Initial commit

Author: sztal

.gitignore

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+# Sandbox folders
+_sandbox/**
+_notebooks/**
+
+# IDEs
+.vscode
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports / benchmarks / profiling
+prof/
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+.benchmarks
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# VIM
+**/*.swp

AUTHORS.rst

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+Authors
+-------
+
+**Development Lead**
+
+* Szymon Talaga <[email protected]>
+
+**Contributors**
+
+None yet. Why not be the first?

CONTRIBUTING.rst

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+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/sztal/pathcensus/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug"
+is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "feature"
+is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+Path census could always use more documentation, whether as part of the
+official Path census docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/sztal/pathcensus/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `pathcensus` for
+local development.
+
+1. Fork_ the `pathcensus` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone [email protected]:your_name_here/pathcensus.git
+
+3. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+Now you can make your changes locally.
+
+4. When you're done making changes, check that your changes pass style and unit
+   tests, including testing other Python versions with tox::
+
+    $ make test-all
+
+You may first need to run ``pip install -r requirements-tests.txt``
+and then ``pip install tox``.
+
+5. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+6. Submit a pull request through the GitHub website.
+
+.. _Fork: https://github.com/sztal/pathcensus/fork
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 3.8+
+   and must pass all tests when running ``make test-all``.
+
+
+Tips
+----
+
+To run a subset of tests::
+
+	 $ pytest test/unweighted/test_pathcensus.py
+
+This will run all tests for the unweighted calculations of path census
+and structural coefficients.

HISTORY.rst

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+.. :changelog:
+
+History
+-------
+
+0.1 (2022-06-01)
+++++++++++++++++++
+
+* First release on PyPI.

LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2021 Szymon Talaga
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

MANIFEST.in

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+include AUTHORS.rst
+include HISTORY.rst
+include LICENSE
+include README.rst

Makefile

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+.PHONY: help clean clean-pyc clean-build clean-test lint test test-all coverage docs release sdist
+
+help:
+	@echo "clean - remove auxiliary files/artifacts"
+	@echo "clean-build - remove build artifacts"
+	@echo "clean-pyc - remove Python file artifacts"
+	@echo "clean-test - remove testing artifacts"
+	@echo "lint - check style with flake8"
+	@echo "test - run tests quickly with the default Python"
+	@echo "test-all - run tests on every Python version with tox"
+	@echo "coverage - compute code coverage quickly with the default Python"
+	@echo "cov-report - display coverage report"
+	@echo "docs - generate Sphinx HTML documentation, including API docs"
+	@echo "release - package and upload a release"
+	@echo "sdist - package"
+
+clean: clean-build clean-py clean-test
+
+clean-build:
+	rm -fr build/
+	rm -fr dist/
+	find . -name '*.egg-info' -exec rm -rf {} +
+	find . -name '*.eggs' -exec rm -rf {} +
+
+clean-py:
+	find . -name '__pycache__' -exec rm -rf {} +
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*.nbc' -exec rm -f {} +
+	find . -name '*.nbi' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+
+clean-test:
+	find . -name '.benchmarks' -exec rm -rf {} +
+	find . -name '.pytest_cache' -exec rm -rf {} +
+	find . -name '.tox' -exec rm -rf {} +
+
+lint:
+	pytest --pylint -m pylint
+
+test:
+	pytest
+
+test-all:
+	tox
+
+cov-run:
+	coverage run --source pathcensus setup.py test
+
+cov-report:
+	coverage report --omit=pathcensus/core/*.py
+	coverage html --omit=pathcensus/core/*.py
+	xdg-open htmlcov/index.html || open htmlcov/index.html
+
+coverage: cov-run cov-report
+
+docs:
+	rm -f docs/pathcensus.rst
+	rm -f docs/modules.rst
+	sphinx-apidoc -o docs/ pathcensus
+	$(MAKE) -C docs clean
+	$(MAKE) -C docs html
+	xdg-open docs/_build/html/index.html || open docs/_build/html/index.html
+
+release: clean
+	python setup.py sdist upload
+	python setup.py bdist_wheel upload
+
+sdist: clean
+	python setup.py sdist
+	python setup.py bdist_wheel upload
+	ls -l dist