fix(ci): repair build and docs workflows

build.yml:
- Enable tests (-DBML_BUILD_TESTS=ON) and add ctest step
- Update upload-artifact to v4

docs.yml:
- Replace nonexistent requirements.txt with pip install .[dev] from
  pyproject.toml
- Update all actions to current major versions (setup-python v5,
  cache v4, configure-pages v4, upload-pages-artifact v3,
  deploy-pages v4)
- Remove broken jobs: lychee link-check (pip install lychee is invalid),
  bandit security scan (irrelevant for C++ project), metrics (wrong
  output), and no-op notify
- Add deployment environment for GitHub Pages

Author: doyaGu

.github/workflows/build.yml

@@ -51,17 +51,21 @@ jobs:
         -DCMAKE_BUILD_TYPE=${{ matrix.configuration }}
         -DVIRTOOLS_SDK_PATH=${{ github.workspace }}/Virtools-SDK-2.1
         -DCMAKE_INSTALL_PREFIX=${{ env.BASE_DIST_DIR }}/${{ matrix.configuration }}
+        -DBML_BUILD_TESTS=ON
 
     - name: Build the project
       run: cmake --build ${{ env.BASE_BUILD_DIR }}/${{ matrix.configuration }} --config ${{ matrix.configuration }}
 
+    - name: Run tests
+      run: ctest --test-dir ${{ env.BASE_BUILD_DIR }}/${{ matrix.configuration }} -C ${{ matrix.configuration }} --output-on-failure
+
     - name: Install binaries to distribution folder
       run: >
         cmake --install ${{ env.BASE_BUILD_DIR }}/${{ matrix.configuration }}
         --prefix ${{ env.BASE_DIST_DIR }}/${{ matrix.configuration }}  --config ${{ matrix.configuration }}
 
     - name: Upload build artifacts
-      uses: actions/upload-artifact@v4.3.3
+      uses: actions/upload-artifact@v4
       with:
         name: ${{ env.PROJECT_NAME }}-${{ env.GIT_SHA }}-${{ matrix.configuration }}
         path: ${{ env.BASE_DIST_DIR }}/${{ matrix.configuration }}

.github/workflows/docs.yml

@@ -0,0 +1,77 @@
+name: Documentation
+
+on:
+  push:
+    branches: [ main ]
+    paths:
+      - 'docs/**'
+      - 'mkdocs.yml'
+      - 'pyproject.toml'
+      - '.github/workflows/docs.yml'
+  pull_request:
+    branches: [ main ]
+    paths:
+      - 'docs/**'
+      - 'mkdocs.yml'
+      - 'pyproject.toml'
+      - '.github/workflows/docs.yml'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install dependencies
+        run: pip install ".[dev]"
+
+      - name: Build documentation
+        run: mkdocs build --clean --strict
+
+      - name: Setup Pages
+        if: github.ref == 'refs/heads/main'
+        uses: actions/configure-pages@v4
+
+      - name: Upload artifact
+        if: github.ref == 'refs/heads/main'
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./site
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: build
+    if: github.ref == 'refs/heads/main'
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4