')).major}.{parse(version('openfe_analysis')).minor}"
+
+# -- 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_click.ext",
+    "sphinxcontrib.autodoc_pydantic",
+    "sphinx_toolbox.collapse",
+    "sphinx.ext.autosectionlabel",
+    "sphinx_design",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autosummary",
+    "docs._ext.sass",
+    "myst_parser",
+    "nbsphinx",
+    "nbsphinx_link",
+    "sphinx.ext.mathjax",
+]
+suppress_warnings = ["config.cache"]  # https://github.com/sphinx-doc/sphinx/issues/12300
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3.9", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+    "scikit.learn": ("https://scikit-learn.org/stable", None),
+    "openmm": ("https://docs.openmm.org/latest/api-python/", None),
+    "rdkit": ("https://www.rdkit.org/docs", None),
+    "openeye": ("https://docs.eyesopen.com/toolkits/python/", None),
+    "mdtraj": ("https://www.mdtraj.org/1.9.5/", None),
+    "openff.units": ("https://docs.openforcefield.org/projects/units/en/stable", None),
+    "gufe": ("https://gufe.openfree.energy/en/latest/", None),
+}
+
+autoclass_content = "both"
+# Make sure labels are unique
+# https://www.sphinx-doc.org/en/master/usage/extensions/autosectionlabel.html#confval-autosectionlabel_prefix_document
+autosectionlabel_prefix_document = True
+
+autodoc_pydantic_model_show_json = False
+
+autodoc_default_options = {
+    "members": True,
+    "member-order": "bysource",
+    "inherited-members": "GufeTokenizable,BaseModel",
+    "undoc-members": True,
+    "special-members": "__call__",
+}
+toc_object_entries_show_parents = "hide"
+
+# 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 = [
+    "_build",
+    "**/Thumbs.db",
+    "**/.DS_Store",
+    "_ext",
+    "_sass",
+    "**/README.md",
+    "ExampleNotebooks",
+]
+
+autodoc_mock_imports = [
+    "cinnabar",
+    "dill",
+    "MDAnalysis",
+    "matplotlib",
+    "mdtraj",
+    "openmmforcefields",
+    "openmmtools",
+    "pymbar",
+    "openff.interchange",
+    "openmmforcefields",
+    "psutil",
+    "py3Dmol",
+    "zstandard",
+]
+
+# Extensions for the myst parser
+myst_enable_extensions = [
+    "dollarmath",
+    "colon_fence",
+    "smartquotes",
+    "replacements",
+    "deflist",
+    "attrs_inline",
+]
+myst_heading_anchors = 3
+
+# -- 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 = "ofe_sphinx_theme"
+html_theme_options = {
+    "logo": {"text": "OpenFE docs"},
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/OpenFreeEnergy/openfe_analysis",
+            "icon": "fa-brands fa-square-github",
+            "type": "fontawesome",
+        }
+    ],
+    "accent_color": "cantina-purple",
+    "navigation_with_keys": False,
+}
+html_logo = "_static/OFE-color-icon.svg"
+html_favicon = "_static/OFE-color-icon.svg"
+# temporary fix, see https://github.com/pydata/pydata-sphinx-theme/issues/1662
+html_sidebars = {
+    "installation": [],
+    "CHANGELOG": [],
+}
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']
+
+
+# replace macros
+rst_prolog = """
+.. |rdkit.mol| replace:: :class:`rdkit.Chem.rdchem.Mol`
+"""
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+html_css_files = [
+    "css/custom.css",
+    "css/custom-api.css",
+    "css/deflist-flowchart.css",
+]
+
+# custom-api.css is compiled from custom-api.scss
+sass_src_dir = "_sass"
+sass_out_dir = "_static/css"
+
+# Clone or update ExampleNotebooks
+example_notebooks_path = Path("ExampleNotebooks")
+try:
+    if example_notebooks_path.exists():
+        repo = git.Repo(example_notebooks_path)
+        try:
+            repo.remote("origin").pull()
+        except git.exc.GitCommandError:
+            # cannot pull if on a tag
+            pass
+    else:
+        repo = git.Repo.clone_from(
+            "https://github.com/OpenFreeEnergy/ExampleNotebooks.git",
+            branch="2025.12.04",
+            to_path=example_notebooks_path,
+        )
+except Exception as e:
+    from sphinx.util.logging import getLogger
+
+    filename = e.__traceback__.tb_frame.f_code.co_filename
+    lineno = e.__traceback__.tb_lineno
+    getLogger("sphinx.ext.openfe_git").warning(
+        f"Getting ExampleNotebooks failed in {filename} line {lineno}: {e}"
+    )
+
+
+# First, create links at top of notebook pages
+# All notebooks are in ExampleNotebooks repo, so link to that
+# Finally, add sphinx reference anchor in prolog so that we can make refs
+nbsphinx_prolog = cleandoc(r"""
+    {%- set gh_repo = "OpenFreeEnergy/ExampleNotebooks" -%}
+    {%- set gh_branch = "main" -%}
+    {%- set path = env.doc2path(env.docname, base=None) -%}
+    {%- if path.endswith(".nblink") -%}
+        {%- set path = env.metadata[env.docname]["nbsphinx-link-target"] -%}
+    {%- endif -%}
+    {%- if path.startswith("ExampleNotebooks/") -%}
+        {%- set path = path.replace("ExampleNotebooks/", "", 1) -%}
+    {%- endif -%}
+    {%- set gh_url =
+        "https://www.github.com/"
+        ~ gh_repo
+        ~ "/blob/"
+        ~ gh_branch
+        ~ "/"
+        ~ path
+    -%}
+    {%- set dl_url =
+        "https://raw.githubusercontent.com/"
+        ~ gh_repo
+        ~ "/"
+        ~ gh_branch
+        ~ "/"
+        ~ path
+    -%}
+
+    .. container:: ofe-top-of-notebook
+
+        .. button-link:: {{gh_url}}
+            :color: primary
+            :shadow:
+            :outline:
+
+            :octicon:`mark-github` View on GitHub
+
+        .. button-link:: {{dl_url}}
+            :color: primary
+            :shadow:
+            :outline:
+
+            :octicon:`download` Download Notebook
+
+    .. _{{ env.doc2path(env.docname, base=None) }}:
+""")
diff --git a/docs/environment.yaml b/docs/environment.yaml
new file mode 100644
index 0000000..e85ad3c
--- /dev/null
+++ b/docs/environment.yaml
@@ -0,0 +1,36 @@
+name: openfe_analysis-docs
+channels:
+- https://conda.anaconda.org/conda-forge
+
+# explicit pins to speed up build:
+dependencies:
+- autodoc-pydantic >= 2.1
+- docutils == 0.20
+- gitpython
+- libsass
+- myst-parser
+- nbsphinx
+- nbsphinx-link
+- openff-toolkit-base == 0.17.0
+- openff-units == 0.3.1
+- packaging
+- pip
+- plugcli >= 0.2.1
+- python
+- pydantic >=2.0.0, <2.12.0  # https://github.com/openforcefield/openff-interchange/issues/1346
+- sphinx ==7.2.6 # TODO: debug "duplicate object" warning with later versions
+- sphinx-click
+- sphinx-design
+- sphinx-toolbox
+- threadpoolctl
+- tqdm
+- pip:
+  - git+https://github.com/OpenFreeEnergy/ofe-sphinx-theme@v0.3.1
+  # pip install these so that we can make sure docs build on main while these packages' docs are under development
+
+# These are added automatically by RTD, so we include them here
+# for a consistent environment.
+- mock
+- pillow
+# - sphinx
+# - sphinx_rtd_theme
diff --git a/docs/index.rst b/docs/index.rst
new file mode 100644
index 0000000..f42d80c
--- /dev/null
+++ b/docs/index.rst
@@ -0,0 +1,26 @@
+.. template taken from SciPy who took it from Pandas (keep the chain going)
+
+.. module:: openfe_analysis
+
+==========================================
+Welcome to OpenFE Analysis' documentation!
+==========================================
+
+The **OpenFE Analysis** toolkit provides a free and open-source framework for analyzing alchemical free energy calculations.
+
+.. grid:: 1 2 2 4
+    :gutter: 3
+
+    .. grid-item-card:: :fas:`code` Python API
+        :text-align: center
+        :link: reference/api/index
+        :link-type: doc
+
+        Comprehensive details of the **openfe** Python API.
+
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+
+   reference/index
diff --git a/docs/reference/api/generated/openfe_analysis.rst b/docs/reference/api/generated/openfe_analysis.rst
new file mode 100644
index 0000000..743b7b6
--- /dev/null
+++ b/docs/reference/api/generated/openfe_analysis.rst
@@ -0,0 +1,37 @@
+openfe\_analysis package
+========================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   openfe_analysis.utils
+
+Submodules
+----------
+
+openfe\_analysis.reader module
+------------------------------
+
+.. automodule:: openfe_analysis.reader
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+openfe\_analysis.rmsd module
+----------------------------
+
+.. automodule:: openfe_analysis.rmsd
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+openfe\_analysis.transformations module
+---------------------------------------
+
+.. automodule:: openfe_analysis.transformations
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/reference/api/generated/openfe_analysis.utils.rst b/docs/reference/api/generated/openfe_analysis.utils.rst
new file mode 100644
index 0000000..df59c30
--- /dev/null
+++ b/docs/reference/api/generated/openfe_analysis.utils.rst
@@ -0,0 +1,29 @@
+openfe\_analysis.utils package
+==============================
+
+Submodules
+----------
+
+openfe\_analysis.utils.multistate module
+----------------------------------------
+
+.. automodule:: openfe_analysis.utils.multistate
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+openfe\_analysis.utils.serialization module
+-------------------------------------------
+
+.. automodule:: openfe_analysis.utils.serialization
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: openfe_analysis.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/reference/api/index.rst b/docs/reference/api/index.rst
new file mode 100644
index 0000000..1d15575
--- /dev/null
+++ b/docs/reference/api/index.rst
@@ -0,0 +1,10 @@
+.. _api:
+
+OpenFE Analysis API Reference
+=============================
+
+.. toctree::
+    :maxdepth: 2
+
+    generated/openfe_analysis.rst
+    generated/openfe_analysis.utils.rst
diff --git a/docs/reference/index.rst b/docs/reference/index.rst
new file mode 100644
index 0000000..c2a34f1
--- /dev/null
+++ b/docs/reference/index.rst
@@ -0,0 +1,9 @@
+Reference
+=========
+
+This contains details of the Python API.
+
+.. toctree::
+    :maxdepth: 2
+
+    api/index
diff --git a/src/openfe_analysis/rmsd.py b/src/openfe_analysis/rmsd.py
index 7d2af13..427ef1a 100644
--- a/src/openfe_analysis/rmsd.py
+++ b/src/openfe_analysis/rmsd.py
@@ -14,22 +14,44 @@
 
 
 def make_Universe(top: pathlib.Path, trj: nc.Dataset, state: int) -> mda.Universe:
-    """Makes a Universe and applies some transformations
+    """
+    Construct an MDAnalysis Universe from a MultiState NetCDF trajectory
+    and apply standard analysis transformations.
+
+    The Universe is created using the custom ``FEReader`` to extract a
+    single state from a multistate simulation.
 
     Identifies two AtomGroups:
-    - protein, defined as having standard amino acid names, then filtered
-      down to CA
+    - protein, defined as having standard amino acid names, then filtered down to CA
     - ligand, defined as resname UNK
 
-    Then applies some transformations.
+    Depending on whether a protein is present, a sequence of trajectory
+    transformations is applied:
 
     If a protein is present:
-    - prevents the protein from jumping between periodic images
-    - moves the ligand to the image closest to the protein
-    - aligns the entire system to minimise the protein RMSD
+    - prevents the protein from jumping between periodic images (class:`NoJump`)
+    - moves the ligand to the image closest to the protein (:class:`Minimiser`)
+    - aligns the entire system to minimise the protein RMSD (:class:`Aligner`)
 
-    If only a ligand:
+    If only a ligand is present:
     - prevents the ligand from jumping between periodic images
+    - Aligns the ligand to minimize its RMSD
+
+    Parameters
+    ----------
+    top : pathlib.Path or Topology
+        Path to a topology file (e.g. PDB) or an already-loaded MDAnalysis
+        topology object.
+    trj : netCDF4.Dataset
+        Open NetCDF dataset produced by
+        ``openmmtools.multistate.MultiStateReporter``.
+    state : int
+        Thermodynamic state index to extract from the multistate trajectory.
+
+    Returns
+    -------
+    MDAnalysis.Universe
+        A Universe with trajectory transformations applied.
     """
     u = mda.Universe(
         top,

From 5c60e835928c5b060b7f7fa9f600d5eee7ad80cf Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 29 Jan 2026 10:25:39 +0000
Subject: [PATCH 2/7] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/openfe_analysis/tests/conftest.py | 28 +++++++++++++++++----------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/src/openfe_analysis/tests/conftest.py b/src/openfe_analysis/tests/conftest.py
index 5fa2db4..19961eb 100644
--- a/src/openfe_analysis/tests/conftest.py
+++ b/src/openfe_analysis/tests/conftest.py
@@ -1,6 +1,6 @@
+import pathlib
 from importlib import resources
 
-import pathlib
 import pooch
 import pytest
 
@@ -9,41 +9,49 @@
     path=POOCH_CACHE,
     base_url="doi:10.5281/zenodo.17916322",
     registry={
-       "openfe_analysis_simulation_output.tar.gz":"md5:09752f2c4e5b7744d8afdee66dbd1414",
-       "openfe_analysis_skipped.tar.gz": "md5:3840d044299caacc4ccd50e6b22c0880",
+        "openfe_analysis_simulation_output.tar.gz": "md5:09752f2c4e5b7744d8afdee66dbd1414",
+        "openfe_analysis_skipped.tar.gz": "md5:3840d044299caacc4ccd50e6b22c0880",
     },
 )
 
+
 @pytest.fixture(scope="session")
 def rbfe_output_data_dir() -> pathlib.Path:
     ZENODO_RBFE_DATA.fetch("openfe_analysis_simulation_output.tar.gz", processor=pooch.Untar())
-    result_dir = pathlib.Path(POOCH_CACHE) / "openfe_analysis_simulation_output.tar.gz.untar/openfe_analysis_simulation_output/"
+    result_dir = (
+        pathlib.Path(POOCH_CACHE)
+        / "openfe_analysis_simulation_output.tar.gz.untar/openfe_analysis_simulation_output/"
+    )
     return result_dir
 
+
 @pytest.fixture(scope="session")
 def rbfe_skipped_data_dir() -> pathlib.Path:
     ZENODO_RBFE_DATA.fetch("openfe_analysis_skipped.tar.gz", processor=pooch.Untar())
-    result_dir = pathlib.Path(POOCH_CACHE) / "openfe_analysis_skipped.tar.gz.untar/openfe_analysis_skipped/"
+    result_dir = (
+        pathlib.Path(POOCH_CACHE) / "openfe_analysis_skipped.tar.gz.untar/openfe_analysis_skipped/"
+    )
     return result_dir
 
+
 @pytest.fixture(scope="session")
 def simulation_nc(rbfe_output_data_dir) -> pathlib.Path:
-    return rbfe_output_data_dir/"simulation.nc"
+    return rbfe_output_data_dir / "simulation.nc"
 
 
 @pytest.fixture(scope="session")
 def simulation_skipped_nc(rbfe_skipped_data_dir) -> pathlib.Path:
-    return rbfe_skipped_data_dir/"simulation.nc"
+    return rbfe_skipped_data_dir / "simulation.nc"
 
 
 @pytest.fixture(scope="session")
 def hybrid_system_pdb(rbfe_output_data_dir) -> pathlib.Path:
-    return rbfe_output_data_dir/"hybrid_system.pdb"
+    return rbfe_output_data_dir / "hybrid_system.pdb"
 
 
 @pytest.fixture(scope="session")
-def hybrid_system_skipped_pdb(rbfe_skipped_data_dir)->pathlib.Path:
-    return rbfe_skipped_data_dir/"hybrid_system.pdb"
+def hybrid_system_skipped_pdb(rbfe_skipped_data_dir) -> pathlib.Path:
+    return rbfe_skipped_data_dir / "hybrid_system.pdb"
 
 
 @pytest.fixture(scope="session")

From ffe13da32b4ff9b802588e79c21c7bae4b71e978 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Thu, 29 Jan 2026 11:33:24 +0100
Subject: [PATCH 3/7] Small fixes

---
 docs/.DS_Store         | Bin 6148 -> 0 bytes
 docs/_ext/.sass.py.swp | Bin 12288 -> 0 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 docs/.DS_Store
 delete mode 100644 docs/_ext/.sass.py.swp

diff --git a/docs/.DS_Store b/docs/.DS_Store
deleted file mode 100644
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From c473cfdbe4205d6c7275206ac909830ebcca7a7a Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Thu, 29 Jan 2026 11:33:42 +0100
Subject: [PATCH 4/7] Small fixes

---
 docs/index.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/index.rst b/docs/index.rst
index f42d80c..2595f4b 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -16,7 +16,7 @@ The **OpenFE Analysis** toolkit provides a free and open-source framework for an
         :link: reference/api/index
         :link-type: doc
 
-        Comprehensive details of the **openfe** Python API.
+        Comprehensive details of the **openfe_analysis** Python API.
 
 
 .. toctree::

From 3b36a89f37900cfd64046d273bd923f1052d353d Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Thu, 29 Jan 2026 11:41:21 +0100
Subject: [PATCH 5/7] Update readthedocs

---
 .readthedocs.yaml | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 76717c6..501592f 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,24 +1,19 @@
-# .readthedocs.yaml
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
 version: 2
 
 build:
-  os: ubuntu-20.04
+  os: "ubuntu-24.04"
   tools:
-    python: "mambaforge-4.10"
+    python: "miniconda3-3.12-24.9"
 
 sphinx:
    configuration: docs/conf.py
    fail_on_warning: true
 
 conda:
-  environment: environment.yml
+  environment: docs/environment.yaml
 
 python:
-  # Install our python package before building the docs so setuptools-scm generates the version for RTD to find.
+  # Install our python package before building the docs
   install:
     - method: pip
       path: .

From af0cbaf3988378adf37685fef484c6888496d88f Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Thu, 29 Jan 2026 11:45:28 +0100
Subject: [PATCH 6/7] add docs badge to readme

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index f182bf6..7c8b701 100644
--- a/README.md
+++ b/README.md
@@ -3,6 +3,7 @@
 [![Logo](https://img.shields.io/badge/OSMF-OpenFreeEnergy-%23002f4a)](https://openfree.energy/)
 [![CI](https://github.com/OpenFreeEnergy/openfe_analysis/actions/workflows/ci.yaml/badge.svg)](https://github.com/OpenFreeEnergy/openfe_analysis/actions/workflows/ci.yaml)
 [![Coverage](https://codecov.io/gh/OpenFreeEnergy/openfe_analysis/graph/badge.svg?token=krb231ftki)](https://codecov.io/gh/OpenFreeEnergy/openfe_analysis)
+[![documentation](https://readthedocs.org/projects/openfe/badge/?version=stable)](https://docs.openfree.energy/en/stable/?badge=stable)
 [![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org)
 
 ## Quickstart

From ece3d15a49ab46d193d040c6383c9d9d52f182d9 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 10 Feb 2026 12:21:02 +0000
Subject: [PATCH 7/7] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/openfe_analysis/tests/conftest.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/openfe_analysis/tests/conftest.py b/src/openfe_analysis/tests/conftest.py
index 949fee2..3b3edc0 100644
--- a/src/openfe_analysis/tests/conftest.py
+++ b/src/openfe_analysis/tests/conftest.py
@@ -33,14 +33,12 @@ def rbfe_output_data_dir() -> pathlib.Path:
     return cached_dir
 
 
-
 @pytest.fixture(scope="session")
 def rbfe_skipped_data_dir() -> pathlib.Path:
     cached_dir = _fetch_and_untar("openfe_analysis_skipped")
     return cached_dir
 
 
-
 @pytest.fixture(scope="session")
 def simulation_nc(rbfe_output_data_dir) -> pathlib.Path:
     return rbfe_output_data_dir / "simulation.nc"