13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps,โฆ
Version-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training, evaluation, and safe checkpoint review. Covers the native 5.0 build and environment API, published 3.0.0 Gymnasium/PettingZoo adaptation, and a pinned historical
Claude Code
$ npx -y skills add K-Dense-AI/scientific-agent-skills --skill pufferlib --agent claude-code
Codex
$ npx skills add K-Dense-AI/scientific-agent-skills --skill pufferlib -a codex -y
Cursor
$ npx skills add K-Dense-AI/scientific-agent-skills --skill pufferlib -a cursor -y
Gemini CLI
$ npx skills add K-Dense-AI/scientific-agent-skills --skill pufferlib -a gemini-cli -y
GitHub Copilot
$ npx skills add K-Dense-AI/scientific-agent-skills --skill pufferlib -a github-copilot -y
OpenCode
$ npx skills add K-Dense-AI/scientific-agent-skills --skill pufferlib -a opencode -y
Windsurf
$ npx skills add K-Dense-AI/scientific-agent-skills --skill pufferlib -a windsurf -y
name: pufferlib description: Version-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training, evaluation, and safe checkpoint review. Covers the native 5.0 build and environment API, published 3.0.0 Gymnasium/PettingZoo adaptation, and a pinned historical 4.0 profile. license: MIT compatibility: Bundled CLIs require Python 3.10+ (standard library only). PufferLib 5.0 requires a native C/CUDA toolchain; CPU builds support evaluation, not training. PyPI 3.0.0 declares Python >=3.9 and needs a native source build with NumPy <2 and Gymnasium <=0.29.1. Native dependencies and network access are needed for installation; bundled checks require neither. allowed-tools: Read Bash Grep Python metadata: version: "1.4" skill-author: "K-Dense Inc." last-reviewed: "2026-10-01"
Choose the version before choosing an API. Reviewed **2026-10-01**:
| Profile | Status | Main use | |---|---|---| | Native source `5.0` | Current default branch and live documentation | C/CUDA environments, native trainer; CPU evaluation only | | `pufferlib==3.0.0` | Latest PyPI release, published 2025-06-23; sdist only | Python/Gymnasium/PettingZoo adaptation and Torch PuffeRL | | Pinned source `4.0` | Historical snapshot | C Ocean interface with an optional Torch fallback |
For **5.0**, read [references/native-5.md](references/native-5.md). The reviewed revision is `6ffa5b10dbbbe4d1e8288367c7d9d3acd3bad4a2`. Its CLI is `./puffer train` after building an environment, not `puffer train ENV_NAME`. There is no 5.0 Python emulation/vector API or `--slowly` fallback.
The bundled plan schema deliberately supports only 3.0 and pinned 4.0; it does not launch training. All native/PufferLib training examples are **source-reviewed, illustrative, and not executed in this review**. Bundled synthetic checks are executed CPU tests, not evidence of PufferLib installation or learning quality. The PyPI sdist was hash-verified and its Python sources inspected; the moving `3.0` branch differs, including its `load_policy` and logger contracts.
1. Start with bundled synthetic, CPU-only, network-free tools. 2. Do not import an arbitrary environment by dotted path. Bundled tools accept only allowlisted built-ins and slug identifiers. 3. Do not install or execute an unreviewed environment package, native extension, ROM, map, checkpoint, or pickle file. 4. Verify official source, immutable revision, licenses, checksums or attestations, and build hooks. Sandbox native builds and first execution. 5. Cap steps, environments, agents, workers, threads, buffers, memory, disk, render size, and wall time. 6. Keep training and evaluation environments/seeds separate. 7. Default logging to local/none. External logging requires explicit opt-in, disclosure acknowledgment, and separate artifact-upload approval. 8. Never pass W&B or Neptune credentials via CLI, INI, JSON, tags, run names, or logger configuration. Never print them. 9. Never dump all environment variables or recursively search for `.env`. 10. Hash checkpoint bytes before trusted, sandboxed loading; metadata inspection is not proof of safety.
All bundled CLIs are dependency-free and emit strict JSON:
python3 scripts/env_template.py --help python3 scripts/env_contract_validator.py python3 scripts/benchmark_vectorization.py --backend serial python3 scripts/train_template.py python3 scripts/validate_plan.py python3 scripts/repro_plan.py
Defaults are synthetic, deterministic, bounded, local, CPU-only, no-network, and dry-run where training would otherwise occur.
PyPI supplies only `pufferlib-3.0.0.tar.gz`:
sha256: 7df3a3e3f5f894d78d2a1f5374097890aec01473183e748abefe4f3faa10eaa9 Requires-Python: >=3.9
After source/build review, create a pinned uv project:
uv venv --python 3.11 uv add --exact --no-sync "pufferlib==3.0.0" uv lock uv sync --frozen
These installation commands are illustrative and were not executed. Commit `pyproject.toml` and `uv.lock`; verify the archive digest and every resolved dependency. The source build can compile native code and fetch build assets, so resolve/build in a sandbox without credentials or sensitive mounts. The archive declares NumPy `<2`, Gymnasium `<=0.29.1`, and PettingZoo `<=1.24.1`; latest Gymnasium/NumPy are not valid substitutes for this profile. Its setup supports Linux/macOS and rejects other systems. Python classifiers alone do not establish a successful native build. The uploaded metadata does not pin Torch or CUDA; do not claim a supported CUDA matrix that PyPI does not declare.
The reviewed branch head on 2026-07-23 was:
25647630e1b15330bb3153a5a0d3ff8d234c3acf
Pin the commit, not branch `4.0`:
uv add --no-sync \ "pufferlib @ git+https://github.com/PufferAI/PufferLib.git@25647630e1b15330bb3153a5a0d3ff8d234c3acf" uv lock
The reviewed 4.0 package declares Python `>=3.10` and Torch `>=2.9`. The reviewed PufferTank snapshot uses Ubuntu 24.04, Python 3.12, and an NVIDIA CUDA 13.0.2/cuDNN development image with the `cu130` Torch index, but does not pin the exact Torch wheel or all system packages. Treat it as a reference, not a complete lock. Never execute a remote installer directly from a pipe.
Read `references/training.md` before any installation or build.
Gymnasium reset returns `(observation, info)`. Step returns:
(observation, reward, terminated, truncated, info)
Validate spaces, shapes, dtypes, finite rewards, booleans, reset-before-step, reset-after-end, seeding, and cleanup. `terminated` is an MDP terminal; `truncated` is an external cutoff such as a time limit. Preserve the distinction for bootstrapping and metrics. Both flags can be true in general Gymnasium. Check autoreset timing and retain the
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