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Updated examples from cookiecutter-mdakit at bf268fa
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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/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: Create a report to help us improve
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---
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## Expected behavior ##
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<!-- A clear and concise description of what you want to do and what you think should happen. (Code to reproduce the behavior can be added below). -->
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## Actual behavior ##
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<!-- What happened instead. Add as much detail as you can. Include (copy and paste) stack traces and any output. -->
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## Code to reproduce the behavior ##
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<!-- Show us how to reproduce the failure. If you can, use trajectory files from the test data. Use the code snipped below as a starting point. -->
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``` python
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import mdakit-Cookie
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...
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```
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## Current environment ##
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- Which version are you using? (run `python -c "import mdakit-Cookie; print(mdakit-Cookie.__version__)"`)
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- Which version of Python (`python -V`)?
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- Which operating system?
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- What is the output of `pip list`?
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- If you use conda, what is the output of `conda list`?

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature request
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about: Suggest an idea for this project
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---
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## Is your feature request related to a problem? ##
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<!-- A clear and concise description of what the problem is. For example, I'm always frustrated when [...] -->
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## Describe the solution you'd like ##
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<!-- A description of what you want to happen. For example, I'd like to be able to do [...] -->
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## Describe alternatives you've considered ##
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<!-- A description of any alternative solutions or features you've considered or possible solutions that you've seen elsewhere. -->
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## Additional context ##
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<!-- Add any other context or screenshots about the feature request here. -->

‎.github/PULL_REQUEST_TEMPLATE.md‎

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<!-- Does this PR fix an issue or relate to an existing discussion? Please link it below after "Fixes #" -->
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Fixes #
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Changes made in this Pull Request:
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<!-- Summarise changes made with dot points below -->
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-
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-
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PR Checklist
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------------
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- [ ] Tests?
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- [ ] Docs?
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- [ ] CHANGELOG updated?
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- [ ] Issue raised/referenced?

‎.github/workflows/gh-ci.yaml‎

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name: GH Actions CI
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on:
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push:
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branches:
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- "**" # main -- replaced main to allow CI to run in example cookie repo
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pull_request:
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branches:
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- "**" # main -- replaced main to allow CI to run in example cookie repo
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schedule:
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# Weekly tests at midnight on Sundays run on main 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 * * 0"
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concurrency:
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# Specific group naming so CI is only cancelled
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# within same PR or on merge to main
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group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
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cancel-in-progress: true
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defaults:
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run:
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shell: bash
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jobs:
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main-tests:
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if: "github.repository == 'other/mdakit-Cookie'"
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macOS-latest, windows-latest]
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mdanalysis-version: ["latest", "develop"]
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python-version: ["3.11", "3.12", "3.13", "3.14"]
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steps:
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- uses: actions/checkout@v4
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- name: Build information
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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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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install testing dependencies
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run: |
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python -m pip install -U pytest pytest-xdist pytest-cov codecov
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- name: Install MDAnalysis version
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uses: MDAnalysis/install-mdanalysis@main
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with:
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version: ${{ matrix.mdanalysis-version }}
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install-tests: false
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installer: pip
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shell: bash
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- name: Install package
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run: |
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python --version
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python -m pip install .
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- name: Python information
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run: |
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which python
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which pip
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pip list
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- name: Run tests
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run: |
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pytest -n 2 -v --cov=cookieKit --cov-report=xml --color=yes cookieKit/tests/
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- name: codecov
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if: github.repository == 'other/mdakit-Cookie' && github.event_name != 'schedule'
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uses: codecov/codecov-action@v5
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with:
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file: coverage.xml
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name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
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verbose: True
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# to upload coverage reports, set a secret called CODECOV_TOKEN
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# in the repository settings
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# (Obtain this from the Codecov website after setting up the repository there)
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token: ${{ secrets.CODECOV_TOKEN }}
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# To fail the CI if there's an error, keep this set to true
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# If repository forks need to run CI, you may need to set this to false
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# Forks can't access the CODECOV_TOKEN secret,
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# and a failed upload registers as an error
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fail_ci_if_error: true
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pylint_check:
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if: "github.repository == 'other/mdakit-Cookie'"
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.12"
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- name: Install Pylint
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run: |
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which pip
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which python
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pip install pylint mdanalysis
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- name: Run Pylint
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env:
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PYLINTRC: .pylintrc
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run: |
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pylint .
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pypi_check:
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if: "github.repository == 'other/mdakit-Cookie'"
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.12"
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- name: Install dependencies
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run: |
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pip install pipx twine
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- name: Build package
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run: |
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python -m pipx run build --sdist
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- name: Check package build
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run: |
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DISTRIBUTION=$(ls -t1 dist/mdakit_cookie-*.tar.gz | head -n 1)
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test -n "${DISTRIBUTION}" || { echo "no distribution dist/mdakit-Cookie-*.tar.gz found"; exit 1; }
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echo "twine check $DISTRIBUTION"
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twine check $DISTRIBUTION

‎.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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# VS Code
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.vscode/
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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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.DS_Store
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# poetry
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poetry.lock

‎.pre-commit-config.yaml‎

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# To install the git pre-commit hook run:
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# pre-commit install
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# To update the pre-commit hooks run:
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# pre-commit install-hooks
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exclude: '^(\.tox|ci/templates|\.bumpversion\.cfg)(/|$)'
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: master
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: debug-statements
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- repo: https://github.com/timothycrosley/isort
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rev: master
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hooks:
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- id: isort
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- repo: https://gitlab.com/pycqa/flake8
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rev: master
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hooks:
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- id: flake8

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