Mjvolk3/torchcell

Mjvolk3/torchcell

Skill Claude CodeCodex

Commit staged changes with an auto-generated bulleted commit message. Run /stage first to stage files.

Mjvolk3/torchcell

Skill Claude CodeCodex

Move a path (dataset, LMDB build, schema, code, note) into the deprecation graveyard instead of deleting it. Use when retiring old data structures or stale builds -- especially before a rebuild -- since rm -rf of directories is blocked. Wraps scripts/deprecate.sh (move + provenance manifest); nothing is auto-deleted…

Mjvolk3/torchcell

Skill Claude CodeCodex

Run the deterministic merge-queue drainer once (land queued worktree branches to main). Normally triggered automatically by /enqueue-merge and a cron; use this only to force a drain by hand.

Mjvolk3/torchcell

Skill Claude CodeCodex

Author a NEW draw.io diagram from scratch by writing the .drawio XML directly -- at true Nature print size, in the repo palette, verified by headless render. Use when asked to draw/diagram a mechanism, workflow, schematic, or concept figure that is not a matplotlib plot. For refreshing plot panels already placed in a…

Mjvolk3/torchcell

Skill Claude CodeCodex

Enqueue a finished worktree branch and watch it land through the single-writer merge queue from this session -- resolving any rebase conflict here, and printing a distinct dove signal when it is merged + cleaned up + safe to close. Takes a branch name (defaults to the current worktree's branch).

Mjvolk3/torchcell

Skill Claude CodeCodex

Audit and refresh the matplotlib SVG panels embedded in a draw.io figure (notes/assets/drawio/.drawio.svg) without opening the GUI -- swap regenerated panels in at true size, rebuild the preview/PDF, and rebuild editing.pdf if it is a paper figure. Use after re-running plot scripts, or to check which panels of a…

Mjvolk3/torchcell

Skill Claude CodeCodex

Pull OCR literature artifacts from the keyed torchcell literature endpoint and verify sha256. Use on the M1 Mac (or any client) to list citation keys, fetch a paper's manifest/markdown/SI, or download an artifact with integrity checking.

Mjvolk3/torchcell

Skill Claude CodeCodex

Merge a worktree branch to main via rebase, then clean up worktree and branch. Takes branch name as argument.

Mjvolk3/torchcell

Skill Claude CodeCodex

Introspect a running or finished tcdb Neo4j/BioCypher KG build on GilaHyper (slurm .out + wandb + the served DB), report a concise status, and diagnose + restart on stall or failure. Use when checking on a builddatabase slurm job, polling a KG build, or driving one to a queryable DB.

Mjvolk3/torchcell

Skill Claude CodeCodex

Run mypy on staged or specified Python files and fix errors following the project's type-checking strategy.

Mjvolk3/torchcell

Skill Claude CodeCodex

Edit the Nature Biotech manuscript (paper/nature-biotech) respecting the section status stoplight, then rebuild editing.pdf. Use for any change to the paper body, sections, or SI.

Mjvolk3/torchcell

Skill Claude CodeCodex

Three scouts explore the codebase in parallel, argue the approach, and a plan-writer agent synthesizes the deliberation into a concise Dendron note. A reducer-critic then smart-tightens the plan (flagging low-value content for cuts, not truncating) until the plan is dense and human-readable. Built for Claude Opus 4.8…

Mjvolk3/torchcell

Skill Claude CodeCodex

Run ruff linter on staged or specified Python files and fix errors following the project's lint strategy.

Mjvolk3/torchcell

Skill Claude CodeCodex

Create a new git worktree or ensure an existing one is properly configured. Wraps scripts/setup-worktree.sh with validation.

Mjvolk3/torchcell

Skill Claude CodeCodex

Smart staging with auto-detected file blocks and interactive override. Use before /commit.

Mjvolk3/torchcell

Skill Claude CodeCodex

End-to-end autonomous pipeline -- plans with /plan-4.8 (3 scouts, deliberator, plan-writer, reducer-critic), then implements with /wt-implement in an isolated worktree. No manual approval between plan and implementation.

Mjvolk3/torchcell

Skill Claude CodeCodex

Meta-skill: update dendron module notes for changed source files, then update the weekly task note. Combines /update-src-notes + /update-tasks-weekly into one command. Run before /stage and /commit.

Mjvolk3/torchcell

Skill Claude CodeCodex

Update dendron module notes for changed source files (Python, Bash, etc.). Checks staged files first, then falls back to modified (unstaged) files. Appends dated sections and stages updated notes.

Mjvolk3/torchcell

Skill Claude CodeCodex

Update the weekly task note with a bullet point linking to reviewed/modified files, then auto-stage the weekly file.

Mjvolk3/torchcell

Skill Claude CodeCodex

Implement an instruction file (plan note, scratch note, .claude/plans/ file) in an isolated git worktree. Creates branch, sets up env, executes the instructions, runs verification, rebases onto main, and optionally merges.

Mjvolk3/torchcell

Skill Claude CodeCodex

Draft and revise long-form prose (manuscripts, proposals, strategy docs, design memos) as Dendron notes inside an isolated git worktree, iterate with the user, then hand off to /merge-worktree. The writing counterpart to /plan-4.8 -- worktree-first, but for words instead of an implementation plan. Use when the…