.gitignore

# Dist files #
##############
/build
/dist
/doc/_build
/vEcoli.egg-info
/Build_sequences.egg-info
/Fast_polymerize_sums.egg-info
/Monte_carlo_complexation.egg-info

*.out
out/
/out
.idea/
*.iml

# User files #
################
user/*
!user/user.txt
*.cprof
.ipynb_checkpoints

# Compiled source #
###################
*.pyc
__pycache__
*.so
/wholecell/utils/*.c
/doc/reference/api/
/doc/notebooks/

# OS generated files #
######################
.DS_Store
.DS_Store?
._*
.python-version
.pytest_cache
.mypy_cache/
.ruff_cache/

# VS Code files #
#################
/.vscode

# Generated Files #
###################
data/blame_test_data.json
data/vivecoli_t2.json
ecoli/composites/ecoli_configs/test_configs/test_export.json
/notebooks/test_files/
cache/

# Nextflow files #
##################
.nextflow*
nextflow_temp
trace-*

# Virtual environment #
#######################
.venv/