Skill: zoeprior/reinvent4 (version 1.0.0)

--- name: reinvent4 description: Help install, configure, run, troubleshoot, and extend MolecularAI REINVENT4 for generative molecular design. Use when the user mentions REINVENT4 or Reinvent 4, asks about `reinvent` or `reinvent_datapre`, needs to choose an install backend like `mac`, `cpu`, `cu126`, `rocm6.4`, or `xpu`, wants help editing `configs/*.toml`, working with sampling, scoring, transfer learning, staged learning, notebooks, or scoring plugins, or needs guidance grounded in the upstream REINVENT4 repository. --- # REINVENT4 Prefer a local REINVENT4 checkout over web summaries. Treat a directory as the repo root when it contains `install.py`, `pyproject.toml`, `reinvent/`, and `configs/`. ## Workflow 1. Classify the request: install, run configuration, data preprocessing, notebook conversion, scoring plugin, or test/troubleshooting. 2. Read only the relevant reference file: - installation or CLI usage: `references/install-and-run.md` - TOML mode selection or parameter mapping: `references/config-modes.md` - plugins, notebooks, or tests: `references/plugins-and-tests.md` 3. Verify commands against the local checkout before proposing them. Prefer `python install.py --help`, `python install.py <backend> --dry-run`, `reinvent --help`, direct file inspection, and existing files under `configs/`. 4. Reuse the example configs in `configs/` instead of inventing schemas from scratch. 5. Keep file paths explicit. Upstream example configs are templates and must be adjusted to local model, SMILES, output, and log paths before execution. ## Installation Rules - Use an isolated Python environment with Python 3.10 or newer. - Map the processor/backend carefully: - macOS CPU: `mac` - Linux CPU: `cpu` - Linux NVIDIA CUDA: upstream examples use values like `cu126` - Linux AMD ROCm: upstream examples use values like `rocm6.4` - Intel XPU: `xpu` - Windows: CPU, CUDA, and XPU are supported, but upstream says Windows is only partially tested - Remember that `install.py` defaults to optional dependency set `all`, which includes extra packages such as `openeye` and `isim`. - Prefer `-d none` for minimal or smoke-test installs unless the user explicitly needs OpenEye ROCS or iSIM-related functionality. - Use `--dry-run` before a real install whenever backend choice or dependency resolution is uncertain. - Verify a finished install with `reinvent --help`. ## Running REINVENT - Main CLI entry point: `reinvent [-l logfile] <config.toml>`. - Data pipeline entry point from `pyproject.toml`: `reinvent_datapre`. - Prefer TOML because upstream ships maintained examples in `configs/`. - When editing configs, update at least device selection, model/prior paths, SMILES inputs, output files, and TensorBoard/log paths. ## Troubleshooting Rules - On macOS, remind the user that upstream documents CPU-only support and says macOS is only partially tested. - If a macOS clone reports path collisions under `contrib/tutorials/maize/adgpu_prepare`, avoid relying on those collided files unless the user specifically needs that tutorial. - For tests, warn that they require a JSON config with a non-existent `MAIN_TEST_PATH`; some tests also require `OE_LICENSE`. - Do not promise a full RL/TL run unless models, datasets, and optional licensed tools are present locally. ## Source Files Use these upstream files as the primary source of truth when they are present in the local checkout: - `README.md` - `install.py` - `pyproject.toml` - `configs/README.md` - `configs/PARAMS.md` - `configs/SCORING.md` - `notebooks/README.md` - `tests/example_config.json`


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