chore(migration): step 07c build the bagel-cli image from the release…

[surchs]

Title: chore(migration): step 07c build the bagel-cli image from the release wheel (R3)
Branch: migration/step-07c

Can be squash-merged or merged; it imports no history.

Summary

• Dockerfile: tools/bagel-cli/Dockerfile is replaced by the plan's wheel-based Dockerfile. It copies tools/bagel-cli/dist/*.whl, fails unless exactly one wheel is present, and pip installs it; nothing is installed from PyPI or from source.
• Ignore file: tools/bagel-cli/Dockerfile.dockerignore contains * and !tools/bagel-cli/dist/*.whl.
• Deleted: Dockerfile.nightly and Dockerfile.nightly.dockerignore, plus the obsolete tools/bagel-cli/.dockerignore (see Deviations).
• just: just build bagel-cli runs rm -rf tools/bagel-cli/dist, uv build --wheel in tools/bagel-cli, then docker build -f tools/bagel-cli/Dockerfile -t neurobagel/bagelcli:local . from the root.
• Docs:
  • bagel-cli README: the Docker section is replaced with the content the plan requires, plus one paragraph on just build bagel-cli, the root build context and the one-wheel check.
  • Root README: an R3 row linking to it.

Checks run

Check	Result
just build bagel-cli; docker run --rm neurobagel/bagelcli:local --version vs. uv run bagel --version	both bagel 0.11.7.dev2145
docker run --rm --entrypoint pip neurobagel/bagelcli:local show -f bagel	lists files under bagel/communities/ (51) and bagel/pipeline-catalog/ (5)
Build with two wheels in tools/bagel-cli/dist	fails at RUN test "$(ls /tmp/*.whl | wc -l)" -eq 1 ... (exit code 1)
ls tools/bagel-cli/Dockerfile.nightly*	nothing
grep -rn "pip install --no-cache-dir bagel$" tools/bagel-cli	nothing
BuildKit "transferring context"	1.24 MB (the wheel only)
scripts/check-unchanged.sh	OK
bagel-cli / api / federation-api tests	215 / 188 / 111 passed
query-tool and annotation-tool static checks; just build api|federation-api|query-tool	pass
just lint	passes

Documentation check: in a fresh --recurse-submodules clone of this branch, from the repository root, the README's three local build commands ran verbatim:

• rm -rf tools/bagel-cli/dist, (cd tools/bagel-cli && uv build --wheel) and docker build -f tools/bagel-cli/Dockerfile -t neurobagel/bagelcli:local . all succeeded.
• docker run --rm neurobagel/bagelcli:local --version printed bagel 0.11.7.dev2146, which equals the wheel's version.
• just build bagel-cli succeeded.
• docker pull neurobagel/bagelcli and docker run --rm neurobagel/bagelcli --help work.
• apptainer pull was not run (Apptainer is not available locally).

Deviations from the plan

• Extra deletion: also deleted tools/bagel-cli/.dockerignore. It served builds with the tool folder as context, is ignored with the root context, and lists dist, the folder the new image builds from. Plan updated.
• Nightly build check: Step 4's skipped Dockerfile.nightly check is now covered here. The single Dockerfile builds an image whose version matches uv run bagel --version.
• Not in CI yet: the bagel-cli image is not built by CI in this step. Nightly (Step 11) and release (Step 13) jobs build it from the uploaded wheel.

🤖 Generated with Claude Code