Remove debug self.save() from build_kbase_genome_from_api - #25
Merged
Conversation
This debug save requires NotebookUtils.save() which is only available in KBase Jupyter notebooks. Callers outside that environment (e.g., REST APIs, CLI scripts) have to monkey-patch BVBRCUtils.save to avoid an AttributeError. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
cshenry
pushed a commit
that referenced
this pull request
Jul 6, 2026
Adds the kbu-run Claude Code skill at src/kbutillib/harness/skills/kbu-run/SKILL.md driving the harness loop: pull from BERIL, classify via PRD-A graduated-execution policy reading preferences.md thresholds (defaulting to full/consult when uncertain), choose local vs h100, run via kbu harness run, verify outputs, append DEVLOG.md, and on success stop and prompt 'Push results back to BERIL now? (y/N)' before pushing; on failure stop, append traceback to DEVLOG, escalate BLOCKED, edit no code. Adds tests/harness/test_skill_bundle.py (21 tests) asserting frontmatter parses with name=kbu-run, a 'Use when ...' description, allowed-tools=[Read,Bash], and user-invocable:true, plus body content checks for all workflow steps (AC #25-#26-#37). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
cshenry
pushed a commit
that referenced
this pull request
Jul 20, 2026
…ule C/D) Adds kbu king install/uninstall/status over a new vendored kbutillib.king_install module implementing the on-disk ~/king-apps/ contract (registry.json, union-recomposed CONTEXT.md, serve-king.sh launch wrapper), so KBUtilLib's modeling app self-installs into a local KING session without any cross-repo dependency or edits under ~/king-stack/king/. Ships the app bundle (bundle.json + skill.md, authored from the frozen kbu model --help surface) as package data and wires it into pyproject package-data so a non-editable install still carries it. Per agent-io/prds/king-integration-apps/fullprompt.md Module C/D, Acceptance Criteria #13-#23, #25. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
self.save("test_genome", genome)debug call fromBVBRCUtils.build_kbase_genome_from_api()(line 335)NotebookUtils.save()which is only available in KBase Jupyter notebooksBVBRCUtils.save = lambda self, name, obj: Noneto avoidAttributeErrorContext
Building the ModelSEED REST API, we call
build_kbase_genome_from_api()from a FastAPI service process where NotebookUtils isn't available. Chris confirmed this save was a testing leftover and can be removed.Test plan
build_kbase_genome_from_api()still works without the save call