NeuralGraph/.gitignore at main · saalfeldlab/NeuralGraph · GitHub

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# Files in root folder (Claude experiment logs)
/*.md
/*.log
/*.txt
!README.md
!instruction_*.md

# Project-specific directories
Data/
scratch/
log/
graphs_data/
tmp_data/
results/
vis/
vis*/
archive/
src/models/data/
src/NeuralGraph/scripts/tmp/
src/NeuralGraph/ODEs/logs/
src/NeuralGraph/ODEs/config/
runs/
Claude_experiments/
papers/
.claude/

# Media and data files
*.png
*.jpg
*.gif
*.tif
*.svg
*.mp4
*.avi
*.pdf
*.xml
*.npz
*.csv
*.ijm
*.bkup
*.html
!assets/landscape_quadrant_interactive.html
!assets/landscape_partitioned_interactive.html
docs/

# Experiment documentation in config folders
config/fly/**/*.md
config/zebrafish/**/*.md

# Exception: allow assets folder images
!assets/*.png
!assets/*.jpg
!assets/*.gif
!assets/*.svg

# Exception: allow PNG figures in LatentEvolution
!src/LatentEvolution/**/*.jpg

# IDE files
*.iml
.idea/
.attach*

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

# C extensions
*.so

# Distribution / packaging
.Python
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/

# 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
.pybuilder/
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
# .python-version

# pipenv
# Pipfile.lock

# poetry
# poetry.lock

# pdm
# pdm.lock
.pdm.toml

# PEP 582
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# 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/

# pytype static type analyzer
.pytype/

# Cython debug symbols
cython_debug/

# Docker
.devcontainer/

# conda environments
.conda_envs/

# claude local settings
.claude/settings.local.json
.claude.md

# nohup logs
nohup*.out

# misc
instantNGP/*.tif
**/*.pth
**/*.npy
instantNGP/imageio_ffmpeg
.julia_env/
.julia/
**/.julia_env/
**/.julia/
**/.nfs*


/.quarto/
**/*.quarto_ipynb