.gitignore

__MACOSX/

# LaminDB
.lamin
docs/pertdb.*.rst
docs/bionty.*.rst
README_stripped.md
docs/scripts/test_artifact_parquet.py
README.ipynb
docs/sample.fasta
docs/faq/sample.fasta
docs/faq/test-acid/
docs/scripts/define_mini_immuno_features_labels.py
docs/scripts/define_mini_immuno_schema_flexible.py
docs/scripts/define_schema_anndata_ensembl_gene_ids_and_valid_features_in_obs.py
docs/scripts/define_valid_features.py
docs/scripts/save_mini_immuno_datasets.py
profile_output*
.coveragerc
uv.lock
*.db
*.lndb
*.jpg
*.zarr/
docsbuild/
docs/lamin.md
docs/guide/data-validation.ipynb
docs/guide/bionty.ipynb
docs/guide/lnschema-core.ipynb
docs/paradisi05_laminopathic_nuclei.jpg
bionty_docs/
lamindb_docs/
_build
mydata/
lamin-intro/
lamin-tutorial/
mytest/
rds/
mydb/
docs/test-registries/
docs/test-annotate-flexible/
docs/lamindb.*
lamin_sphinx
docs/conf.py
lamindb/setup/.env
_secrets.py
_configuration.py
lamin.db
docs/generated/*
_docs_tmp*
docs/guide/Laminopathic_nuclei.jpg
docs/guide/paradisi05_laminopathic_nuclei.jpg
nocodb
docs/guide/SRR4238351_subsamp.fastq.gz
docs/faq/paradisi05_laminopathic_nuclei.jpg
docs/faq/tostore/
docs/faq/mydata_postgres/
docs/guide/myobjects/
docs/faq/test-run-inputs/
docs/intro/paradisi05_laminopathic_nuclei.jpg
docs/guide/figures/
docs/test-annotate/
docs/test-track/
suo22/
docs/biology/test-flow/
docs/biology/test-scrna/
docs/biology/test-registries/
docs/biology/test-multimodal/
default_storage
default_storage_unit_core
default_storage_unit_storage
testdb-integrations/
test.ipynb
test2.ipynb
run-tests
test-django-validation/
curate.tiledbsoma
small_dataset.tiledbsoma
nonregistered_storage
registered_storage
tests/pydata/notebooks/no-uid-renamed.ipynb

# General
.DS_Store

# 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

# ruff
.ruff_cache

# Pyre type checker
.pyre/

# data files
data/
_build
*.csv
*.fcs
*.zip
*.feather
*.h5ad
*.h5mu
*.parquet
*.bam
*.fastq.gz
*.pt

# Pycharm
.idea

# VSCode
.vscode

# CELLxGENE
!lamindb/examples/cellxgene/cellxgene_schema_versions.csv

# ml
lightning_logs
mlruns
download_mnist
checkpoints
test_lightning