FermiLib v0.1a0 (#2)

Submitted on behalf of Ryan Babbush (Google), Jarrod McClean (LBNL), Damian Steiger (ETH, Google), Ian Kivlichan (Harvard University), Thomas Häner (ETH), Vojtech Havlicek, Matthew Neeley (Google), and Wei Sun (Google)

.gitignore

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+*.pyc
+__pycache__/
+.DS_Store
+.ipynb_checkpoints/
+*lastfailed
+*coverage

.travis.yml

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+sudo: false
+language: python
+matrix:
+  include:
+  - os: linux
+    python: "2.7"
+    addons:
+      apt:
+        sources: ['ubuntu-toolchain-r-test']
+        packages: ['gcc-4.9', 'g++-4.9']
+    env: CC=gcc-4.9 CXX=g++-4.9 PYTHON=2.7
+  - os: linux
+    python: "3.4"
+    addons:
+      apt:
+        sources: ['ubuntu-toolchain-r-test']
+        packages: ['gcc-4.9', 'g++-4.9']
+    env: CC=gcc-4.9 CXX=g++-4.9 PYTHON=3.4
+  - os: linux
+    python: "3.5"
+    addons:
+      apt:
+        sources: ['ubuntu-toolchain-r-test']
+        packages: ['gcc-4.9', 'g++-4.9']
+    env: CC=gcc-4.9 CXX=g++-4.9 PYTHON=3.5
+  - os: linux
+    python: "3.6"
+    addons:
+      apt:
+        sources: ['ubuntu-toolchain-r-test']
+        packages: ['gcc-4.9', 'g++-4.9']
+    env: CC=gcc-4.9 CXX=g++-4.9 PYTHON=3.5
+
+before_install:
+  - pip$PY install --upgrade pip setuptools wheel
+
+install:
+  - if [ "${PYTHON:0:1}" = "3" ]; then export PY=3; fi
+  - pip$PY install --only-binary=numpy,scipy numpy scipy
+  - pip$PY install pybind11
+  - pip$PY install -r requirements.txt
+  - pip$PY install pytest-cov
+  - pip$PY install coveralls
+
+# command to run tests
+script: cd src && pytest fermilib --cov fermilib
+
+after_success:
+  - coveralls
+

MANIFEST.in

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+include LICENSE
+include MANIFEST.in
+include NOTICE
+include README.rst
+include requirements.txt
+include setup.py
+
+recursive-include src *.py *.hdf5 *.npy

NOTICE

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+FermiLib (www.projectq.ch)
+
+The first release of FermiLib (v0.1a0) was developed by Ryan Babbush (Google), Jarrod McClean (LBNL*), Damian Steiger (ETH, Google), Ian Kivlichan (Harvard University), Thomas Häner (ETH), Vojtech Havlicek, Matthew Neeley (Google), and Wei Sun (Google).
+
+*FermiLib Copyright (c) 2017, All contributors including but not limited to The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
+
+NOTICE.  This Software was developed partially under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit others to do so.
+
+This first release (v0.1a0) is licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

README.rst

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+FermiLib - An open source software for analyzing quantum simulation algorithms
+==============================================================================
+
+.. image:: https://travis-ci.org/ProjectQ-Framework/FermiLib.svg?branch=master
+    :target: https://travis-ci.org/ProjectQ-Framework/FermiLib
+
+.. image:: https://coveralls.io/repos/github/ProjectQ-Framework/FermiLib/badge.svg
+    :target: https://coveralls.io/github/ProjectQ-Framework/FermiLib
+
+
+FermiLib is an open source effort for analyzing quantum simulation algorithms.
+
+The first version (v0.1a0) is an alpha release which features data structures and tools for obtaining and manipulating representations of fermionic Hamiltonians. FermiLib is designed as a library on top of ProjectQ and leverages ProjectQ to compile, emulate and simulate quantum circuits.
+
+Getting started
+---------------
+
+To start using FermiLib, simply follow the installation instructions in the `intro <https://github.com/ProjectQ-Framework/FermiLib/tree/master/docs/intro.html>`__. There, you will also find `code examples <https://github.com/ProjectQ-Framework/FermiLib/tree/master/examples.html>`__. Also, make sure to check out the `ProjectQ
+website <http://www.projectq.ch>`__ and the detailed `code documentation <https://github.com/ProjectQ-Framework/FermiLib/tree/master/docs/>`__.
+
+How to contribute
+-----------------
+
+To contribute code please adhere to the following very simple rules:
+
+1. Make sure your new code comes with extensive tests!
+2. Make sure you adhere to our style guide. Until we release a code style 
+   guide, just have a look at our code for clues. We mostly follow pep8 and use the pep8 linter to check for it.
+3. Put global constants and configuration parameters into src/config.py, and
+   add 'from config import *' in the file that uses the constants/parameters.
+
+Documentation can be found `here <https://github.com/ProjectQ-Framework/FermiLib/tree/master/docs/>`_.
+
+Authors
+-------
+
+The first release of FermiLib (v0.1a0) was developed by `Ryan Babbush <https://research.google.com/pubs/RyanBabbush.html>`__, `Jarrod McClean <https://crd.lbl.gov/departments/computational-science/ccmc/staff/alvarez-fellows/jarrod-mcclean/>`__, `Damian S. Steiger <http://www.comp.phys.ethz.ch/people/person-detail.html?persid=165677>`__, `Ian D. Kivlichan <http://aspuru.chem.harvard.edu/ian-kivlichan/>`__, `Thomas
+Häner <http://www.comp.phys.ethz.ch/people/person-detail.html?persid=179208>`__, `Vojtech Havlicek <https://github.com/VojtaHavlicek>`__, `Matthew Neeley <https://maffoo.net/>`__, and `Wei Sun <https://github.com/Spaceenter>`__.
+
+License
+-------
+
+FermiLib is released under the Apache 2 license.
+
+
+
+
+
+
+
+
+
+

docs/Makefile

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+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  applehelp  to make an Apple Help Book"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  epub3      to make an epub3"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@echo "  coverage   to run coverage check of the documentation (if enabled)"
+	@echo "  dummy      to check syntax errors of document sources"
+
+.PHONY: clean
+clean:
+	rm -rf $(BUILDDIR)/*
+
+.PHONY: html
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: dirhtml
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+.PHONY: singlehtml
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+.PHONY: pickle
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+.PHONY: json
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+.PHONY: htmlhelp
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+.PHONY: qthelp
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/FermiLib.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/FermiLib.qhc"
+
+.PHONY: applehelp
+applehelp:
+	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
+	@echo
+	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
+	@echo "N.B. You won't be able to view it unless you put it in" \
+	      "~/Library/Documentation/Help or install it in your application" \
+	      "bundle."
+
+.PHONY: devhelp
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/FermiLib"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/FermiLib"
+	@echo "# devhelp"
+
+.PHONY: epub
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+.PHONY: epub3
+epub3:
+	$(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
+	@echo
+	@echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
+
+.PHONY: latex
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+.PHONY: latexpdf
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: latexpdfja
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: text
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+.PHONY: man
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+.PHONY: texinfo
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+.PHONY: info
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+.PHONY: gettext
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+.PHONY: changes
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+.PHONY: linkcheck
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+.PHONY: doctest
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+.PHONY: coverage
+coverage:
+	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+	@echo "Testing of coverage in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/coverage/python.txt."
+
+.PHONY: xml
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+.PHONY: pseudoxml
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+
+.PHONY: dummy
+dummy:
+	$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
+	@echo
+	@echo "Build finished. Dummy builder generates no files."