New compasUtils file

.github/workflows/comment-evolution-plot.yml

@@ -0,0 +1,97 @@
+name: Comment PR with Evolution Plot
+
+on:
+  workflow_run:
+    workflows:
+      - COMPAS compile test
+    types:
+      - completed
+
+permissions:
+  actions: read
+  contents: read
+  issues: write
+  pull-requests: write
+
+jobs:
+  comment-with-plot:
+    name: Post evolution plot comment
+    runs-on: ubuntu-22.04
+    if: >
+      github.event.workflow_run.conclusion == 'success' &&
+      github.event.workflow_run.event == 'pull_request' &&
+      github.event.workflow_run.pull_requests[0].number
+
+    env:
+      ARTIFACT_NAME: detailedEvolutionPlot.png
+
+    steps:
+      - name: Download evolution plot artifact from triggering run
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const fs = require('fs');
+            const path = require('path');
+            const runId = context.payload.workflow_run.id;
+            const runNumber = context.payload.workflow_run.run_number;
+            const artifactName = `evolution-plot-${runNumber}`;
+            const { owner, repo } = context.repo;
+
+            const artifacts = await github.paginate(
+              github.rest.actions.listWorkflowRunArtifacts,
+              { owner, repo, run_id: runId, per_page: 100 }
+            );
+            const artifact = artifacts.find((entry) => entry.name === artifactName);
+
+            if (!artifact) {
+              core.setFailed(`Artifact '${artifactName}' not found for workflow run ${runId}`);
+              return;
+            }
+
+            const download = await github.rest.actions.downloadArtifact({
+              owner,
+              repo,
+              artifact_id: artifact.id,
+              archive_format: 'zip',
+            });
+
+            fs.writeFileSync(
+              path.join(process.env.GITHUB_WORKSPACE, 'evolution-plot.zip'),
+              Buffer.from(download.data)
+            );
+
+      - name: Unpack evolution plot artifact
+        run: |
+          set -e
+          mkdir -p evolution-plot
+          unzip -o evolution-plot.zip -d evolution-plot
+          test -f "evolution-plot/${ARTIFACT_NAME}"
+
+      - name: Post PR comment
+        env:
+          REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PR_NUMBER: ${{ github.event.workflow_run.pull_requests[0].number }}
+          HEAD_SHA: ${{ github.event.workflow_run.head_sha }}
+          RUN_ID: ${{ github.event.workflow_run.id }}
+        run: |
+          set -e
+
+          cat <<EOF > report.md
+          ## ✅ COMPAS Build Successful!
+
+          | Item | Value |
+          |------|-------|
+          | **Commit** | [\`$(echo "$HEAD_SHA" | cut -c1-7)\`]($GITHUB_SERVER_URL/$GITHUB_REPOSITORY/commit/$HEAD_SHA) |
+          | **Logs** | [View workflow]($GITHUB_SERVER_URL/$GITHUB_REPOSITORY/actions/runs/$RUN_ID) |
+
+          ### Detailed Evolution Plot
+          <details><summary>Click to view evolution plot</summary>
+
+          ![](./evolution-plot/${ARTIFACT_NAME})
+          </details>
+
+          ---
+          <sub>Generated by COMPAS CI</sub>
+          EOF
+
+          npx -y @dvcorg/cml@0.20.6 comment create --target=pr/"$PR_NUMBER" report.md

.github/workflows/compas-compile-ci.yml

@@ -19,6 +19,9 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+permissions:
+  contents: read
+
 jobs:
   compas:
     env:
@@ -40,7 +43,7 @@ jobs:
           echo "Building COMPAS from source..."
           cd src
           make clean 2>/dev/null || echo 'No existing build to clean'
-          make -j $(nproc) -f Makefile
+          make DOCKER_BUILD=1 CPP="g++" -j "$(nproc)" -f Makefile
           ./COMPAS -v
           echo "COMPAS build completed successfully!"
 
@@ -106,51 +109,3 @@ jobs:
           echo "- Python Dependencies: Success" >> $GITHUB_STEP_SUMMARY
           echo "- Example COMPAS Job: Success" >> $GITHUB_STEP_SUMMARY
           echo "- Pytest Suite: Success" >> $GITHUB_STEP_SUMMARY
-
-  comment-with-plot:
-    name: Comment PR with Evolution Plot
-    runs-on: ubuntu-22.04
-    container: docker://ghcr.io/iterative/cml:0-dvc2-base1
-    needs: compas
-    if: github.event_name == 'pull_request'
-
-    env:
-      ARTIFACT_NAME: detailedEvolutionPlot.png
-
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-
-      - name: Download evolution plot
-        uses: actions/download-artifact@v4
-        with:
-          name: evolution-plot-${{ github.run_number }}
-
-      - name: Create report with evolution plot
-        env:
-          REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          echo "## ✅ COMPAS Build Successful!" >> report.md
-          echo "" >> report.md
-          echo "| Item | Value |" >> report.md
-          echo "|------|-------|" >> report.md
-          echo "| **Commit** | [\`$(echo $GITHUB_SHA | cut -c1-7)\`](${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}/commit/${GITHUB_SHA}) |" >> report.md
-          echo "| **Logs** | [View workflow](${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}) |" >> report.md
-          echo "" >> report.md
-
-          if [ -f "${{ env.ARTIFACT_NAME }}" ]; then
-            echo "### Detailed Evolution Plot" >> report.md
-            echo "<details><summary>Click to view evolution plot</summary>" >> report.md
-            echo "" >> report.md
-            echo "![](./${{ env.ARTIFACT_NAME }})" >> report.md
-            echo "</details>" >> report.md
-          else
-            echo "### ⚠️ Evolution plot not found" >> report.md
-          fi
-
-          echo "" >> report.md
-          echo "---" >> report.md
-          echo "<sub>Generated by COMPAS CI </sub>" >> report.md
-
-          # Post the report using CML
-          cml comment create report.md

.github/workflows/native-linux-bundle.yml

@@ -0,0 +1,199 @@
+name: Native Linux bundle
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - dev
+    paths:
+      - src/**
+      - misc/cicd-scripts/**
+      - .github/workflows/native-linux-bundle.yml
+  push:
+    branches:
+      - dev
+    paths:
+      - src/**
+      - misc/cicd-scripts/**
+      - .github/workflows/native-linux-bundle.yml
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  native-linux-bundle:
+    name: Build native Linux bundle
+    runs-on: ubuntu-22.04
+
+    env:
+      BUNDLE_DIR: dist/COMPAS-linux-x86_64
+      BUNDLE_TARBALL: dist/COMPAS-linux-x86_64.tar.gz
+      CCACHE_DIR: ${{ github.workspace }}/.ccache
+      CCACHE_BASEDIR: ${{ github.workspace }}
+      CCACHE_COMPILERCHECK: content
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Restore compiler cache
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.CCACHE_DIR }}
+          key: ${{ runner.os }}-native-linux-bundle-ccache-${{ hashFiles('src/Makefile', 'misc/cicd-scripts/linux-dependencies', '.github/workflows/native-linux-bundle.yml') }}-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-native-linux-bundle-ccache-${{ hashFiles('src/Makefile', 'misc/cicd-scripts/linux-dependencies', '.github/workflows/native-linux-bundle.yml') }}-
+
+      - name: Install native build dependencies
+        run: |
+          # Keep this workflow lean: install only the native compiler and link dependencies.
+          bash misc/cicd-scripts/linux-dependencies native-build
+
+      - name: Build COMPAS from source
+        working-directory: src
+        run: |
+          ccache --zero-stats || true
+          ccache --max-size=500M || true
+          make DOCKER_BUILD=1 CPP="ccache g++" -j "$(nproc)" -f Makefile
+          ./COMPAS -v
+          ccache --show-stats || true
+
+      - name: Run native smoke test
+        working-directory: src
+        run: |
+          rm -rf smoke-output
+          ./COMPAS \
+            -n 1 \
+            --initial-mass-1 35 \
+            --initial-mass-2 31 \
+            -a 3.5 \
+            --random-seed 0 \
+            --metallicity 0.001 \
+            --quiet \
+            -o smoke-output
+          test -d smoke-output
+          find smoke-output -maxdepth 2 -type f | sort | sed -n '1,40p'
+
+      - name: Inspect runtime dependencies
+        run: |
+          echo "Runtime dependencies for native build:"
+          ldd src/COMPAS
+
+      - name: Package portable Linux bundle
+        run: |
+          bash misc/cicd-scripts/package-linux-bundle.sh src/COMPAS "$BUNDLE_DIR"
+
+      - name: Test bundled launcher
+        run: |
+          "$BUNDLE_DIR/run_compas.sh" -v
+
+          BUNDLE_SMOKE_DIR="${RUNNER_TEMP}/compas-bundle-smoke"
+          rm -rf "$BUNDLE_SMOKE_DIR"
+
+          "$BUNDLE_DIR/run_compas.sh" \
+            -n 1 \
+            --initial-mass-1 35 \
+            --initial-mass-2 31 \
+            -a 3.5 \
+            --random-seed 0 \
+            --metallicity 0.001 \
+            --quiet \
+            -o "$BUNDLE_SMOKE_DIR"
+
+          test -d "$BUNDLE_SMOKE_DIR"
+
+          echo "Runtime dependencies for bundled binary with bundled lib/:"
+          LD_LIBRARY_PATH="${GITHUB_WORKSPACE}/$BUNDLE_DIR/lib" ldd "$BUNDLE_DIR/bin/COMPAS"
+
+      - name: Archive bundle tarball
+        run: |
+          tar -C dist -czf "$BUNDLE_TARBALL" COMPAS-linux-x86_64
+
+      - name: Upload bundle artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: COMPAS-linux-x86_64
+          path: ${{ env.BUNDLE_TARBALL }}
+          if-no-files-found: error
+
+  verify-native-linux-bundle:
+    name: Verify bundled artifact on fresh runner
+    runs-on: ubuntu-22.04
+    needs: native-linux-bundle
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Download bundle artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: COMPAS-linux-x86_64
+          path: downloaded-artifact
+
+      - name: Install Python runner only
+        run: |
+          python -m pip install --no-deps -e .
+
+      - name: Unpack bundled artifact
+        run: |
+          mkdir -p bundle-test
+          tar -xzf downloaded-artifact/COMPAS-linux-x86_64.tar.gz -C bundle-test
+          test -x bundle-test/COMPAS-linux-x86_64/run_compas.sh
+
+      - name: Inspect downloaded bundle dependencies
+        run: |
+          LD_LIBRARY_PATH="${GITHUB_WORKSPACE}/bundle-test/COMPAS-linux-x86_64/lib" \
+            ldd bundle-test/COMPAS-linux-x86_64/bin/COMPAS | tee bundle-test/ldd.txt
+
+          ! grep -q 'not found' bundle-test/ldd.txt
+          grep -q 'bundle-test/COMPAS-linux-x86_64/lib/libhdf5_serial' bundle-test/ldd.txt
+          grep -q 'bundle-test/COMPAS-linux-x86_64/lib/libgsl' bundle-test/ldd.txt
+          grep -q 'bundle-test/COMPAS-linux-x86_64/lib/libboost_program_options' bundle-test/ldd.txt
+
+      - name: Run downloaded bundle smoke test
+        run: |
+          ./bundle-test/COMPAS-linux-x86_64/run_compas.sh -v
+
+          ARTIFACT_SMOKE_DIR="${RUNNER_TEMP}/compas-downloaded-bundle-smoke"
+          rm -rf "$ARTIFACT_SMOKE_DIR"
+
+          ./bundle-test/COMPAS-linux-x86_64/run_compas.sh \
+            -n 1 \
+            --initial-mass-1 35 \
+            --initial-mass-2 31 \
+            -a 3.5 \
+            --random-seed 0 \
+            --metallicity 0.001 \
+            --quiet \
+            -o "$ARTIFACT_SMOKE_DIR"
+
+          test -d "$ARTIFACT_SMOKE_DIR"
+
+      - name: Run Python runner against downloaded bundle
+        env:
+          COMPAS_BUNDLE_ROOT: ${{ github.workspace }}/bundle-test/COMPAS-linux-x86_64
+        run: |
+          compas_run --print-path
+          compas_run -v
+
+          PYTHON_RUNNER_SMOKE_DIR="${RUNNER_TEMP}/compas-python-runner-smoke"
+          rm -rf "$PYTHON_RUNNER_SMOKE_DIR"
+
+          compas_run \
+            -n 1 \
+            --initial-mass-1 35 \
+            --initial-mass-2 31 \
+            -a 3.5 \
+            --random-seed 0 \
+            --metallicity 0.001 \
+            --quiet \
+            -o "$PYTHON_RUNNER_SMOKE_DIR"
+
+          test -d "$PYTHON_RUNNER_SMOKE_DIR"