By drannarosen
Domain-agnostic research-coding workflow discipline for computational science (JAX/Python research family). 48 skills across collaborate / scope / build-correctly / verify / review / record / communicate / reproduce — the core evidence-first / numerical-validation / reproducibility discipline plus computational-physics code review (numerical / JAX / physics / error-handling / structure), figure faithfulness & publication-quality plotting, and MyST documentation authoring (voice + page-anatomy + deploy/CI) — eight self-limiting enforcement hooks (deletion, no-secrets-in-git, test-integrity, no-silent-except, myst-docs-hygiene, provenance, evidence-before-done, no-stub-when-done) and per-domain lenses (e.g. MESA, REBOUND) for reference-parity work.
Based on adoption, maintenance, documentation, and repository signals. Not a security audit or endorsement.
Go/no-go checkpoint before an expensive or irreversible run (high-impact-checkpoint).
Inspect or enable the research-workflow hook decision log (RWF_HOOK_DEBUG).
Reference-parity audit against an external reference, loading the matching domain lens.
Capture a reproducibility contract for the current work — env lock, seeds, precision, inputs, commit.
Multi-lens scientific code & figure review of a changeset, running the Review-cluster skills (correctness, numerics, JAX, robustness, craft, figures).
Use when you have a result you are about to trust — to red-team it against confirmation bias and the stable-but-wrong failure mode (numerical artifact, latent bug, boundary effect, or a mundane alternative explanation that fits the same data). Produces the strongest attacks plus the cheapest discriminating test for each. Don't use for reviewing CODE (→ scientific-code-reviewer and the Review cluster), the neutral close-out format (→ verification-gate), reporting the result's uncertainty budget (→ uncertainty-reporting-gate), or explaining a convergence/refinement-floor behavior (→ numerical-method-validation).
Use when relying on code, math, or facts the AI assistant itself produced — apply EXTRA scrutiny precisely because the model's signature failure is confident fabrication: hallucinated library APIs, plausible-but-wrong algebra, invented constants/citations, and tests written to pass rather than to catch. The stance that points generic skepticism at the assistant's own output. Don't use as the concrete check itself — route to the specific gate: API existence (→ verify against docs), formulas (→ derivation-before-implementation), constants/citations (→ provenance-of-constants), result size (→ plausibility-envelope), test/claim integrity (→ evidence-first-execution).
Use when a research session produces meaningful results and you need durable manifests, payloads, plot scripts, and a completion note so later sessions can reason from artifacts instead of memory. Don't use for the in-the-moment command discipline (→ evidence-first-execution), the go/no-go close-out (→ verification-gate), or pinning the runtime environment itself (→ reproducible-environment-contract).
Use when a result or model rests on simplifying assumptions, approximations, fixed parameters, or regime-of-validity choices — keep an explicit running ledger of what each result depends on, so when an assumption later breaks you know exactly which conclusions die with it. Don't use for citing the source of a value (→ provenance-of-constants), recording a decision and its rationale (→ decision-log-and-commits), or quantifying the numeric error a kept assumption induces (→ uncertainty-reporting-gate).
Use when verifying performance claims, characterizing scaling, comparing implementations, or validating against analytic solutions for performance-critical kernels (integrators, force solvers, renderers). Don't use for small analysis scripts (overkill) or for designing a test plan before code exists (→ testing-strategist).
Executes bash commands
Hook triggers when Bash tool is used
Modifies files
Hook triggers on file write and edit operations
Domain-agnostic research-coding workflow discipline for computational science (the JAX/Python research family — gravax, stellax, progenax, radax, …), packaged as a Claude Code plugin. The human is the scientist-in-the-loop, PI-level collaborator, and supervisor; the skills enforce evidence-first execution, structural correctness over compatibility, falsifiability, and reproducible artifacts. Domain specifics (e.g. MESA parity) live in thin lenses, so the stances stay sharp while the suite stays general.
| Phase | Skill |
|---|---|
| Collaborate | researcher-in-the-loop · high-impact-checkpoint |
| Scope | minimal-falsifiable-slice · discriminating-experiment-design · testing-strategist |
| Build correctly | ownership-and-structure · correct-cutover · numerical-precision · derivation-before-implementation · staleness-sweep · no-silent-except |
| Verify | evidence-first-execution · verification-gate · numerical-method-validation · gradient-validation · reference-parity-audit · adversarial-result-check · uncertainty-reporting-gate · plausibility-envelope · ai-self-distrust · seed-and-stochasticity · prior-sensitivity · systematic-error-hunting · no-stub-when-done |
| Review (audit written code/figures) | scientific-code-reviewer · numerical-methods-auditor · jax-code-validator · error-handling-reviewer · code-craft-reviewer · benchmark-generator · plot-faithfulness-inspector |
| Record | decision-log-and-commits · provenance-of-constants · experiment-tracking · data-provenance · data-io-validator · null-result-integrity · assumption-ledger · no-secrets-in-git |
| Communicate (docs & figures) | myst-expert · docs-writing-voice · myst-ci · interactive-figures · mystmd-plugin-dev · plot-design-inspector · publication-figure-validator |
| Reproduce | artifact-first-reproducibility · reproducible-environment-contract |
Each skill's description carries a "Don't use when… (→ sibling)" partition and a ## Related block, so the suite reads as one ordered protocol. reference-parity-audit loads a domain lens when one exists (lenses/mesa.md and lenses/nbody.md ship; lenses/rad-transfer.md is added on first need).
The Review and Communicate clusters and several MyST references were consolidated in v1.2.0 from the former astro-code-review and myst plugins (now retired) — see the Status section. MyST authoring skills ship co-located references (myst-cheatsheet, math-and-gotchas, myst-projects-and-workflows, voice-fingerprint, page-anatomy) and the shippable mystmd-plugins/interactive.mjs directive bundle.
The skills document the discipline; eight path-/command-scoped, self-limiting hooks (hooks/hooks.json) enforce it. Each stays inert outside research code (e.g. during course work or quick edits) and fails open on any error, so it never blocks legitimate work.
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