.gitignore

# Byte-compiled / optimized / DLL files
__pycache__/
.DS_Store
*.py[cod]
*$py.class
# *.json

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
#  Usually these files are written by a python script from a template
#  before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/
cover/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# celery beat schedule file
celerybeat-schedule

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/


*pt

# macOS
.DS_Store

# temporary files
src/tooluniverse/test/MeSH_desc2025.xml
src/tooluniverse/test/drugbank_full_database.xml

# IDE
.vscode/
.idea/
*.swp
*.swo
*~

# Auto-generated API documentation
docs/api/tooluniverse.*.rst
!docs/api/core.rst
!docs/api/mcp.rst
!docs/api/tools.rst
!docs/api/modules.rst
!docs/old_files/

src/tooluniverse/web_tools/

# Auto-generated tool files (moved to temporary folder)
src/tooluniverse/tools_generated/FILE_ORGANIZATION_LIST.md
temp_docs_and_tests/

# Parked tools pending API keys (not ready for publishing)
temp_tools/

# Session documentation (temporary - never push)
*_SUMMARY.md
*_REPORT.md
SESSION_*.md
IMPLEMENTATION_*.md
BUG_ANALYSIS_*.md
FIX_SUMMARY.md
CORRECT_FIX.md
AGENT_*.md
DEVTU_*.md
!README.md
!CHANGELOG.md
!LICENSE.md

# Root-level ad-hoc test scripts (not part of test suite)
/test_*.py

# Claude Code configuration
.claude/
.tooluniverse/

# Benchmark harness — dev-only, kept locally but never tracked.
# Plugin build doesn't include skills/evals/ in dist, and .gitattributes
# already excludes it from `git archive` release tarballs.
skills/evals/

# Skill iteration / evaluation workspaces — `tooluniverse-*-workspace/`
# directories hold with-skill-vs-without-skill comparison runs produced
# by the skill evaluator. They have no SKILL.md (not real skills), match
# the sync-skills.sh `tooluniverse-*` glob accidentally, and bloat plugin/
# without ever shipping to users. Keep locally for dev, never track.
**/tooluniverse-*-workspace/

# One-off outputs from working-example scripts that write to cwd
# (e.g. ddi_working_example.py). Outputs should go to /tmp or an explicit
# --output-dir, never beside the example source.
**/DDI_report_*.md
**/*_metabolomics_report*.md

# Superseded skill source — when SKILL.md is rewritten, keep the prior
# version in git history (git log / git show) instead of beside the new
# one as SKILL_OLD.md, where it ships to users and causes confusion.
**/SKILL_OLD.md
**/SKILL_v[0-9]*.md

# Dev iteration notes that lived inside skill source: comparison
# write-ups, test feedback diaries, "fixed" twin implementations.
# Belong in git history or PR descriptions, not the shipped skill tree.
**/COMPARISON_*.md
**/*_FEEDBACK.md
**/*_implementation_fixed.py
**/*_implementation_v[0-9]*.py

# Per-user auto-memory / private session notes (never push)
memory/
MEMORY.md
CLAUDE.md

# API keys & secrets
.env
.env.local
credentials.json
*_api_key*
*_token*

# Local-only harness sweep artifacts (test-all command output)
TOOL_TEST_REPORT.md
TOOL_SWEEP_TRIAGE.md

# Local-only runtime artifact from test_new_tools.py
tool_relationship_graph.json