# Scientific dependencies for OpenScientist executor container
# This is a minimal set - no web framework, no database

# Core scientific computing
pandas>=3.0.0
numpy>=2.2.0,<2.4
scipy>=1.15.0
scikit-learn>=1.6.0

# Visualization
matplotlib>=3.7.0
seaborn>=0.12.0

# Statistics
statsmodels>=0.14.0

# Domain-specific
networkx>=3.0

# Single-cell genomics
scanpy>=1.12.0
anndata>=0.12.0
h5py>=3.10.0

# File format support
openpyxl>=3.1.0
pyarrow>=14.0.0

# HTTP requests (for KBase, external APIs)
requests>=2.31.0

# SPARQL queries against remote endpoints
SPARQLWrapper>=2.0.0

# Bioinformatics
biopython>=1.84

# Dimensionality reduction and clustering
umap-learn>=0.5.0
leidenalg>=0.10.0
python-igraph>=0.11.0

# Better statistical tests (effect sizes, ANOVA, mixed models)
pingouin>=0.5.0

# Fast DataFrames for large datasets
polars>=1.0.0

# Interactive visualization
plotly>=5.0.0

# Differential expression analysis
pydeseq2>=0.4.0
