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Ralf Grubenmann
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Merge branch 'add_unicode_support' of github.com:Panaetius/cwltool into add_unicode_support
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‎.github/ISSUE_TEMPLATE.md

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This issue tracker is for reporting bugs in cwltool (the CWL reference implementation) itself. Please use the [Gitter channel](https://gitter.im/common-workflow-language/common-workflow-language) or [Biostars forum](https://www.biostars.org/) for general questions about using cwltool to create/run workflows or issues not related to cwltool. Don't forget to use cwl tag when posting on Biostars Forum.
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This issue tracker is for reporting bugs in cwltool (the CWL reference implementation) itself. Please use the [Gitter channel](https://gitter.im/common-workflow-language/common-workflow-language) or [CWL Discourse Forum](https://cwl.discourse.group/) for general questions about using cwltool to create/run workflows or issues not related to cwltool. Don't forget to use cwl tag when posting on Biostars Forum.
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If you'd like to report a bug, fill out the template below and provide any extra information that may be useful / related to your problem. Ideally, you create an [a Minimal, Complete, and Verifiable example](http://stackoverflow.com/help/mcve) reproducing the problem before opening an issue to ensure it's not caused by something in your code.
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‎.github/ISSUE_TEMPLATE/config.yml

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contact_links:
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- name: CWL Community Forum
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url: https://cwl.discourse.group/c/q-and-a/5
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about: Please ask and answer questions here.

‎.github/workflows/ci-tests.yml

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name: Continous integration tests
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on:
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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workflow_dispatch:
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env:
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singularity_version: 3.6.4
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jobs:
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tox:
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name: CI tests via Tox
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runs-on: ubuntu-20.04
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strategy:
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matrix:
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py-ver-major: [3]
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py-ver-minor: [6, 7, 8, 9]
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step: [lint, unit, bandit, mypy]
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env:
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py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }}
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TOXENV: ${{ format('py{0}{1}-{2}', matrix.py-ver-major, matrix.py-ver-minor, matrix.step) }}
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: Set up Singularity
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if: ${{ matrix.step == 'unit' || matrix.step == 'mypy' }}
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uses: eWaterCycle/setup-singularity@v6
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with:
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singularity-version: ${{ env.singularity_version }}
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- name: Give the test runner user a name to make provenance happy.
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if: ${{ matrix.step == 'unit' || matrix.step == 'mypy' }}
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run: sudo usermod -c 'CI Runner' $(whoami)
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: ${{ env.py-semver }}
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- name: Cache for pip
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uses: actions/cache@v2
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ matrix.step }}-${{ hashFiles('requirements.txt', 'tox.ini') }}
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- name: Upgrade setuptools and install tox
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run: |
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pip install -U pip setuptools wheel
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pip install tox tox-gh-actions
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- name: MyPy cache
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if: ${{ matrix.step == 'mypy' }}
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uses: actions/cache@v2
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with:
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path: .mypy_cache/${{ env.py-semver }}
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key: mypy-${{ env.py-semver }}
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- name: Test with tox
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run: tox
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- name: Upload coverage to Codecov
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if: ${{ matrix.step == 'unit' }}
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uses: codecov/codecov-action@v1
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with:
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fail_ci_if_error: true
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tox-style:
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name: CI linters via Tox
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runs-on: ubuntu-20.04
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strategy:
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matrix:
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step: [lint-readme, shellcheck, pydocstyle]
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env:
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py-semver: 3.9
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TOXENV: ${{ format('py39-{0}', matrix.step) }}
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: ${{ env.py-semver }}
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- name: Cache for pip
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uses: actions/cache@v2
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ matrix.step }}-${{ hashFiles('requirements.txt') }}
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- name: Upgrade setuptools and install tox
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run: |
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pip install -U pip setuptools wheel
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pip install tox tox-gh-actions
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- if: ${{ matrix.step == 'pydocstyle' && github.event_name == 'pull_request'}}
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name: Create local branch for diff-quality for PRs
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run: git branch ${{github.base_ref}} origin/${{github.base_ref}}
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- name: Test with tox
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run: tox
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conformance_tests:
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name: CWL spec conformance tests
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runs-on: ubuntu-20.04
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strategy:
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matrix:
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cwl-version: [v1.0, v1.1, v1.2]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: 3.9
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- name: Cache for pip
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uses: actions/cache@v2
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-conformance-${{ matrix.step }}-${{ hashFiles('requirements.txt') }}
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- name: Run CWL conformance tests ${{ matrix.cwl-version }}
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env:
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version: ${{ matrix.cwl-version }}
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run: ./conformance-test.sh
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release_test:
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name: cwltool release test
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runs-on: ubuntu-20.04
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steps:
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- uses: actions/checkout@v2
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- name: Set up Singularity
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uses: eWaterCycle/setup-singularity@v6
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with:
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singularity-version: ${{ env.singularity_version }}
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: 3.9
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- name: Give the test runner user a name to make provenance happy.
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run: sudo usermod -c 'CI Runner' $(whoami)
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- name: Cache for pip
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uses: actions/cache@v2
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-release-${{ hashFiles('requirements.txt', 'test-requirements.txt') }}
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- name: Install packages
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run: |
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pip install -U pip setuptools wheel
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pip install virtualenv
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- name: Release test
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env:
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RELEASE_SKIP: head
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run: ./release-test.sh

‎.github/workflows/codeql-analysis.yml

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name: "Code scanning - action"
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on:
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push:
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pull_request:
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schedule:
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- cron: '0 10 * * 2'
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jobs:
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CodeQL-Build:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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with:
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# We must fetch at least the immediate parents so that if this is
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# a pull request then we can checkout the head.
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fetch-depth: 2
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# If this run was triggered by a pull request event, then checkout
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# the head of the pull request instead of the merge commit.
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- run: git checkout HEAD^2
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if: ${{ github.event_name == 'pull_request' }}
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# Initializes the CodeQL tools for scanning.
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- name: Initialize CodeQL
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uses: github/codeql-action/init@v1
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with:
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languages: python
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- name: Perform CodeQL Analysis
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uses: github/codeql-action/analyze@v1

‎.gitignore

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.cache/
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cache/
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.coverage
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.coverage.*
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coverage.xml
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htmlcov
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output
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test.txt
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time.txt
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value
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.python-version

‎.mergify.yml

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pull_request_rules:
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- name: Automatic merge on approval and when when GitHub branch protection passes on main
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conditions:
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- "#approved-reviews-by>=1"
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- -draft
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- base=main
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actions:
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merge:
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method: merge
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strict: smart+fasttrack
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pull_request_rules:
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- name: Automatic merge for leadership team members when there are no reviewers and the label is "ready"
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conditions:
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- "#review-requested=0"
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- "#changes-requested-reviews-by<1"
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- -draft
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- base=main
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- author=@leadership
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- label=ready
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actions:
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merge:
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method: merge
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strict: smart+fasttrack

‎.travis.singularity_key.txt

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‎.travis.yml

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