Bump dependencies to fix 47 Dependabot security alerts

[rjpower]

Bump direct dep floor pins (ray 2.54, black 26.3.1, markdownify 0.14.1,
cryptography 46.0.6, requests 2.33, deepdiff 8.6.2, flask 3.1.3,
PyJWT 2.12, lxml-html-clean 0.4.4) and run uv lock --upgrade to pull
in transitive fixes for authlib, litellm, aiohttp, nltk, gradio,
tornado, orjson, cbor2, pyasn1, pygments, werkzeug, and others.
Remove unnecessary pydantic>=2.12.5 pin from iris.

Remaining unfixable: pillow (trackio caps <12), xgrammar (vllm-tpu
pins 0.1.27), diskcache/sqlitedict (no upstream fix), lz4_flex (cargo
already at latest compatible).

[claude]

Claude finished @rjpower's task in 1m 11s —— View job

---

PR Review: Dependency Security Bumps

• Review pyproject.toml changes
• Review Cargo.lock changes
• Verify no risky dependency changes
• Post review summary

---

Looks good overall — straightforward security bumps with a clean Cargo.lock prune. A few observations:

Python dependency changes (4 pyproject.toml files):

Package	Old	New	Notes
ray	==2.53.0	==2.54.0	Pinned across fray, levanter, marin — consistent ✅
flask	unpinned / missing	>=3.1.3	Security fix
cryptography	>=45	>=46.0.6	Security fix
deepdiff	unpinned	>=8.6.2	Pinned in levanter + marin
requests	unpinned	>=2.33.0	Security fix
PyJWT	>=2.8.0	>=2.12.0	Security fix
markdownify	==0.12.1	>=0.14.1	Exact pin → floor pin (see below)
black	==25.9.0	>=26.3.1	Exact pin → floor pin (see below)
pydantic (iris)	>=2.12.5	>=2.0	Relaxed — removal of unnecessary pin
lxml-html-clean	—	>=0.4.4	New explicit dep

Two items worth a second look:

1. markdownify changed from ==0.12.1 to >=0.14.1 — The old exact pin suggests there may have been a reason to lock this version (e.g. output format differences affecting snapshots/tests). If the test suite passes with the new version, this is fine. If there are snapshot tests for HTML→Markdown conversion, worth confirming they still match.

2. black changed from ==25.9.0 to >=26.3.1 — Note that infra/pre-commit.py hardcodes uvx black@25.9.0 (line 175), so the actual formatting version used by CI is still 25.9.0 regardless of this pin. The pyproject.toml pin only affects uv run black invocations. This mismatch is harmless now but could cause confusion later — consider either bumping the hardcoded version in pre-commit.py to match, or keeping the exact pin in pyproject.toml.

Rust Cargo.lock: Clean removal of unused transitive deps (arrow-csv, arrow-json, csv, serde/serde_json, indexmap, simdutf8, etc.) and a minor lz4_flex bump (0.12.0 → 0.12.1). This just trims the dependency tree — no concerns.

Verdict: LGTM with the caveat on the markdownify and black pin changes above. If CI (tests + lint) passes, this is safe to merge.

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[rjpower]

@claude pls rebase and fix conflicts

[claude]

Claude finished @rjpower's task in 6m 56s —— View job

---

Rebased dep-security-bumps onto main ✅

• Unshallow the runner checkout (needed — base was 285 commits behind main)
• Rebase the 6 branch commits onto origin/main (b42d3d1)
• Resolve lib/marin/pyproject.toml conflict: kept main's marin-fray / marin-rigging renames (drop old fray, rigging, ddsketch, floret, lz4) while applying the branch's version bumps (deepdiff>=8.6.2, flask>=3.1.3, markdownify>=0.14.1, lxml-html-clean>=0.4.4)
• Regenerate uv.lock via uv lock after each conflicted step (4 steps); yielded clean upgrades — ray 2.53→2.54, cryptography 46.0.5→46.0.7, deepdiff 8.6.1→9.0.0, markdownify 0.12.1→1.2.2, flask 3.1.2→3.1.3, pyjwt 2.10.1→2.12.1, requests 2.32.5→2.33.1, black 25.9.0→26.3.1, etc.
• Preserve the other 5 commits from the branch (markdownify 1.x migration, snapshots, chex, optax<0.2.7 pin, tensorstore<0.1.82 pin)
• Force-push with --force-with-lease → 07f14df71…8065f0181

Testing

• ./infra/pre-commit.py --all-files --fix → OK (ruff, black, pyrefly, license headers, markdown pre-commit all pass)
• uv run --package marin pytest tests/test_markdown.py → 10 passed
• uv run --package marin pytest tests/ -k "snapshot or markdown or resiliparse or wiki" --ignore=tests/integration → 68 passed, 4 skipped

Resulting branch history

8065f0181 Pin tensorstore<0.1.82 to avoid zarr3 S3/R2 StorageGeneration regression
2dd40d7f4 Pin optax<0.2.7 to avoid tree flatten_up_to regression
f339ab7ad Update markdown test expectations for markdownify 1.x
446d2eae7 Add chex to levanter's main deps (optax no longer pulls it in)
d2d2777d8 Migrate MyMarkdownConverter to markdownify 1.x API
80b964532 Bump dependencies to fix 47 Dependabot security alerts
b42d3d19c [iris] docs: lead §Connecting with --cluster auto-tunnel (#5001) ← origin/main

Note: I did not bump the hardcoded uvx black@25.9.0 in infra/pre-commit.py as flagged in the earlier code review — that's orthogonal to the rebase and should be addressed separately if desired.
· branch

[yonromai]

🚀