pixi.toml

[workspace]
name = "analysis-template"
version = "0.1.0"
description = "Template for single-cell/spatial analysis projects (pixi-managed)"
authors = ["Your Name <your.email@example.com>"]
channels = ["conda-forge"]
platforms = ["osx-arm64", "linux-64"]

[pypi-options]
extra-index-urls = ["https://pypi.nvidia.com"]

[tasks]
lab = "jupyter lab"
test = "pytest"
install-kernel = "python -m ipykernel install --user --name=analysis-template --display-name='Analysis Template (Pixi)'"

[dependencies]
python = "3.12.*"
# Pin numpy to avoid conda/pypi conflicts with numba
numpy = ">=2.0,<2.2"

# CellRank accelerated linear algebra (PETSc/SLEPc)
# Pre-built from conda-forge; PyPI wheels require building from source
petsc4py = "*"
slepc4py = "*"

# Shapely from conda to avoid pygeos build issues
shapely = "*"

[target.osx-arm64.pypi-dependencies]
# CPU-only JAX on macOS (MPS handled automatically by torch)
jax = "<0.9.0"

[target.linux-64.pypi-dependencies]
# GPU stack for Linux (CUDA 12)
rapids-singlecell = { version = ">=0.13", extras = ["rapids12"] }
jax = { version = "<0.9.0", extras = ["cuda12"] }

[pypi-dependencies]
# Compatibility fix: cuML (rapids dependency) incompatible with sklearn 1.8
# https://github.com/rapidsai/cuml/issues/6426
scikit-learn = "<1.8"

# Core single-cell stack
scanpy = ">=1.10"
squidpy = "*"
scvi-tools = "*"
cellrank = "*"
torch = "*"

# Notebook workflow
jupyterlab = "*"
ipykernel = "*"
ipywidgets = "*"
# Pin pandas < 3.0 until anndata supports Arrow-backed strings
# https://github.com/scverse/anndata/issues/1434
pandas = ">=2.0, <3"
matplotlib = "*"
seaborn = "*"

# Utilities
pre-commit = "*"
pytest = "*"
session-info2 = "*"

# Local editable package for path helpers
myanalysis = { path = ".", editable = true }
igraph = ">=1.0.0, <2"
celltypist = ">=1.7.1, <2"