rbio: add compose:* + new dev:* + test:all (local dev surface)

[davidsmejia]

Issue Number

#3572

Purpose/Implementation Notes

• bin/lib/compose.py (new) - wraps docker compose for the local stack. Takes ownership of the rename: compose:up / compose:down replace dev:up / dev:down (which are removed). compose:manage is new - runs a Django management command in a named service container; collapses what would have been separate "manage" + "shell" commands since shell is itself a manage.py subcommand.

• bin/lib/dev.py (rewrite) - higher-level local workflows. Replaces the old cmd_dev_up/down (moved to compose.py) with three orchestration commands:

  • dev:pipeline - survey an accession, drain its job queue locally (port of scripts/run_full_pipeline.py, talks to compose directly)
  • dev:job - run a single downloader/processor job in a worker container (replaces workers/run_job.sh, image as positional arg so no implicit default-to-downloaders surprise)
  • dev:janitor - run cleanup logic in a smasher container (replaces workers/run_janitor.sh; no memory cap — local does not mirror Batch limits, Batch has its own)

• bin/lib/test/all.py (new) - test:all chains common:update + each
  test:* sequentially. Matches scripts/run_all_tests.sh behavior.

• bin/lib/test/init.py - register test:all in the aggregated COMMANDS.

• bin/rbio - register the compose namespace.

Methods

N/A

Types of changes

• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)

Functional tests

rbio smoketesting

Checklist

• Lint and unit tests pass locally with my changes

Screenshots

N/A