docs: Add initial RTD content

Author: Alan Christie

.gitignore

@@ -6,8 +6,8 @@ venv/
 **/__pycache__
 .mypy_cache/
 ./config.yaml
-xchemalign/xchem_align.egg-info/
-xchemalign/_version.py
+src/xchemalign.egg-info/
+src/xchemalign/_version.py
 test-data/outputs/upload_*
 test-data/outputs/upload-v2/upload_*
 test-data/outputs/upload-v2/*.log

.readthedocs.yaml

@@ -0,0 +1,27 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+   - requirements: requirements.txt

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    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+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/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/_static/README.md

@@ -0,0 +1 @@
+# A placeholder file

docs/source/_static/css/custom.css

@@ -0,0 +1,38 @@
+/* Newlines (\a) and/* spaces (\20) before each parameter */
+.sig-param::before {
+    content: "\a\20\20\20\20\20\20\20\20\20\20\20\20\20\20\20\20";
+    white-space: pre;
+}
+
+/* Newline after the last parameter (so the closing bracket is on a new line) */
+dt em.sig-param:last-of-type::after {
+    content: "\a";
+    white-space: pre;
+}
+
+/* To have blue background of width of the block (instead of width of content) */
+dl.class > dt:first-of-type {
+    display: block !important;
+}*/
+
+/*Newlines (\a) and spaces (\20) before each parameter*/
+dl.class em:not([class])::before {
+    content: "\a\20\20\20\20\20\20\20\20\20\20\20\20\20\20\20\20";
+    white-space: pre;
+}
+
+/*Newline after the last parameter (so the closing bracket is on a new line)*/
+dl.class em:not([class]):last-of-type::after {
+    content: "\a";
+    white-space: pre;
+}
+
+/*To have blue background of width of the block (instead of width of content)*/
+dl.class > dt:first-of-type {
+    display: block !important;
+}
+
+/*To use the full window width for content*/
+.wy-nav-content {
+    max-width: none;
+}

docs/source/_templates/README.md

@@ -0,0 +1 @@
+# A placeholder file

docs/source/conf.py

@@ -0,0 +1,60 @@
+# 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
+# sys.path.insert(0, os.path.abspath('.'))
+
+# -- Project information -----------------------------------------------------
+
+project = 'XChem Align'
+copyright = '2025, Diamond Light Source'  # pylint: disable=redefined-builtin
+author = 'Diamond Light Source'
+
+# -- 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.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.imgmath',
+    'myst_parser',
+]
+
+# 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 = []
+
+master_doc = 'index'
+
+
+# -- 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 = 'sphinx_rtd_theme'
+html_css_files = ["css/custom.css"]
+
+# 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']

docs/source/index.md

@@ -0,0 +1,4 @@
+
+# XChem Align
+
+Placeholder file for XCHem Align documentation root.

requirements.tst

@@ -0,0 +1,6 @@
+# Requirements for a ReadTheDocs documentation setup.
+sphinx==7.2.6
+sphinx_rtd_theme==2.0.0
+sphinx-notfound-page==1.1.0
+
+myst-parser==4.*