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Initial import.
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‎.dockerignore‎

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*.pyc
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__pycache__
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default.cfg.template
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.env
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example.env
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example.cfg
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.github

‎.github/dependabot.yml‎

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version: 2
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updates:
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# Maintain dependencies for GitHub Actions
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "daily"

‎.github/workflows/publish-docker-images.yml‎

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name: Publish docker images
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on:
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push:
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branches:
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- main
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release:
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types: [published]
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jobs:
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publish-pypi:
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name: Publish script-runner to pypi
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runs-on: ubuntu-latest
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steps:
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- name: Publish a Python distribution to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}
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publish-docker:
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name: Publish script-runner to dockerhub
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runs-on: ubuntu-latest
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steps:
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- name: Check out the repo
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uses: actions/checkout@v2
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- name: Prepare
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id: prep
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run: |
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PYTHON_IMAGE_TAG=alpine
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DOCKER_IMAGE=labflow/swabseq-analysis-server
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VERSION=latest
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if [[ $GITHUB_REF == refs/tags/* ]]; then
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VERSION=${GITHUB_REF#refs/tags/}
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elif [[ $GITHUB_REF == refs/heads/* ]]; then
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VERSION=$(echo ${GITHUB_REF#refs/heads/} | sed -r 's#/+#-#g')
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elif [[ $GITHUB_REF == refs/pull/* ]]; then
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VERSION=pr-${{ github.event.number }}
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fi
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TAGS="${DOCKER_IMAGE}:${PYTHON_IMAGE_TAG}-latest,${DOCKER_IMAGE}:${PYTHON_IMAGE_TAG}-${VERSION}"
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if [ "${{ github.event_name }}" = "push" ]; then
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TAGS="$TAGS,${DOCKER_IMAGE}:${PYTHON_IMAGE_TAG}-sha-${GITHUB_SHA::8}"
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fi
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echo ::set-output name=version::${VERSION}
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echo ::set-output name=tags::${TAGS}
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echo ::set-output name=created::$(date -u +'%Y-%m-%dT%H:%M:%SZ')
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echo ::set-output name=hashtag::"sha-${GITHUB_SHA::8}"
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echo ::set-output name=pyversion::"${PYTHON_IMAGE_TAG}"
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- name: Set up Docker Buildx
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id: buildx
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uses: docker/setup-buildx-action@v1
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- name: Cache Docker layers
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uses: actions/cache@v2.1.4
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with:
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path: /tmp/.buildx-cache
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key: ${{ runner.os }}-buildx-${{ github.sha }}
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restore-keys: |
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${{ runner.os }}-buildx-
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- name: Login to DockerHub
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if: github.event_name != 'pull_request'
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uses: docker/login-action@v1
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with:
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username: ${{ secrets.DOCKER_USERNAME }}
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password: ${{ secrets.DOCKER_PASSWORD }}
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- name: Push to Docker Hub
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uses: docker/build-push-action@v2
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with:
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context: ./docker
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file: ./Dockerfile
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builder: ${{ steps.buildx.outputs.name }}
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push: ${{ github.event_name != 'pull_request' }}
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tags: ${{ steps.prep.outputs.tags }}
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cache-from: type=local,src=/tmp/.buildx-cache
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cache-to: type=local,dest=/tmp/.buildx-cache
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labels: |
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org.opencontainers.image.source=${{ github.event.repository.clone_url }}
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org.opencontainers.image.created=${{ steps.prep.outputs.created }}
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org.opencontainers.image.revision=${{ github.sha }}
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build-args: |
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SCRIPT_RUNNER_VERSION=${{ steps.prep.outputs.version }}
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PYTHON_IMAGE_TAG=${{ steps.prep.outputs.pyversion }}

‎.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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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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cover/
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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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.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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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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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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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# Don't commit secrets!
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*.env
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!example.env
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.basespace/*
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!.basespace/.gitkeep
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.Rproj.user
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swabseq-analysis.Rproj
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# VSCode
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.vscode/
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# This is autogenerated during CD
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VERSION

‎LICENSE‎

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MIT License
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Copyright (c) 2021 LabGrid and Octant Bio and Kyle Kovary and Joshua Bloom and Nate Lubock and Scott Simpkins and Aaron Cooper
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎Pipfile‎

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[[source]]
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url = "https://pypi.python.org/simple"
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verify_ssl = true
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name = "pypi"
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[packages]
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celery = "*"
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flask = "*"
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flask-cors = "*"
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flask-restx = "*"
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jsonpath-ng = "*"
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python-jose = "*"
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pydantic = "*"
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redis = "*"
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typing_extensions = "*"
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Werkzeug = "*"
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gunicorn = "*"
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[dev-packages]
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pylint = "*"
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pylint-flask = "*"
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pydocstyle = "*"
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pipenv-setup = "*"

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