[build-system]
requires = ["setuptools>=68", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "reverso-mvp"
version = "0.1.0"
description = "Sickle cell drug repurposing MVP — disease signature + drug profile matching via CMap-style connectivity scoring"
readme = "README.md"
requires-python = ">=3.11,<3.14"
license = { text = "Proprietary" }
authors = [{ name = "Reverso" }]

dependencies = [
    "pandas>=2.0",
    "numpy>=1.24",
    "scipy>=1.11",
    "requests>=2.31",
    "chembl_webresource_client>=0.10",   # ChEMBL API client
    "GEOparse>=2.0",                      # GEO dataset access
    "pydeseq2>=0.4",                      # Differential expression in Python
    "cmapPy>=4.0",                        # Reference CMap connectivity implementation
    "pyarrow>=14.0",                      # Parquet I/O
    "jupyter>=1.0",
    "matplotlib>=3.7",                    # Sanity-check plots
    "seaborn>=0.13",
    "pydantic>=2.0",                      # Schema validation for signatures/profiles
    "mygene>=3.2",                        # Gene symbol -> Entrez/Ensembl mapping
]

[project.optional-dependencies]
dev = [
    "pytest>=8.0",
    "ruff>=0.5",
]
# Structure-based binding track (PLAN §12); see docs/structure_binding_notes.md.
# Non-pip tools (install separately): AutoDock Vina binary (tools/vina, from the AutoDock-Vina
# GitHub release) and open-babel (brew). Boltz-2 + cuequivariance run only in the Modal GPU image
# (gpu/modal_app.py), not locally.
structure = [
    "rdkit>=2024.3",        # ligand prep, fingerprints
    "requests>=2.31",       # PubChem / RCSB fetch
    "gemmi>=0.6",           # structure parsing + superposition
    "spyrmsd>=0.9",         # symmetry-corrected pose RMSD
    "meeko>=0.7",           # production docking ligand prep
    "modal>=1.5",           # ephemeral GPU orchestration
]

[tool.setuptools.packages.find]
where = ["."]
include = ["src*"]

[tool.ruff]
line-length = 100
target-version = "py311"

[tool.pytest.ini_options]
testpaths = ["tests"]