Addition of some software maintenance tools (#71)

* add codeql action

* Add codecov report upload to CI.yml

* fix environment to handle testing

* add secret token for uploading codecov reports

Author: CalCraven

.github/workflows/codeql.yml

@@ -0,0 +1,41 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  schedule:
+    - cron: "41 4 * * 6"
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ python ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        with:
+          languages: ${{ matrix.language }}
+          queries: +security-and-quality
+
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v3
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3
+        with:
+          category: "/language:${{ matrix.language }}"

.github/workflows/run_test.yml

@@ -46,5 +46,12 @@ jobs:
     - name: Install package
       run: micromamba run -n grouper-dev pip install -e .
 
-    - name: Run tests with pytest
-      run: micromamba run -n grouper-dev pytest Grouper/tests
+    - name: Test (OS -> ${{ matrix.os }} / Python -> ${{ matrix.python-version }})
+      run: micromamba run -n grouper-dev python -m pytest -v --cov-append --cov-config=pyproject.toml --color yes --pyargs Grouper
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        verbose: true
+        files: ./coverage.xml

Grouper/codecov.yml

@@ -0,0 +1,9 @@
+ignore:
+  - "Grouper/tests"
+  - "Grouper/images"
+  - "Grouper/packages"
+  - "Grouper/submission_scripts"
+  - "Grouper/.github/ISSUE_TEMPLATE"
+  - "Grouper/.github/PULL_REQUEST_TEMPLATE.md"
+  - "run_random_generate.py"
+  - "run_exhaustive_generate.py"

environment.yml

@@ -23,6 +23,9 @@ dependencies:
   - pytorch
   - pytest-benchmark
   - pytest
+  - pytest-cov 
+  - coverage 
+  - codecov 
   - nlohmann_json
   - python-igraph
   - dash

pyproject.toml

@@ -14,4 +14,17 @@ cmake.minimum-version = "3.15"
 wheel.expand-macos-universal-tags = true
 
 [tool.setuptools]
-packages = ["Grouper"]
+packages = ["Grouper"]
+
+[tool.pytest.ini_options]
+addopts = "--cov=Grouper --cov-report=xml:coverage.xml"
+
+[tool.coverage.run]
+source = ["Grouper"] # Adjust based on your project structure
+branch = true # Include branch coverage
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+]