make-anonymous-branch

# Make Anonymous Branch for Double-Blind Submission **Core idea: one branch (`anon-submission`) carries the entire blinded artefact** — code, data, paper, derived results — in-tree. anonymous.4open.science mirrors that branch with `.git/` stripped. `main` stays untouched throughout; all destructive edits live on the anon branch. This skill is **flexible**. The phases and gotchas transfer; the exact file paths depend on the project. Adapt, don't blindly follow. ## When this skill is wrong - Repo has > ~1 GB of data, or single files > 100 MB → use git-lfs, or host data externally and link from the paper. anonymous.4open.science inherits GitHub's 50 MB warn / 100 MB hard limits. - Submission venue forbids supplementary code/data → don't blind, don't submit. - Authors are not yet sure whether to submit → don't preemptively delete the named-authors paper version on `main`. ## Phase 0: Pre-flight Run these BEFORE proposing edits — they shape every later decision: ```bash # 1. Total payload size (excluding things that won't ship) du -sh results figures investigations data 2>/dev/null # 2. Largest tracked files (sorted descending) git ls-files | xargs -I{} ls -l {} 2>/dev/null | awk '$5 > 20000000 {print $5, $9}' | sort -rn | head -20 # 3. Confirm main is clean and you know what you're branching from git status git log main --oneline -5 ``` ### Can the data ship in the repo? (Decide first — this gates everything else.) anonymous.4open.science mirrors a regular GitHub branch, so **GitHub's git-blob limits apply**: - **50 MB**: GitHub warns the user on push (still accepted) - **100 MB**: GitHub hard-blocks the push without git-lfs - **~1 GB**: practical repo-size ceiling for reviewer clone times; above this, anonymous.4open.science responsiveness also degrades Decision tree: | Situation | Hosting decision | |---|---| | Largest single file < 50 MB **and** total payload < ~250 MB | **In-repo.** Simplest path. No LFS, no external host, no second anonymization step. | | Single files in 50–100 MB **or** total 250 MB–1 GB | **In-repo with caveats.** Acceptable but: warn user about clone times; consider whether some intermediate artefacts can be regenerated by scripts and dropped from the branch. | | Any single file > 100 MB **or** total > ~1 GB | **External or LFS.** git-lfs adds complexity; HF/Zenodo adds a second account to anonymize. Pick the one with less identity surface. | | Sensitive / non-redistributable data | **Don't ship.** Describe how to obtain it; have reviewers email an anonymized contact (some venues provide one). | The default to push for: **in-repo if it fits**. The reason is concrete — every external host (HuggingFace, Zenodo, S3 bucket, Google Drive) adds another account/identity that needs separate anonymization, doubling the leakage surface. If the data is in the repo, anonymizing the repo anonymizes the data. ### Verify the in-repo decision before committing to it Run before `git checkout -b`: ```bash # Find anything that would push you over 50/100 MB on the anon branch git ls-files | xargs -I{} ls -l {} 2>/dev/null | awk '$5 > 50000000 {print $5, $9}' # Total tracked-file size (rough — doesn't include things you'll add later) git ls-files | xargs -I{} stat -c %s {} 2>/dev/null | awk '{s+=$1} END {printf "tracked: %.1f MB\n", s/1024/1024}' # If a wandb/ or build-artefact dir is currently tracked, surface it now: du -sh $(git ls-files | xargs -I{} dirname {} | sort -u | head -50) 2>/dev/null | sort -h | tail -10 ``` Any single result > 50 MB → revisit the hosting decision; > 100 MB → must use LFS or external. ### Other upfront decisions - **Branch lineage**: branch from `main`, never modify `main` until the anon branch is shipped. - **Squash needed?**: anonymous.4open.science strips `.git/`, so reviewers don't see commit history via the proxy. But if the public GitHub repo will *also* be visible (typical), past commits authored by your real GitHub account will leak. Decide whether to squash to a single anon-author commit (defense in depth). ## Phase 1: Audit (parallel Haiku Explore subagents) The dominant failure mode is missing an identity leak. Dispatch **3 Haiku Explore subagents in parallel** — they're cheap, thorough, and find things you'd miss by eye: 1. **Identity sweep agent**: scan `investigations/`, `docs/`, `notes/`, all .md/.py files for: author names, GitHub usernames, institution names, advisor names, home-directory paths (`/home/<user>`, `/Users/<user>`), email addresses (`@gmail`, `@<institution>`), hostnames, wandb run URLs. 2. **Build-dependency agent**: list every file slated for deletion, then verify nothing in `tests/`, `scripts/`, `src/`, or LaTeX `\input{}` chain depends on it. The classic gotcha: a paper-macros test that hardcodes a path to the named-authors `.tex`. 3. **README/JSON/PDF agent**: skim root files (`README.md`, `pyproject.toml`, `CLAUDE.md`, `.gitignore`), audit a sample of large JSON files for `email`/`username`/`hostname`/`wandb_run_id` keys, list figure PDFs that may carry matplotlib `Author` metadata. See `superpowers:dispatching-parallel-agents` for how to launch these concurrently. ## Phase 2: Plan the deletions and edits From the audit, build three lists: **A. `git rm` — identity-bearing files** (typical patterns; project-specific paths): - Named-authors paper wrapper(s) and their compiled PDFs (often archived, e.g. `paper/archive/`) - Historical paper versions (often `paper/historical_papers/`, `paper/historical_sections/`) - Personal-path files: any `*.log` containing `/home/<user>/...` stack traces - Internal working docs: citation audits, paper checklists, todo files - `paper/CLAUDE.md`, root `CLAUDE.md` if they contain personal paths - `wandb/` directory if tracked — `wandb-metadata.json` contains your email - Upload-to-HF scripts (often have your HF org name + author names in docstrings) - macOS/IDE noise: `.DS_Store`, `__MACOSX/` **B. `git rm` — internal-only docs** (not identity leaks, but reduce review surface): - Citation verification reports, paper-writing checklists, workshop-submission TODOs - `original_vs_workshop_audit.md`-style internal comparison docs - Personal todo files **C. In-place scrubs** — files that stay but contain identifying lines: - `USER_AGENT = "...(<your-email>)"` in build scripts → drop the email - "Investigator: Claude (under <name>)" in research notes → "under the lead author" - "Raise blockers against <name>" → "with the lead investigator" - Anywhere prose names you/your collaborators (rare in research notes) ## Phase 3: Branch creation and surgery ```bash # Branch from main — DO NOT switch back to main with uncommitted changes git checkout main && git pull git checkout -b anon-submission ``` **Pause and verify before any bulk delete.** Run `git branch --show-current` and `git status` to confirm you're on `anon-submission` with main's tree intact. Real-session pattern: users sometimes ask to "check the branch" before the first `git rm` — that's healthy. A bulk delete on the wrong branch is recoverable (the files are still in main's history) but disorienting; better to confirm than rush. ```bash # Apply the deletions (group by category for reviewable diffs) git rm -r paper/archive paper/historical_papers paper/historical_sections git rm paper/<named-author-wrapper>.{tex,pdf} git rm paper/CLAUDE.md paper/<internal-investigation>.md git rm scripts/<upload-to-hf>.py git rm -r wandb git rm <log-with-home-paths> # ... etc per audit findings git rm --ignore-unmatch .DS_Store paper/.DS_Store # Apply in-place edits (use Edit tool on each file) # - drop email from USER_AGENT # - rename "<name>" mentions to "the lead author" / "the investigator" ``` ## Phase 4: pdf.js compatibility (LaTeX papers) **anonymous.4open.science renders PDFs via pdf.js (Mozilla)**, which handles default LaTeX URW Times Type 1 fonts poorly — visible as smushed-together characters / broken kerning. The fix is two lines in the LaTeX preamble, *before* `microtype` and the conference style file: ```latex \usepackage{cmap} % must come BEFORE fontenc \usepackage[T1]{fontenc} % T1 encoding has glyph-width tables pdf.js handles ``` `cmap` is sometimes missing from minimal TeX distributions: ```bash tlmgr install cmap # if you get "File `cmap.sty' not found" ``` After adding these, **page count typically does not change** (verify; if it does shift across the venue's main-paper page limit, back out and pick a different fix like `\usepackage{newtxtext,newtxmath}`). **Visual confirmation is mandatory** — page count tells you nothing about kerning. After the anon URL is live, ask the user to open the PDF preview on anonymous.4open.science (or open it yourself if you have a browser tool) and confirm characters aren't smushed. A passing build with bad rendering is the failure mode this fix addresses. ## Phase 5: PDF metadata scrub Even with anonymous LaTeX (`\icmlauthor{Anonymous Authors}{anon}`), hyperref and pdfTeX bake the title, anonymized author string, subject, and creator into PDF metadata. **This survives the LaTeX-side anonymization.** Scrub via pypdf: ```python # uv run --with pypdf python <<'EOF' from pypdf import PdfReader, PdfWriter from pathlib import Path pdfs = sorted(set(Path("figures").rglob("*.pdf")) | {Path("paper/<main>.pdf")}) for p in pdfs: if not p.exists(): continue r = PdfReader(str(p)) w = PdfWriter(clone_from=r) w.add_metadata({ "/Author": "", "/Creator": "", "/Title": "", "/Subject": "", "/Keywords": "", "/Producer": "", }) tmp = p.with_suffix(".pdf.scrubtmp") with open(tmp, "wb") as f: w.write(f) tmp.replace(p) EOF ``` **Re-run this after every LaTeX rebuild** — `latexmk` writes fresh metadata each pass. ## Phase 6: Verify Critical and non-negotiable. The whole point of the branch is that these checks pass. ```bash # 1. Build still works cd paper && latexmk -pdf -interaction=nonstopmode <main>.tex && cd .. # 2. Tests still pass (skip slow GPU tests if needed) uv run pytest # 3. Final identity-string sweep — all should return ZERO tracked-text hits git grep -i -n -I -E "<your-name-tokens>|<github-handle>|<institution>|<advisor>|@gmail|@<institution>" git grep -n -I -E "/home/<user>|/Users/<user>" # 4. PDF metadata uv run --with pypdf python -c " from pypdf import PdfReader import sys for p in sys.argv[1:]: md = PdfReader(p).metadata or {} bad = {k: v for k, v in md.items() if v and any(s in str(v).lower() for s in ['<your-name-lowercase>','<institution-lowercase>'])} print(p, '→', 'CLEAN' if not bad else f'LEAKS: {bad}') " paper/<main>.pdf figures/**/*.pdf ``` **Triage the grep hits:** - Identity hits in source files / docs → real leaks, fix. - Identity hits in **binary files** (PNG, PDF stream bytes) → almost always false positives in compressed image data. Verify via `pdftotext` / `strings` extraction; if no actual rendered text contains the name, ignore. - Identity hits in **dataset CSVs/JSONLs** as part of LLM-generated text (e.g. a Tevet completion mentions "Matthew" as a Bible character) → not a leak, common name in eval data. - Bibliography entries citing advisor's papers → **not a leak** under most double-blind rules; third-person citations of one's own / advisor's prior work are explicitly allowed. ## Phase 7: Commit + push ```bash # Use an explicitly anonymous identity (defense in depth — safe even if # repo is later shared without anonymous.4open.science in front) git add -A git -c user.name="Anonymous" -c user.email="anonymous@example.com" \ commit -m "<venue> submission" # Push to remote (regular GitHub; anonymous.4open.science fetches from there) git push -u origin anon-submission # OPTIONAL: full single-commit orphan branch (drops inherited git history # from main entirely — only matters if reviewers may clone the public repo # directly, bypassing anonymous.4open.science). Destructive of the branch # ref; ASK USER before doing this. ``` ## Phase 8: After receiving the anonymous URL ### Order of operations (subtle but matters) 1. **Push `anon-submission` to GitHub first** with placeholder URLs intact (Phase 7). 2. **User submits the GitHub URL** (e.g. `github.com/<user>/<repo>/tree/anon-submission`) to anonymous.4open.science. 3. **anonymous.4open.science returns a stable mirror URL** like `https://anonymous.4open.science/r/<repo>-67E6/` (random 4-character hash suffix). 4. **NOW you can update the `\projectGithubUrl` macro** to the anon URL. Rebuild, re-scrub metadata, commit, push. 5. **Mirror to `main` with the real URL** in the same `\projectGithubUrl` slot. The chicken-and-egg trap: you can't put the anon URL into the paper before submitting, and submitting requires the paper. The pattern above breaks the cycle by accepting one round-trip — push placeholder, submit, push real URL. ### The macro-as-unifying-device pattern Define `\projectGithubUrl` once per branch in the LaTeX preamble (different value per branch). Every footnote, prose mention, and "Released artefacts" paragraph references the macro, never the literal URL. Result: - The same `\input{}`'d section files (`01_motivation.tex` etc.) work on both `main` and `anon-submission` — the URL changes by virtue of the per-branch macro definition. - You can re-apply identical `Edit` calls to both branches when changing footnote prose. - **Do not cherry-pick** the `main` URL-update commit onto `anon-submission` (or vice versa). Cherry-pick brings the `\newcommand{\projectGithubUrl}{...}` line, which has the wrong URL for the destination branch. Re-do the prose Edits on the second branch instead; the macro definition stays branch-local. ### What to update 1. **On `anon-submission`**: replace placeholder `\projectGithubUrl` macro / footnote text with the anon URL. If data ships in-repo, also update the prose where the dataset is described to point at its in-repo path (e.g. "released as a public dataset under `results/<dataset>/` in the project repository"). Place the URL in **footnote 1** — usually the first paragraph of the body section that mentions code release; reviewers shouldn't have to flip pages to find it. Rebuild → re-scrub PDF metadata → commit (anonymous identity) → push. 2. **On `main`**: same prose updates, but with the **real** repo URL (`https://github.com/<user>/<repo>`). Bundle the cmap/T1 fontenc fix into this commit too, so `main`'s PDF benefits from the same pdf.js compatibility. Commit (regular identity), and **ask before pushing main** — pushing to a public repo is a shared-state action; the user owns that decision. ## Common gotchas (caught in real sessions) - **Test files hardcoding the anonymized .tex path.** `tests/test_paper_macros.py` (or equivalent) often reads the named-authors paper to verify macros resolve. Switch the test to read the anonymous wrapper. Easy to miss because tests pass on `main` but break on `anon-submission` after deletion. - **`wandb/` is tracked.** Sometimes a developer didn't add `wandb/` to `.gitignore`. The directory contains `wandb-metadata.json` with your literal email address. Always grep for `wandb/` in the audit; `git rm -r wandb/` if tracked. - **Untracked-then-tracked scripts.** A file that was untracked at session start can become tracked between audit and commit. Re-run `git grep` for personal paths AFTER all `git rm`s, AFTER all edits, BEFORE pushing. - **`git grep` matches in binary files.** Compressed image streams in PNGs/PDFs occasionally contain byte sequences that match a name. Verify with `strings` (PNG) or `pdftotext` (PDF). If the rendered text doesn't contain the string, it's a false positive.