pyproject.toml

[project]
name = "spimquant"
dynamic = ["version"]
description = "BIDS App for quantifying SPIM (lightsheet) microscopy data"
readme = "README.md"
license = "MIT"
authors = [{ name = "Ali R. Khan", email = "alik@robarts.ca" }]
requires-python = ">=3.11,<3.14"
# Dependencies are conda packages, declared once in [tool.pixi.package.run-dependencies]
dependencies = []

[project.scripts]
spimquant = "spimquant.run:app.run"

[build-system]
build-backend = "hatchling.build"
requires = ["hatchling", "hatch-vcs"]

[tool.hatch.version]
source = "vcs"

[tool.hatch.version.raw-options]
tag_regex = "^v(?P<version>.+)$"
fallback_version = "0.0.0.dev0"
version_scheme = "no-guess-dev"
local_scheme = "no-local-version"

[tool.hatch.build.targets.wheel]
packages = ["spimquant"]


# ----------------------------------------------------------------------
# Pixi workspace
# ----------------------------------------------------------------------

[tool.pixi.workspace]
channels = ["conda-forge", "bioconda", "https://prefix.dev/akhanf/khanlab"]
# all inline tables, as snakefmt's toml parser rejects mixed arrays
platforms = [
    { platform = "linux-64" },
    { name = "linux-64-cuda", platform = "linux-64", cuda = "12.0" },
]
preview = ["pixi-build"]


# ----------------------------------------------------------------------
# Conda package
#
# The run-dependencies below are the single list of runtime dependencies:
# they are what the published package requires, and the pixi environments
# get them by depending on this package from source (see the runtime
# feature), which pixi installs in editable mode.
# ----------------------------------------------------------------------

[tool.pixi.package]
name = "spimquant"
# set from the release tag by the publish workflow
version = "0.0.0.dev0"
publish = true

[tool.pixi.package.build.backend]
name = "pixi-build-python"
version = "*"
channels = ["conda-forge"]

[tool.pixi.package.host-dependencies]
hatchling = "*"
hatch-vcs = "*"

[tool.pixi.package.run-dependencies]
snakemake = ">=9.5.1,<10"
snakebids = ">=0.15.0,<0.16"
snakemake-storage-plugin-s3 = ">=0.3.3,<0.4"
snakemake-storage-plugin-gcs = ">=1.1.4,<2"
snakemake-storage-plugin-fs = ">=1.1.2,<2"
snakemake-storage-plugin-cached-http = ">=0.3.0,<0.4.0"
snakemake-storage-plugin-zenodo = ">=0.1.5,<0.2"
snakemake-executor-plugin-slurm = ">=1.4.0,<2"
conda = ">=25.5.0,<26"
gcsfs = ">=2025.5.1,<2026"
s3fs = ">=2025.5.1,<2026"
universal-pathlib = ">=0.2.6,<0.3"
# image I/O and processing
zarrnii = ">=0.22.0,<0.23.0"
zarr = ">=3.1.6,<4"
dask = ">=2026.3.0"
h5py = ">=3.14.0"
simpleitk = ">=2.4.0"
nibabel = ">=5.3.2,<6"
scipy = ">=1.11.0,<2"
scikit-image = ">=0.26.0,<0.27"
scikit-learn = ">=1.8.0,<2"
skan = ">=0.13.1,<0.14"
greedyreg = "==0.0.20250712"
antspyx = "==0.6.1"
pyarrow = ">=18.0.0,<19"
# QC and reports
matplotlib = ">=3.7.0,<4"
seaborn = ">=0.12.0,<1"
nilearn = ">=0.12.1,<0.13"
# deep learning segmentation (vesselFM, LANTERN)
vesselfm = ">=0.2.1"
dynamic-network-architectures = ">=0.4"
monai = ">=1.5.2,<2"
hydra-core = ">=1.3.2,<2"
omegaconf = ">=2.3.0,<3"
lightning = ">=2.6.0,<3"
huggingface_hub = ">=1.3.7,<2"
tensorboard = ">=2.20.0,<3"
wandb = ">=0.24.1,<0.25"
gpustat = ">=1.1.1,<2"
tqdm = ">=4.67.2,<5"

[tool.pixi.package.run-constraints]
# pins on transitive dependencies (snakemake reports)
markdown-it-py = "<4"
docutils = "<0.22"


# ----------------------------------------------------------------------
# Runtime environments
# ----------------------------------------------------------------------

[tool.pixi.feature.runtime.dependencies]
spimquant = { path = "." }

# the CUDA platform is only solved for the gpu environment
[tool.pixi.feature.cpu]
platforms = ["linux-64"]

[tool.pixi.feature.gpu]
platforms = ["linux-64-cuda"]

[tool.pixi.feature.gpu.dependencies]
cuda-version = "12.6.*"
pytorch-gpu = "*"
# cohort template building (khanlab fork, from akhanf/khanlab)
fireants = ">=1.4.0.post1"
fireants-fused-ops = ">=1.2.0"


# ----------------------------------------------------------------------
# Development
# ----------------------------------------------------------------------

[tool.pixi.feature.dev.dependencies]
# snakefmt 0.10 fails on python 3.13
python = ">=3.11,<3.13"
black = ">=26.0.0,<27.0.0"
isort = ">=5.10.1,<6.0.0"
snakefmt = ">=2.1.0,<3.0.0"
pytest = "*"
jupyterlab = ">=4.4.7,<5"

[tool.pixi.feature.dev.tasks]
quality_check = "isort --profile black spimquant/*.py -c && black spimquant --check && snakefmt spimquant --check"
quality_fix = "isort --profile black spimquant/*.py && black spimquant && snakefmt spimquant"

[tool.pixi.feature.vis.dependencies]
napari = ">=0.6.6,<0.7"
napari-ome-zarr = ">=0.6.1,<0.7"
pyqt = ">=5.15.11,<6"
micro_sam = ">=1.6.2,<2"


# ----------------------------------------------------------------------
# Environments
# ----------------------------------------------------------------------

[tool.pixi.environments]
default = ["runtime", "cpu"]
gpu = ["runtime", "gpu"]
dev = ["runtime", "dev", "vis", "cpu"]
dev-only = { features = ["dev", "cpu"], no-default-feature = true }