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Release 2026.3.2 - #121
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Release 2026.3.2#121
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Exits 1 without writing when schema.json is out of date, so the check doesn't depend on the working tree being clean.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.
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.
Agent harness: AGENTS.md, bin/check and bin/t
Opening or pushing to a PR moves its linked issues to In review, and merging it into a release branch moves them to Pending release. A release PR into the default branch gets a Closes line for every issue its branch picked up, so GitHub closes them when the release merges. Issues only ever move forward. Adds a pull request template whose Closes line feeds the automation.
GitHub turns a Closes line into an issue link only on PRs into the default branch. On a PR into a release branch it stays a plain mention, so the workflow missed issues named that way. The script now reads closing lines from PR descriptions as well as the sidebar links.
…s-automation ci: move linked issues across the backlog board from PR events
agct downloads the hg19<->hg38 chain files on first use, through certifi. certifi 2026.10.18 dropped the emSign roots that UCSC's certificate chain ends at, so every mapping job in the rebuilt 2026.3.1 image failed on liftover with CERTIFICATE_VERIFY_FAILED. Download both files at build time with curl, which uses the system trust store, verify them against UCSC's md5s, and write them under WAGS_TAILS_DIR with the names agct's wags-tails lookup expects. The build runs a test that loads both converters with agct's downloader patched to raise, so a change in that naming fails the build rather than production. Pinning certifi was rejected: it only defers the next root change.
…c-chainfiles fix(docker): bake the UCSC liftover chain files into the image
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coverage: 0.0%. remained the same — mavedb-dev into mavedb-main |
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Fixes mapping, which has failed in every environment since the 2026.3.1 image was deployed: the image now ships the UCSC liftover chain files instead of downloading them at runtime (#118, closes #117). The other changes are repo tooling and CI only (#113, #116).
Merge after the version bump (#120) lands on
mavedb-dev.After deploy: rerun mapping for the score sets whose mapping failed since 2026-10-19 16:56 UTC.