Update v0.6 of the hafnian library

.circleci/config.yml

@@ -4,7 +4,40 @@
 #
 version: 2.1
 jobs:
-  tests:
+  cpptests:
+    docker:
+      - image: gcc:latest
+    working_directory: ~/circleci-googletest
+    environment:
+      TEST_RESULTS: /tmp/test-results
+    steps:
+      - run:
+          name: Install Dependencies
+          command: |
+            apt-get -y -q update
+            apt-get -y -q install cmake gcc libomp-dev libeigen3-dev
+      - run:
+          name: Install Google Test
+          working_directory: ~/googletest
+          command: |
+            wget -qO - https://github.com/google/googletest/archive/release-1.8.1.tar.gz | tar -xz
+            cmake -D CMAKE_INSTALL_PREFIX:PATH=$HOME/googletest -D CMAKE_BUILD_TYPE=Release googletest-release-1.8.1
+            make install
+      - checkout
+      - run:
+          name: Build unit tests
+          command: |
+            cd src/tests
+            GOOGLETEST_DIR=/root/googletest make cpptests
+      - run:
+          name: Run unit tests
+          command: |
+            cd src/tests && ./cpptests
+      - store_test_results:
+          # This option doesn't expand $TEST_RESULTS if used.
+          path: /tmp/test-results
+
+  pythontests:
     docker:
       - image: circleci/python:3.6.8-stretch
     working_directory: ~/tests
@@ -19,7 +52,6 @@ jobs:
           command: |
             sudo apt-get -qq update;
             sudo apt-get install -y gcc gfortran libeigen3-dev;
-            curl -sL -o src/linpack_q_complex.f90 https://raw.githubusercontent.com/josh146/linpack_q_complex/master/linpack_q_complex.f90
             python3 -m venv venv
             . venv/bin/activate
             pip install -r requirements.txt
@@ -45,7 +77,7 @@ jobs:
       - image: circleci/python:3.6.8-stretch
     environment:
       CIBW_SKIP: "cp27-* cp34-* *i686"
-      CIBW_BEFORE_BUILD_LINUX: curl -sL -o {project}/src/linpack_q_complex.f90 https://raw.githubusercontent.com/josh146/linpack_q_complex/master/linpack_q_complex.f90 && curl -OsL https://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz && tar xzf 3.3.7.tar.gz eigen-eigen-323c052e1731/Eigen --strip-components 1 && cp -rf Eigen {project}/src && pip install numpy scipy cython
+      CIBW_BEFORE_BUILD_LINUX: curl -OsL https://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz && tar xzf 3.3.7.tar.gz eigen-eigen-323c052e1731/Eigen --strip-components 1 && cp -rf Eigen {project}/src && pip install numpy scipy cython
       CIBW_TEST_REQUIRES: numpy scipy pytest pytest-cov
       CIBW_TEST_COMMAND: python -m pytest {project}/hafnian
     steps:
@@ -78,7 +110,7 @@ jobs:
       xcode: "10.0.0"
     environment:
       CIBW_SKIP: "cp27-* cp34-* *i686"
-      CIBW_BEFORE_BUILD_MACOS: wget -O {project}/src/linpack_q_complex.f90 https://raw.githubusercontent.com/josh146/linpack_q_complex/master/linpack_q_complex.f90 && brew cask uninstall --force oclint && brew install gcc eigen libomp || true; brew install gcc eigen libomp && pip install numpy scipy cython
+      CIBW_BEFORE_BUILD_MACOS: brew cask uninstall --force oclint && brew install gcc eigen libomp || true; brew install gcc eigen libomp && pip install numpy scipy cython
       CIBW_TEST_REQUIRES: numpy scipy pytest pytest-cov
       CIBW_TEST_COMMAND: python -m pytest {project}/hafnian
     steps:
@@ -87,6 +119,7 @@ jobs:
           name: Build the OS X wheels.
           command: |
             pip install --user cibuildwheel
+            export PATH=$PATH:/Users/distiller/Library/Python/2.7/bin
             cibuildwheel --output-dir wheelhouse
       - run:
           name: Upload OS X wheels.
@@ -108,4 +141,6 @@ workflows:
   version: 2
   all-tests:
     jobs:
+      - cpptests
       - linux-wheels
+      - osx-wheels

.github/pull_request_template.md

@@ -0,0 +1,22 @@
+### Pull request template
+
+Make sure you are up to date on the
+[Hafnian workflow](https://github.com/XanaduAI/hafnianplus/wiki/Hafnian-GitHub-Flow)
+before submitting the pull request.
+
+When ready to submit, delete everything above the dashed line and fill in the pull
+request template.
+
+Please include as much detail as possible regarding the changes made/new features
+added/performance improvements. If including any bug fixes, mention the issue numbers
+associated with the bugs.
+
+------------------------------------------------------------------------------------------------------------
+
+**Description of the Change:**
+
+**Benefits:**
+
+**Possible Drawbacks:**
+
+**Related GitHub Issues:**

.gitignore

@@ -15,4 +15,7 @@ coverage_html_report
 hafnian/lib
 src/*.o
 src/timing
-
+src/tests/*.o
+src/tests/cpptests
+docs/doxyoutput/*
+docs/hafnian_cpp_api/*

.pylintrc

@@ -28,4 +28,4 @@ ignored-classes=numpy,ctypes,hafnian.lib,hafnian.lib.libhaf,hafnian.lib.libperm,
 # can either give multiple identifier separated by comma (,) or put this option
 # multiple time (only on the command line, not in the configuration file where
 # it should appear only once).
-disable=line-too-long,invalid-name,too-many-lines,redefined-builtin,too-many-locals,duplicate-code
+disable=line-too-long,invalid-name,too-many-lines,redefined-builtin,too-many-locals,duplicate-code,bad-continuation

.travis.yml

@@ -2,12 +2,11 @@ language: python
 env:
   global:
   - CIBW_SKIP="cp27-* cp34-* *i686"
-  - CIBW_BEFORE_BUILD_LINUX='curl -sL -o {project}/src/linpack_q_complex.f90 https://raw.githubusercontent.com/josh146/linpack_q_complex/master/linpack_q_complex.f90
-    && curl -OsL https://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
+  - CIBW_BEFORE_BUILD_LINUX='curl -OsL https://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
     && tar xzf 3.3.7.tar.gz eigen-eigen-323c052e1731/Eigen --strip-components 1
     && cp -rf Eigen {project}/src && pip install numpy scipy cython'
-  - CIBW_BEFORE_BUILD_MACOS='wget -O {project}/src/linpack_q_complex.f90 https://raw.githubusercontent.com/josh146/linpack_q_complex/master/linpack_q_complex.f90
-    && brew cask uninstall --force oclint && brew install gcc eigen libomp || true; brew install gcc eigen libomp && pip install numpy scipy cython'
+  - CIBW_BEFORE_BUILD_MACOS='brew cask uninstall --force oclint && brew install gcc eigen libomp || true;
+    brew install gcc eigen libomp && pip install numpy scipy cython'
   - CIBW_TEST_REQUIRES="numpy scipy pytest pytest-cov"
   - CIBW_TEST_COMMAND="python -m pytest {project}/hafnian"
   - WHEELHOUSE_UPLOADER_USERNAME=AKIAJOU6ECM5Q7T6UUQQ
@@ -46,7 +45,6 @@ before_install:
 install:
 - |
   if [ "$WHEEL" = "0" ]; then
-    curl -sL -o src/linpack_q_complex.f90 https://raw.githubusercontent.com/josh146/linpack_q_complex/master/linpack_q_complex.f90
     pip install -r requirements.txt
     pip install pytest pytest-cov wheel codecov
     pip install -e .

Makefile

@@ -10,12 +10,12 @@ help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  install            to install Hafnian"
 	@echo "  libperm            to compile the Fortran permanent library"
-	@echo "  libtor             to compile the Fortran torontonian library"
 	@echo "  wheel              to build the Hafnian wheel"
 	@echo "  dist               to package the source distribution"
 	@echo "  clean              to delete all temporary, cache, and build files"
 	@echo "  clean-docs         to delete all built documentation"
-	@echo "  test               to run the test suite"
+	@echo "  test-cpp           to run the C++ test suite"
+	@echo "  test               to run the Python test suite"
 	@echo "  coverage           to generate a coverage report"
 
 .PHONY: install
@@ -46,8 +46,16 @@ doc:
 
 .PHONY : clean-docs
 clean-docs:
+	rm -rf docs/hafnian_cpp_api
 	make -C docs clean
 
+test-cpp:
+	make -C src/tests clean
+	echo "Going to compile C++ tests"
+	make -C src/tests
+	echo "Compilation done for C++ tests"
+	make -C src/tests runtest
+
 test:
 	$(PYTHON) $(TESTRUNNER)
 

README.rst

@@ -1,40 +1,27 @@
 Hafnian
 #######
 
-.. image:: https://img.shields.io/travis/XanaduAI/hafnian/master.svg?style=for-the-badge
-    :alt: Travis
-    :target: https://travis-ci.org/XanaduAI/hafnian
+.. image:: https://circleci.com/gh/XanaduAI/hafnianplus.svg?style=svg&circle-token=e34895951dd90ef61a72c1928b4db7ba1e856f48
+    :alt: CircleCI
+    :target: https://circleci.com/gh/XanaduAI/hafnianplus
 
 .. image:: https://ci.appveyor.com/api/projects/status/6wt68c81f8ly583s/branch/master?svg=true
     :alt: Appveyor
     :target: https://ci.appveyor.com/project/josh146/hafnianplus/branch/master
 
-.. image:: https://img.shields.io/codecov/c/github/xanaduai/hafnian/master.svg?style=for-the-badge
-    :alt: Codecov coverage
-    :target: https://codecov.io/gh/XanaduAI/hafnian
 
-.. image:: https://img.shields.io/codacy/grade/df94d22534cf4c05b1bddcf697011a82.svg?style=for-the-badge
-    :alt: Codacy grade
-    :target: https://app.codacy.com/app/XanaduAI/hafnian?utm_source=github.com&utm_medium=referral&utm_content=XanaduAI/hafnian&utm_campaign=badger
-
-.. image:: https://img.shields.io/readthedocs/hafnian.svg?style=for-the-badge
-    :alt: Read the Docs
-    :target: https://hafnian.readthedocs.io
-
-.. image:: https://img.shields.io/pypi/pyversions/hafnian.svg?style=for-the-badge
-    :alt: PyPI - Python Version
-    :target: https://pypi.org/project/hafnian
-
-The fastest exact hafnian library for real and complex matrices. For more information, please see the `documentation <https://hafnian.readthedocs.io>`_.
+The fastest exact hafnian library. For more information, please see the `documentation <https://hafnian.readthedocs.io>`_.
 
 Features
 ========
 
-* The fastest calculation of the hafnian, loop hafnian, permanent, and torontonian,
-  of general and certain structured matrices.
+* The fastest calculation of the hafnians, loop hafnians, and torontonians of general and certain structured matrices.
+
+* An easy to use interface to use the loop hafnian for quantum state calculations
 
-* An easy to use interface to use the loop hafnian to calculate Fock matrix
-  elements of Gaussian states via the included quantum module.
+* State of the art algorithms to sample from hafnian and torontonians of graphs.
+
+* Efficient classical methods for approximating the hafnian of non-negative matrices.
 
 Installation
 ============
@@ -51,7 +38,7 @@ Pre-built binary wheels are available for the following platforms:
 | Python 3.7 |  ✅         |  ✅              |   ✅          |
 +------------+-------------+------------------+---------------+
 
-These can be installed using ``pip``:
+To install, simply run
 
 .. code-block:: bash
 
@@ -69,7 +56,6 @@ Hafnian depends on the following Python packages:
 In addition, to compile the included Fortran and C++ extensions, the following dependencies are required:
 
 * A Fortran compiler, such as ``gfortran``
-* The LINPACK_Q quadruple precision linear algebra library
 * A C++11 compiler, such as ``g++`` >= 4.8.1, ``clang`` >= 3.3, ``MSVC`` >= 14.0/2015
 * `Eigen3 <http://eigen.tuxfamily.org/index.php?title=Main_Page>`_ - a C++ header library for linear algebra.
 
@@ -78,14 +64,12 @@ On Debian-based systems, these can be installed via ``apt`` and ``curl``:
 .. code-block:: console
 
     $ sudo apt install g++ gfortran libeigen3-dev
-    $ curl -sL -o src/linpack_q_complex.f90 https://raw.githubusercontent.com/josh146/linpack_q_complex/master/linpack_q_complex.f90
 
 or using Homebrew on MacOS:
 
 .. code-block:: console
 
     $ brew install gcc eigen
-    $ curl -sL -o src/linpack_q_complex.f90 https://raw.githubusercontent.com/josh146/linpack_q_complex/master/linpack_q_complex.f90
 
 Alternatively, you can download the Eigen headers manually:
 
@@ -142,6 +126,32 @@ To ensure that the Hafnian library is working correctly after installation, the
 
     $ make test
 
+To run the low-level C++ test suite, `Googletest <https://github.com/google/googletest>`_
+will need to be installed. In Ubuntu-based distributions, this can be done as follows:
+
+.. code-block:: console
+
+    sudo apt-get install cmake libgtest-dev
+    cd /usr/src/googletest/googletest
+    sudo cmake
+    sudo make
+    sudo cp libgtest* /usr/lib/
+    sudo mkdir /usr/local/lib/googletest
+    sudo ln -s /usr/lib/libgtest.a /usr/local/lib/googletest/libgtest.a
+    sudo ln -s /usr/lib/libgtest_main.a /usr/local/lib/googletest/libgtest_main.a
+
+Alternatively, the latest Googletest release can be installed from source:
+
+.. code-block:: console
+
+    sudo apt install cmake
+    wget -qO - https://github.com/google/googletest/archive/release-1.8.1.tar.gz | tar -xz
+    cmake -D CMAKE_INSTALL_PREFIX:PATH=$HOME/googletest -D CMAKE_BUILD_TYPE=Release googletest-release-1.8.1
+    make install
+
+If installing Googletest from source, make sure that the included headers and
+libraries are available on your include/library paths.
+
 Documentation
 =============
 
@@ -151,12 +161,15 @@ The Hafnian+ documentation is currently not hosted online. To build it locally,
 * `sphinxcontrib-bibtex <https://sphinxcontrib-bibtex.readthedocs.io/en/latest/>`_ >=0.3.6
 * `nbsphinx <https://github.com/spatialaudio/nbsphinx>`_
 * `Pandoc <https://pandoc.org/>`_
+* `breathe <https://breathe.readthedocs.io/en/latest/>`_ >=4.12.0
+* `exhale <https://exhale.readthedocs.io/en/latest/>`_
+* `Doxygen <http://www.doxygen.nl/>`_
 
 They can be installed via a combination of ``pip`` and ``apt`` if on a Debian-based system:
 ::
 
-    $ sudo apt install pandoc
-    $ pip3 install sphinx sphinxcontrib-bibtex nbsphinx --user
+    $ sudo apt install pandoc doxygen
+    $ pip3 install sphinx sphinxcontrib-bibtex nbsphinx breathe exhale
 
 To build the HTML documentation, go to the top-level directory and run the command
 

appveyor.yml

@@ -4,7 +4,7 @@ environment:
       APPVEYOR_SKIP_FINALIZE_ON_EXIT: true
       EIGEN_INCLUDE_DIR: C:\eigen-eigen-323c052e1731\
       TEST_TIMEOUT: 1000
-      CIBW_BEFORE_BUILD: copy "C:\linpack_q_complex.f90" "{project}\src" && pip install numpy scipy cython
+      CIBW_BEFORE_BUILD: pip install numpy scipy cython
       CIBW_SKIP: "cp27-* cp33-* cp34-* *win32"
       CIBW_TEST_REQUIRES: "numpy scipy pytest pytest-cov"
       CIBW_TEST_COMMAND: "python -m pytest {project}/hafnian"
@@ -21,7 +21,6 @@ matrix:
 
 
 install:
-  - ps: wget https://raw.githubusercontent.com/josh146/linpack_q_complex/master/linpack_q_complex.f90 -outfile C:\linpack_q_complex.f90
   - ps: wget http://bitbucket.org/eigen/eigen/get/3.3.7.zip -outfile eigen3.zip
   - cmd: 7z x eigen3.zip -o"C:\" -y > nul
 
@@ -34,6 +33,8 @@ artifacts:
   - path: "wheelhouse\\*.whl"
     name: Wheels
 
+skip_branch_with_pr: true
+
 configuration: Debug
 
 # override common configuration