queue intake: Strong Lensing Cosmology with Population-level Calibrated Neural Ratio Estimation #11
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| name: Queue filing | |
| # The dashboard's 📥 `queue-intake` / 📑 `queue-cite` buttons open prefilled | |
| # issues — from the reading queue or from either suggestion tier | |
| # (`arxiv-inbox.md`, `arxiv-interests.md`), which the issue's `file:` names; | |
| # this workflow has Claude file the named paper — bibliography entry, | |
| # wiki sources section (minimal for cite, full stub for intake, the human's | |
| # notes folded in), DONE-mark on the queue line — and opens a reviewable PR | |
| # that closes the issue. Merge stays human. | |
| # | |
| # Trigger is `labeled` only: GitHub fires it both for labels applied at | |
| # creation (the dashboard path) and for labels added later, and using it alone | |
| # avoids the double-run an `opened`+`labeled` pair would cause. Only | |
| # owner/member/collaborator-authored issues act (public repo — same gate as | |
| # queue_actions.yml), and only triage+ users can apply labels at all. | |
| # | |
| # The PR is created with the runner's GITHUB_TOKEN, so `pull_request` | |
| # workflows (validate.yml) do NOT run on it — `make validate` + pytest run | |
| # here as the gate instead, before anything is pushed. | |
| # | |
| # Claude runs with tools scoped to workspace edits plus arXiv lookups; the | |
| # deterministic steps below stage explicit paths only — never `git add -A`. | |
| on: | |
| issues: | |
| types: [labeled] | |
| # contents: write → push the filing branch; pull-requests/issues: write → the | |
| # PR + failure comment; id-token: write → claude-code-action's OIDC startup | |
| # (same requirement as PyAutoMind's arxiv_papers.yml). | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| issues: write | |
| id-token: write | |
| concurrency: | |
| group: queue-filing-${{ github.event.issue.number }} | |
| cancel-in-progress: false | |
| jobs: | |
| file-paper: | |
| if: >- | |
| contains(fromJSON('["queue-intake", "queue-cite"]'), | |
| github.event.label.name) && | |
| contains(fromJSON('["OWNER", "MEMBER", "COLLABORATOR"]'), | |
| github.event.issue.author_association) | |
| runs-on: ubuntu-latest | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| # gh needs explicit repo context in the pre-checkout secret-guard step. | |
| GH_REPO: ${{ github.repository }} | |
| ISSUE: ${{ github.event.issue.number }} | |
| steps: | |
| - name: Require the Claude OAuth token | |
| env: | |
| TOKEN: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }} | |
| run: | | |
| if [ -z "$TOKEN" ]; then | |
| echo "::error::CLAUDE_CODE_OAUTH_TOKEN is not set on this repo — add it under Settings → Secrets and variables → Actions to enable queue filing." | |
| gh issue comment "$ISSUE" --body \ | |
| "Queue filing is not enabled yet: the CLAUDE_CODE_OAUTH_TOKEN secret is missing on this repo (Settings → Secrets and variables → Actions). File this paper from a Claude Code session instead, or add the secret and re-apply the label." | |
| exit 1 | |
| fi | |
| - uses: actions/checkout@v4 | |
| # The board tests import the family look from the Brain | |
| # (PyAutoBrain/board/_theme.py — moved there in dcd1e2c, which added | |
| # this step to validate.yml and knowledge_board.yml but not here). | |
| # Without it the gate's pytest — and Claude's own in-prompt gate, which | |
| # is told to fix its own mistakes until green but cannot fix a missing | |
| # checkout — dies on 30 tests/test_board.py errors after the filing | |
| # work is already done. So it lands before the Claude step, not just | |
| # before the gate. | |
| - uses: actions/checkout@v4 | |
| with: | |
| repository: PyAutoLabs/PyAutoBrain | |
| path: PyAutoBrain | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| # The gate below (and Claude's own in-sandbox check) runs pytest; the | |
| # bare runner doesn't ship it — its absence failed the first live run. | |
| - name: Install the test runner | |
| run: pip install pytest | |
| - name: Stash the request for Claude | |
| env: | |
| # env, never inline interpolation — issue text is untrusted input. | |
| ISSUE_BODY: ${{ github.event.issue.body }} | |
| LABEL: ${{ github.event.label.name }} | |
| run: | | |
| printf '%s' "$ISSUE_BODY" > /tmp/issue_body.txt | |
| printf '%s' "$LABEL" > /tmp/issue_label.txt | |
| - name: File the paper with Claude | |
| uses: anthropics/claude-code-action@v1 | |
| with: | |
| # Claude subscription OAuth token — NOT an API key (the org pattern | |
| # from PyAutoMind arxiv_papers.yml / morning_status.yml). | |
| claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }} | |
| # Default-hidden output masks real failures — surface everything. | |
| show_full_output: true | |
| # Workspace edits + the repo's own gates + arXiv metadata lookups. | |
| # No git/gh: the deterministic steps below own branch/commit/PR. | |
| claude_args: '--allowedTools "Read,Glob,Grep,Edit,Write,Bash(make:*),Bash(python:*),Bash(python3:*),WebFetch(domain:arxiv.org),WebFetch(domain:export.arxiv.org)"' | |
| prompt: | | |
| You are filing one paper into this PyAutoMemory checkout. | |
| Read /tmp/issue_body.txt (a dashboard queue request). Extract: | |
| - `file:` — which file the line lives in: `reading-queue.md` | |
| (already queued to read), or one of the two overnight suggestion | |
| tiers, NOT yet in the queue — `arxiv-inbox.md` (strong lensing) | |
| and `arxiv-interests.md` (everything else). Absent means | |
| reading-queue.md. | |
| - `section:` — the reading-queue section header, | |
| - `line:` — the exact line as written. A suggestion-tier line is | |
| prefixed `<YYYY-MM-DD> — `, and an arxiv-interests.md one may | |
| carry a further `[Topic] ` after that date. Neither is part of | |
| the title: strip both before using the title anywhere. (The | |
| topic is the same value as `section:`, kept on the line so the | |
| file round-trips on its own.) | |
| - `notes:` — the human's free-text notes; treat as absent if it | |
| still holds the "(optional — replace this…)" placeholder. | |
| Read /tmp/issue_label.txt: `queue-intake` (full filing) or | |
| `queue-cite` (minimal, citeable-only). | |
| Follow this repo's documented workflow — bibliography/README.md | |
| "Adding a paper" and wiki/CLAUDE.md's schema: | |
| 1. Identify the paper. Use the arXiv ref if the line has one; | |
| otherwise search arXiv by title (WebFetch against arxiv.org / | |
| export.arxiv.org only). Get authoritative metadata: authors, | |
| year, arXiv id, journal if published. | |
| 2. Add the canonical BibTeX entry to the bibliography (the single | |
| canonical .bib file per bibliography/README.md). Follow the | |
| README's key convention exactly. | |
| 3. Wiki sources page: pick the sub-wiki whose domain matches the | |
| section (e.g. "Strong Lensing" → wiki/lensing/); check the | |
| sub-wiki index if unsure. In the matching sources/*.md page: | |
| - queue-cite → add a MINIMAL section: heading, the | |
| `**Canonical BibTeX key:**` marker with the new key, and the | |
| human's notes (lightly cleaned up) — nothing deeper. | |
| - queue-intake → add a full stub section per wiki/CLAUDE.md, | |
| folding the notes into the summary. | |
| 4. Record it as read, which depends on `file:`: | |
| - `reading-queue.md` → prefix the exact `line:` inside its | |
| `## section` with `DONE <today's date> — ` (never delete it). | |
| - `arxiv-inbox.md` or `arxiv-interests.md` → there is no queue | |
| line yet. Append `DONE <today's date> — <title>[ — <ref>]` to | |
| the end of the `## section` in reading-queue.md (the paper is | |
| being filed now, so it enters the queue already read), then | |
| delete the line from whichever of those two files `file:` | |
| names. A suggestion line is not reading history, so deleting | |
| it is correct — the DONE line it becomes is the history. | |
| 5. Run `make validate` and `python -m pytest tests/ -q`; fix your | |
| own filing mistakes until both are green. | |
| Touch ONLY bibliography/, wiki/, reading-queue.md, | |
| arxiv-inbox.md and arxiv-interests.md. Do not | |
| commit — the workflow handles git. If the paper cannot be | |
| identified confidently, write the reason to /tmp/filing_error.txt | |
| and stop without editing anything. | |
| - name: Abort cleanly if Claude could not identify the paper | |
| run: | | |
| if [ -f /tmp/filing_error.txt ]; then | |
| gh issue comment "$ISSUE" --body-file /tmp/filing_error.txt | |
| echo "::error::filing aborted — reason posted to the issue" | |
| exit 1 | |
| fi | |
| - name: Gate the filing (validate + tests) | |
| run: | | |
| make validate | |
| python -m pytest tests/ -q | |
| - name: Branch, commit, push, open the PR (explicit paths only) | |
| run: | | |
| git config user.name "github-actions[bot]" | |
| git config user.email "github-actions[bot]@users.noreply.github.com" | |
| branch="queue-filing/issue-${ISSUE}" | |
| git checkout -b "$branch" | |
| git add bibliography/ wiki/ reading-queue.md arxiv-inbox.md arxiv-interests.md | |
| if git diff --cached --quiet; then | |
| echo "::error::Claude produced no changes"; exit 1 | |
| fi | |
| git commit -m "queue: file paper from #${ISSUE}" | |
| # claude-code-action rewires the checkout git credentials for its | |
| # own short-lived OIDC token (the first live run died here with | |
| # 'Invalid username or token') — push with the job token explicitly. | |
| git push "https://x-access-token:${GH_TOKEN}@github.com/${GH_REPO}.git" "HEAD:refs/heads/${branch}" | |
| { | |
| echo "Files the paper requested in #${ISSUE} (label: $(cat /tmp/issue_label.txt))." | |
| echo | |
| echo "Rendered by claude-code-action from the issue's section/line/notes;" | |
| echo "\`make validate\` + \`pytest tests/\` ran green in the filing workflow" | |
| echo "(GITHUB_TOKEN-created PRs do not trigger validate.yml)." | |
| echo | |
| echo "Closes #${ISSUE}." | |
| } > /tmp/pr_body.md | |
| if gh pr create --base main --head "$branch" \ | |
| --title "queue filing: paper from #${ISSUE}" \ | |
| --body-file /tmp/pr_body.md; then | |
| gh issue comment "$ISSUE" --body \ | |
| "Filing PR opened: $(gh pr view "$branch" --json url --jq .url). Review and merge to complete the intake." | |
| else | |
| # Repo/org policy can forbid Actions-created PRs. The branch is | |
| # pushed and gated — degrade to a one-tap PR link, not a failure. | |
| gh issue comment "$ISSUE" --body \ | |
| "Filing branch pushed and gated: \`${branch}\` — but this repo's policy blocks Actions from opening PRs. Open it with one tap: ${GITHUB_SERVER_URL}/${GH_REPO}/compare/main...${branch}?expand=1 — or enable 'Allow GitHub Actions to create and approve pull requests' (Settings → Actions → General) to make this automatic." | |
| fi | |
| - name: Report failure on the issue | |
| if: failure() | |
| run: | | |
| gh issue comment "$ISSUE" --body \ | |
| "Queue filing failed — see the workflow run: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}. The issue stays open; file manually from a Claude Code session if needed." || true |