.gitignore

output_reports/
error_reports/
*.test*
*.validation*
*.training*
*.meta*
gnn/data/*
gnn/results/*
artificial_data/results
ae_imputation/ae_hyperopt


phenotyping
Jupyter/**
data/restore/*
data/af_tracker/*
data/tumor_s3_snr/*
data/tumor_s3_non_snr/*
data/tumor_mesmer/*
data/tumor_mesmer_sp_46/*
data/tumor_mesmer_sp_92/*
data/tumor_mesmer_sp_138/*
data/tumor_mesmer_sp_184/*
data/tumor_mesmer_sp_23/*
data/tumor_mesmer_z_scores/*/
data/cleaned_data/*
unmicst_s3_non_snr/tumor_in_patient_hyper/*
unmicst_s3_non_snr/tumor_out_patient_hyper/*
unmicst_s3_non_snr/tumor_in_patient/9_*
unmicst_s3_non_snr/tumor_out_patient/9_*
unmicst_s3_non_snr/tumor_in_patient_en/9_*
unmicst_s3_non_snr/tumor_out_patient_en/9_*

unmicst_s3_snr/tumor_in_patient/9_*
unmicst_s3_snr/tumor_in_patient_en/9_*
unmicst_s3_snr/tumor_in_patient_hyper/9_*
unmicst_s3_snr/tumor_out_patient/9_*
unmicst_s3_snr/tumor_out_patient_en/9_*
unmicst_s3_snr/tumor_out_patient_hyper/9_*

ae/ae_hyperopt/*
ae_sp_46/ae_hyperopt/*
ae_imputation/ip/*
ae_imputation/op/*
ae_imputation/exp/*


mesmer/tumor_in_patient/9_*
mesmer/tumor_in_patient_en/9_*
mesmer/tumor_in_patient_hyper/9_*
mesmer/tumor_out_patient/9_*
mesmer/tumor_out_patient_en/9_*
mesmer/tumor_out_patient_hyper/9_*
mesmer/tumor_in_patient_sp_46/9_*
mesmer/tumor_in_patient_sp_92/9_*
mesmer/tumor_out_patient_sp_46/9_*
mesmer/tumor_out_patient_sp_92/9_*
mesmer/tumor_out_patient_sp_138/9_*
mesmer/tumor_out_patient_sp_184/9_*
mesmer/tumor_in_patient_sp_138/9_*
mesmer/tumor_in_patient_sp_184/9_*
mesmer/tumor_in_patient_sp_23/9_*
mesmer/tumor_out_patient_sp_23/9_*

mesmer/tumor_exp_patient_en/9_*
mesmer/tumor_exp_patient/9_*
mesmer/tumor_exp_patient_z_scores/9_*
mesmer/tumor_exp_patient_sp_23/9_*
mesmer/tumor_exp_patient_sp_46/9_*
mesmer/tumor_exp_patient_sp_92/9_*
mesmer/tumor_exp_patient_sp_138/9_*
mesmer/tumor_exp_patient_sp_184/9_*
mesmer/tumor_exp_patient_hyper/9_*







new_me_vae/checkpoints
*.c
*.so
*.zarr
# Byte-compiled / optimized / DLL files
__pycache__/
mlruns/*
LatentSpaceExplorer/tmp/*
src/VAE/results/*
*.py[cod]
*$py.class
.idea
.DS_Store
results/*
ludwig_experiments/*
# C extensions
*.so
*.png
# 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
.DS_Store

# 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/

tumor_cycif.csv
data/tumor_cycif_v2.csv
*.csv
.vscode/settings.json
mlruns.zip
*.eps
ludwig_prediction.err
artificial_data/.lock_preprocessing