git:20260726.ec471db to git:20260727.b2ef5f3

---

name: presubmit

description: Run the standalone presubmit CLI. Adversarial 30+ stage peer-review pipeline.

argument-hint: "[path to your draft to review, or describe the setup task]"

---

# Presubmit Activator

A launcher and setup wizard for the [`presubmit`](https://github.com/scdenney/presubmit) Python CLI — the standalone, API-driven adversarial peer-review pipeline that writes a consolidated review report to disk. The review itself happens in the CLI against the Anthropic API (~30 stages, ~$5–10 per full run on a typical manuscript); this skill verifies the install and the key, settles where output lands, launches the run, and reports where the report ended up.

This is for self-audit of your own drafts pre-submission. Peer-reviewing other people's manuscripts goes through the separate `reviews/` workflow with its own agents-based `CLAUDE.md` — not here.

## Setup phase (run once per machine)

Before any per-paper invocation, verify the install and the config. Run only the steps whose check fails.

### Step 1 — Is `presubmit` installed?

```bash

command -v presubmit && presubmit --help | head -3

```

If the usage banner comes back, skip to Step 2. If not, ask the user where they keep cloned repos (that choice becomes `PRESUBMIT_DIR`, used throughout below), then:

```bash

PRESUBMIT_DIR=~/repos/presubmit # wherever the user keeps clones

# Clone (or update) the repo

git clone https://github.com/scdenney/presubmit "$PRESUBMIT_DIR" \

|| git -C "$PRESUBMIT_DIR" pull

cd "$PRESUBMIT_DIR"

# Create a venv

python3 -m venv .venv

source .venv/bin/activate

# Install — first time pulls marker-pdf + PyTorch, ~5–10 min.

# pyproject.toml pins anthropic>=0.60 directly; verify the resolver honored it:

pip install -e .

pip show anthropic | head -2 # must be >= 0.60; if not: pip install -U 'anthropic>=0.60'

```

Confirm with `"$PRESUBMIT_DIR/.venv/bin/presubmit" --help | head -3`. The CLI lives in the venv: either source the venv each session (`source "$PRESUBMIT_DIR/.venv/bin/activate"`) or invoke the absolute binary path.

Warn the user that the **first PDF conversion** is slow — marker-pdf downloads ~3–5 GB of OCR / layout / table-recognition model weights into its local Hugging Face cache (macOS `~/Library/Caches/datalab/models/`, Linux `~/.cache/datalab/models/`), bandwidth-limited. Subsequent runs reuse the cache.

### Step 2 — Is `ANTHROPIC_API_KEY` set?

```bash

[ -n "$ANTHROPIC_API_KEY" ] && case "$ANTHROPIC_API_KEY" in sk-ant-*) echo "key OK";; *) echo "key set but unexpected prefix: ${ANTHROPIC_API_KEY:0:8}…";; esac

```

If empty, check whether it's defined in `~/.zshrc` but unsourced in the current shell:

```bash

eval "$(grep -E '^export ANTHROPIC_API_KEY=' ~/.zshrc | head -1)" 2>/dev/null && [ -n "$ANTHROPIC_API_KEY" ] && case "$ANTHROPIC_API_KEY" in sk-ant-*) echo "found in .zshrc";; esac

```

If still missing, walk the user through:

1. Generate a key at <https://console.anthropic.com/> → **Settings → API Keys → Create Key**.

2. Add to `~/.zshrc` (or equivalent shell rc), placed **above** any wrapper functions that re-set `ANTHROPIC_API_KEY` to an empty string to route the `claude` CLI to local Ollama models — those would shadow the real key:

```bash

export ANTHROPIC_API_KEY="sk-ant-api03-..."

```

3. `source ~/.zshrc` or open a new terminal.

4. Confirm a positive credit balance on the account. presubmit fails fast on credit/billing 400s rather than burning the retry budget — an empty balance halts the run on the first call.

### Step 3 — Where should outputs live?

Read `~/.config/presubmit/config.json` for an existing `output_base`; if the path is writable, use it. Otherwise ask (`AskUserQuestion`) — "Where should presubmit reviews be stored by default?" — offering at least these plus a custom path:

- `~/presubmit-reviews/` — generic, no project-folder assumption

- `~/Documents/presubmit/` — under Documents

- `~/Documents/GitHub/pre-submission/` — for users who keep all repos under `~/Documents/GitHub/`

Write the choice to `~/.config/presubmit/config.json`:

```json

{

"output_base": "/absolute/path/the/user/picked",

"saved_at": "ISO 8601 timestamp"

}

```

That config file is the source of truth for this skill. Also *offer* to write `export PRESUBMIT_OUTPUT_BASE=…` to `~/.zshrc` so the bare CLI picks up the same default — ask first, never write to `.zshrc` silently.

## Per-paper run phase

### Step 1 — Slug

Derive a default slug from the input filename: extension and path stripped, lowercased, runs of non-alphanumerics collapsed to single hyphens (underscores preserved), leading/trailing hyphens and underscores trimmed. Target shape is `<lastname>_<year>_<short-title>` — e.g. `Denney_2026_What-Were-They-Thinking.pdf` → `denney_2026_what-were-they-thinking`. Confirm the proposed slug with the user (`AskUserQuestion`); allow override.

### Step 2 — Mode

Ask which run mode (`AskUserQuestion`):

- **Smoke** — `--stop-stage 2.0`. Metadata extraction + Red Team + numbers auditor. ~15–25 min on a 70-page paper, ~$1–2. Useful for verifying setup or catching show-stoppers fast.

- **Custom** — ask for additional flags (`--code-dir`, `--math`, `--supp`, `--no-copyedit`, `--no-editor-note`, `--start-stage`, `--stop-stage`, `--skip-size-check`).

### Step 3 — Construct paths and run

```bash

WORK_DIR="$OUTPUT_BASE/$SLUG/presubmit_run"

mkdir -p "$WORK_DIR"

"$PRESUBMIT_DIR/.venv/bin/presubmit" "$PAPER_PATH" \

--work-dir "$WORK_DIR" \

-o "$OUTPUT_BASE/$SLUG/report.txt" \

$EXTRA_FLAGS

```

Always pass both. `-o / --output` controls the *final report copy* only; without it a stray `report.txt` lands in the invoking directory. Without `--work-dir`, stage outputs go to a temp dir that gets garbage-collected.

Launch with the Bash tool's `run_in_background: true` and stream the log to a file. Tell the user the expected wall time, the `tail -f` path for the live log, and what files to expect in `$WORK_DIR` as stages complete.

### Step 4 — Report when done

1. Confirm exit code 0 and no `FATAL: Claude refused` in the log. (A `--stop-stage` smoke run also exits 0, printing `Stopped at stage N as requested`; judge it by the per-stage files in `$WORK_DIR`, since no consolidated report exists by design.)

2. Locate the consolidated report: `$WORK_DIR/<slug>_*.txt` (presubmit auto-names it `<author_title_uuid>.txt`), with a stable-named copy at the `-o` path.

3. Report wall time, total tokens (input + output across stages, at the end of the log), and the end-of-run dollar total (pricing.csv carries current Claude rates; cross-check the Anthropic console if rates have changed).

4. Offer to open the report and to write a per-paper README.md alongside the work_dir capturing invocation date, flags, models, wall time.

If the run failed:

- **`Messages.create() got an unexpected keyword argument 'thinking'`** — anthropic SDK is < 0.60. Fix: `pip install -U 'anthropic>=0.60'` in the venv.

- **`FATAL: Claude refused the request (likely safety policy)`** — a Red Team prompt tripped Claude's safety filters. The message does not name the stage; find the last `► Executing <stage>` line above it in the log, then locate that stage's prompt under `$PRESUBMIT_DIR/src/presubmit/prompts/`. Soften it to attack the manuscript's claims, not the authors. Re-run; the pipeline is resumable.

- **Marker conversion failure** — surface the specific PipelineError. Common cause: marker-pdf install incomplete; verify `pip show marker-pdf` succeeds in the venv.

- **Out-of-credit** — top up at <https://console.anthropic.com/>, then re-run. The pipeline picks up where it stopped.

## File-naming and organization convention

```

$OUTPUT_BASE/ (from config; user-chosen)

└── <slug>/ (one folder per paper)

├── README.md (offered after the run — never silently written)

├── report.txt (stable-named copy of the report, via -o)

└── presubmit_run/ (the --work-dir)

├── <author_title_uuid>.txt ← THE main consolidated report

├── original_source.pdf (cached source)

├── paper.md (marker conversion of source)

├── metadata.json

├── pipeline_execution.log

├── 00a_metadata.txt … 09c_copyedit.txt (intermediate per-stage outputs)

└── 10_latex_body.txt (body without LaTeX framing)

```

`<author_title_uuid>.txt` consolidates all stages into one file: header, disclaimer, overview, Editor's Note, Summary (Is It Credible? + Bottom Line), Potential Issues, Future Research, Copyediting, Proofreading. Read it first. The rest are intermediates — though the raw `01a_breaker.txt`, `01b_butcher.txt`, etc. carry unfiltered Red Team findings that are sometimes sharper than the consolidated version.

## When to use this skill vs. `paper-review-lite`

| | `presubmit` (this skill) | `paper-review-lite` (sister skill) |

|---|---|---|

| Where the work happens | Outside Claude Code — Python CLI calls Anthropic API | Inside Claude Code — parallel sub-agents read the paper |

| Cost | Per-token, billed to your API key (~$5–10/run) | Subscription only (no per-token bill) |

| Wall time | 30–90 min unattended | Minutes; you control each pass |

| Depth | 30+ stages: Red Team (Breaker, Butcher, Shredder, Collector, Void) + Blue Team defence + verification cascade + legal pass + copyedit + Writer Mode | ~11 sub-agents: content/argument, numbers, references, DOIs, writing, CONSORT, pre-reg, figures, archive, plus 2 cross-checkers |

| Output | Single consolidated `.txt` deliverable + ~30 intermediate files | Structured pre-submit report in-conversation + `.review-tmp/` scratch files |

| Resumable | Yes — checkpointed per stage to disk | No — single conversation pass |

| Math audit | Yes (`--math`, requires Mathpix) | No |

| Replication-code audit | Yes (`--code-dir`) | Partial (Agent 9 checks archive completeness; doesn't compare claims to code) |

| Refusal risk | Moderate (some Red Team stages adversarial enough to trip safety) | Low (single-pass personas, quote-grounded) |

| When to use | Deep audit before submission; standalone deliverable; math or code audit | Quick in-flow check; routine self-audit; no API spend |

`paper-review-lite` is the everyday tool; `presubmit` is the heavy-artillery final pass before submission.

## Known gotchas (current as of 2026-06)

1. **anthropic SDK version conflict.** presubmit's `pyproject.toml` pins `anthropic>=0.60` directly (core.py's `Messages.create(thinking=…)` needs it), but `marker-pdf 1.10.x` transitively caps anthropic at `<0.47`. pip resolves the conflict by backtracking marker-pdf to an older release, or by warning. After install, check `pip show anthropic marker-pdf`; if anthropic landed below 0.60, force it with `pip install -U 'anthropic>=0.60'` — runtime is unaffected, since presubmit doesn't use marker's optional anthropic-LLM mode.

2. **`use_search=True` is a no-op.** Stage 00a (metadata) silently degrades for published papers needing a citation lookup; fine for unpublished manuscripts.

3. **Older checkouts exit 1 on intentional `--stop-stage` runs.** Current presubmit exits 0 with `Stopped at stage N as requested`; if you see exit 1 with "did not produce a final report" after a smoke run, the install predates the fix — `git pull && pip install -e .`.