Automate Ubuntu dependency baseline generation (closes #617)

.github/workflows/generate-baseline.yml

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+name: Generate Ubuntu Baseline
+
+on:
+  workflow_dispatch:
+
+jobs:
+  generate:
+    if: github.actor != 'github-actions[bot]'
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Python deps
+        run: pip install PyYAML
+
+      - name: Generate baseline
+        run: |
+          python3 scripts/generate_ubuntu_baseline.py \
+            --lts 22.04 24.04
+
+      - name: Commit if changed
+        run: |
+          git config user.name github-actions
+          git config user.email [email protected]
+          git add _data/ubuntu-baseline.yml
+
+          if git diff --cached --quiet; then
+            echo "No changes"
+          else
+            git commit -m "Update Ubuntu baseline"
+            git push
+          fi

_data/ubuntu-baseline.yml

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+generated_at: '2026-02-28T11:28:15.149816+00:00'
+ubuntu:
+  '22.04':
+    optional:
+      libopenmpi-dev: 4.1.2
+      petsc-dev: 3.15.5+dfsg1
+      python3-dev: 3.10.6
+      python3-numpy: 1.21.5
+    required:
+      build-essential: 12.9ubuntu3
+      cmake: 3.22.1
+      libboost-all-dev: 1.74.0.3ubuntu7
+      libeigen3-dev: 3.4.0
+      libxml2-dev: 2.9.13+dfsg
+  '24.04':
+    optional:
+      libopenmpi-dev: 4.1.6
+      petsc-dev: 3.19.6+dfsg1
+      python3-dev: 3.12.3
+      python3-numpy: 1.26.4+ds
+    required:
+      build-essential: 12.10ubuntu1
+      cmake: 3.28.3
+      libboost-all-dev: 1.83.0.1ubuntu2
+      libeigen3-dev: 3.4.0
+      libxml2-dev: 2.9.14+dfsg

scripts/dependencies.yml

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+packages:
+  required:
+    - build-essential
+    - cmake
+    - libeigen3-dev
+    - libxml2-dev
+    - libboost-all-dev
+
+  optional:
+    - libopenmpi-dev
+    - petsc-dev
+    - python3-dev
+    - python3-numpy

scripts/generate_ubuntu_baseline.py

@@ -0,0 +1,124 @@
+#!/usr/bin/env python3
+
+import subprocess
+import yaml
+import argparse
+from pathlib import Path
+from datetime import datetime, UTC
+
+ROOT = Path(__file__).resolve().parent.parent
+DEPENDENCIES_FILE = ROOT / "scripts" / "dependencies.yml"
+OUTPUT_FILE = ROOT / "_data" / "ubuntu-baseline.yml"
+
+
+def load_dependencies():
+    with open(DEPENDENCIES_FILE, "r") as f:
+        data = yaml.safe_load(f)
+
+    packages = data.get("packages", {})
+
+    return {
+        "required": sorted(packages.get("required", [])),
+        "optional": sorted(packages.get("optional", [])),
+    }
+
+
+def run_command(cmd):
+    result = subprocess.run(
+        cmd,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+        text=True,
+    )
+    if result.returncode != 0:
+        print(result.stderr)
+        return None
+    return result.stdout.strip()
+
+
+def get_version_docker(ubuntu_version, package):
+    cmd = [
+        "docker",
+        "run",
+        "--rm",
+        f"ubuntu:{ubuntu_version}",
+        "bash",
+        "-c",
+        f"apt-get update -qq && apt-cache policy {package} | grep Candidate | awk '{{print $2}}'",
+    ]
+    raw = run_command(cmd)
+
+    if not raw or raw == "(none)":
+        return None
+
+    # Remove epoch (e.g. "1:")
+    if ":" in raw:
+        raw = raw.split(":", 1)[1]
+
+    # Remove Debian revision (e.g. "-1ubuntu1")
+    raw = raw.split("-", 1)[0]
+
+    return raw
+
+
+def get_version_mock(package):
+    return "0.0.0-mock"
+
+
+def generate_data(lts_versions, mock=False):
+    package_groups = load_dependencies()
+
+    result = {
+        "generated_at": datetime.now(UTC).isoformat(),
+        "ubuntu": {},
+    }
+
+    for version in lts_versions:
+        result["ubuntu"][version] = {
+            "required": {},
+            "optional": {},
+        }
+
+        for group in ["required", "optional"]:
+            for pkg in package_groups[group]:
+                if mock:
+                    ver = get_version_mock(pkg)
+                else:
+                    ver = get_version_docker(version, pkg)
+
+                result["ubuntu"][version][group][pkg] = ver or "not-found"
+
+    return result
+
+
+def write_yaml(data):
+    OUTPUT_FILE.parent.mkdir(parents=True, exist_ok=True)
+    with open(OUTPUT_FILE, "w") as f:
+        yaml.dump(data, f, sort_keys=True)
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Generate Ubuntu baseline package versions using Docker."
+    )
+    parser.add_argument(
+        "--mock",
+        action="store_true",
+        help="Use mock versions instead of querying Docker (useful for testing the pipeline).",
+    )
+    parser.add_argument(
+        "--lts",
+        nargs="+",
+        required=True,
+        help="Ubuntu LTS versions to query (e.g. 22.04 24.04)",
+    )
+    args = parser.parse_args()
+
+    data = generate_data(args.lts, mock=args.mock)
+    write_yaml(data)
+
+    print(f"Generated {OUTPUT_FILE}")
+
+
+if __name__ == "__main__":
+    main()