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Merge branch 'main' into 873-metadata-entry-not-filled-should-show-null
2 parents f1db5fe + 898bcd2 commit 209c413

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‎.dockerignore‎

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.venv

‎.flake8‎

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[flake8]
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max-line-length = 180
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extend-ignore = E203, E266, E501, W503, E741, E711, E712
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exclude = .svn,CVS,.bzr,.hg,.git,__pycache__,venv/*,src/*,.rst,build
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max-complexity=16

‎.github/workflows/backend.yaml‎

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uses: docker/setup-buildx-action@v2
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-
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name: Checkout
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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-
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name: Login to DockerHub
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if: github.event_name != 'pull_request'
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name: Build and push
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uses: docker/build-push-action@v3
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with:
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context: ./backend
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context: .
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file: ./backend/Dockerfile
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platforms: linux/amd64,linux/arm64
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push: ${{ github.event_name != 'pull_request' }}
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tags: ${{ steps.backendMeta.outputs.tags }}
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name: Build and push
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uses: docker/build-push-action@v3
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with:
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context: ./backend
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context: .
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file: ./backend/heartbeat.Dockerfile
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platforms: linux/amd64,linux/arm64
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push: ${{ github.event_name != 'pull_request' }}
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tags: ${{ steps.heartbeatMeta.outputs.tags }}
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file: ./backend/heartbeat.Dockerfile
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labels: ${{ steps.heartbeatMeta.outputs.labels }}
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-
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name: Build and push
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uses: docker/build-push-action@v3
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with:
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context: ./backend
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context: .
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file: ./backend/messages.Dockerfile
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platforms: linux/amd64,linux/arm64
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push: ${{ github.event_name != 'pull_request' }}
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tags: ${{ steps.messagesMeta.outputs.tags }}
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file: ./backend/messages.Dockerfile
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labels: ${{ steps.messagesMeta.outputs.labels }}
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labels: ${{ steps.messagesMeta.outputs.labels }}

‎.github/workflows/black.yml‎

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: psf/black@stable
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- uses: psf/black@23.3.0

‎.github/workflows/codegen.yaml‎

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timeout-minutes: 10
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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node:
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- "14"
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steps:
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- name: Set up QEMU
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uses: docker/setup-qemu-action@v2
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v2
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- name: Checkout
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Build Backend no push
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uses: docker/build-push-action@v3
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with:
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context: ./backend
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context: .
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file: ./backend/Dockerfile
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platforms: linux/amd64
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push: false
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tags: github-action
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- name: Start containers
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run: docker-compose -f "docker-compose.test.yml" up -d --build
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run: docker compose -f "docker-compose.yml" up -d --build
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# setup node
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- name: Install node
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uses: actions/setup-node@v3
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with:
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node-version: ${{ matrix.node }}
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node-version: 16
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- name: Install dependencies
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working-directory: frontend
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- name: Run Codegen
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working-directory: frontend
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run: npm run codegen:v2:test
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- name: Verify Changed files
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uses: tj-actions/verify-changed-files@v14
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id: verify-changed-files
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- name: Stop containers
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if: always()
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run: docker-compose -f "docker-compose.test.yml" down
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run: docker compose -f "docker-compose.yml" down

‎.github/workflows/helm-release.yaml‎

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name: Release Helm Charts
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defaults:
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run:
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working-directory: deployments/kubernetes/charts/clowder2
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on:
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release:
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types: [published]
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env:
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MAIN_REPO: clowder-framework/clowder2
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jobs:
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release:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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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: Get dependencies
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run: |
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helm repo add bitnami https://charts.bitnami.com/bitnami
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helm repo add ncsa https://opensource.ncsa.illinois.edu/charts
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helm dep build
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- name: Get release info
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id: release_info
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run: |
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version="$(awk '/^version:/ { print $2} ' Chart.yaml)"
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changelog="$(sed -e "1,/^### ${version}/d" -e "/^###/,\$d" -e '/^$/d' README.md)"
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changelog="${changelog//'%'/'%25'}"
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changelog="${changelog//$'\n'/'%0A'}"
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changelog="${changelog//$'\r'/'%0D'}"
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echo "version=${version}" >> $GITHUB_ENV
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echo "changelog=${changelog}" >> $GITHUB_ENV
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echo "version: ${version}"
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echo "changelog: ${changelog}"
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- name: Print Github Info
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run: |
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echo "github.event_name: ${{ github.event_name }}"
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echo "github.repository: ${{ github.repository }}"
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echo "github.ref: ${{ github.ref }}"
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- name: run helm template
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run: helm template .
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- name: Publish to NCSA OpenSource
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if: |
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github.event_name != 'pull_request'
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&& github.repository == env.MAIN_REPO
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uses: bsord/[email protected]
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with:
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username: ${{ secrets.HELM_USERNAME }}
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password: ${{ secrets.HELM_PASSWORD }}
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registry-url: "https://opensource.ncsa.illinois.edu/charts"
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chart-folder: "deployments/kubernetes/charts/clowder2"
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force: true

‎.github/workflows/pytest.yml‎

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name: Pytest
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on: push
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defaults:
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run:
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working-directory: backend
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jobs:
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test:
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uv-example:
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name: python
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runs-on: ubuntu-latest
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timeout-minutes: 10
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steps:
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- name: Check out repository code
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uses: actions/checkout@v2
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.9"
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- name: Install pipenv
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run: |
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python -m pip install --upgrade pipenv wheel
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- uses: actions/checkout@v4
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- id: cache-pipenv
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uses: actions/cache@v3
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with:
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path: ~/.local/share/virtualenvs
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key: ${{ runner.os }}-pipenv-${{ hashFiles('**/Pipfile.lock') }}
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- name: Install uv
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uses: astral-sh/setup-uv@v5
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- name: Install dependencies
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if: steps.cache-pipenv.outputs.cache-hit != 'true'
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run: |
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pipenv install --deploy --dev
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- name: Install the project
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run: uv sync --all-extras --dev
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- name: Start env
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run: docker-compose -f ../docker-compose.dev.yml up -d
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run: docker compose -f ../docker-compose.dev.yml up -d
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# wait for docker containers to come up before running tests
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- name: Sleep for 60 seconds
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run: sleep 60s
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shell: bash
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- name: Run test suite
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run: |
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pipenv run pytest -v
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- name: Run tests
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run: uv run pytest app/tests/

‎.gitignore‎

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# ignore clowder chart deps
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deployments/kubernetes/charts/clowder2/charts
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deployments/kubernetes/charts/clowder2/*clowder2-software-dev.yaml
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*secret*.yaml
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# Environments
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.env
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# faker
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official.csv
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fact.png
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jupyterhub/.env-dev

‎.pre-commit-config.yaml‎

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repos:
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- repo: local
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hooks:
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- id: extract-openapi
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name: extract-openapi
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entry: python backend/extract-openapi.py app.main:app
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language: system
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pass_filenames: false
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- repo: local
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hooks:
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- id: generate-frontend-api-client
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name: generate-frontend-api-client
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entry: bash -c 'cd frontend && npm run codegen:v2:file'
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language: system
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pass_filenames: false
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- repo: local
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hooks:
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- id: eslint
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name: eslint
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entry: bash -c "cd frontend && npx eslint --fix src"
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language: system
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- repo: local
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hooks:
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- id: prettier
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name: prettier
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entry: bash -c "cd frontend && npx prettier src --write"
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language: system
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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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- id: check-yaml
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exclude: deployments/kubernetes/charts
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- id: end-of-file-fixer
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exclude: 'openapi.json|frontend/src/openapi/v2/'
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- id: trailing-whitespace
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exclude: 'openapi.json|frontend/src/openapi/v2/'
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- repo: https://github.com/astral-sh/ruff-pre-commit
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# Ruff version.
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rev: v0.9.4
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hooks:
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# Run the linter.
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- id: ruff
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args: [ --fix ]
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# Run the formatter.
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- id: ruff-format

‎.python-version‎

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3.10

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