Presubmit Activator

A launcher and setup wizard for the 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?

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:

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?

[ -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:

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:

   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:

{
  "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.
• Standard — full pipeline. ~30–90 min, ~$2–4 on a 70–80-page paper (a short article of a few thousand words runs well under $2). The default for a real audit.
• Custom — ask for additional flags (--code-dir, --math, --supp, --no-copyedit, --no-editor-note, --start-stage, --stop-stage, --skip-size-check).

Cost depends on which of four model tiers (mechanical/forensic/adversarial/synthesis, mapped to Haiku/Sonnet/Opus/Fable) each stage routes to — see the upstream repo's README "Model tier mapping" section for the full breakdown. These are estimates, not a guarantee. The end-of-run cost report has the real total.

Step 3 — Construct paths and run

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 ..