Renaming the hafnian library to The Walrus

.circleci/config.yml

@@ -29,12 +29,12 @@ jobs:
       - run:
           name: Build unit tests
           command: |
-            cd src/tests
+            cd tests
             GOOGLETEST_DIR=/root/googletest make cpptests
       - run:
           name: Run unit tests
           command: |
-            cd src/tests && ./cpptests
+            cd tests && ./cpptests
 
   pythoncoverage:
     docker:
@@ -75,9 +75,9 @@ jobs:
       - image: circleci/python:3.6.8-stretch
     environment:
       CIBW_SKIP: "cp27-* cp34-* *i686"
-      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_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}/include && pip install numpy scipy cython
       CIBW_TEST_REQUIRES: numpy scipy pytest pytest-cov
-      CIBW_TEST_COMMAND: python -m pytest {project}/hafnian
+      CIBW_TEST_COMMAND: python -m pytest {project}/thewalrus
     steps:
       - checkout
       - setup_remote_docker
@@ -110,7 +110,7 @@ jobs:
       CIBW_SKIP: "cp27-* cp34-* *i686"
       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
+      CIBW_TEST_COMMAND: python -m pytest {project}/thewalrus
     steps:
       - checkout
       - run:

.coveragerc

@@ -1,7 +1,7 @@
 # .coveragerc to control coverage.py
 [run]
-source = hafnian
-omit = hafnian/tests/*
+source = thewalrus
+omit = thewalrus/tests/*
 
 [report]
 # Regexes for lines to exclude from consideration
@@ -30,9 +30,9 @@ exclude_lines =
     raise IndexError
     raise FileNotFoundError
     raise NotADirectoryError
-    return __version__ 
-    if len(lst) != self._num_modes: 
-    elif max(lst) >= self._trunc: 
+    return __version__
+    if len(lst) != self._num_modes:
+    elif max(lst) >= self._trunc:
     except NotImplementedError as err
 
     # Don't complain if non-runnable code isn't run:

.gitignore

@@ -3,21 +3,20 @@
 docs/_build
 build
 dist
-hafnian.egg-info
+thewalrus.egg-info
 .idea
 examples/*ipynp*
 .eggs/*
 *.egg-info*
-hafnian/__pycache__/*
+thewalrus/__pycache__/*
+thewalrus/*.so
 tests/__pycache__/*
 .coverage
 coverage_html_report
-hafnian/lib
-src/*.o
-src/timing
-src/tests/*.o
-src/tests/cpptests
+include/*.o
+tests/*.o
+tests/cpptests
 docs/doxyoutput/*
-docs/hafnian_cpp_api/*
+docs/libwalrus_cpp_api/*
 docs/.ipynb_checkpoints/*
 coverage.xml

.pylintrc

@@ -2,20 +2,20 @@
 # A comma-separated list of package or module names from where C extensions may
 # be loaded. Extensions are loading into the active Python interpreter and may
 # run arbitrary code
-extension-pkg-whitelist=numpy,hafnian.lib,hafnian.lib.libhaf,hafnian.lib.libperm,hafnian.lib.libtor,hafnian.lib.libhafapprox
+extension-pkg-whitelist=numpy,thewalrus.libwalrus
 
 [TYPECHECK]
 
 # List of module names for which member attributes should not be checked
 # (useful for modules/projects where namespaces are manipulated during runtime
 # and thus existing member attributes cannot be deduced by static analysis. It
 # supports qualified module names, as well as Unix pattern matching.
-ignored-modules=numpy,ctypes,hafnian.lib.libhaf,hafnian.lib.libperm,hafnian.lib,hafnian.lib.libtor,hafnian.lib.libhafapprox
+ignored-modules=numpy,ctypes,thewalrus.libwalrus
 
 # List of classes names for which member attributes should not be checked
 # (useful for classes with attributes dynamically set). This supports can work
 # with qualified names.
-ignored-classes=numpy,ctypes,hafnian.lib,hafnian.lib.libhaf,hafnian.lib.libperm,hafnian.lib.libtor,hafnian.lib.libhafapprox
+ignored-classes=numpy,ctypes,thewalrus.libwalrus
 
 [MESSAGES CONTROL]
 

MANIFEST.in

@@ -2,5 +2,6 @@ include README.rst
 include docs/*
 include LICENSE
 include examples/*
-include src/*/*
+include include/*
+include tests/*
 include octave/*

Makefile

@@ -2,15 +2,15 @@ PYTHON3 := $(shell which python3 2>/dev/null)
 COVERAGE3 := $(shell which coverage3 2>/dev/null)
 
 PYTHON := python3
-COVERAGE := --cov=hafnian --cov-report term-missing --cov-report=html:coverage_html_report --cov-report=xml:coverage.xml
-TESTRUNNER := -m pytest hafnian
+COVERAGE := --cov=thewalrus --cov-report term-missing --cov-report=html:coverage_html_report --cov-report=xml:coverage.xml
+TESTRUNNER := -m pytest thewalrus
 
 .PHONY: help
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  install            to install Hafnian"
+	@echo "  install            to install The Walrus"
 	@echo "  libperm            to compile the Fortran permanent library"
-	@echo "  wheel              to build the Hafnian wheel"
+	@echo "  wheel              to build the The Walrus 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"
@@ -21,7 +21,7 @@ help:
 .PHONY: install
 install:
 ifndef PYTHON3
-	@echo "To install Hafnian you need to have Python 3 installed"
+	@echo "To install The Walrus you need to have Python 3 installed"
 endif
 	$(PYTHON) setup.py install
 
@@ -35,9 +35,9 @@ dist:
 
 .PHONY : clean
 clean:
-	make -C src clean
-	rm -rf hafnian/__pycache__
-	rm -rf hafnian/tests/__pycache__
+	make -C include clean
+	rm -rf thewalrus/__pycache__
+	rm -rf thewalrus/tests/__pycache__
 	rm -rf dist
 	rm -rf build
 
@@ -46,21 +46,18 @@ doc:
 
 .PHONY : clean-docs
 clean-docs:
-	rm -rf docs/hafnian_cpp_api
+	rm -rf docs/libwalrus_cpp_api
 	make -C docs clean
 
 test-cpp:
-	make -C src/tests clean
+	make -C tests clean
 	echo "Going to compile C++ tests"
-	make -C src/tests
+	make -C tests cpptests
 	echo "Compilation done for C++ tests"
-	make -C src/tests runtest
+	make -C tests
 
 test:
 	$(PYTHON) $(TESTRUNNER)
 
 coverage:
 	$(PYTHON) $(TESTRUNNER) $(COVERAGE)
-
-libperm:
-	make libperm -C src

README.rst

@@ -1,31 +1,31 @@
-Hafnian
-#######
-    
-.. image:: https://circleci.com/gh/XanaduAI/hafnian/tree/master.svg?style=svg&circle-token=209b57390082a2b2fe2cdc9ee49a301ddc29ca5b
+The Walrus
+##########
+
+.. image:: https://circleci.com/gh/XanaduAI/thewalrus/tree/master.svg?style=svg&circle-token=209b57390082a2b2fe2cdc9ee49a301ddc29ca5b
     :alt: CircleCI
-    :target: https://circleci.com/gh/XanaduAI/hafnian/tree/master
+    :target: https://circleci.com/gh/XanaduAI/thewalrus/tree/master
 
 .. image:: https://ci.appveyor.com/api/projects/status/9udscqldo1xd25yk/branch/master?svg=true
     :alt: Appveyor
-    :target: https://ci.appveyor.com/project/josh146/hafnian/branch/master
+    :target: https://ci.appveyor.com/project/josh146/thewalrus/branch/master
 
-.. image:: https://img.shields.io/codecov/c/github/xanaduai/hafnian/master.svg?style=flat
+.. image:: https://img.shields.io/codecov/c/github/xanaduai/thewalrus/master.svg?style=flat
     :alt: Codecov coverage
-    :target: https://codecov.io/gh/XanaduAI/hafnian
+    :target: https://codecov.io/gh/XanaduAI/thewalrus
 
 .. image:: https://img.shields.io/codacy/grade/df94d22534cf4c05b1bddcf697011a82.svg?style=flat
     :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
+    :target: https://app.codacy.com/app/XanaduAI/thewalrus?utm_source=github.com&utm_medium=referral&utm_content=XanaduAI/thewalrus&utm_campaign=badger
 
-.. image:: https://img.shields.io/readthedocs/hafnian.svg?style=flat
+.. image:: https://img.shields.io/readthedocs/thewalrus.svg?style=flat
     :alt: Read the Docs
-    :target: https://hafnian.readthedocs.io
+    :target: https://thewalrus.readthedocs.io
 
-.. image:: https://img.shields.io/pypi/pyversions/hafnian.svg?style=flat
+.. image:: https://img.shields.io/pypi/pyversions/thewalrus.svg?style=flat
     :alt: PyPI - Python Version
-    :target: https://pypi.org/project/hafnian
+    :target: https://pypi.org/project/thewalrus
 
-The fastest exact hafnian library. For more information, please see the `documentation <https://hafnian.readthedocs.io>`_.
+The fastest exact hafnian library. For more information, please see the `documentation <https://thewalrus.readthedocs.io>`_.
 
 Features
 ========
@@ -57,13 +57,13 @@ To install, simply run
 
 .. code-block:: bash
 
-    pip install hafnian
+    pip install thewalrus
 
 
 Compiling from source
 =====================
 
-Hafnian depends on the following Python packages:
+The Walrus depends on the following Python packages:
 
 * `Python <http://python.org/>`_ >=3.5
 * `NumPy <http://numpy.org/>`_  >=1.13.3
@@ -94,47 +94,47 @@ Alternatively, you can download the Eigen headers manually:
     $ tar xzf eigen3.tar.gz eigen-eigen-323c052e1731/Eigen --strip-components 1
     $ export EIGEN_INCLUDE_DIR=$HOME/.local/eigen3
 
-Note that we export the environment variable ``EIGEN_INCLUDE_DIR`` so that Hafnian can find the Eigen3 header files (if not provided, Hafnian will by default look in ``/use/include/eigen3`` and ``/usr/local/include/eigen3``).
+Note that we export the environment variable ``EIGEN_INCLUDE_DIR`` so that The Walrus can find the Eigen3 header files (if not provided, The Walrus will by default look in ``/use/include/eigen3`` and ``/usr/local/include/eigen3``).
 
-Once all dependencies are installed, you can compile the latest stable version of the Hafnian library as follows:
+Once all dependencies are installed, you can compile the latest stable version of the The Walrus library as follows:
 
 .. code-block:: console
 
-    $ python -m pip install hafnian --no-binary :all:
+    $ python -m pip install thewalrus --no-binary :all:
 
 Alternatively, you can compile the latest development version by cloning the git repository, and installing using pip in development mode.
 
 .. code-block:: console
 
-    $ git clone https://github.com/XanaduAI/hafnian.git
-    $ cd hafnian && python -m pip install -e .
+    $ git clone https://github.com/XanaduAI/thewalrus.git
+    $ cd thewalrus && python -m pip install -e .
 
 
 OpenMP
 ------
 
-The Hafnian library uses OpenMP to parallelize both the permanent and the hafnian calculation. **At the moment, this is only supported on Linux using the GNU g++ compiler, due to insufficient support using Windows/MSCV and MacOS/Clang.**
+``libwalrus`` uses OpenMP to parallelize both the permanent and the hafnian calculation. **At the moment, this is only supported on Linux using the GNU g++ compiler, due to insufficient support using Windows/MSCV and MacOS/Clang.**
 
 
 
 Using LAPACK, OpenBLAS, or MKL
 ------------------------------
 
-If you would like to take advantage of the highly optimized matrix routines of LAPACK, OpenBLAS, or MKL, you can optionally compile the Hafnian library such that Eigen uses these frameworks as backends. As a result, all calls in the Hafnian library to Eigen functions are silently substituted with calls to LAPACK/OpenBLAS/MKL.
+If you would like to take advantage of the highly optimized matrix routines of LAPACK, OpenBLAS, or MKL, you can optionally compile the ``libwalrus`` such that Eigen uses these frameworks as backends. As a result, all calls in the ``libwalrus`` library to Eigen functions are silently substituted with calls to LAPACK/OpenBLAS/MKL.
 
 For example, for LAPACK integration, make sure you have the ``lapacke`` C++ LAPACK bindings installed (``sudo apt install liblapacke-dev`` in Ubuntu-based Linux distributions), and then compile with the environment variable ``USE_LAPACK=1``:
 
 .. code-block:: console
 
-    $ USE_LAPACK=1 python -m pip install hafnian --no-binary :all:
+    $ USE_LAPACK=1 python -m pip install thewalrus --no-binary :all:
 
 Alternatively, you may pass ``USE_OPENBLAS=1`` to use the OpenBLAS library.
 
 
 Software tests
 ==============
 
-To ensure that the Hafnian library is working correctly after installation, the test suite can be run by navigating to the source code folder and running
+To ensure that The Walrus library is working correctly after installation, the test suite can be run by navigating to the source code folder and running
 
 .. code-block:: console
 
@@ -169,7 +169,9 @@ libraries are available on your include/library paths.
 Documentation
 =============
 
-The Hafnian+ documentation is currently not hosted online. To build it locally, you need to have the following packages installed:
+The Walrus documentation is available online on `Read the Docs <https://thewalrus.readthedocs.io>`_.
+
+To build it locally, you need to have the following packages installed:
 
 * `Sphinx <http://sphinx-doc.org/>`_ >=1.5
 * `sphinxcontrib-bibtex <https://sphinxcontrib-bibtex.readthedocs.io/en/latest/>`_ >=0.3.6
@@ -200,23 +202,23 @@ Authors
 
 Nicolás Quesada, Brajesh Gupt, and Josh Izaac.
 
-All contributions are acknowledged in the `acknowledgments page <https://github.com/XanaduAI/hafnian/blob/master/.github/ACKNOWLEDGMENTS.md>`_.
+All contributions are acknowledged in the `acknowledgments page <https://github.com/XanaduAI/thewalrus/blob/master/.github/ACKNOWLEDGMENTS.md>`_.
 
-If you are doing research using Hafnian, please cite `our paper <https://dl.acm.org/citation.cfm?id=3325111>`_:
+If you are doing research using The Walrus, please cite `our paper <https://dl.acm.org/citation.cfm?id=3325111>`_:
 
  Andreas Björklund, Brajesh Gupt, and Nicolás Quesada. A faster hafnian formula for complex matrices and its benchmarking on a supercomputer, Journal of Experimental Algorithmics (JEA) 24 (1), 11 (2019)
 
 
 Support
 =======
 
-- **Source Code:** https://github.com/XanaduAI/hafnian
-- **Issue Tracker:** https://github.com/XanaduAI/hafnian/issues
+- **Source Code:** https://github.com/XanaduAI/thewalrus
+- **Issue Tracker:** https://github.com/XanaduAI/thewalrus/issues
 
 If you are having issues, please let us know by posting the issue on our Github issue tracker.
 
 
 License
 =======
 
-Hafnian is **free** and **open source**, released under the Apache License, Version 2.0.
+The Walrus is **free** and **open source**, released under the Apache License, Version 2.0.

appveyor.yml

@@ -7,7 +7,7 @@ environment:
       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"
+      CIBW_TEST_COMMAND: "python -m pytest {project}/thewalrus"
       CIBW_BUILD_VERBOSITY: 3
       WHEELHOUSE_UPLOADER_USERNAME: AKIAJOU6ECM5Q7T6UUQQ
       WHEELHOUSE_UPLOADER_SECRET:

docs/Doxyfile

@@ -32,7 +32,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "Hafnian C++"
+PROJECT_NAME           = "libwalrus C++"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -873,7 +873,7 @@ RECURSIVE              = NO
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = 
+EXCLUDE                =
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded