# ====================
# Project-specific
# ====================
.notebook_contexts.json
.factory_hashes.json

# ====================
# Python
# ====================
test.py
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python

# Benchmarks - ignore data directories but keep code
benchmarks/bixbench/data/
benchmarks/bixbench/results/
benchmarks/bixbench/workspaces/
benchmarks/bixbench/groundtruth/
benchmarks/bixbench/test_capsules/
benchmarks/bixbench/__pycache__/
benchmarks/single_cell_benchmark/results/
benchmarks/single_cell_benchmark/workspaces/
benchmarks/single_cell_benchmark/benchmark_data/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
*.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/
tmp/

# Translations
*.mo
*.pot

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

# Flask
instance/
.webassets-cache

# Scrapy
.scrapy

# Sphinx documentation
docs/_build/
docs/source/_build/

# PyBuilder
.pybuilder/
target/

# Jupyter Notebook
.ipynb_checkpoints
*.ipynb

# IPython
profile_default/
ipython_config.py

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

# ====================
# Package Managers
# ====================

# pipenv
#Pipfile.lock

# UV
#uv.lock

# poetry
#poetry.lock

# pdm
#pdm.lock
.pdm.toml
.pdm-python
.pdm-build/

# PEP 582
__pypackages__/

# ====================
# Type Checkers & Linters
# ====================

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

# Pyre
.pyre/

# pytype
.pytype/

# ====================
# IDEs & Editors
# ====================

# PyCharm / IntelliJ
.idea

# VSCode
.vscode/

# Spyder
.spyderproject
.spyproject

# Rope
.ropeproject

# ====================
# Project Specific
# ====================

# Workspaces
my-app-workspace/
chatroom-workspace/
.pantheon-chatroom*/
.pantheon-chatroom-workspace*/
.pantheon-test-default-workspace/
.pantheon/

# NATS JetStream storage
jetstream_storage/

# Temporary & development
try/
tmp/
.executor/
workdir**

# Session metadata and task tracking
.notebook_sessions_metadata.json
.pantheon_tasks.json

# Ignore all markdown files in root except README.md
/*.md
!/README.md

# Ignore all JSON files in root (configs, session data, etc.)
/*.json

# Ignore test files in project root (test_*.py)
/test_*.py

# ====================
# Other
# ====================

# Celery
celerybeat-schedule
celerybeat.pid

# SageMath
*.sage.py

# Cython debug symbols
cython_debug/

# mkdocs
/site

workdir/
backup/
*.h5ad
evolution_results/

# Evolution example results (only programs/ with individual JSON files)
examples/evolution_*/*/*/programs/
examples/evolution_*/*/programs/
examples/evolution_*/data
examples/code_distillation/*/programs/

# Code distillation large files (model and cached data)
examples/code_distillation/*.pkl
examples/code_distillation/data/*.npz

.DS_Store
.uploaded_files/
*.aux
.claude/worktrees/
.worktrees/
