[project]
name = "mfass"
version = "0.1.0"
description = "MFASS splice-variant prioritisation benchmark"
requires-python = ">=3.11"
dependencies = ["rewirebench"]

# SpliceAI 1.3.1 is a 2019 package: it needs pkg_resources (so setuptools<82) and
# pulls TensorFlow. Kept optional so the core benchmark installs without it.
[project.optional-dependencies]
spliceai = ["spliceai==1.3.1", "tensorflow>=2.16", "setuptools<82", "pyfaidx>=0.5", "pandas>=2"]
# Pangolin is installed from git; it needs torch, gffutils, pyvcf3 and pyfastx.
pangolin = ["torch>=2", "gffutils>=0.13", "pyvcf3", "pyfastx", "setuptools<82"]
dnabert2-pilot = ["torch==2.2.2", "transformers==4.29.2", "einops==0.6.1",
                  "safetensors==0.7.0", "numpy==1.26.4"]

[project.scripts]
mfass-build = "mfass.build_dataset:main"
mfass-split = "mfass.split:main"
mfass-baseline = "mfass.run_baseline:main"
mfass-spliceai = "mfass.run_spliceai:main"
mfass-compare = "mfass.compare:main"
mfass-subgroups = "mfass.subgroups:main"
mfass-pangolin = "mfass.run_pangolin:main"
mfass-dnabert2-pilot = "mfass.run_dnabert2_pilot:main"
mfass-dnabert2 = "mfass.run_dnabert2:main"

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.hatch.build.targets.wheel]
packages = ["src/mfass"]