Reuel albert dev patch 1

.github/workflows/publish-pypi.yml

@@ -7,6 +7,8 @@ on:
 jobs:
   release-build:
     name: Build distribution
+    permissions:
+      contents: read
     runs-on: ubuntu-latest
     needs: [checks]
     steps:
@@ -31,6 +33,8 @@ jobs:
           path: dist/
 
   checks:
+    permissions:
+      contents: read
     uses: ./.github/workflows/shared.yml
 
   pypi-publish:

.github/workflows/pyre.yml

@@ -0,0 +1,46 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# This workflow integrates Pyre with GitHub's
+# Code Scanning feature.
+#
+# Pyre is a performant type checker for Python compliant with
+# PEP 484. Pyre can analyze codebases with millions of lines
+# of code incrementally – providing instantaneous feedback
+# to developers as they write code.
+#
+# See https://pyre-check.org
+
+name: Pyre
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+    contents: read
+
+jobs:
+  pyre:
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Run Pyre
+        uses: facebook/pyre-action@60697a7858f7cc8470d8cc494a3cf2ad6b06560d
+        with:
+          # To customize these inputs:
+          # See https://github.com/facebook/pyre-action#inputs
+          repo-directory: './'
+          requirements-path: 'requirements.txt'

.github/workflows/python-app.yml

@@ -0,0 +1,39 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest