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‎.coveragerc‎

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[run]
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relative_files = True
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# Use 'source' instead of 'omit' in order to ignore 'tests/unit/__init__.py'
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source = hello_world

‎.github/CODEOWNERS‎

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* @Sage-Bionetworks-IT/sagebio-it @Sage-Bionetworks-IT/infra-oversight-committee

‎.github/PULL_REQUEST_TEMPLATE.md‎

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DELETE THIS TEMPLATE BEFORE SUBMITTING
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PR Checklist:
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[ ] Clearly explain your change with a desriptive commit message
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[ ] Setup pre-commit and run the validators (info in README.md)
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To validate files run: `pre-commit run --all-files`

‎.github/actions/sam-build/action.yaml‎

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name: sam-build
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runs:
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# This creates a composite action to be used as a step in a job
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# https://docs.github.com/en/actions/creating-actions/creating-a-composite-action
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using: "composite"
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steps:
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# Convert Pipfile.lock to requirements.txt for sam
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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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- run: pip install -U pipenv
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shell: bash
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# This needs to be in the 'CodeUri' directory
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- run: pipenv requirements > requirements.txt
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shell: bash
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# Install aws-sam-cli
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- uses: aws-actions/setup-sam@v2
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with:
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use-installer: true
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# Use a lambda-like docker container to build the lambda artifact
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- run: sam build --use-container
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shell: bash

‎.github/workflows/periodic.yaml‎

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name: periodic
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on:
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# Run once a month
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schedule:
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- cron: '30 16 15 * *' # 16:30 UTC (9:30 PST) on the 15th of the month
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jobs:
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# Check that our current dependencies still work
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dependency-check:
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uses: "./.github/workflows/test.yaml"

‎.github/workflows/post-merge.yaml‎

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name: post-merge
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on:
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# Run on merges to main or tag pushes
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push:
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branches: [ 'main' ]
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tags: [ '*' ]
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concurrency:
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group: ${{ github.workflow }}
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jobs:
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lambda-test:
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uses: "./.github/workflows/test.yaml"
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package-and-publish:
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runs-on: ubuntu-latest
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needs: lambda-test
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permissions:
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id-token: write
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env:
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BOOTSTRAP_BUCKET: bootstrap-awss3cloudformationbucket-19qromfd235z9
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ESSENTIALS_BUCKET: essentials-awss3lambdaartifactsbucket-x29ftznj6pqw
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steps:
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- uses: actions/checkout@v4
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# Install sam-cli and run "sam build"
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- uses: ./.github/actions/sam-build
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# authenticate with AWS via OIDC
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- uses: aws-actions/configure-aws-credentials@v4
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with:
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aws-region: us-east-1
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role-to-assume: arn:aws:iam::745159704268:role/sagebase-github-oidc-lambda-template-deploy-sageit
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role-session-name: GHA-${{ github.event.repository.name }}-${{ github.run_id }} # Must not exceed 64 chars
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role-duration-seconds: 900
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# upload the lambda artifact to s3 and generate a cloudformation template referencing it
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- run: sam package --template-file .aws-sam/build/template.yaml --s3-bucket $ESSENTIALS_BUCKET --s3-prefix ${{ github.event.repository.name }}/${{ github.ref_name }} --output-template-file .aws-sam/build/${{ github.event.repository.name }}.yaml
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# upload the generated cloudformation template to s3
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- run: aws s3 cp .aws-sam/build/${{ github.event.repository.name }}.yaml s3://$BOOTSTRAP_BUCKET/${{ github.event.repository.name }}/${{ github.ref_name }}/

‎.github/workflows/pre-merge.yaml‎

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name: pre-merge
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on:
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# Run on open pull requests
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pull_request:
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jobs:
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lambda-test:
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uses: "./.github/workflows/test.yaml"

‎.github/workflows/test.yaml‎

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name: lambda-test
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on:
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# This is a dispatched workflow to be called as a job in other workflows
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# https://docs.github.com/en/actions/using-workflows/reusing-workflows#creating-a-reusable-workflow
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workflow_call:
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jobs:
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pre-commit:
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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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- uses: pre-commit/action@v3.0.1
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pytest:
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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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- run: pip install -U pipenv
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- run: pipenv sync --dev
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- run: pipenv run coverage run -m pytest tests/ -svv
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- run: pipenv run coverage lcov
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- name: upload coverage to coveralls
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uses: coverallsapp/github-action@v2
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with:
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file: coverage.lcov
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fail-on-error: false
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sam-build-and-lint:
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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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- uses: ./.github/actions/sam-build
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- run: sam validate --lint --template .aws-sam/build/template.yaml

‎.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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coverage.lcov
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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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db.sqlite3
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db.sqlite3-journal
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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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# 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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# jetbrains
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.idea/
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# generated dynamically from Pipfile
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requirements.txt

‎.pre-commit-config.yaml‎

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ci:
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autoupdate_schedule: monthly
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v5.0.0
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hooks:
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# On Windows, git will convert all CRLF to LF, but only after all hooks are done executing.
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# yamllint will fail before git has a chance to convert line endings, so line endings must be explicitly converted before yamllint
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- id: mixed-line-ending
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args: ['--fix=lf']
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description: Forces to replace line ending by the UNIX 'LF' character
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- id: end-of-file-fixer
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- id: trailing-whitespace
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- id: check-ast
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- repo: https://github.com/adrienverge/yamllint
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rev: v1.37.1
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hooks:
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- id: yamllint
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- repo: https://github.com/awslabs/cfn-python-lint
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rev: v1.34.2
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hooks:
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- id: cfn-python-lint
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files: template\.(json|yml|yaml)$
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- repo: https://github.com/Lucas-C/pre-commit-hooks
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rev: v1.5.5
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hooks:
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- id: remove-tabs
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- repo: https://github.com/aristanetworks/j2lint.git
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rev: v1.2.0
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hooks:
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- id: j2lint

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