Deflake CI: record DOI fixtures, retry Jupyter execution e2e tests

[mmcky]

Fixes #29

Context

Four flake incidents today alone, culminating in the live-DOI test failing all three node jobs simultaneously on the sync PR #59 (doi.org throttling the runner IP range). Of the issue's options this implements (4) the real fix for the DOI tests plus (2) targeted per-test retry for the Jupyter tests — deliberately not the workflow-level retry, so genuinely deterministic tests still fail fast.

DOI tests → recorded fixtures

• doi.spec.ts now uses a mock session whose fetch serves recorded doi.org content-negotiation responses (fixtures/doi.json, captured today with the proper Accept headers — including the month=Sept quirk that previously caused live drift).
• Coverage preserved: URL normalization (the "strange characters" cases still construct a real URL), content negotiation by Accept header, and the full BibTeX/CSL-JSON parsing pipeline all still run — only the network is fixed.
• TEST_LIVE_DOI=1 runs the same cases against live doi.org as well (16 tests total; verified passing) — for fixture refresh or upstream-drift checks, e.g. from a scheduled workflow later.
• Side benefit: 8 tests run in ~30ms instead of ~4s of network round-trips.

Jupyter execution tests → targeted retry

• The e2e runner (endToEnd.spec.ts) moves from test.each to per-case test(title, { retry }, fn) so cases can declare vitest options; exports.yml gains retry: 2 on exactly the two known-environmental cases (Serial execution, Concurrent execution), each attempt with a fresh timeout. All other e2e cases keep retry: 0.

Testing

• Full monorepo build + test pass (all 56 e2e cases green through the new runner)
• DOI suite green in both recorded (8) and live (16) modes

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR aims to deflake CI by removing reliance on live doi.org network calls in DOI resolver tests (using recorded fixtures) and by enabling targeted per-test retries for known flaky Jupyter execution end-to-end cases.

Changes:

• Add retry support to the e2e test runner and set retry: 2 for the two known flaky Jupyter execution cases in exports.yml.
• Replace live-network doi.org test behavior with recorded fixtures, while keeping an opt-in mode for live DOI verification via TEST_LIVE_DOI.
• Add a changeset documenting the CI deflaking changes.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
packages/mystmd/tests/exports.yml	Adds retry: 2 for the known flaky Serial/Concurrent Jupyter execution cases.
packages/mystmd/tests/endToEnd.spec.ts	Switches away from test.each to allow per-case vitest options (notably retries).
packages/myst-cli/src/transforms/fixtures/doi.json	Adds recorded doi.org responses used by the mocked DOI test session.
packages/myst-cli/src/transforms/doi.spec.ts	Introduces a mocked DOI session backed by fixtures and optional live-doi mode.
.changeset/ci-deflake.md	Records the deflaking change as a myst-cli patch changeset.

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