[denniswu28]

Summary

Sets up CI that tests the whole repository with coverage, and adds fault-injection ("chaos monkey") and survey-workflow test suites. Stacked on ram/clean-up; retarget to dev/main once that merges.

CI (.github/workflows/ci.yml)

• Runs on pull requests into any branch (so stacked branches like this one get CI), pushes to main/dev, and manual dispatch.
• One test matrix: Python 3.9–3.14 on Ubuntu 24.04, plus 3.9 and 3.14 on macOS. Every job installs sshd and runs the whole suite with the loopback SSH tests, which previously ran only 2 files in a separate job.
• A coverage job combines coverage from all 8 jobs, writes the report to the job summary, uploads XML/HTML, uploads to Codecov (OIDC, no secret), and enforces a 90% floor in CI itself. Codecov statuses are informational.
• distribution-and-docs additionally runs twine check --strict and smoke-tests both hm and hallmark.
• Actions updated to current majors; ruff exclusions moved so ruff check . works.

Nightly (.github/workflows/nightly.yml): chaos tests with fresh seeds and 2,000 random operations per seed (Linux 3.9/3.14, macOS 3.14), and live downloads of ~2 MB from DESI DR1 and EHT/CyVerse. It also runs on PRs that touch these tests, since schedules only start from main.

Tests

• test/http_server.py: a real loopback HTTP server (python/Apache/CyVerse listings) with scripted faults: resets, short and unannounced-length bodies, 404/429/5xx, stalls, slow drips, bit flips, redirects.
• test/test_survey.py (-m survey): one scenario per doc/usecase.rst use case, plus DESI-like and EHT-like releases, release updates, silent corruption, Git and snapshot clones. No request leaves the machine.
• test/test_chaos_*.py (-m chaos): network faults, full disk and I/O errors, SIGKILL at chosen calls, and seeded random operation sequences checked against repository invariants.
• test/test_survey_live.py (-m survey_live, opt-in): real DESI DR1 and EHT downloads, size-capped, and skipped when an archive is down.

Bugs found (strict expected failures; each fix goes on its own branch)

• Truncated download accepted when the catalog has a size but no checksum: Truncated download accepted when the catalog records a size but no checksum #54
• Dothm.save_state writes state files non-atomically, so a failed add can leave mixed generations: A failed add can leave config.yml, meta.yml and data.tsv from different states #55
• A checkout killed partway cannot be rerun: A checkout interrupted partway cannot be rerun #56
• add_worktree rerun after a crash leaves the worktree without files: add_worktree rerun after an interruption leaves the worktree without files #57
• Checkout before the first commit raises a raw GitCommandError: Checkout before the first commit shows a raw Git error #58

Also fixes a Python 3.9-only test failure caused by Click 8.1's CliRunner (it never ran in CI on ram/clean-up).

Needs an org admin

Install the Codecov GitHub App on lanisrc, then rerun the coverage job. Until then the upload step logs a warning and CI is gated by the in-workflow floor.

Testing

• Local mirror of CI: full suite with SSH tests on Python 3.9, 3.13 and 3.14 → 701–702 passed, 7 strict expected failures, only opt-in skips; combined branch coverage 91.9%.
• actionlint on both workflows; codecov.yml validated; twine check/Sphinx -W pass.
• Network chaos module run 40× on Python 3.9 with no failures; both monkeys run with 20 seeds × 300 steps.
• Also confirmed hm add . from a subfolder drops staged files outside it #53 (hm add . from a subfolder drops staged rows); not fixed here.
• Live tests: DESI DR1 passes; CyVerse was degraded at the time of testing (slow listings, 503s), which the tests now skip instead of failing.
• GitHub Actions on this PR: all 15 checks green. Each of the 8 test jobs ran the whole suite with SSH enabled (701–702 passed, 7 strict expected failures, no SSH skips); combined coverage on CI is 91.93% (floor 90, unchanged since floor(total) − 1 = 90). Nightly also ran through its path filter: chaos (3 seeds × 300 steps per lane) passed on Linux 3.9/3.14 and macOS 3.14; live DESI and one EHT test passed, one EHT test skipped because CyVerse timed out.
• The Codecov step obtained an OIDC token, but downloading Codecov's CLI failed with a TLS handshake error on cli.codecov.io, so nothing was uploaded; the step is non-blocking. Uploads also need the Codecov app installed (above).

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[denniswu28]

Retiring this draft. Work has moved from ram/clean-up to codex/function-atomic-replay-20260928, and #61 ports the CI plumbing from here onto that branch. The chaos and survey suites and nightly.yml weren't ported; they stay on ci/test-automation if we want them later.