linting changes

.flake8

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

.github/ISSUE_TEMPLATE/1-bug.yml

@@ -39,7 +39,9 @@ body:
       value: https://jira.cdisc.org/projects/CORERULES/issues/CORERULES-
   - type: markdown
     attributes:
-      value: "\nIn the next fields, please provide a [Minimal Reproducible Example](https://stackoverflow.com/help/minimal-reproducible-example)."
+      value: |
+        In the next fields, please provide a
+        [Minimal Reproducible Example](https://stackoverflow.com/help/minimal-reproducible-example).
   - type: input
     id: cli_command
     validations:

.github/workflows/build-binary.yml

@@ -27,13 +27,46 @@ jobs:
 
       - name: Build Binary (Linux)
         if: runner.os == 'Linux'
-        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
+        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
       - name: Build Binary (Mac)
         if: runner.os == 'macOS'
-        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
+        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
       - name: Build Binary (Windows)
         if: runner.os == 'Windows'
-        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"
+        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"
       - name: Archive Binary
         uses: actions/upload-artifact@v6
         with:

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

@@ -29,9 +29,12 @@ jobs:
         run: |
           npm i prettier
           npx prettier resources/schema/rule-merged/*.json --write
-      - uses: CatChen/check-git-status-action@7b45cb4ce3e00a8bce4910dc2d5f2785235a6d7e # v2.1.2
+      - uses: CatChen/check-git-status-action@7b45cb4ce3e00a8bce4910dc2d5f2785235a6d7e  # v2.1.2
         with:
           fail-if-not-clean: true
           request-changes-if-not-clean: ${{ github.event_name == 'pull_request' }}
-          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.
+          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.
           targets: resources/schema/rule-merged

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

@@ -16,7 +16,11 @@ permissions:
   contents: read
 
 env:
-  creds: '{"clientId":"${{ vars.AZURE_CLIENT_ID }}","clientSecret":"${{ secrets.AZURE_CLIENT_SECRET }}","subscriptionId":"${{ vars.AZURE_SUBSCRIPTION_ID }}","tenantId":"${{ vars.AZURE_TENANT_ID }}"}'
+  creds: >-
+    {"clientId":"${{ vars.AZURE_CLIENT_ID }}",
+    "clientSecret":"${{ secrets.AZURE_CLIENT_SECRET }}",
+    "subscriptionId":"${{ vars.AZURE_SUBSCRIPTION_ID }}",
+    "tenantId":"${{ vars.AZURE_TENANT_ID }}"}
   functionAppName: cdisc-library-conformance-rules-generator-dev
   PYTHON_VERSION: "3.12"
 
@@ -34,7 +38,8 @@ jobs:
         with:
           app-name: ${{ env.functionAppName }}
           mask-inputs: false
-          app-settings-json: '{"WEBSITE_ENABLE_SYNC_UPDATE_SITE": "1"}' # wait for this step to complete before the webapps-deploy step
+          # wait for this step to complete before the webapps-deploy step
+          app-settings-json: '{"WEBSITE_ENABLE_SYNC_UPDATE_SITE": "1"}'
           general-settings-json: '{"linuxFxVersion": "PYTHON|${{ env.PYTHON_VERSION }}"}'
           slot-name: ${{ vars.AZURE_WEBAPP_SLOT }}
 

.github/workflows/lint-format.yml

@@ -7,32 +7,34 @@ on:
       - main
 permissions:
   contents: read
-
 jobs:
   get_changed_files:
     runs-on: ubuntu-latest
     outputs:
       py: ${{ steps.changes.outputs.py_all_changed_files }}
-      pretty: ${{ steps.changes.outputs.pretty_all_changed_files }}
+      yaml: ${{ steps.changes.outputs.yaml_all_changed_files }}
+      md: ${{ steps.changes.outputs.md_all_changed_files }}
+      json: ${{ steps.changes.outputs.json_all_changed_files }}
     steps:
       - name: Checkout repository
         uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Get changed files
         id: changes
-        uses: tj-actions/changed-files@7dee1b0c1557f278e5c7dc244927139d78c0e22a # v47.0.4
+        uses: tj-actions/changed-files@7dee1b0c1557f278e5c7dc244927139d78c0e22a  # v47.0.4
         with:
           files_yaml: |
             py: 
               - '**.py'
-            pretty: 
-              - '**.json'
-              - '**.md'
+            yaml:
               - '**.yaml'
               - '**.yml'
+            md:
+              - '**.md'
+            json:
+              - '**.json'
           separator: " "
-
   check_python_files:
     runs-on: ubuntu-latest
     needs: get_changed_files
@@ -57,19 +59,50 @@ jobs:
       - name: Run black
         run: |
           black --check ${{needs.get_changed_files.outputs.py}}
-
-  check_prettier_files:
+  check_json_files:
     runs-on: ubuntu-latest
     needs: get_changed_files
-    # only run if there are changed files
-    if: ${{needs.get_changed_files.outputs.pretty}}
+    if: ${{needs.get_changed_files.outputs.json}}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - name: Run json lint
+        run: |
+          for f in ${{needs.get_changed_files.outputs.json}}; do
+            python -m json.tool $f > /dev/null && echo "$f OK" || exit 1
+          done
+  check_yaml_files:
+    runs-on: ubuntu-latest
+    needs: get_changed_files
+    if: ${{needs.get_changed_files.outputs.yaml}}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+      - name: Install yamllint
+        run: |
+          pip install yamllint -c requirements-dev.txt
+      - name: Run yamllint
+        run: |
+          yamllint ${{needs.get_changed_files.outputs.yaml}}
+  check_markdown_files:
+    runs-on: ubuntu-latest
+    needs: get_changed_files
+    if: ${{needs.get_changed_files.outputs.md}}
     steps:
       - name: Checkout repository
         uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - uses: actions/setup-node@v6
-      - name: Run prettier
+      - name: Run markdownlint
         run: |
-          npm i prettier
-          npx prettier --check ${{needs.get_changed_files.outputs.pretty}}
+          npm i markdownlint-cli2
+          npx markdownlint-cli2 ${{needs.get_changed_files.outputs.md}}

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

@@ -13,7 +13,8 @@ jobs:
         with:
           # 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
           # git bash: ssh-keygen -t ed25519 -C "github-actions@cdisc.org"
-          # Add public key (.pub one) as a deploy key at Your repo -> Settings -> Security -> Deploy keys, check "Allow write access".
+          # Add public key (.pub one) as a deploy key at 
+          # Your repo -> Settings -> Security -> Deploy keys, check "Allow write access".
           # Add private key as a secret at Your repo -> Settings -> Security -> Secrets and variables -> Actions
           ssh-key: ${{ secrets.GH_ACTION_PRIVATE_KEY }}
 

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

@@ -21,9 +21,9 @@ jobs:
         uses: actions/checkout@v6
         with:
           # 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
-          # git bash: ssh-keygen -t ed25519 -C "github-actions@cdisc.org"
-          # Add public key (.pub one) as a deploy key at Your repo -> Settings -> Security -> Deploy keys, check "Allow write access".
-          # Add private key as a secret at Your repo -> Settings -> Security -> Secrets and variables -> Actions
+          # Generate SSH key: ssh-keygen -t ed25519 -C "github-actions@cdisc.org"
+          # Add public key as deploy key (Settings -> Security -> Deploy keys, allow write access)
+          # Add private key as secret (Settings -> Security -> Secrets and variables -> Actions)
           ssh-key: ${{ secrets.GH_ACTION_PRIVATE_KEY }}
 
       - name: Set up Python