pyproject.toml

[build-system]
requires = ["setuptools>=77.0.3", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "chatspatial"
version = "1.5.3"
description = "ChatSpatial: Natural language-driven spatial transcriptomics analysis via Model Context Protocol (MCP) integration"
readme = "README.md"
license = "MIT"
license-files = ["LICENSE"]
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",
    "Operating System :: MacOS",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
requires-python = ">=3.11,<3.15"
dependencies = [
    # ========== Core Foundation (Essential) ==========
    # MCP 2026-07-28 protocol and data processing
    "mcp>=2.0.0,<3.0",
    "anyio>=4.9.0,<5.0",
    "numpy>=1.21.0",
    "pandas>=1.3.0",
    "scipy>=1.7.0",
    "scikit-learn>=1.0.0",
    "statsmodels>=0.13.0,<1.0",
    "certifi>=2024.2.2",
    "cloudpickle>=2.2.0",
    "typing-extensions>=4.12.0",
    "zarr>=2.18.0,<4.0",
    
    # Visualization
    "matplotlib>=3.5.0",
    "seaborn>=0.11.0",
    "Pillow>=8.0.0",
    
    # Single-cell analysis core
    # Modern releases are required for the declared Python 3.11-3.14 range.
    # Older releases can resolve to numba/llvmlite builds that do not support it.
    "scanpy>=1.11.0,<2.0",
    "anndata>=0.11.0",  # Updated for scvi-tools 1.3.x compatibility
    "squidpy>=1.6.0,<2.0",

    # Default Python-native spatial variable gene backend
    "flashs>=0.2.1,<0.3",
    
    # 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>=2.12.0,<3.0",
    "click>=8.0.0",
    
    # Heavy method-specific packages live in optional extras below. The default
    # install includes every default backend; optional methods report clear
    # installation guidance only when their extra has not been installed.
]

[project.optional-dependencies]
# Deep learning methods (scVI, scANVI, VeloVI, DestVI, Cell2location backend)
deep-learning = [
    "torch>=2.0.0,<3.0",
    "scvi-tools>=1.0.0,<2.0",
]

# RNA velocity methods
velocity = [
    "scvelo-modern>=0.3.4.post2,<0.4",
]

# Trajectory methods. CellRank is available on Python 3.12 and newer.
trajectory = [
    "cellrank>=2.3.2,<3.0; python_version >= '3.12'",
    "palantir>=1.0.0",
]

# Cell-cell communication methods
cell-communication = [
    "liana>=1.4.0,<2.0; python_version < '3.14'",
    "cellphonedb>=5.0.0,<6.0",
]

# Focused FastCCC statistical runtime. The maintained distribution omits the
# unused HTML report layer, so it has no Jinja2 conflict with CellRank/pyGPCCA.
fastccc = [
    "fastccc-modern>=1.0.1.post1,<1.1",
]

# Batch integration methods that do not require the deep-learning stack
integration = [
    "harmonypy>=0.0.9",
    "bbknn>=1.5.0",
    "scanorama>=1.7.0",
]

# Spatial statistics extensions
spatial-stats = [
    "esda>=2.4.0",
    "libpysal>=4.6.0",
    "networkx>=2.6.0",
]

# Spatial deconvolution methods
deconvolution = [
    "flashdeconv>=0.1.0",
    "cell2location>=0.1.4",
]

# Cell type annotation and spatial mapping methods.
annotation = [
    "tangram-sc>=1.0.0",
    "singler>=0.4.0; sys_platform != 'win32'",
    "singlecellexperiment>=0.4.0; sys_platform != 'win32'",
    "celldex>=0.3.0; sys_platform != 'win32'",
    "mllmcelltype>=0.1.0",
]

# Gene-set enrichment and enrichment-map visualization.
enrichment = [
    "gseapy>=1.0.0",
    "enrichmap>=0.1.0",
    "requests>=2.31.0,<3.0",
]

# Copy-number inference.
cnv = [
    "infercnvpy>=0.4.0",
]

# Pseudobulk differential expression.
differential = [
    "pydeseq2>=0.4.0",
]

# Pairwise and multi-slice spatial registration.
registration = [
    "torch>=2.0.0,<3.0",
    "POT>=0.9.0",
    "paste-modern>=1.4.0.post1,<1.5",
    "stalign-modern>=1.0.post1,<1.1",
]

# Optional statistically rigorous spatial-variable-gene backend.
spatial-genes = [
    "spatialde-modern>=1.1.3.post2,<1.2",
]

# PyTorch port of RCTD. Kept separate because it downloads a large likelihood
# table on first use and has a faster release cadence than the core package.
rctd-python = [
    "rctd-py>=0.3.7,<0.4",
]

# Bridges for methods implemented in R. Kept out of [full] because rpy2 must
# inspect and link against a system R installation while it is being installed;
# the required R packages are managed separately from Python package metadata.
r-backends = [
    "rpy2>=3.6.7,<3.7",
    "anndata2ri>=1.3.0",
]

# Broadest mutually compatible Python installation. R bridges, AESTETIK, and
# RCTD remain isolated because they impose platform, system, or dependency
# constraints that cannot be expressed as one portable environment.
full = [
    # Deep learning and dynamics
    "torch>=2.0.0,<3.0",
    "scvi-tools>=1.0.0,<2.0",
    "scvelo-modern>=0.3.4.post2,<0.4",
    "cellrank>=2.3.2,<3.0; python_version >= '3.12'",
    "palantir>=1.0.0",

    # Cell communication
    "liana>=1.4.0,<2.0; python_version < '3.14'",
    "cellphonedb>=5.0.0,<6.0",
    "fastccc-modern>=1.0.1.post1,<1.1",

    # Integration and spatial statistics
    "harmonypy>=0.0.9",
    "bbknn>=1.5.0",
    "scanorama>=1.7.0",
    "esda>=2.4.0",
    "libpysal>=4.6.0",
    "networkx>=2.6.0",

    # Deconvolution and annotation
    "flashdeconv>=0.1.0",
    "cell2location>=0.1.4",
    "tangram-sc>=1.0.0",
    "singler>=0.4.0; sys_platform != 'win32'",
    "singlecellexperiment>=0.4.0; sys_platform != 'win32'",
    "celldex>=0.3.0; sys_platform != 'win32'",
    "mllmcelltype>=0.1.0",

    # Enrichment, CNV, and differential expression
    "gseapy>=1.0.0",
    "enrichmap>=0.1.0",
    "requests>=2.31.0,<3.0",
    "infercnvpy>=0.4.0",
    "pydeseq2>=0.4.0",

    # Spatial domains and variable genes
    "graphst-modern>=1.1.1.post3,<1.2",
    "stagate-modern>=1.0.0.post1,<1.1",
    "spagcn-modern>=1.3.0,<1.4",
    "pybanksy>=1.3.5,<2.0; python_version < '3.14'",
    "spatialde-modern>=1.1.3.post2,<1.2",

    # Spatial registration
    "POT>=0.9.0",
    "paste-modern>=1.4.0.post1,<1.5",
    "stalign-modern>=1.0.post1,<1.1",
]

# 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")'
# Install the [r-backends] extra after installing R.

# Spatial domain methods. The maintained SpaGCN distribution uses igraph's
# built-in Leiden implementation and does not require the obsolete louvain
# extension. BANKSY does not yet publish Python 3.14-compatible metadata.
spatial-domains = [
    "torch>=2.0.0,<3.0",
    "graphst-modern>=1.1.1.post3,<1.2",
    "stagate-modern>=1.0.0.post1,<1.1",
    "spagcn-modern>=1.3.0,<1.4",
    "pybanksy>=1.3.5,<2.0; python_version < '3.14'",
]

# AESTETIK multi-modal spatial domain identification. Kept in its own family
# because it does not yet support Python 3.14 and because it pulls a
# torchvision/lightning stack that the other spatial-domain backends do not
# need. The environment marker keeps the 3.14 CI leg resolvable.
aestetik = [
    "aestetik>=0.3.1,<0.4; python_version < '3.14'",
]

# Dependencies used by the manuscript reproducibility scripts. Core scientific
# packages such as NumPy, pandas, Scanpy, and scikit-learn are already required
# by ChatSpatial itself, so this extra only declares the additional packages.
reproducibility = [
    "requests>=2.31.0,<3.0",
    "statsmodels>=0.13.0,<1.0",
]

# Development dependencies
dev = [
    "pytest>=8.0.0",
    "pytest-asyncio>=0.23.0,<2.0",
    "black==25.12.0",
    "mypy>=1.0.0,<2.0",
    "types-requests>=2.31.0",
    "ruff==0.14.11",
    "isort==7.0.0",
    "pre-commit>=3.0.0,<5.0",
]

# Deliberately pinned: these tools create the immutable public artifacts.
release = [
    "build==1.5.0",
    "twine==7.0.0",
]

[project.urls]
Homepage = "https://github.com/cafferychen777/ChatSpatial"
Documentation = "https://docs.cafferyang.com/"
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 -m 'not slow' --strict-markers"
# Fix pytest-asyncio warning
asyncio_mode = "auto"
asyncio_default_fixture_loop_scope = "function"
markers = [
    "unit: Unit tests for pure functions",
    "integration: Multi-component integration tests",
    "e2e: End-to-end workflow tests through public tool interfaces",
    "slow: Heavy dependency or long-running tests (excluded by default)",
]
[tool.black]
line-length = 88
target-version = ["py311"]

[tool.ruff]
line-length = 88
target-version = "py311"

[tool.ruff.lint.mccabe]
max-complexity = 40

[tool.isort]
profile = "black"
line_length = 88
skip_gitignore = true

[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"]