rae

Plugin rae from marketplace reproducible_agent_environment in peabody124/reproducible_agent_environment. Commands read from the repo's manifest — 5 days ago.

Skills (27)

• audit-repo

  Audit the current repository against RAE standards. Use when the user says "audit repo", "check repo standards", "sync with RAE", "check for drift", "compare against template", or when you want to verify a repo follows RAE conventions. Compares pyproject.toml, CLAUDE.md, ruff config, pytest/coverage

• bead-driven-development

  This skill should be used when the user asks to "execute plan with beads", "implement with persistent tracking", "bead-driven execution", "run plan with subagents", "track tasks across sessions", "use beads for planning", or wants planning + subagents + beads + code review unified. Orchestrates writ

• camera-model

  Use when working with camera projections, intrinsics, extrinsics, triangulation, reprojection, coordinate transforms between world/camera frames, or any code that touches camera_params dicts. Covers unit conventions (mm vs meters), the OpenCV world-to-camera extrinsic convention, and the required AP

• config-improvement

  Propose improvements to upstream RAE repository

• consult-guidelines

  Review relevant coding guidelines before starting a task. Use when the user says "consult guidelines", "check standards", "what are the rules for", "review guidelines", or when starting Python, git, refactoring, debugging, or code review work. Also useful when asking "what line length", "how should

• datajoint-biomechanics-schema

  Use when working with biomechanics DataJoint pipeline - querying KinematicReconstruction, understanding Video-Session relationships, using bridging algorithms, debugging schema issues across PosePipeline/MultiCameraTracking/BodyModels, or working with method 137 results

• deslop

  Clean up AI-generated slop from code changes. Use when the user says "deslop", "clean up code", "remove slop", "review for AI artifacts", "check for anti-patterns in diff", or before committing to ensure code quality. Also activates when reviewing staged changes or preparing a commit.

• efficient-rendering

  Use when building or speeding up visualization that renders 3D meshes, point clouds, skeletons/keypoints, or overlays onto video — especially offscreen/headless (EGL) rendering, differentiable rasterization in JAX, compositing renders over real camera footage, or anything that must align with a cali

• enforce-guidelines

  Mandatory skill that ensures all work follows RAE guidelines. Activates automatically before any code task.

• excalidraw

  Use when asked to create diagrams, flowcharts, architecture diagrams, wireframes, visual drawings, or .excalidraw files, or to assemble a composite scientific overview figure (rendered chart/3D panels embedded under a vector annotation layer). Generates valid Excalidraw JSON, embeds raster panels, r

• fetching-synchronized-data

  Use when fetching 2D keypoints synchronized with kinematic reconstruction qpos, aligning video frames with reconstruction frames, working with fetch_keypoints, handling camera parameter ordering between Calibration and SingleCameraVideo, or debugging temporal misalignment between observations and po

• gait-lab-dataset

  Query and analyze clinical gait lab (marker-based motion capture) data. Use when asked about c3d files, gait lab sessions, mocap markers, MocapProjection synchronization, video-mocap temporal alignment, GaitLab-MMC trial matching, gait events, gait parameters, forceplate/EMG analog data, or comparin

• gait-metrics

  Use when analyzing gait data, computing spatiotemporal metrics, finding valid walking segments, calculating step length/cadence/velocity, joint ROM per gait cycle, gait phase percentages, asymmetry indices, Gait Deviation Index (GDI), GaitAnalytics table queries, or normative gait comparisons from k

• github-activity-review

  Use when the user asks for a periodic review of their GitHub activity, wants a summary of what they've been working on, asks "what have I done recently", "review my commits", "summarize my GitHub activity", or wants a cross-repository progress report. Also use when asked to review team activity, lab

• golden-test-harness

  Set up self-generating golden/parity integration tests where a config-driven test harness generates the golden data on first run and the golden files are .gitignored, not committed. Use when adding parity tests, comparison tests, integration tests, or golden fixtures; when deciding whether to commit

• investigation

  Scaffolds a structured investigation in scratch/ for empirical research and documentation. Use when the user says "start an investigation" or wants to: trace code paths or data flow ("trace from X to Y", "what touches X", "follow the wiring"), document system architecture comprehensively ("document

• isr-paper-writing

  Guide, scaffold, edit, and critique scientific manuscripts in R. James Cotton's authentic pre-2026 (non-AI-written) scientific voice using the canonical Reproducible Agent Environment (RAE) MyST paper template (templates/myst-paper with dual ISR single-column preprint and IEEE two-column builds). En

• jax-config

  Set up JAX/Equinox-compatible configuration for a project. Use when the user says "set up config", "add configuration", "make a config", "jax config", or when creating dataclass configs that will be passed through JAX-traced code. Also use when debugging recompilation issues or pytree registration p

• jax-jit-and-fusion

  Find and fix JIT/fusion-hygiene misses in JAX/Equinox code: expensive work running eager (un-jitted), under-fused (many tiny jits, or per-element Python loops calling un-jitted forwards), or missing `eqx.filter_jit` on a hot path. Use when "every step is slow", "GPU sits idle", "low GPU utilization"

• jax-memory-and-retracing

  Diagnose and prevent GPU/host memory OOMs, memory leaks, and JIT retracing in JAX/Equinox projects. Use when a process is "killed" with no traceback, when you see "OOM", "out of memory", "GPU OOM", "RESOURCE_EXHAUSTED", "memory leak", "host RAM grows", "retracing", "recompiling every step", "every s

• jax-multi-gpu

  Make multi-GPU JAX data-parallel training correct, survivable and worth the hardware — both legacy `jax.pmap` and its `jax.jit` + `NamedSharding` / `jax.shard_map` replacement. Use when a multi-device run "hangs" with no traceback, when you see "Acquire clique", "rendezvous.cc", "Expected N threads

• pose-datajoint

  Use when writing Python code to query biomechanics DataJoint tables - counting videos/sessions, filtering by video_project or participant_id/subject_id, fetching keypoints or kinematic reconstructions, synchronizing keypoints with qpos, understanding Session-Video relationships for both multi-camera

• rae-jax-profiling

  Canonical RAE standard for JAX/Equinox JIT compilation hygiene, zero-recompilation verification, bf16 tensor-core GEMMs, analytic custom_jvp kinematic Jacobians, multi-iteration lax.scan fusion, and cold-vs-warm profiling across eqx_pose repositories. Use when implementing new JAX/Equinox algorithms

• scaffold-repo

  Initialize a new Python repository with correct structure following RAE guidelines. Use when the user says "new repo", "new project", "initialize", "scaffold", "create a project", "set up a repo", or "start a new package". Creates src/ layout, pyproject.toml, tests, .gitignore, and optionally a devc

• semi-formal-code-reasoning

  Structured semi-formal reasoning templates for agentic code analysis. Use this skill whenever Claude is asked to reason deeply about code semantics without executing it — including: comparing two patches or code changes for equivalence, reviewing pull requests or diffs for correctness, localizing bu

• ste100-spec

  Author, audit, and maintain ~80% ASD-STE100 (Simplified Technical English) specifications and technical explanations for repositories (docs/SPEC.md or docs/specs/), scientific manuscripts (docs/papers/<slug>/SPEC.md), and PR/bug walkthroughs. Trigger when asked to "write a spec", "STE-100", "STE100"

• tufte-data-viz

  Use when creating, reviewing, or styling charts, graphs, dashboards, sparklines, or any data visualization. Applies to Recharts, ECharts, Chart.js, matplotlib, Plotly, seaborn, D3.js, and SVG. Enforces Tufte principles (data-ink ratio, direct labeling, range-frame axes) plus modern screen-first stan

Slash commands (1)

• /rae:bead-driven-development

  Execute plan with beads tracking

Hooks (1)

• SessionStart

  bash ${CLAUDE_PLUGIN_ROOT}/hooks/scripts/load-guidelines.sh

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