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SFJohnson24RamilCDISC
SFJohnson24
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RamilCDISC
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linting changes (#1748)
Co-authored-by: RamilCDISC <113539111+RamilCDISC@users.noreply.github.com>
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‎.flake8‎

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@@ -6,5 +6,6 @@ exclude = .github,
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.pytest_cache,
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cdisc_rules_engine/resources,
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venv,
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.venv,
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build,
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dist

‎.github/ISSUE_TEMPLATE/1-bug.yml‎

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value: https://jira.cdisc.org/projects/CORERULES/issues/CORERULES-
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- type: markdown
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attributes:
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value: "\nIn the next fields, please provide a [Minimal Reproducible Example](https://stackoverflow.com/help/minimal-reproducible-example)."
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value: |
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In the next fields, please provide a
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[Minimal Reproducible Example](https://stackoverflow.com/help/minimal-reproducible-example).
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- type: input
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id: cli_command
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validations:

‎.github/workflows/build-binary.yml‎

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- name: Build Binary (Linux)
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if: runner.os == 'Linux'
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run: pyinstaller --onedir --contents-directory "." core.py --icon=resources/assets/CORE_logo_sm.ico --dist ./dist/output/${{ inputs.name }} --collect-submodules pyreadstat --add-data=$pythonLocation/lib/python3.12/site-packages/xmlschema/schemas:xmlschema/schemas --add-data=resources/cache:resources/cache --add-data=resources/templates:resources/templates --add-data=resources/schema:resources/schema --add-data=resources/datasets:resources/datasets --add-data=resources/jsonata:resources/jsonata
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run: >-
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pyinstaller --onedir --contents-directory "." core.py
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--icon=resources/assets/CORE_logo_sm.ico
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--dist ./dist/output/${{ inputs.name }}
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--collect-submodules pyreadstat
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--add-data=$pythonLocation/lib/python3.12/site-packages/xmlschema/schemas:xmlschema/schemas
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--add-data=resources/cache:resources/cache
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--add-data=resources/templates:resources/templates
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--add-data=resources/schema:resources/schema
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--add-data=resources/datasets:resources/datasets
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--add-data=resources/jsonata:resources/jsonata
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- name: Build Binary (Mac)
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if: runner.os == 'macOS'
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run: pyinstaller --onedir --contents-directory "." core.py --icon=resources/assets/CORE_logo_sm.icns --dist ./dist/output/${{ inputs.name }} --collect-submodules pyreadstat --add-data=$pythonLocation/lib/python3.12/site-packages/xmlschema/schemas:xmlschema/schemas --add-data=resources/cache:resources/cache --add-data=resources/templates:resources/templates --add-data=resources/schema:resources/schema --add-data=resources/datasets:resources/datasets --add-data=resources/jsonata:resources/jsonata
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run: >-
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pyinstaller --onedir --contents-directory "." core.py
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--icon=resources/assets/CORE_logo_sm.icns
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--dist ./dist/output/${{ inputs.name }}
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--collect-submodules pyreadstat
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--add-data=$pythonLocation/lib/python3.12/site-packages/xmlschema/schemas:xmlschema/schemas
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--add-data=resources/cache:resources/cache
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--add-data=resources/templates:resources/templates
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--add-data=resources/schema:resources/schema
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--add-data=resources/datasets:resources/datasets
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--add-data=resources/jsonata:resources/jsonata
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- name: Build Binary (Windows)
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if: runner.os == 'Windows'
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run: pyinstaller --onedir --contents-directory "." core.py --icon=resources/assets/CORE_logo_sm.ico --dist ./dist/output/${{ inputs.name }} --collect-submodules pyreadstat --add-data="$env:pythonLocation\Lib\site-packages\xmlschema\schemas;xmlschema/schemas" --hidden-import numpy --hidden-import numpy.core._methods --hidden-import numpy.lib.format --add-data="resources/cache;resources/cache" --add-data="resources/templates;resources/templates" --add-data="resources/schema;resources/schema" --add-data="resources/datasets;resources/datasets" --add-data="resources/jsonata;resources/jsonata"
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run: >-
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pyinstaller --onedir --contents-directory "." core.py
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--icon=resources/assets/CORE_logo_sm.ico
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--dist ./dist/output/${{ inputs.name }}
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--collect-submodules pyreadstat
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--add-data="$env:pythonLocation\Lib\site-packages\xmlschema\schemas;xmlschema/schemas"
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--hidden-import numpy
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--hidden-import numpy.core._methods
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--hidden-import numpy.lib.format
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--add-data="resources/cache;resources/cache"
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--add-data="resources/templates;resources/templates"
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--add-data="resources/schema;resources/schema"
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--add-data="resources/datasets;resources/datasets"
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--add-data="resources/jsonata;resources/jsonata"
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- name: Archive Binary
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uses: actions/upload-artifact@v6
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with:

‎.github/workflows/check-schema-markdown.yml‎

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run: |
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npm i prettier
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npx prettier resources/schema/rule-merged/*.json --write
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- uses: CatChen/check-git-status-action@7b45cb4ce3e00a8bce4910dc2d5f2785235a6d7e # v2.1.2
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- uses: CatChen/check-git-status-action@7b45cb4ce3e00a8bce4910dc2d5f2785235a6d7e # v2.1.2
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with:
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fail-if-not-clean: true
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request-changes-if-not-clean: ${{ github.event_name == 'pull_request' }}
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request-changes-comment: Updated schema has not been merged with markdown descriptions. Please run the "Merge Schema with Markdown Descriptions" workflow to update the merged schema files.
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request-changes-comment: >-
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Updated schema has not been merged with markdown descriptions.
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Please run the "Merge Schema with Markdown Descriptions" workflow
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to update the merged schema files.
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targets: resources/schema/rule-merged

‎.github/workflows/deploy-rule-tester.yml‎

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contents: read
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env:
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creds: '{"clientId":"${{ vars.AZURE_CLIENT_ID }}","clientSecret":"${{ secrets.AZURE_CLIENT_SECRET }}","subscriptionId":"${{ vars.AZURE_SUBSCRIPTION_ID }}","tenantId":"${{ vars.AZURE_TENANT_ID }}"}'
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creds: >-
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{"clientId":"${{ vars.AZURE_CLIENT_ID }}",
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"clientSecret":"${{ secrets.AZURE_CLIENT_SECRET }}",
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"subscriptionId":"${{ vars.AZURE_SUBSCRIPTION_ID }}",
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"tenantId":"${{ vars.AZURE_TENANT_ID }}"}
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functionAppName: cdisc-library-conformance-rules-generator-dev
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PYTHON_VERSION: "3.12"
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with:
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app-name: ${{ env.functionAppName }}
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mask-inputs: false
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app-settings-json: '{"WEBSITE_ENABLE_SYNC_UPDATE_SITE": "1"}' # wait for this step to complete before the webapps-deploy step
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# wait for this step to complete before the webapps-deploy step
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app-settings-json: '{"WEBSITE_ENABLE_SYNC_UPDATE_SITE": "1"}'
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general-settings-json: '{"linuxFxVersion": "PYTHON|${{ env.PYTHON_VERSION }}"}'
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slot-name: ${{ vars.AZURE_WEBAPP_SLOT }}
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‎.github/workflows/lint-format.yml‎

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- main
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permissions:
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contents: read
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jobs:
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get_changed_files:
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runs-on: ubuntu-latest
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outputs:
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py: ${{ steps.changes.outputs.py_all_changed_files }}
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pretty: ${{ steps.changes.outputs.pretty_all_changed_files }}
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yaml: ${{ steps.changes.outputs.yaml_all_changed_files }}
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md: ${{ steps.changes.outputs.md_all_changed_files }}
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json: ${{ steps.changes.outputs.json_all_changed_files }}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v6
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with:
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fetch-depth: 0
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- name: Get changed files
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id: changes
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uses: tj-actions/changed-files@7dee1b0c1557f278e5c7dc244927139d78c0e22a # v47.0.4
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uses: tj-actions/changed-files@7dee1b0c1557f278e5c7dc244927139d78c0e22a # v47.0.4
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with:
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files_yaml: |
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py:
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- '**.py'
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pretty:
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- '**.json'
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- '**.md'
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yaml:
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- '**.yaml'
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- '**.yml'
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md:
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- '**.md'
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json:
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- '**.json'
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separator: " "
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check_python_files:
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runs-on: ubuntu-latest
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needs: get_changed_files
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- name: Run black
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run: |
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black --check ${{needs.get_changed_files.outputs.py}}
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check_prettier_files:
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check_json_files:
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runs-on: ubuntu-latest
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needs: get_changed_files
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# only run if there are changed files
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if: ${{needs.get_changed_files.outputs.pretty}}
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if: ${{needs.get_changed_files.outputs.json}}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v6
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with:
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fetch-depth: 0
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- name: Run json lint
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run: |
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for f in ${{needs.get_changed_files.outputs.json}}; do
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python -m json.tool $f > /dev/null && echo "$f OK" || exit 1
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done
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check_yaml_files:
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runs-on: ubuntu-latest
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needs: get_changed_files
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if: ${{needs.get_changed_files.outputs.yaml}}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v6
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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@v6
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with:
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python-version: "3.12"
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- name: Install yamllint
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run: |
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pip install yamllint -c requirements-dev.txt
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- name: Run yamllint
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run: |
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yamllint ${{needs.get_changed_files.outputs.yaml}}
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check_markdown_files:
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runs-on: ubuntu-latest
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needs: get_changed_files
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if: ${{needs.get_changed_files.outputs.md}}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v6
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with:
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fetch-depth: 0
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- uses: actions/setup-node@v6
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- name: Run prettier
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- name: Run markdownlint
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run: |
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npm i prettier
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npx prettier --check ${{needs.get_changed_files.outputs.pretty}}
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npm i markdownlint-cli2
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npx markdownlint-cli2 ${{needs.get_changed_files.outputs.md}}

‎.github/workflows/prerelease-update-cache.yml‎

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with:
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# https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key
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# git bash: ssh-keygen -t ed25519 -C "github-actions@cdisc.org"
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# Add public key (.pub one) as a deploy key at Your repo -> Settings -> Security -> Deploy keys, check "Allow write access".
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# Add public key (.pub one) as a deploy key at
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# Your repo -> Settings -> Security -> Deploy keys, check "Allow write access".
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# Add private key as a secret at Your repo -> Settings -> Security -> Secrets and variables -> Actions
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ssh-key: ${{ secrets.GH_ACTION_PRIVATE_KEY }}
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‎.github/workflows/prerelease-update-version.yml‎

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uses: actions/checkout@v6
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with:
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# https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key
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# git bash: ssh-keygen -t ed25519 -C "github-actions@cdisc.org"
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# Add public key (.pub one) as a deploy key at Your repo -> Settings -> Security -> Deploy keys, check "Allow write access".
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# Add private key as a secret at Your repo -> Settings -> Security -> Secrets and variables -> Actions
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# Generate SSH key: ssh-keygen -t ed25519 -C "github-actions@cdisc.org"
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# Add public key as deploy key (Settings -> Security -> Deploy keys, allow write access)
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# Add private key as secret (Settings -> Security -> Secrets and variables -> Actions)
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ssh-key: ${{ secrets.GH_ACTION_PRIVATE_KEY }}
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- name: Set up Python

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