From mims-harvard-tooluniverse
Enforces safe GitHub push workflow for ToolUniverse: moves temp files to cleanup, activates pre-commit hooks with ruff, runs pytest tests, rebases main, and pushes with force-with-lease. Use for commits, CI fixes, or staging cleanups.
npx claudepluginhub joshuarweaver/cascade-data-analytics --plugin mims-harvard-tooluniverseThis skill uses the workspace's default tool permissions.
Safely push ToolUniverse code to GitHub by enforcing pre-push cleanup, pre-commit hooks, and test validation.
Conducts multi-round deep research on GitHub repos via API and web searches, generating markdown reports with executive summaries, timelines, metrics, and Mermaid diagrams.
Dynamically discovers and combines enabled skills into cohesive, unexpected delightful experiences like interactive HTML or themed artifacts. Activates on 'surprise me', inspiration, or boredom cues.
Generates images from structured JSON prompts via Python script execution. Supports reference images and aspect ratios for characters, scenes, products, visuals.
Safely push ToolUniverse code to GitHub by enforcing pre-push cleanup, pre-commit hooks, and test validation.
When the user wants to push code, fix CI, or prepare a commit, follow this workflow:
# Move session markdown files to temp_docs_and_tests/
for f in $(ls *.md 2>/dev/null | grep -v README.md | grep -v CHANGELOG.md | grep -v LICENSE.md); do
mv "$f" temp_docs_and_tests/
done
# Move root-level test scripts to temp_docs_and_tests/
for f in $(ls test_*.py 2>/dev/null); do
mv "$f" temp_docs_and_tests/
done
git status --short
Red flags - these should NEVER be staged:
*_SUMMARY.md, *_REPORT.md, SESSION_*.md in roottest_*.py in root (these are ad-hoc scripts, not real tests).env or credential filestemp_docs_and_tests/ contentspre-commit install
This enables automatic checks on every git commit:
ruff check --fix - Python linting with auto-fixruff format - Code formattingls -la .git/hooks/pre-commit
python -m pytest tests/ -x --tb=short -q
git add . or git add -A):git add src/tooluniverse/specific_file.py tests/specific_test.py
git commit -m "Clear, descriptive message"
git fetch origin
git stash # stash any uncommitted work
git rebase origin/main
git stash pop # restore uncommitted work
If rebase conflicts arise, resolve them (keep our newer changes), then:
git add <conflicted-file>
git rebase --continue
git push --force-with-lease origin <branch-name>
After pushing, verify the PR is conflict-free:
gh pr view <PR-number> --json mergeable,mergeStateStatus
# Must show: "mergeable":"MERGEABLE"
These are session notes created during development. Move to temp_docs_and_tests/ before committing:
| Pattern | Example |
|---|---|
*_SUMMARY.md | API_DISCOVERY_SESSION_SUMMARY.md |
*_REPORT.md | SKILL_TESTING_REPORT.md, TOOLUNIVERSE_BUG_REPORT.md |
SESSION_*.md | SESSION_2026_02_13.md |
IMPLEMENTATION_*.md | IMPLEMENTATION_COMPLETE.md |
BUG_ANALYSIS_*.md | BUG_ANALYSIS_DETAILED.md |
FIX_*.md | FIX_SUMMARY.md, CORRECT_FIX.md |
AGENT_*.md | AGENT_DESIGN_UPDATES.md |
Exception: README.md, CHANGELOG.md, LICENSE.md are real docs and MUST stay.
Ad-hoc test scripts like test_*.py in root are NOT part of the test suite (tests/ directory is). Move them to temp_docs_and_tests/:
| File | Purpose |
|---|---|
test_clear_tools.py | One-off tool cleanup test |
test_finemapping_tools.py | Ad-hoc tool validation |
test_metabolomics_tools.py | Ad-hoc tool validation |
test_original_bug.py | Bug reproduction |
test_pathway_tools.py | Ad-hoc tool validation |
test_protein_interaction_skill.py | Skill test |
test_reload_fix.py | Bug reproduction |
test_round10_tools.py | Ad-hoc tool validation |
.env - Environment variables with secretstemp_docs_and_tests/ - Already in .gitignore.claude/ - Claude Code configuration__pycache__/, *.pyc - Python bytecode.DS_Store - macOS metadataSymptom: KeyError: 'role' when accessing message dicts
Fix: Add return_message=True to tu.run() and use .get():
messages = tu.run(calls, use_cache=True, return_message=True)
if msg.get("role") == "tool":
Symptom: TypeError: 'Mock' object is not subscriptable
Fix: Use real dicts for all_tool_dict and add _get_tool_instance:
mock_tu.all_tool_dict = {"Tool": mock_tool}
mock_tu._get_tool_instance = lambda name, cache=True: mock_tu.all_tool_dict.get(name)
Fix F841 (unused variable): Use _ prefix or _ = func()
Fix E731 (lambda assignment): Replace with def
Symptom: git status shows temp files as modified/staged
Fix:
git rm -r --cached temp_docs_and_tests/
git rm --cached API_DISCOVERY_SESSION_SUMMARY.md
git commit -m "Remove temp files from tracking"
The project uses .pre-commit-config.yaml:
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
hooks: [end-of-file-fixer, trailing-whitespace, check-yaml, check-toml]
- repo: https://github.com/astral-sh/ruff-pre-commit
hooks: [ruff-check --fix, ruff-format]
Scope: Only files matching ^(ToolUniverse/)?src/tooluniverse/
| Task | Command |
|---|---|
| Activate hooks | pre-commit install |
| Run all tests | pytest tests/ -x --tb=short -q |
| Run specific test | pytest tests/path/test.py::Class::method -xvs |
| Check staged files | git status --short |
| Unstage a file | git restore --staged <file> |
| Remove from tracking | git rm --cached <file> |
| Move temp files | See Phase 1 commands |
| Run hooks manually | pre-commit run --all-files |
Before every push, verify:
temp_docs_and_tests/test_*.py scripts moved to temp_docs_and_tests/pre-commit install)pytest tests/ -x).env, no temp files)git add <specific-files> instead of git add .