Merge pull request #174 from kbase/remove_black_autocommit

Removing the black autocommit action and doing some general housekeep…

.github/workflows/codacy.yaml

@@ -9,41 +9,41 @@
 name: Codacy Security Scan
 
 on:
-  workflow_call:
+    workflow_call:
 
 permissions:
-  contents: read
+    contents: read
 
 jobs:
-  codacy-security-scan:
-    permissions:
-      contents: read # for actions/checkout to fetch code
-      security-events: write # for github/codeql-action/upload-sarif to upload SARIF results
-    name: Codacy Security Scan
-    runs-on: ubuntu-latest
-    steps:
-      # Checkout the repository to the GitHub Actions runner
-      - name: Checkout code
-        uses: actions/checkout@v3
+    codacy-security-scan:
+        permissions:
+            contents: read # for actions/checkout to fetch code
+            security-events: write # for github/codeql-action/upload-sarif to upload SARIF results
+        name: Codacy Security Scan
+        runs-on: ubuntu-latest
+        steps:
+            # Checkout the repository to the GitHub Actions runner
+            - name: Checkout code
+              uses: actions/checkout@v4
 
-      # Execute Codacy Analysis CLI and generate a SARIF output with the security issues identified during the analysis
-      - name: Run Codacy Analysis CLI
-        uses: codacy/codacy-analysis-cli-action@5cc54a75f9ad88159bb54046196d920e40e367a5
-        with:
-          # Check https://github.com/codacy/codacy-analysis-cli#project-token to get your project token from your Codacy repository
-          # You can also omit the token and run the tools that support default configurations
-          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
-          verbose: true
-          output: results.sarif
-          format: sarif
-          # Adjust severity of non-security issues
-          gh-code-scanning-compat: true
-          # Force 0 exit code to allow SARIF file generation
-          # This will handover control about PR rejection to the GitHub side
-          max-allowed-issues: 2147483647
+            # Execute Codacy Analysis CLI and generate a SARIF output with the security issues identified during the analysis
+            - name: Run Codacy Analysis CLI
+              uses: codacy/codacy-analysis-cli-action@5cc54a75f9ad88159bb54046196d920e40e367a5
+              with:
+                  # Check https://github.com/codacy/codacy-analysis-cli#project-token to get your project token from your Codacy repository
+                  # You can also omit the token and run the tools that support default configurations
+                  project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+                  verbose: true
+                  output: results.sarif
+                  format: sarif
+                  # Adjust severity of non-security issues
+                  gh-code-scanning-compat: true
+                  # Force 0 exit code to allow SARIF file generation
+                  # This will handover control about PR rejection to the GitHub side
+                  max-allowed-issues: 2147483647
 
-      # Upload the SARIF file generated in the previous step
-      - name: Upload SARIF results file
-        uses: github/codeql-action/upload-sarif@v2
-        with:
-          sarif_file: results.sarif
+            # Upload the SARIF file generated in the previous step
+            - name: Upload SARIF results file
+              uses: github/codeql-action/upload-sarif@v2
+              with:
+                  sarif_file: results.sarif

.github/workflows/codeql.yaml

@@ -1,40 +1,40 @@
 name: "CodeQL"
 
 on:
-  workflow_call:
+    workflow_call:
 
 jobs:
-  analyze:
-    name: Analyze
-    runs-on: ubuntu-latest
-    permissions:
-      actions: read
-      contents: read
-      security-events: write
+    analyze:
+        name: Analyze
+        runs-on: ubuntu-latest
+        permissions:
+            actions: read
+            contents: read
+            security-events: write
 
-    strategy:
-      fail-fast: false
-      matrix:
-        language: [ 'python' ]
-        # python-version: ["3.9", "3.10"]
-        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
-        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+        strategy:
+            fail-fast: false
+            matrix:
+                language: ["python"]
+                python-version: ["3.10", "3.11", "3.12"]
+                # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+                # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
 
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v3
+        steps:
+            - name: Checkout repository
+              uses: actions/checkout@v4
 
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
-      with:
-        languages: ${{ matrix.language }}
-        # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file.
-        # Prefix the list here with "+" to use these queries and those in the config file.
+            # Initializes the CodeQL tools for scanning.
+            - name: Initialize CodeQL
+              uses: github/codeql-action/init@v2
+              with:
+                  languages: ${{ matrix.language }}
+                  # If you wish to specify custom queries, you can do so here or in a config file.
+                  # By default, queries listed here will override any specified in a config file.
+                  # Prefix the list here with "+" to use these queries and those in the config file.
 
-        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
-        # queries: security-extended,security-and-quality
+                  # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+                  # queries: security-extended,security-and-quality
 
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+            - name: Perform CodeQL Analysis
+              uses: github/codeql-action/analyze@v2

.github/workflows/on_branch_merge.yaml

@@ -1,20 +1,20 @@
 name: Merge to main / develop
 
 on:
-  push:
-    branches:
-      - main
-      - develop
+    push:
+        branches:
+            - main
+            - develop
 
 jobs:
-  run_unit_tests:
-    uses: ./.github/workflows/run_tests.yaml
+    run_unit_tests:
+        uses: ./.github/workflows/run_tests.yaml
 
-  run_code_ql:
-    uses: ./.github/workflows/codeql.yaml
+    run_code_ql:
+        uses: ./.github/workflows/codeql.yaml
 
-  run_codacy:
-    uses: ./.github/workflows/codacy.yaml
+    run_codacy:
+        uses: ./.github/workflows/codacy.yaml
 
-  run_trivy:
-    uses: ./.github/workflows/trivy.yaml
+    run_trivy:
+        uses: ./.github/workflows/trivy.yaml

.github/workflows/on_pr.yaml

@@ -1,26 +1,22 @@
 name: Standard PR workflow
 
 on:
-  pull_request:
-    types:
-    - opened
-    - reopened
-    - synchronize
-    - ready_for_review
+    pull_request:
+        types:
+            - opened
+            - reopened
+            - synchronize
+            - ready_for_review
 
 jobs:
-  format_files:
-    uses: ./.github/workflows/black.yaml
+    run_unit_tests:
+        uses: ./.github/workflows/run_tests.yaml
 
-  run_unit_tests:
-    uses: ./.github/workflows/run_tests.yaml
-    needs: format_files
+    run_code_ql:
+        uses: ./.github/workflows/codeql.yaml
 
-  run_code_ql:
-    uses: ./.github/workflows/codeql.yaml
+    run_codacy:
+        uses: ./.github/workflows/codacy.yaml
 
-  run_codacy:
-    uses: ./.github/workflows/codacy.yaml
-
-  run_trivy:
-    uses: ./.github/workflows/trivy.yaml
+    run_trivy:
+        uses: ./.github/workflows/trivy.yaml