From 23f0b45614bb2bde0d3d194598387a6b2a2ae9e6 Mon Sep 17 00:00:00 2001
From: Tibo De Peuter <tibo.depeuter@ugent.be>
Date: Sat, 4 Apr 2026 18:10:38 +0200
Subject: [PATCH] feat(hpc): add structured env/hpc config and requirements
 export script

- env/hpc/modules.txt: curated list of HPC EasyBuild modules loaded by vsc-venv
- env/hpc/requirements.txt: pip packages not covered by HPC modules (auto-generated)
- scripts/export_hpc_requirements.py: developer utility to regenerate requirements.txt
  from pyproject.toml; to be called by CI when pyproject.toml changes
---
 env/hpc/modules.txt                |  7 +++
 env/hpc/requirements.txt           |  9 ++++
 scripts/export_hpc_requirements.py | 76 ++++++++++++++++++++++++++++++
 3 files changed, 92 insertions(+)
 create mode 100644 env/hpc/modules.txt
 create mode 100644 env/hpc/requirements.txt
 create mode 100644 scripts/export_hpc_requirements.py

diff --git a/env/hpc/modules.txt b/env/hpc/modules.txt
new file mode 100644
index 0000000..0955932
--- /dev/null
+++ b/env/hpc/modules.txt
@@ -0,0 +1,7 @@
+jax/0.4.25-gfbf-2023a-CUDA-12.1.1
+Flax/0.8.4-gfbf-2023a-CUDA-12.1.1
+Optax/0.2.2-gfbf-2023a-CUDA-12.1.1
+wandb/0.16.1-GCC-12.3.0
+matplotlib/3.7.2-gfbf-2023a
+PyYAML/6.0-GCCcore-12.3.0
+FFmpeg/5.1.2-GCCcore-12.3.0
diff --git a/env/hpc/requirements.txt b/env/hpc/requirements.txt
new file mode 100644
index 0000000..9007c36
--- /dev/null
+++ b/env/hpc/requirements.txt
@@ -0,0 +1,9 @@
+biorobot==0.4.2
+cleanrl>=0.4.8
+evosax==0.2.0
+gymnasium>=1.2.3
+ipykernel==7.2.0
+mediapy==1.2.6
+pyopengl>=3.1.10
+pyopengl-accelerate>=3.1.10
+tyro>=1.0.10
diff --git a/scripts/export_hpc_requirements.py b/scripts/export_hpc_requirements.py
new file mode 100644
index 0000000..feeb66d
--- /dev/null
+++ b/scripts/export_hpc_requirements.py
@@ -0,0 +1,76 @@
+#!/usr/bin/env python3
+"""Export HPC pip requirements from pyproject.toml.
+
+This is a LOCAL DEVELOPER UTILITY — run it on your own machine before pushing
+code whenever pyproject.toml dependencies change. It reads the full dependency
+list from pyproject.toml and subtracts packages already provided by HPC modules
+(listed in env/hpc/modules.txt), then writes the remainder to
+env/hpc/requirements.txt for use by vsc-venv on the cluster.
+
+Usage:
+    uv run scripts/export_hpc_requirements.py
+"""
+
+from __future__ import annotations
+
+import importlib.util
+import re
+import sys
+from pathlib import Path
+
+ROOT = Path(__file__).parent.parent
+
+# Packages provided by HPC modules (PyPI name → Python import name).
+# We skip any pyproject.toml dep whose import can be found after loading
+# the HPC modules. As this script runs locally (without those modules), we
+# maintain an explicit exclusion list keyed by normalised PyPI package name.
+EXCLUDED_BY_MODULE = {
+    "jax",
+    "flax",
+    "optax",
+    "wandb",
+    "matplotlib",
+    "pyyaml",  # PyYAML module
+    "ffmpeg",  # FFmpeg is a system tool, not a Python package
+}
+
+
+def normalise(name: str) -> str:
+    """Normalise a PyPI package name for comparison."""
+    return re.sub(r"[-_.]+", "-", name).lower()
+
+
+def pkg_name(dep: str) -> str:
+    """Extract the bare package name from a PEP 508 dependency string."""
+    return re.split(r"[\[=><~!;]", dep)[0].strip()
+
+
+def main() -> None:
+    try:
+        import tomllib  # Python ≥ 3.11
+    except ImportError:
+        import tomli as tomllib  # type: ignore[no-redef]
+
+    pyproject_path = ROOT / "pyproject.toml"
+    with pyproject_path.open("rb") as f:
+        data = tomllib.load(f)
+
+    deps: list[str] = data.get("project", {}).get("dependencies", [])
+
+    missing: list[str] = []
+    for dep in deps:
+        name = normalise(pkg_name(dep))
+        if name in EXCLUDED_BY_MODULE:
+            print(f"  [skip – provided by HPC module] {dep}", file=sys.stderr)
+            continue
+        missing.append(dep)
+        print(f"  [pip] {dep}", file=sys.stderr)
+
+    output_path = ROOT / "env" / "hpc" / "requirements.txt"
+    output_path.parent.mkdir(parents=True, exist_ok=True)
+    output_path.write_text("\n".join(missing) + "\n")
+    print(f"\nWrote {len(missing)} requirement(s) to {output_path}", file=sys.stderr)
+
+
+if __name__ == "__main__":
+    main()