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‎.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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title: ''
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labels: ''
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assignees: ''
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---
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### Describe the bug
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A clear and concise description of what the bug is.
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### To Reproduce
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Code snippet or clear steps to reproduce the behaviour.
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### Expected behavior
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A clear and concise description of what you expected to happen.
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### Screenshots
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If applicable, add screenshots to help explain your problem.
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### Version
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- Version info such as v0.1.0
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### Additional context
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Add any other context about the problem here.

‎.github/ISSUE_TEMPLATE/config.yml‎

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blank_issues_enabled: false

‎.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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title: ''
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labels: ''
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assignees: ''
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---
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### Is your feature request related to a problem? Please describe.
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
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### Describe the solution you'd like
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A clear and concise description of what you want to happen.
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### Describe alternatives you've considered
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A clear and concise description of any alternative solutions or features you've considered.
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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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# PR Type
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[Feature | Fix | Documentation | Refactor | Other]
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# Short Description
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Add a short description of what is in this PR.
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# Tests Added
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Describe the tests that have been added to ensure the codes correctness, if applicable.

‎.github/workflows/code_checks.yml‎

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name: code checks
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on:
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push:
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branches:
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- main
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paths:
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- .pre-commit-config.yaml
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- .github/workflows/code_checks.yml
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- '**.py'
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- poetry.lock
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- pyproject.toml
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- '**.ipynb'
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pull_request:
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branches:
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- main
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paths:
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- .pre-commit-config.yaml
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- .github/workflows/code_checks.yml
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- '**.py'
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- poetry.lock
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- pyproject.toml
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- '**.ipynb'
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jobs:
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run-code-check:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/[email protected]
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- name: Install and configure Poetry
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uses: snok/install-poetry@v1
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with:
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virtualenvs-create: true
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virtualenvs-in-project: true
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- uses: actions/[email protected]
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with:
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python-version: '3.9'
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cache: 'poetry'
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- name: Install dependencies and check code
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run: |
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poetry env use '3.9'
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source .venv/bin/activate
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poetry install --with test --all-extras
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pre-commit run --all-files
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- name: pip-audit (gh-action-pip-audit)
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uses: pypa/[email protected]
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with:
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virtual-environment: .venv/
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ignore-vulns: GHSA-cqh9-jfqr-h9jj

‎.github/workflows/integration_tests.yml‎

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name: integration tests
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on:
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push:
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branches:
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- main
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paths:
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- .pre-commit-config.yaml
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- .github/workflows/code_checks.yml
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- .github/workflows/integration_tests.yml
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- '**.py'
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- '**.ipynb'
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- poetry.lock
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- pyproject.toml
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- '**.rst'
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- '**.md'
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pull_request:
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branches:
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- main
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paths:
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- .pre-commit-config.yaml
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- .github/workflows/code_checks.yml
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- .github/workflows/integration_tests.yml
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- '**.py'
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- '**.ipynb'
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- poetry.lock
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- pyproject.toml
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- '**.rst'
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- '**.md'
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jobs:
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integration-tests:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/[email protected]
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- name: Install poetry
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run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
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- uses: actions/[email protected]
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with:
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python-version: '3.9'
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- name: Install dependencies and check code
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run: |
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poetry env use '3.9'
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source $(poetry env info --path)/bin/activate
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poetry install --with test
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pytest -m integration_test

‎.github/workflows/publish.yml‎

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name: publish package
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on:
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release:
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types: [published]
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jobs:
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deploy:
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name: Upload release to PyPI
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/mmlearn
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permissions:
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id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
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steps:
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- name: Install apt dependencies
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run: |
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sudo apt-get update
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sudo apt-get install libcurl4-openssl-dev libssl-dev
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- uses: actions/[email protected]
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- name: Install poetry
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run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
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- uses: actions/[email protected]
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with:
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python-version: '3.9'
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- name: Build package
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run: poetry build
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- name: Publish package
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uses: pypa/gh-action-pypi-publish@release/v1

‎.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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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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pip-wheel-metadata/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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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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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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# Translations
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*.mo
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*.pot
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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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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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.python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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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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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pycharm
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.idea/
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# vscode
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.vscode/
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# wandb
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wandb/
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# hydra
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outputs/
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# slurm
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*slurm-*

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.6.0 # Use the ref you want to point at
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hooks:
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- id: trailing-whitespace
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- id: check-ast
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- id: check-builtin-literals
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- id: check-docstring-first
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- id: check-executables-have-shebangs
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- id: debug-statements
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- id: end-of-file-fixer
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- id: mixed-line-ending
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args: [--fix=lf]
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- id: detect-private-key
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- id: check-yaml
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- id: check-toml
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- repo: https://github.com/python-poetry/poetry
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rev: 1.8.3
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hooks:
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- id: poetry-check
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args: [--lock]
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.5.7
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hooks:
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- id: ruff
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args: [--fix, --exit-non-zero-on-fix]
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types_or: [ python, pyi, jupyter ]
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- id: ruff-format
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types_or: [ python, pyi, jupyter ]
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- repo: https://github.com/crate-ci/typos
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rev: v1.23.6
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hooks:
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- id: typos
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args: []
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v1.11.1
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hooks:
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- id: mypy
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entry: python3 -m mypy --show-error-codes --pretty --config-file pyproject.toml
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types: [python]
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exclude: "tests"
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- repo: https://github.com/nbQA-dev/nbQA
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rev: 1.8.7
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hooks:
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- id: nbqa-ruff
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args: [--fix, --exit-non-zero-on-fix]
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- repo: local
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hooks:
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- id: pytest
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name: pytest
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language: system
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entry: python3 -m pytest -m "not integration_test"
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pass_filenames: false
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always_run: true

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