chore: lint code & non-code files

.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/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
 
@@ -67,12 +68,12 @@ 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:

.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 +48,3 @@ 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 +47,3 @@ 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:
@@ -99,4 +100,4 @@ jobs:
         run: poetry install --only=lint --no-interaction --no-root
 
       - name: Check spellings
-        run: poetry run typos . 
+        run: poetry run typos .

.github/workflows/code_test_unit.yaml

@@ -1,3 +1,4 @@
+---
 name: Code Test Unit
 
 on:
@@ -30,7 +31,11 @@ jobs:
         run: poetry install --only=test --no-interaction
 
       - 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

.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 +44,9 @@ 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)
+
+  # TODO: Add when cache PR is merged
+  # pre-commit:
+  #   name: Pre-commit checks

.github/workflows/vulnerabilities.yaml

@@ -1,3 +1,4 @@
+---
 name: Vulnerability Test
 
 on:

.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

.pre-commit-config.yaml

@@ -0,0 +1,59 @@
+---
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+# Common commands:
+# pre-commit install
+# pre-commit autoupdate
+# pre-commit run --all-files --hook-stage commit
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-builtin-literals
+      - id: check-added-large-files
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-toml
+      - id: check-vcs-permalinks
+      - id: debug-statements
+      - id: destroyed-symlinks
+      - id: detect-private-key
+        exclude: |
+          (?x)^(
+            deployment/charts/tesk/templates/.*\.yaml|deployment/charts/tesk/tls_secret_name\.yml-TEMPLATE
+          )$
+      - id: double-quote-string-fixer
+      - id: fix-byte-order-marker
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=auto]
+      - id: trailing-whitespace
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.5
+    hooks:
+      - id: ruff
+      - id: ruff-format
+        args: [--check]
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.17
+    hooks:
+      - id: mdformat
+        additional_dependencies:
+          - mdformat-config
+          - mdformat-black
+          - mdformat-frontmatter
+        args: [--wrap=80]
+        # exclude: _.+\.md|CHANGELOG\.md  # Add when changelog is implemented
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.35.1
+    hooks:
+      - id: yamllint
+        exclude: ^deployment/charts
+  - repo: https://github.com/pappasam/toml-sort
+    rev: v0.23.1
+    hooks:
+      - id: toml-sort-fix
+        args: [--in-place, --all, --trailing-comma-inline-array]
+        exclude: poetry\.lock

.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 +46,3 @@ security-updates:
   dependency-vulnerabilities:
     auto-security-updates-limit:
       - patch
-

.yamllint.yaml

@@ -0,0 +1,10 @@
+---
+# https://yamllint.readthedocs.io/en/stable/configuration.html#default-configuration
+extends: default
+
+ignore: |
+  ^deployment/charts
+
+rules:
+  document-start:
+    level: error

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 \