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Exits 1 without writing when schema.json is out of date, so the check doesn't depend on the working tree being clean.
bin/check runs ruff check, the format check and the schema.json check in about 3 s and reports every failure in one pass. bin/t wraps pytest with CI's MAVEDB_BASE_URL. Both use .venv when present and python3 otherwise, so CI runs the same commands.
AGENTS.md (CLAUDE.md imports it) covers what the code doesn't show: the fork's branch flow, which tests run where, the schema.json contract, the GA4GH dependency pin, and the SeqRepo refget rule.
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coverage: 0.0%. remained the same — feature/bencap/agent-harness into mavedb-dev |
Deny --no-verify and reads of ~/.aws and ~/.pgpass. Ask before pushes, AWS and Elastic Beanstalk commands, the prod-API dev server and dependency changes. The same file lives in the workspace and in each repo, because Claude Code reads settings only from the folder a session starts in. These are guardrails, not a security boundary: a rewritten command can get past them.
Sessions get AWS_PROFILE=mavedb-agent-readonly, so aws commands use the read-only role (see deployment/environments/aws/agent-access.md) and fail rather than fall back to full credentials where the profile is missing. Choosing another profile asks first, replacing the blanket prompt on aws. Reading ~/.ssh is now blocked, alongside ~/.aws and ~/.pgpass.
Edits to AGENTS.md, CLAUDE.md and anything under .claude/ now ask first. Those files shape every later session, and settings.json holds the guardrails. The rules cover Edit and Write; a shell redirect into one of these files is not caught.
Prompts now cover force pushes, pushes to main, mavedb-main, mavedb-dev or release-*, AWS with an explicit profile, eb, adding a dependency and edits to settings.json itself. Ordinary feature-branch pushes, dependency updates and edits to AGENTS.md, CLAUDE.md and .claude/rules no longer ask; the never rule in the workspace AGENTS.md still covers those edits, and PR review sees the diffs.
The ui checks it with Prettier, so every copy uses that layout.
bencap
marked this pull request as ready for review
October 16, 2026 23:33
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Gives coding agents (and new contributors) the facts about this repo they can't get from the code, and one command for the checks CI runs. The mapper counterpart of VariantEffect/mavedb-api#926 and VariantEffect/mavedb-ui#746.
Changes
scripts/generate_schema.py --checkexits 1 without writing whenschema.jsonis out of date. CI used to regenerate the file and rungit diff --exit-code, which also fails on a correct schema change that isn't committed yet.bin/checkrunsruff check, the format check and the schema check in about 3 s, and reports every failure in one pass.bin/twraps pytest and setsMAVEDB_BASE_URLthe way CI does (the requests are mocked). Both use.venvwhen it exists andpython3otherwise, so CI now calls the same scripts.AGENTS.md(CLAUDE.mdimports it) covers:mavedb-dev→mavedb-main) and opening PRs with-R VariantEffect/dcd_mapping2;schema.jsonas the api's contract;bin/checkandbin/tinstead of plainpytest..claude/settings.jsonholds shared permission rules for Claude Code sessions. It blocks--no-verifyand reading~/.aws,~/.sshor~/.pgpass; setsAWS_PROFILEto the read-only agent role (VariantEffect/mavedb-deployment#54); and asks only before hard-to-undo actions: force pushes, pushes tomain,mavedb-main,mavedb-devorrelease-*, AWS with an explicit profile,eb, the prod-API dev server, adding a dependency, and edits tosettings.jsonitself. Identical copies live in each repo and the workspace, because Claude Code reads settings only from the folder a session starts in. They catch honest mistakes; they aren't a security boundary.Review notes
vrs_mapfailures only need BLAT.test_transcript.py('str' object has no attribute 'urn') andtest_seqrepo_contract.py('ChainedSeqFetcher' object has no attribute 'seq_fetchers') look like real breakage. This PR doesn't touch them.AGENTS.mdin VariantEffect/mavedb-workspace, which is private for now.Testing
bin/checkpasses. A deliberately staleschema.jsonfails--check.bin/t tests/test_mavedb_data.pypasses, as do the offline modules such astests/test_variant_projection.py.