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

# C extensions
*.so

# Distribution / packaging
.Python
src/czitools/_version.py
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/

# 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

# pipenv
#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
#   However, in case of collaboration, if having platform-specific dependencies or dependencies
#   having no cross-platform support, pipenv may install dependencies that don't work, or not
#   install all needed dependencies.
#Pipfile.lock

# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__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/
examples/pylibCZIrw_docu/newczi_mdata.czi
examples/pylibCZIrw_docu/newczi_tilewise.czi
examples/pylibCZIrw_docu/newCZI_z=16_ch=3.czi
examples/pylibCZIrw_docu/newCZI_zloc.czi
examples/pylibCZIrw_docu/newCZI_zscenes.czi

# fuse crap
.fuse_hidden*
.vscode/settings.json
/.vscode/
/.idea/
/.idea
/.vscode
/.vs

# skip folders
**/examples/pylibCZIrw_docu/**
**/demo/experimental/**
/.vscode/
**/experimental/**
**/demo/pylibCZIrw_docu/**
demo/experimental/
demo/experimental/**
demo/testing/
demo/testing/**
demo/notebooks/.ipynb_checkpoints/
data/*.zarr
data/*.xml
**/data/*.zarr
data/*.xml
data/*.html
notebooks/*.html
notebooks/*.csv
**/notebooks/data/**
**/notebooks/data/
**/notebooks/_experimental/**
demo/notebooks/_experimental/**
/old
/demo/notebooks/exports
/demo/notebooks/exports/**
/demo/notebooks/*.zarr
/demo/notebooks/*.log
/demo/notebooks/old
/demo/notebooks/old/**
/demo/notebooks/__marimo__
**/_archive/**



# skip specific files
data/CH=1_16bit.czi
data/Fluorescence_RGB.czi
/demo/experimental/lazy_read6d.py
data/CellDivision_T=3_Z=5_CH=2_X=240_Y=170_comp1.czi
data/CellDivision_T=3_Z=5_CH=2_X=240_Y=170_comp2.czi
data/CellDivision_T=10_Z=15_CH=2_DCV_small.czi
/data/w96_A1+A2_SlidePreview.czi
/data/Tumor_HE_Orig_small_Label.czi
/data/Tumor_HE_Orig_small_SlidePreview.czi
/data/est_ngff_plate.zarr
/data/est_ngff_plate.zarr
**/czitools/*.old
data/nuc_small_new.czi
data/meta_nuc_small.png
data/nuc_small.czi
data/nuc_small.czi
data/nuc_small_green.czi
data/nuc_small.czi
data/Tumor_HE_Orig_small_disp.czi
data/Tumor_HE_RGB_disp.czi
.pylintrc

/demo/omezarr_testing/HCS_ZARR_METADATA_FIX.md
/demo/omezarr_testing/1_image_loading.ipynb
/demo/omezarr_testing/2_image_writing.ipynb
/demo/omezarr_testing/3_simple_dask.ipynb
/demo/notebooks/_experimental
/.github/pr_descriptions
/.tools
data/WP96_4Pos_B4-10_DAPI_planetable.csv
# pixi environments
.pixi/*
!.pixi/config.toml
/_notes/
/.pixi

# Local-only Claude skill files
.claude/
.claude/skills/

# Local-only activation overrides (machine/corporate specific)
scripts/activate.local.*

czitools/.benchmarks
czitools/.github/pr_descriptions
