.gitignore

# 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/
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/

# templates
.github/templates/*
.DS_Store
data/temp/*
.sync-conflict*
notebooks/tests/mytest2
notebooks/tests/mytest
notebooks/tests/wandb
data/GroundTruth/*
data/adamson
data/fasta/*
data/scGPT_human
wandb/*
*/lightning_logs/*
data/tensorboard/*
notebooks/tests/*/
data/logs/*
.lr_find_*
step_*_.*
data/main/embeddings.parquet
slurm-*.out
notebooks/tests/step_0_.h5ad
data/main/gene_embeddings.parquet
data/main/main_scenic+.parquet
scdataloader.out
data/main/9606.protein.links.v12.0.txt.gz
data/main/motifs-v10-nr.hgnc-m0.00001-o0.0.tbl
data/main/main_scenic+_database.feather
*.npy
*.joblib
notebooks/tests/collator_output.txt
notebooks/tests/curr_genes_mouse.csv
notebooks/tests/curr_genes.csv
notebooks/tests/precision_recall_plot.png
notebooks/tests/lightning_logs/*
notebooks/additional/lightning_logs/*
lightning_logs/
collator_output.txt
data/bias_sparse.npz
todel/
tests/out_*.h5ad
data/*.h5ad
notebooks/**/*.h5ad
notebooks/*.h5ad
*.ckpt
data/main/bias_sparse.npz
*.gv.*
*.gv
data/log/
file.txt