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lothianlothian
committedApr 10, 2021
Initial commit after CMS Cookiecutter creation, version 1.5
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‎.codecov.yml

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# Codecov configuration to make it a bit less noisy
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coverage:
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status:
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patch: false
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project:
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default:
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threshold: 50%
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comment:
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layout: "header"
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require_changes: false
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branches: null
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behavior: default
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flags: null
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paths: null

‎.github/CONTRIBUTING.md

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# How to contribute
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We welcome contributions from external contributors, and this document
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describes how to merge code changes into this pycc.
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## Getting Started
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* Make sure you have a [GitHub account](https://github.com/signup/free).
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* [Fork](https://help.github.com/articles/fork-a-repo/) this repository on GitHub.
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* On your local machine,
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[clone](https://help.github.com/articles/cloning-a-repository/) your fork of
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the repository.
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## Making Changes
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* Add some really awesome code to your local fork. It's usually a [good
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idea](http://blog.jasonmeridth.com/posts/do-not-issue-pull-requests-from-your-master-branch/)
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to make changes on a
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[branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/)
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with the branch name relating to the feature you are going to add.
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* When you are ready for others to examine and comment on your new feature,
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navigate to your fork of pycc on GitHub and open a [pull
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request](https://help.github.com/articles/using-pull-requests/) (PR). Note that
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after you launch a PR from one of your fork's branches, all
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subsequent commits to that branch will be added to the open pull request
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automatically. Each commit added to the PR will be validated for
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mergability, compilation and test suite compliance; the results of these tests
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will be visible on the PR page.
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* If you're providing a new feature, you must add test cases and documentation.
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* When the code is ready to go, make sure you run the test suite using pytest.
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* When you're ready to be considered for merging, check the "Ready to go"
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box on the PR page to let the pycc devs know that the changes are complete.
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The code will not be merged until this box is checked, the continuous
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integration returns checkmarks,
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and multiple core developers give "Approved" reviews.
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# Additional Resources
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* [General GitHub documentation](https://help.github.com/)
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* [PR best practices](http://codeinthehole.com/writing/pull-requests-and-other-good-practices-for-teams-using-github/)
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* [A guide to contributing to software packages](http://www.contribution-guide.org)
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* [Thinkful PR example](http://www.thinkful.com/learn/github-pull-request-tutorial/#Time-to-Submit-Your-First-PR)

‎.github/PULL_REQUEST_TEMPLATE.md

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## Description
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Provide a brief description of the PR's purpose here.
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## Todos
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Notable points that this PR has either accomplished or will accomplish.
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- [ ] TODO 1
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## Questions
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- [ ] Question1
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## Status
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- [ ] Ready to go

‎.github/workflows/CI.yaml

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name: CI
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on:
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# GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
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# Existing codes likely still have "master" as the primary branch
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# Both are tracked here to keep legacy and new codes working
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push:
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branches:
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- "master"
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- "main"
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pull_request:
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branches:
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- "master"
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- "main"
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schedule:
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# Nightly tests run on master by default:
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# Scheduled workflows run on the latest commit on the default or base branch.
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# (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
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- cron: "0 0 * * *"
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jobs:
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test:
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name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [macOS-latest, ubuntu-latest, windows-latest]
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python-version: [3.7, 3.8, 3.9]
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steps:
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- uses: actions/checkout@v1
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- name: Additional info about the build
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shell: bash
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run: |
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uname -a
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df -h
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ulimit -a
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# More info on options: https://github.com/conda-incubator/setup-miniconda
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- uses: conda-incubator/setup-miniconda@v2
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with:
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python-version: ${{ matrix.python-version }}
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environment-file: devtools/conda-envs/test_env.yaml
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channels: conda-forge,defaults
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activate-environment: test
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auto-update-conda: false
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auto-activate-base: false
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show-channel-urls: true
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- name: Install package
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# conda setup requires this special shell
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shell: bash -l {0}
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run: |
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python -m pip install . --no-deps
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conda list
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- name: Run tests
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# conda setup requires this special shell
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shell: bash -l {0}
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run: |
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pytest -v --cov=pycc --cov-report=xml --color=yes pycc/tests/
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- name: CodeCov
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uses: codecov/codecov-action@v1
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with:
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file: ./coverage.xml
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flags: unittests
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name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}

‎.gitignore

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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env/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.coverage.*
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.cache
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.pytest_cache
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nosetests.xml
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coverage.xml
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*.cover
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.hypothesis/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# pyenv
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.python-version
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# celery beat schedule file
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celerybeat-schedule
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# SageMath parsed files
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*.sage.py
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# dotenv
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.env
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# virtualenv
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.venv
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venv/
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ENV/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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# profraw files from LLVM? Unclear exactly what triggers this
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# There are reports this comes from LLVM profiling, but also Xcode 9.
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*profraw

‎.lgtm.yml

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# Configure LGTM for this package
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extraction:
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python: # Configure Python
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python_setup: # Configure the setup
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version: 3 # Specify Version 3
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path_classifiers:
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library:
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- versioneer.py # Set Versioneer.py to an external "library" (3rd party code)
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- devtools/*
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generated:
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- pycc/_version.py

‎CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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## Our Pledge
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In the interest of fostering an open and welcoming environment, we as
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contributors and maintainers pledge to making participation in our project and
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our community a harassment-free experience for everyone, regardless of age,
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body size, disability, ethnicity, gender identity and expression, level of
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experience, nationality, personal appearance, race, religion, or sexual
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identity and orientation.
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## Our Standards
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Examples of behavior that contributes to creating a positive environment include:
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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* The use of sexualized language or imagery and unwelcome sexual attention or advances
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* Trolling, insulting/derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or electronic address, without explicit permission
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* Other conduct which could reasonably be considered inappropriate in a professional setting
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## Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable
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behavior and are expected to take appropriate and fair corrective action in
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response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or
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reject comments, commits, code, wiki edits, issues, and other contributions
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that are not aligned to this Code of Conduct, or to ban temporarily or
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permanently any contributor for other behaviors that they deem inappropriate,
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threatening, offensive, or harmful.
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Moreover, project maintainers will strive to offer feedback and advice to
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ensure quality and consistency of contributions to the code. Contributions
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from outside the group of project maintainers are strongly welcomed but the
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final decision as to whether commits are merged into the codebase rests with
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the team of project maintainers.
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## Scope
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This Code of Conduct applies both within project spaces and in public spaces
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when an individual is representing the project or its community. Examples of
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representing a project or community include using an official project e-mail
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address, posting via an official social media account, or acting as an
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appointed representative at an online or offline event. Representation of a
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project may be further defined and clarified by project maintainers.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported by contacting the project team at 'crawdad@vt.edu'. The project team will
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review and investigate all complaints, and will respond in a way that it deems
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appropriate to the circumstances. The project team is obligated to maintain
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confidentiality with regard to the reporter of an incident. Further details of
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specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good
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faith may face temporary or permanent repercussions as determined by other
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members of the project's leadership.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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version 1.4, available at
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[http://contributor-covenant.org/version/1/4][version]
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[homepage]: http://contributor-covenant.org
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[version]: http://contributor-covenant.org/version/1/4/

‎LICENSE

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Copyright 2021 T Daniel Crawford
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Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
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following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
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disclaimer in the documentation and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote
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products derived from this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
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INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
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THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎MANIFEST.in

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include LICENSE
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include MANIFEST.in
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include CODE_OF_CONDUCT.md
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include versioneer.py
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graft pycc
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global-exclude *.py[cod] __pycache__ *.so

‎README.md

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PyCC
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==============================
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[//]: # (Badges)
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[![GitHub Actions Build Status](https://github.com/REPLACE_WITH_OWNER_ACCOUNT/pycc/workflows/CI/badge.svg)](https://github.com/REPLACE_WITH_OWNER_ACCOUNT/pycc/actions?query=workflow%3ACI)
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[![codecov](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/PyCC/branch/master/graph/badge.svg)](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/PyCC/branch/master)
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A Python-based coupled cluster implementation.
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### Copyright
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Copyright (c) 2021, T Daniel Crawford
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#### Acknowledgements
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Project based on the
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[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.5.

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