chore: lint code & non-code files (#182)

.dockerignore

@@ -18,4 +18,4 @@
 # Scripts and tools
 ./scripts
 Makefile
-PULL_REQUEST_TEMPLATE.md
+PULL_REQUEST_TEMPLATE.md

.github/ISSUE_TEMPLATE/general-purpose.md

@@ -1,33 +1,47 @@
-Your issue may already be reported!
-Please search on the [issue tracker](https://github.com/elixir-cloud-aai/TESK/issues) before creating one.
+Your issue may already be reported! Please search on the
+[issue tracker](https://github.com/elixir-cloud-aai/TESK/issues) before creating
+one.
 
 ## Expected Behavior
+
 <!--- If you're describing a bug, tell us what should happen -->
+
 <!--- If you're suggesting a change/improvement, tell us how it should work -->
 
 ## Current Behavior
+
 <!--- If describing a bug, tell us what happens instead of the expected behavior -->
+
 <!--- If suggesting a change/improvement, explain the difference from current behavior -->
 
 ## Possible Solution
+
 <!--- Not obligatory, but suggest a fix/reason for the bug, -->
+
 <!--- or ideas how to implement the addition or change -->
 
 ## Steps to Reproduce (for bugs)
+
 <!--- Provide a link to a live example, or an unambiguous set of steps to -->
+
 <!--- reproduce this bug. Include code to reproduce, if relevant -->
+
+1.
+1.
+1.
 1.
-2.
-3.
-4.
 
 ## Context
+
 <!--- How has this issue affected you? What are you trying to accomplish? -->
+
 <!--- Providing context helps us come up with a solution that is most useful in the real world -->
 
 ## Your Environment
+
 <!--- Include as many relevant details about the environment you experienced the bug in -->
-* Version used:
-* Browser Name and version:
-* Operating System and version (desktop or mobile):
-* Link to your project:
+
+- Version used:
+- Browser Name and version:
+- Operating System and version (desktop or mobile):
+- Link to your project:

.github/actions/setup/poetry/action.yaml

@@ -1,30 +1,32 @@
+---
 name: Setup Python and Poetry Action
-description: Install and configure the system, Python, Poetry and requested deps with cache management.
+description: Configure system, Python, Poetry and deps and cache management.
 
 inputs:
   os:
     default: ubuntu-latest
     description: The operating system to use
   python-version:
-    default: "3.11"
+    default: '3.11'
     description: The version of Python to use
   poetry-version:
-    default: "1.8.2"
+    default: '1.8.2'
     description: The version of Poetry to install
   poetry-install-options:
-    default: ""
+    default: ''
     description: Additional options to pass to poetry install
   poetry-export-options:
-    default: ""
-    description: Options to pass to poetry export for hash generation for cache invalidation
+    default: ''
+    description: Options to pass to poetry export for hash generation for cache
+                 invalidation
 
 runs:
   using: composite
   steps:
-    - uses: "actions/setup-python@v5"
+    - uses: 'actions/setup-python@v5'
       id: setup-python
       with:
-        python-version: "${{ inputs.python-version }}"
+        python-version: '${{ inputs.python-version }}'
 
     - name: Setup pipx environment Variables
       id: pipx-env-setup
@@ -47,33 +49,44 @@ runs:
       uses: actions/cache@v4
       with:
         path: ${{ steps.pipx-env-setup.outputs.pipx-cache-path }}
-        key: ${{ runner.os }}-python-${{ steps.setup-python.outputs.python-version }}-pipx-${{ steps.pipx-env-setup.outputs.pipx-version }}-poetry-${{ inputs.poetry-version }}
+        key: ${{ runner.os }}-python-
+             ${{ steps.setup-python.outputs.python-version }}-
+             pipx-${{ steps.pipx-env-setup.outputs.pipx-version }}-
+             poetry-${{ inputs.poetry-version }}
 
     - name: Install poetry
       if: steps.pipx-cache.outputs.cache-hit != 'true'
       id: install-poetry
       shell: bash
-      run: |-
-        pipx install poetry --python "${{ steps.setup-python.outputs.python-path }}"
+      run: |
+        pipx install poetry \
+        --python "${{ steps.setup-python.outputs.python-path }}"
 
     - name: Read poetry cache location
       id: poetry-cache-location
       shell: bash
-      run: echo "poetry-venv-location=$(poetry config virtualenvs.path)" >> $GITHUB_OUTPUT
+      run: |
+        echo "poetry-venv-location=$(poetry config virtualenvs.path)" \
+        >> $GITHUB_OUTPUT
 
     - name: Generate hash only for required deps
       run: |
-        poetry export ${{ inputs.poetry-export-options }} --format=requirements.txt --output=requirements.txt
-        echo "DEP_HASH=$(sha256sum requirements.txt | cut -d ' ' -f 1)" >> $GITHUB_ENV
+        poetry export ${{ inputs.poetry-export-options }} \
+        --format=requirements.txt --output=requirements.txt
+        echo "DEP_HASH=$(sha256sum requirements.txt | cut -d ' ' -f 1)" \
+         >> $GITHUB_ENV
       shell: bash
 
     - uses: actions/cache@v4
       name: Poetry cache
       with:
         path: ${{ steps.poetry-cache-location.outputs.poetry-venv-location }}
-        key: ${{ runner.os }}-[python-${{ steps.setup-python.outputs.python-version }}]-[${{ env.DEP_HASH }}]-[${{ inputs.poetry-install-options }}]
+        key: ${{ runner.os }}-[python-
+             ${{ steps.setup-python.outputs.python-version }}]-[
+             ${{ env.DEP_HASH }}]-[${{ inputs.poetry-install-options }}]
 
-    - name: "Poetry install"
+    - name: 'Poetry install'
       if: steps.poetry-cache.outputs.cache-hit != 'true'
       shell: bash
-      run: poetry install ${{ inputs.poetry-install-options }} --no-interaction
+      run: poetry install ${{ inputs.poetry-install-options }} --no-interaction
+...

.github/workflows/build_and_publish_charts.yaml

@@ -1,3 +1,4 @@
+---
 name: Build and Publish Helm Charts
 
 on:
@@ -18,12 +19,12 @@ jobs:
         uses: actions/[email protected]
         with:
           fetch-depth: 0
-            
+
       - name: Create k3s Cluster
         uses: debianmaster/[email protected]
         with:
           version: 'latest'
-            
+
       - name: Create namespace
         run: kubectl create ns tesk
 
@@ -67,15 +68,16 @@ jobs:
         uses: actions/[email protected]
         with:
           fetch-depth: 0
-            
+
       - name: Configure Git
         run: |
           git config user.name "$GITHUB_ACTOR"
           git config user.email "[email protected]"
-    
+
       - name: Run chart-releaser
         uses: helm/[email protected]
         with:
           skip_existing: true
         env:
           CR_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+...

.github/workflows/build_and_publish_filer.yaml

@@ -1,9 +1,10 @@
+---
 name: Build and Publish Filer
 
 on:
   push:
-    branches: [ 'testing-gh-action' ]
-    tags: [ '*' ]
+    branches: ['testing-gh-action']
+    tags: ['*']
 
   workflow_dispatch:
     inputs:
@@ -38,7 +39,7 @@ jobs:
         with:
           images: |
             elixircloud/${{ github.workflow }}
-      
+
       - name: Build and push Docker images
         uses: docker/build-push-action@v3
         with:
@@ -47,4 +48,4 @@ jobs:
           file: ./deployment/containers/filer.Dockerfile
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
-
+...

.github/workflows/build_and_publish_taskmaster.yaml

@@ -1,9 +1,10 @@
+---
 name: Build and Publish Taskmaster
 
 on:
   push:
-    branches: [ 'testing-gh-action' ]
-    tags: [ '*' ]
+    branches: ['testing-gh-action']
+    tags: ['*']
 
   workflow_dispatch:
     inputs:
@@ -37,7 +38,7 @@ jobs:
         with:
           images: |
             elixircloud/${{ github.workflow }}
-      
+
       - name: Build and push Docker images
         uses: docker/build-push-action@v3
         with:
@@ -46,4 +47,4 @@ jobs:
           file: ./deployment/containers/taskmaster.Dockerfile
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
-
+...

.github/workflows/code_quality.yaml

@@ -1,3 +1,4 @@
+---
 name: Code Quality
 
 on:
@@ -80,3 +81,4 @@ jobs:
 
       - name: Check spellings
         run: poetry run typos .
+...

.github/workflows/code_test_unit.yaml

@@ -1,3 +1,4 @@
+---
 name: Code Test Unit
 
 on:
@@ -25,7 +26,11 @@ jobs:
           poetry-export-options: "--with=test"
 
       - name: Run tests and generate coverage as test_unit.xml
-        run: poetry run pytest --cov-report term --cov-report xml:test_unit.xml --cov=tests/test_unit
+        run: |
+          poetry run pytest \
+            --cov-report term \
+            --cov-report xml:test_unit.xml \
+            --cov=tests/test_unit
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
@@ -35,3 +40,4 @@ jobs:
           files: ./test_unit.xml
           fail_ci_if_error: true
           verbose: true
+...

.github/workflows/validation_pr.yaml

@@ -1,3 +1,4 @@
+---
 name: PR Evaluation
 
 on:
@@ -6,10 +7,11 @@ on:
     branches: ['main']
 
 jobs:
-  semantic_pr: 
+  semantic_pr:
     name: Semantic PR title
     runs-on: ubuntu-latest
-    if: ${{ github.event.action != 'edited' || github.event.changes.title != null }}
+    if: ${{ github.event.action != 'edited' ||
+            github.event.changes.title != null }}
     steps:
       - uses: amannn/action-semantic-pull-request@v5
         env:
@@ -31,7 +33,8 @@ jobs:
           subjectPatternError: |
             The subject "{subject}" found in the pull request title "{title}"
             didn't match the configured pattern. Please ensure that the subject
-            doesn't start with an uppercase character & not have more than 50 characters.
+            doesn't start with an uppercase character & not have more than 50
+            characters.
 
   detect-unresolved-conflicts:
     name: Detect unresolved merge conflicts
@@ -41,5 +44,6 @@ jobs:
       - uses: actions/checkout@v3
       - name: List files with merge conflict markers
         run: git --no-pager grep "<<<<<<<" ":(exclude).github/" || true
-      - name: Fail or succeed job if any files with merge conflict markers have been checked in
+      - name: Fail or succeed job if any files with merge conflict markers
         run: exit $(git grep "<<<<<<<" ":(exclude).github/" | wc --lines)
+...

.github/workflows/vulnerabilities.yaml

@@ -1,3 +1,4 @@
+---
 name: Vulnerability Test
 
 on:
@@ -44,3 +45,4 @@ jobs:
 
       - name: Check dependency vulnerabilities with safety
         run: poetry run safety check --full-report
+...

.gitignore

@@ -173,4 +173,4 @@ poetry.toml
 # LSP config files
 pyrightconfig.json
 
-# End of https://www.toptal.com/developers/gitignore/api/python
+# End of https://www.toptal.com/developers/gitignore/api/python

.safety-policy.yml

@@ -1,3 +1,4 @@
+---
 version: '3.0'
 
 scanning-settings:
@@ -9,15 +10,15 @@ scanning-settings:
 
 security:
   ignore-vulnerabilities:
-      65213:
-          reason: 'Fix is downgrading the pyopenssl package to 21.0.0, doing that breaks all the test.'
-          expires: '2025-5-18'
-      67599:
-          reason: 'No fix available.'
-          expires: '2025-5-18'
-      70612:
-          reason: 'No fix available.'
-          expires: '2025-5-18'
+    65213:
+      reason: 'Need the pyopenssl== 21.0.0, which breaks the test.'
+      expires: '2025-5-18'
+    67599:
+      reason: 'No fix available.'
+      expires: '2025-5-18'
+    70612:
+      reason: 'No fix available.'
+      expires: '2025-5-18'
 
 report:
   dependency-vulnerabilities:
@@ -28,7 +29,6 @@ report:
         unpinned-requirements: true
       cvss-severity: []
 
-
 fail-scan-with-exit-code:
   dependency-vulnerabilities:
     enabled: true
@@ -46,4 +46,4 @@ security-updates:
   dependency-vulnerabilities:
     auto-security-updates-limit:
       - patch
-
+...

Makefile

@@ -153,7 +153,7 @@ run-service:
 		exit 1; \
 	fi
 
-.PHONY: clean-service-image 
+.PHONY: clean-service-image
 clean-service-image:
 		@if [ -x "$(BUILDAH_CMD)" ]; then \
 				if $(BUILDAH_CMD) inspect $(ELIXIR_CLOUD_REGISTRY)/tesk-core-$(IMAGE):$(TAG) > /dev/null 2>&1; then \