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Merge pull request #1236 from Sage-Bionetworks/develop
Schematic Release v23.6.1
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‎.github/workflows/api_test.yml‎

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# Built from:
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# https://github.com/Sage-Bionetworks/schematic/blob/develop/.github/workflows/test.yml
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name: Test schematic API
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on:
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workflow_dispatch:
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inputs:
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perform_benchmarking:
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required: true
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type: boolean
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description: perform benchmarking test (True) or skip (False)
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jobs:
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test:
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runs-on: ubuntu-latest
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env:
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POETRY_VERSION: 1.2.0
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.9", "3.10"]
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steps:
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#----------------------------------------------
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# check-out repo and set-up python
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#----------------------------------------------
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- name: Check out repository
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uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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#----------------------------------------------
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# install & configure poetry
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#----------------------------------------------
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- name: Install Poetry
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run: |
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curl -sSL https://install.python-poetry.org \
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| python3 - --version ${{ env.POETRY_VERSION }};
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poetry config virtualenvs.create true;
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poetry config virtualenvs.in-project true;
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#----------------------------------------------
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# load cached venv if cache exists
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#----------------------------------------------
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- name: Load cached venv
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id: cached-poetry-dependencies
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uses: actions/cache@v2
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with:
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path: .venv
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key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
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#----------------------------------------------
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# install dependencies if cache does not exist
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#----------------------------------------------
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- name: Install dependencies
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if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
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run: poetry install --no-interaction --no-root --all-extras
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#----------------------------------------------
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# install your root project, if required
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#----------------------------------------------
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- name: Install library
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run: poetry install --no-interaction
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#----------------------------------------------
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# run API test suite
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#----------------------------------------------
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- name: Run all API tests
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env:
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SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }}
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SERVICE_ACCOUNT_CREDS: ${{ secrets.SERVICE_ACCOUNT_CREDS }}
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if: ${{ inputs.perform_benchmarking }}
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run: >
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source .venv/bin/activate;
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pytest -m "schematic_api"
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- name: Run API tests + Exclude Benchmarks
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env:
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SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }}
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SERVICE_ACCOUNT_CREDS: ${{ secrets.SERVICE_ACCOUNT_CREDS }}
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if: ${{ false == inputs.perform_benchmarking }}
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run: >
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source .venv/bin/activate;
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pytest -m "schematic_api and not rule_benchmark"

‎.github/workflows/docker.yml‎

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on:
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push:
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tags: ['v[0-9]*', '[0-9]+.[0-9]+*'] # Match tags that resemble a version
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tags: ['^v\d+\.\d+\.\d+$'] # Match tags that resemble a version, but exclude minior releases. For example, v0.1.1-beta would not get included
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workflow_dispatch:
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jobs:

‎.github/workflows/docker_build.yml‎

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# Taken from https://github.com/Sage-Bionetworks/data_curator/blob/schematic-rest-api/.github/workflows/docker_build.yml
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# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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name: Create and publish a Docker image
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on:
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push:
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tags:
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- '*beta*'
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env:
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REGISTRY: ghcr.io
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IMAGE_PATH: ghcr.io/${{ github.repository }}
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jobs:
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build-and-push-image:
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runs-on: ubuntu-latest
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permissions:
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contents: read
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packages: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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- name: Log in to the Container registry
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uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
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with:
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images: ${{ env.IMAGE_PATH }}
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tags: |
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type=ref,event=branch
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type=ref,event=pr
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type=semver,pattern={{raw}}
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- name: Build and push Docker image
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uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
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with:
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file: schematic_api/Dockerfile
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}

‎.github/workflows/pdoc.yml‎

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run: poetry install --no-interaction --no-root
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# create documentation
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- run: poetry add pdoc@13.0.0
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- run: poetry show pdoc
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- run: poetry run pdoc --docformat google -o docs/schematic schematic/manifest schematic/models schematic/schemas schematic/store schematic/utils schematic/visualization
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‎.github/workflows/publish.yml‎

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on:
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push:
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tags:
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- '*'
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- 'v[1-9][0-9].[0-9]+.[0-9]+'
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branches: [main]
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jobs:

‎.github/workflows/test.yml‎

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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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pull_request:
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branches: ['*']
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workflow_dispatch: # Allow manually triggering the workflow
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concurrency:
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# cancel the current running workflow from the same branch, PR when a new workflow is triggered
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# cancel the current running workflow from the same branch, PR when a new workflow is triggered
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# when the trigger is not a PR but a push, it will use the commit sha to generate the concurrency group
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# {{ github.workflow }}: the workflow name is used to generate the concurrency group. This allows you to have more than one workflows
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# {{ github.ref_type }}: the type of Git ref object created in the repository. Can be either branch or tag
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# {{ github.event.pull_request.number}}: get PR number
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# {{ github.sha }}: full commit sha
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# {{ github.ref_type }}: the type of Git ref object created in the repository. Can be either branch or tag
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# {{ github.event.pull_request.number}}: get PR number
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# {{ github.sha }}: full commit sha
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# credit: https://github.com/Sage-Bionetworks-Workflows/sagetasks/blob/main/.github/workflows/ci.yml
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group: >-
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${{ github.workflow }}-${{ github.ref_type }}-
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test:
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runs-on: ubuntu-latest
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env:
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POETRY_VERSION: 1.2.0rc1
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POETRY_VERSION: 1.2.0
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.7", "3.8", "3.9", "3.10"]
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python-version: ["3.9", "3.10"]
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steps:
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#----------------------------------------------
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# check-out repo and set-up python
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# check-out repo and set-up python
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#----------------------------------------------
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- name: Check out repository
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uses: actions/checkout@v2
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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#----------------------------------------------
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# install & configure poetry
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# install & configure poetry
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#----------------------------------------------
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- name: Install Poetry
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run: |
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curl -sSL https://install.python-poetry.org \
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| python3 - --version ${{ env.POETRY_VERSION }};
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poetry config virtualenvs.create true;
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poetry config virtualenvs.in-project true;
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poetry config virtualenvs.create true;
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poetry config virtualenvs.in-project true;
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#----------------------------------------------
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# load cached venv if cache exists
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# load cached venv if cache exists
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#----------------------------------------------
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- name: Load cached venv
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id: cached-poetry-dependencies
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key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
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#----------------------------------------------
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# install dependencies if cache does not exist
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# install dependencies if cache does not exist
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#----------------------------------------------
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- name: Install dependencies
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if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
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run: poetry install --no-interaction --no-root
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run: poetry install --no-interaction --no-root --all-extras
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#----------------------------------------------
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# install your root project, if required
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#----------------------------------------------
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# install your root project, if required
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#----------------------------------------------
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- name: Install library
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run: poetry install --no-interaction
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#----------------------------------------------
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# perform linting
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#----------------------------------------------
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#----------------------------------------------
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# Disabled until we agree to turn it on
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# - name: Lint with flake8
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# run: |
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#----------------------------------------------
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# check formatting
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#----------------------------------------------
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# Disabled until we agree to turn it on
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# - name: Code formatting with black
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# run: |
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# # run black in check mode
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# # if files are not formatted correctly, the build will not go through
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# black . --check
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- name: Code formatting with black
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run: |
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# ran only on certain files for now
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# add here when checked
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poetry run black schematic/configuration.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py --check
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# run test suite
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# type checking/enforcement
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#----------------------------------------------
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- name: Type checking with mypy
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run: |
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# ran only on certain files for now
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# add here when checked
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poetry run mypy --install-types --non-interactive schematic/configuration.py
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# add here when enforced
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poetry run mypy --disallow-untyped-defs --install-types --non-interactive schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py
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#----------------------------------------------
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# linting
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#----------------------------------------------
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- name: Lint with pylint
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run: |
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# ran only on certain files for now
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# add here when checked
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poetry run pylint schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py
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#----------------------------------------------
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# run test suite
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- name: Run regular tests and rule combination tests
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env:
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run: >
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source .venv/bin/activate;
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pytest --cov-report=term --cov-report=html:htmlcov --cov=schematic/
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-m "not (google_credentials_needed or table_operations)"
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-m "not (google_credentials_needed or schematic_api or table_operations)"
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- name: Run tests
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env:
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SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }}
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pytest --cov-report=term --cov-report=html:htmlcov --cov=schematic/
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-m "not (google_credentials_needed or rule_combos or schematic_api or table_operations)"
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- name: Upload pytest test results
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uses: actions/upload-artifact@v2
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with:

‎.pylintrc‎

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[MAIN]
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load-plugins=pylint.extensions.docparams

‎.readthedocs.yml‎

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python: "3.9"
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jobs:
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post_install:
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- pip install poetry==1.2.0b1
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- pip install poetry==1.2.0
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- poetry config virtualenvs.create false
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- poetry install --with doc
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#Poetry will install my dependencies into the virtualenv created by readthedocs if I set virtualenvs.create=false

‎Dockerfile‎

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PIP_NO_CACHE_DIR=off \
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PIP_DISABLE_PIP_VERSION_CHECK=on \
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PIP_DEFAULT_TIMEOUT=200 \
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POETRY_VERSION=1.2.0rc1
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POETRY_VERSION=1.2.0
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WORKDIR /usr/src/app
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COPY . ./
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RUN poetry install --no-interaction --no-ansi --only-root
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RUN poetry install --only-root

‎README.md‎

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# Installation
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## Installation Requirements
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* Python 3.7.1 or higher
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* Python version 3.9.0≤x<3.11.0
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Note: You need to be a registered and certified user on [`synapse.org`](https://www.synapse.org/), and also have the right permissions to download the Google credentials files from Synapse.
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