Pipfile

[[source]]
url = "https://pypi.org/simple"
verify_ssl = true
name = "pypi"

[packages]
# JupyterHub and system libraries (e.g., Spark, MinIO, etc.)
jupyterlab= "==4.2.5"
jupyterhub = "==5.2.1"
jupyterhub-nativeauthenticator = "==1.3.0"
dockerspawner = "==13.0.0"
jupyterlab_favorites = "==3.2.2"
sidecar = "==0.7.0"
json5 = "==0.9.25"
pycurl = "==7.45.3"
pyspark= "==3.5.3"
boto3 = "==1.35.48"
minio = "==7.2.10"
delta-spark = "==3.2.0"  # should match JAR version (DELTA_SPARK_VER) specified in the Dockerfile
PyMySQL = "==1.1.1"
urllib3 = "==2.2.3"
jupyterlab-git = "==0.50.1"
cdm-jupyterlab-brand-extension = {file = "https://github.com/kbaseincubator/cdm_jupyterlab_brand_extension/raw/main/dist/cdm_jupyterlab_brand_extension-0.1.0-py3-none-any.whl"}

# Jupyter AI libraries
jupyter-ai = "==2.26.0"
langchain-openai = "==0.1.25"
langchain-anthropic = "==0.1.23"
huggingface_hub = "==0.26.0"
jupyter-ai-cborg = {git = "https://github.com/kbaseincubator/cdm-jupyter-ai-cborg.git", ref = "v0.1.0"}


# Frequently utilized data visualization libraries by the science team
plotly = "==5.24.1"
tqdm = "==4.66.5"
ipywidgets = "==8.1.5"
pygraphviz = "==1.14"
scipy = "==1.14.1"
scikit-learn = "==1.5.2"
biopython = "==1.84"
seaborn = "==0.13.2"
pandas = "==2.2.3"
pyarrow = "==17.0.0"
itables = "==2.2.2"

[dev-packages]
pytest = "==8.3.3"
coverage = "==7.6.4"
pytest-cov = "==5.0.0"
ipython = "==8.29.0"

[requires]
python_version = "3.11"