[build-system]
requires = ["setuptools>=42", "wheel"]
build-backend = "setuptools.build_meta"
[project]
name = "chatspatial"
version = "1.1.1"
description = "ChatSpatial: Natural language-driven spatial transcriptomics analysis via Model Context Protocol (MCP) integration"
readme = "README.md"
license = {text = "MIT"}
authors = [
{name = "Chen Yang", email = "cafferychen777@tamu.edu"}
]
keywords = ["spatial-transcriptomics", "single-cell", "mcp", "llm", "bioinformatics", "scanpy", "squidpy"]
classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
requires-python = ">=3.11,<3.14"
dependencies = [
# ========== Core Foundation (Essential) ==========
# MCP and data processing
# Updated to 1.17.0 for full Pydantic v2 and ImageContent support
"mcp>=1.17.0",
"numpy>=1.21.0",
"pandas>=1.3.0",
"scipy>=1.7.0",
"scikit-learn>=1.0.0",
# Visualization
"matplotlib>=3.5.0",
"seaborn>=0.11.0",
"Pillow>=8.0.0",
# Single-cell analysis core
"scanpy>=1.9.0,<2.0",
"anndata>=0.11.0", # Updated for scvi-tools 1.3.x compatibility
"squidpy>=1.2.0",
# Clustering and dimensionality reduction
"umap-learn>=0.5.0",
"igraph>=0.9.0",
"leidenalg>=0.8.0", # Leiden is preferred over Louvain (better algorithm, fewer compilation issues on macOS)
# MCP server framework
"pydantic>=2.0.0,<3.0",
"click>=8.0.0",
"aiohttp>=3.8.0",
# Version constraints
"jinja2>=3.0.0", # Handle conflict with pygpcca
# ========== High-Frequency Features (Extended Default) ==========
# Most commonly used advanced features based on usage analysis
# Multi-tool dependency (24 references in codebase)
"scvi-tools>=1.0.0,<2.0",
"mudata>=0.2.0", # Core dependency of scvi-tools (not optional)
# RNA velocity (7 references)
"scvelo>=0.2.5", # Removed upper bound for better compatibility
# Cell communication (10 references combined)
"liana", # No version constraint - let pip choose compatible version
"cellphonedb>=5.0.0,<6.0",
"fastccc>=0.1.0", # FFT-based ultra-fast cell-cell communication (Nature Communications 2025)
# Batch integration (frequently needed)
"harmonypy>=0.0.9",
"bbknn>=1.5.0",
# Spatial statistics extensions
"esda>=2.4.0", # Exploratory spatial data analysis
"libpysal>=4.6.0", # Core spatial analysis library
# Gene set enrichment (commonly used)
"gseapy>=1.0.0",
# Spatial deconvolution (default method)
"flashdeconv>=0.1.0", # Ultra-fast deconvolution using random sketching
]
[project.optional-dependencies]
# Full installation with all features (recommended)
full = [
# ========== Deep Learning Frameworks ==========
"torch>=2.0.0,<3.0", # Required for many advanced methods
# ========== Advanced Spatial Domains ==========
"SpaGCN>=1.2.5,<2.0", # Graph convolutional network for spatial domains
"GraphST>=1.1.0", # Graph self-supervised contrastive learning for spatial domains
# "STAGATE>=1.0.0", # Spatial domain identification with graph attention
# ========== Advanced Deconvolution ==========
"cell2location>=0.1.4", # Bayesian deconvolution (0.1.4+ fixes scvi-tools one_hot compatibility)
# ========== Advanced Trajectory Analysis ==========
"cellrank>=2.0.0,<3.0", # RNA velocity-based fate mapping
"palantir>=1.0.0", # Probabilistic trajectory inference
# CellRank acceleration (optional but recommended, Unix only)
# Note: PETSc requires Cygwin on Windows, not supported in native Windows Python
"petsc4py>=3.18.0,<4.0; sys_platform != 'win32'",
"slepc4py>=3.18.0,<4.0; sys_platform != 'win32'",
# ========== Additional Integration Methods ==========
"scanorama>=1.7.0", # Cross-dataset integration
# ========== Spatial Variable Genes ==========
"spatialde>=1.1.3", # Gaussian process-based method
"scikit-misc>=0.5.0", # Required for Seurat v3 HVG selection (used by GraphST)
# ========== Advanced Cell Type Annotation ==========
"tangram-sc>=1.0.0", # Spatial mapping of cell types
# SingleR requires C++ dependencies (mattress, knncolle) that fail on Windows
# Error: MinGW "too many sections" compilation error (Windows PE format limitation)
"singler>=0.4.0; sys_platform != 'win32'", # SingleR Python implementation
"singlecellexperiment>=0.4.0; sys_platform != 'win32'", # Required for SingleR
"celldex>=0.3.0; sys_platform != 'win32'", # Reference datasets for SingleR
"mllmcelltype>=0.1.0", # LLM-based cell type annotation
# ========== R Interface (for specific methods) ==========
# IMPORTANT: rpy2 3.6.x requires R 4.5 which has compatibility issues
# We pin to 3.5.x which works well with R 4.4.1
# Note: Requires R to be installed (GitHub Actions installs R 4.4.1)
"rpy2>=3.5.0,<3.7", # Compatible with R 4.4.x, required for RCTD, SPOTlight, etc.
"anndata2ri>=1.3.0", # Sparse matrix support for R deconvolution (85.9% memory savings)
# ========== Extended Spatial Analysis ==========
"pysal>=2.6.0", # Full Python spatial analysis library
"statsmodels>=0.13.0", # Statistical modeling
"networkx>=2.6.0", # Network analysis for spatial graphs
# ========== Spatial Registration ==========
"POT>=0.9.0", # Python optimal transport
# "STalign>=1.0.0", # Spatial alignment tool (install from GitHub, not on PyPI)
"paste-bio>=1.0.0", # PASTE spatial registration
# ========== CNV Analysis ==========
"infercnvpy>=0.4.0", # Copy number variation inference from spatial transcriptomics
# Note: Numbat CNV analysis also supported via rpy2 (requires R package: install.packages('numbat'))
# ========== Advanced Differential Expression ==========
"pydeseq2>=0.4.0", # Python DESeq2 for pseudobulk differential expression
# ========== Spatial Enrichment Extensions ==========
"enrichmap", # Enrichment map visualization (Python >=3.10)
"statannotations>=0.2.0", # Statistical annotations for plots
"pygam>=0.8.0", # Generalized additive models
"scikit-gstat>=1.0.0", # Geostatistical analysis
"adjustText>=0.8.0", # Automatic label placement
"splot>=1.1.0", # Spatial plotting
# ========== Emerging Technologies ==========
"spatialdata>=0.2.0", # Emerging spatial data format standard
]
# SCTransform normalization (variance-stabilizing transformation)
# Note: SCTransform now uses R's sctransform package via rpy2 (more stable than pySCTransform)
# Requirements: R with sctransform package installed
# Install R package: R -e 'install.packages("sctransform")'
# rpy2 is already included in the [full] optional dependencies
# Development dependencies
dev = [
"pytest>=8.0.0",
"pytest-asyncio>=0.23.0,<2.0",
"black>=22.0.0,<26.0",
"mypy>=1.0.0,<2.0",
"ruff>=0.1.0",
"isort>=5.0.0",
"pre-commit>=3.0.0,<5.0",
]
[project.urls]
Homepage = "https://github.com/cafferychen777/ChatSpatial"
Documentation = "https://chatspatial.readthedocs.io"
Repository = "https://github.com/cafferychen777/ChatSpatial"
Issues = "https://github.com/cafferychen777/ChatSpatial/issues"
[project.scripts]
chatspatial = "chatspatial.__main__:main"
[tool.pytest.ini_options]
minversion = "6.0"
testpaths = ["tests"]
python_files = "test_*.py"
python_classes = "Test*"
python_functions = "test_*"
addopts = "-v"
# Fix pytest-asyncio warning
asyncio_mode = "auto"
asyncio_default_fixture_loop_scope = "function"
# Suppress known upstream dependency version warnings
filterwarnings = [
"ignore:.*jinja2.*:UserWarning",
"ignore:.*numpy.*version.*:UserWarning",
]
[tool.black]
line-length = 88
target-version = ["py311"]
[tool.isort]
profile = "black"
line_length = 88
[tool.mypy]
python_version = "3.11"
warn_return_any = false
warn_unused_ignores = true
ignore_missing_imports = true
plugins = ["pydantic.mypy"]
[tool.pydantic-mypy]
init_forbid_extra = true
init_typed = true
warn_required_dynamic_aliases = true
[tool.setuptools.packages.find]
where = ["."]
include = ["chatspatial", "chatspatial.*"]
exclude = ["tests", "tests.*", "chatspatial.tests", "chatspatial.tests.*"]
[tool.setuptools.package-data]
chatspatial = ["py.typed"]
