read the docs started!

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 = 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

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+@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/conf.py

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+# 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 = 'Symmer'
+copyright = '2023, Alexis Ralli, Tim Weaving'
+author = 'Alexis Ralli, Tim Weaving'
+
+
+# -- 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.intersphinx',
+ 'sphinx.ext.extlinks',
+ 'sphinx.ext.napoleon',
+ 'sphinx.ext.linkcode',
+ 'myst_nb',
+ "sphinx_design",
+ 'sphinx_copybutton'
+# 'autoapi.extension',
+]
+
+# msyt_nb configuration
+nb_execution_mode = "off"
+myst_heading_anchors = 4
+myst_enable_extensions = [
+ "amsmath",
+ "colon_fence",
+ "deflist",
+ "dollarmath",
+ "html_image",
+]
+
+# 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 = []
+
+
+# -- 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 = 'alabaster'
+
+# 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']
+
+def linkcode_resolve(domain, info):
+ if domain != 'py':
+ return None
+ if not info['module']:
+ return None
+ filename = info['module'].replace('.', '/')
+ return "https://somesite/sourcerepo/%s.py" % filename

docs/source/index.rst

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+.. Symmer documentation master file, created by
+ sphinx-quickstart on Wed Aug 23 14:45:04 2023.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+.. image:: ./_static/symmer_logo.png
+ :width: 800px
+Welcome to Symmer's documentation!
+==================================
+.. image:: https://github.com/UCL-CCS/symmer/actions/workflows/pull_request.yaml/badge.svg
+ :target: https://github.com/UCL-CCS/symmer/actions/workflows/pull_request.yaml
+ :alt: Continuous_Integration
+.. image:: https://codecov.io/gh/UCL-CCS/symmer/branch/main/graph/badge.svg?token=PZzJNZuEEW
+ :target: https://codecov.io/gh/UCL-CCS/symmer
+ :alt: codecov
+.. image:: https://img.shields.io/badge/Supported%20By-UNITARY%20FUND-brightgreen.svg?style=for-the-badge
+ :target: http://unitary.fund
+ :alt: Unitary Fund
+
+`symmer <https://github.com/UCL-CCS/symmer>`_ is an easy and **fast** python library
+for manipulations of *'Pauli operators and Quantum States'*. One of the primary
+goals of the library is to reduce the qubit requirements of a quantum simulation problem
+by tapering and/or mapping the problem into a contextual subspace. The most useful classes of
+library, that form a base for all operations, are:
+
+.. grid:: 2
+
+ .. grid-item-card:: PauliwordOp
+ :img-bottom: _images/noncontextual-graph.png
+
+ The :mod:`PauliwordOp` class contains tools for working with
+ **Pauli operators**. It has a particular focus on:
+
+ * fast operations (multiplication, addition, subtraction)
+ * fast expectation value determination
+ * output to various other backends:
+ `openfermion <https://github.com/quantumlib/OpenFermion>`_ and
+ `qiskit <https://github.com/Qiskit/qiskit>`_
+ * Find commutation relations between Pauli operators in an efficient manor.
+
+ .. grid-item-card:: QuantumState
+
+ The :mod:`QuantumState` class contains tools for working with
+ **'quantum states'**. With this you can:
+
+ * resample a state :math:`10^{15}` times in nanoseconds (useful for bootstrapping)
+ * evaluate expectation values with a :mod:`PauliwordOp` in linear time
+ * compute various quantities including entanglement measures
+ * Implement partial traces
+ * Plot quantum state
+ * Make examining real NISQ data more streamlined
+
+
+User Guide
+----------
+
+The following guides give a basic introduction to the various parts:
+
+.. toctree::
+ :maxdepth: 1
+
+ installation
+
+
+
+.. _examples:
+
+
+Examples
+--------
+
+The following guides, generated from the notebooks in `notebooks <https://github.com/UCL-CCS/symmer/tree/main/notebooks>`_,
+provide a beginners guide and demonstrate some more advanced features or complete usage:
+
+.. toctree::
+ :numbered:
+ :maxdepth: 2
+
+ ./notebooks/1_Basic_Usage/1.1 PauliwordOp Usage.ipynb
+ ./notebooks/1_Basic_Usage/1.2 QuantumState Usage.ipynb
+ ./notebooks/1_Basic_Usage/1.3 Importing Hamiltonian Data.ipynb
+ ./notebooks/1_Basic_Usage/1.4 QubitSubspaceManager Usage.ipynb
+
+.. toctree::
+ :numbered:
+ :maxdepth: 2
+ ./notebooks/2_Applications
+

docs/source/installation.rst

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+============
+Installation
+============
+
+Note `symmer <https://github.com/UCL-CCS/symmer>`_ is a pure python package and can now be found on `PyPI <https://pypi.org/project/symmer/>`_.
+To install run the following:
+
+.. code-block:: bash
+
+ pip install symmer
+
+The code is hosted on `github <https://github.com/UCL-CCS/symmer>`_. A development version can be installed from source
+by running:
+
+.. code-block:: bash
+
+ git clone https://github.com/UCL-CCS/symmer.git
+ pip install .