integrate and harden useful upstream patches#193
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The wrapper masked a signal-killed child (spawnSync status === null) as a clean exit 0. A subprocess killed by SIGINT/SIGTERM/SIGKILL therefore looked successful to callers and CI. Report failure using the shell convention 128 + signal number when status is null and a signal is present, and fall back to exit 1 for the no-status/no-signal case.
Add NMR compound inference skill for 1D 1H/13C spectrum analysis. Uses nmrglue for processing Bruker/NMRPipe/text data, generates spectrum plots and peak tables, and compares against BMRB, HMDB, SDBS, and nmrshiftdb2 reference libraries. - SKILL.md with full OpenScience frontmatter - scripts/nmr_candidate_report.py: evidence package generator - references/standard-libraries.md: library targets and comparison rules
Bumps the actions group with 4 updates: [github/codeql-action/init](https://github.com/github/codeql-action), [github/codeql-action/analyze](https://github.com/github/codeql-action), [github/codeql-action/upload-sarif](https://github.com/github/codeql-action) and [actions/stale](https://github.com/actions/stale). Updates `github/codeql-action/init` from 4.36.3 to 4.37.0 - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@54f647b...99df26d) Updates `github/codeql-action/analyze` from 4.36.3 to 4.37.0 - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@54f647b...99df26d) Updates `github/codeql-action/upload-sarif` from 4.36.3 to 4.37.0 - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@54f647b...99df26d) Updates `actions/stale` from 10.3.0 to 10.4.0 - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@eb5cf3a...1e223db) --- updated-dependencies: - dependency-name: github/codeql-action/init dependency-version: 4.37.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: github/codeql-action/analyze dependency-version: 4.37.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: github/codeql-action/upload-sarif dependency-version: 4.37.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: actions/stale dependency-version: 10.4.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com>
… regress_out (synthetic-sciences#102) Complements the thread-cap already in main (pythonThreadCapEnv) with the axes it doesn't cover: - Reap orphaned workers: python/R kernels now spawn detached (own process group) and every kill path (timeout, abort, idle-reap, shutdown, process-exit) routes through Shell.killTree/killTreeSync, so joblib/BLAS worker children die with the kernel instead of lingering and thrashing swap. Group kill only fires when the child leads its own group (verified via /proc on Linux). - Bound concurrent compute subagents (biology/ml/physics) with an abort-aware counting semaphore (OPENSCIENCE_MAX_COMPUTE_SUBAGENTS, default 2): N parallel subagent kernels each holding a dataset copy no longer sum to an OOM. A cancelled subagent still queued unblocks immediately and leaks no slot. - Scanpy template: size regress_out's n_jobs to the worker copies that fit in RAM and skip (with guidance) only when even one won't fit; warn on a dense adata.X. regress_out stays enabled by default. Full suite green (1138 pass).
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Constraint: OpenScience exposes subscription access as openai-codex, not plain openai. Rejected: Treat all OpenAI OAuth sessions as Codex | plain OpenAI OAuth must not inherit Codex request shaping. Confidence: high Scope-risk: narrow Directive: Keep subscription-specific request shaping keyed to openai-codex OAuth credentials. Tested: bun test test/session/llm.test.ts test/plugin/codex-401-retry.test.ts test/plugin/codex-refresh.test.ts test/session/billing-gate.test.ts; bun run typecheck; live streamText smoke openai-codex/gpt-5.4-mini returned openscience-codex-ok. Not-tested: Browser interactive connect callback completion; live smoke reused existing Codex OAuth refresh token.
The science agents' prompts carry a static Skill Routing Table (ml.txt,
biology.txt, physics.txt) that names skills like peft/unsloth. When those
skills aren't loaded in the current environment the model still routes to
them and skill({name}) fails with "not found". Inject a runtime
<available-skills> section built from the real loaded registry (permission
-filtered, grouped by category) so routing targets skills that resolve;
when none are loaded, tell the model not to call the skill tool. The
curated tables stay intact as guidance.
Complements main's cross-turn text doom-loop guard, which can't see a model that re-emits the same block many times WITHIN one turn (only one finished turn exists, so the 3-turn cross-turn check never fills). Observed live with a local qwen3:4b re-printing the same research-state block ~7x in a single generation. Detect a repeated tail as the assistant text streams (throttled, O(window), bounded to the last 8KB) and break the stream — disposing the iterator aborts the underlying request so the model stops instead of spinning. The aborted turn is finalized as 'stop' so the outer loop ends cleanly. Full suite green (1135 pass).
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Summary
This integrates the useful upstream PR backlog into one validated branch, while fixing conflicts and correctness gaps found during review.
Validation
bun testfrombackend/cli: 1156 passed, 1 intentionally skipped, 0 failedbun run typecheck: 7/7 packages passedbun run buildfromfrontend/workspace: passedgit diff --check: passedThe JavaScript SDK was not regenerated because this patch does not change the generated SDK schema or route surface.