[WIP] Adding tutorial for building AlchemicalNetworks for consumption with fah-alchemy

devtools/conda-envs/client.yml

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+name: fah-alchemy-client
+channels:
+  - jaimergp/label/unsupported-cudatoolkit-shim
+  - conda-forge
+  - openeye
+dependencies:
+  - python =3.9
+
+  # gufe dependencies
+  - numpy
+  - networkx
+  - rdkit
+  - pip
+  - pydantic
+  - openff-toolkit
+  - openff-units
+  - typing-extensions
+
+  # perses dependencies
+  - tqdm
+  - openmm
+
+  ## cli
+  - click
+
+  # needed for openfe
+  - lomap2>=2.1.0
+
+  ## needed for perses
+  - openmmtools
+  - openmmforcefields
+  - openmoltools
+  - cloudpathlib
+  - dask
+  - distributed
+  - openeye-toolkits
+
+  - pip:
+    - git+https://github.com/OpenFreeEnergy/gufe
+    - git+https://github.com/OpenFreeEnergy/openfe
+    - git+https://github.com/OpenFreeEnergy/openfe-benchmarks
+    - git+https://github.com/mikemhenry/openff-models.git@support_nested_models
+    - git+https://github.com/choderalab/perses@protocol-neqcyc

docs/Makefile

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+# 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/conf.py

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+# 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
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'fah-alchemy'
+copyright = '2022, "OpenFE and OpenFF developers"'
+author = '"OpenFE and OpenFF developers"'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = []
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']

docs/index.rst

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+.. fah-alchemy documentation master file, created by
+   sphinx-quickstart on Wed Nov 23 20:51:04 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to fah-alchemy's documentation!
+=======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+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