pyproject.toml

[project]
name = "biostatistics"
version = "0.1.0"
readme = "README.md"
requires-python = "==3.12"

## pyproject.toml
#[tool.pixi.pypi-options.dependency-overrides]
#numpy = ">=2.0.0"

[tool.pixi.workspace]
channels = [
    "conda-forge",
    "bioconda",
]
platforms = ["linux-64"]

[tool.pixi.pypi-dependencies]
biostatistics = { path = ".", editable = true }

[tool.pixi.tasks]
install-parquet-cli = { cmd = "bash -lc 'cargo install parquet@57.0.0 --features=cli --locked --root ${CONDA_PREFIX}'" }
parquet-fromcsv = { cmd = "parquet-fromcsv" }
install-mr = """
mkdir -p r-libs && \
Rscript -e "if (!requireNamespace('TwoSampleMR', quietly = TRUE)) install.packages('TwoSampleMR', repos=c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org'))"
"""
install-raps= """
mkdir -p r-libs && \
Rscript -e "if (!requireNamespace('mr.raps', quietly = TRUE)) install.packages('mr.raps', repos=c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org'))"
"""
install-lava = """
mkdir -p r-libs && \
Rscript -e "if (!require('remotes', quietly=TRUE)) install.packages('remotes', repos='https://cloud.r-project.org'); if (!requireNamespace('LAVA', quietly=TRUE)) remotes::install_github('josefin-werme/LAVA')"
"""
[tool.setuptools]
packages = ["mecfs_bio"]

[tool.pixi.activation]
env = { R_LIBS_USER = "r-libs" }

[tool.pixi.feature.analysis.dependencies]
pysam = ">=0.24,<0.25"
pixi-pycharm = ">=0.0.11,<0.0.12"
ruff = ">=0.15.11,<0.16"
bedops = ">=2.4.42,<3"
pyarrow = ">=22.0.0,<23"
rust = ">=1.96,<1.97"
duckdb = ">=1.4.1,<2"
pandoc = ">=3.8.2.1,<4"
bcftools = ">=1.22,<2"
typos = ">=1.41.0,<2"
r-base = ">=4.0,<4.6"
bioconductor-celldex = ">=1.16.0,<2"
pixi = "*"
make = ">=4.4.1,<5"
r-dplyr = ">=1.1.4,<2"
"r-data.table" = ">=1.17.8,<2"
r-jsonlite = ">=2.0.0,<3"
r-httr = ">=1.4.7,<2"
r-ggplot2 = ">=4.0.2,<5"
r-cowplot = ">=1.2.0,<2"
r-knitr = ">=1.51,<2"
r-markdown = ">=2.0,<3"
r-plyr = ">=1.8.9,<2"
r-reshape2 = ">=1.4.5,<2"
r-stringr = ">=1.6.0,<2"
r-xml2 = ">=1.5.1,<2"
r-magrittr = ">=2.0.4,<3"
r-ieugwasr = ">=1.1.0,<2"
r-glmnet = ">=4.1.10,<5"
r-mass = ">=7.3.65,<8"
r-mendelianrandomization = ">=0.10.0,<0.11"
gh = ">=2.86.0,<3"
lychee = ">=0.24.1,<0.25"
r-susier = ">=0.14.2,<0.15"
tomli-w = ">=1.2.0,<2"
awscli = ">=2.33.8,<3"
r-rfast = ">=2.1.5.2,<3"
r-seurat = ">=5.4.0,<6"
r-cpp11 = ">=0.5,<1"
ty = ">=0.0.55,<0.0.56"
actionlint = ">=1.7.12,<2"
shellcheck = ">=0.11.0,<0.12"

[tool.pixi.feature.analysis.pypi-dependencies]
attrs = ">=25.3.0"
cattrs = ">=25.2.0"
emoji = ">=2.15.0"
geneview = ">=0.2.1"
gwaslab = "==4.1.9"
invoke = ">=2.2.0"
loguru = ">=0.7.3"
matplotlib = ">=3.8"
narwhals = ">=2.6.0"
networkx = ">=3.5"
numpy = "*"
osfclient = ">=0.0.5"
pandas = ">=2.3.3"
pandasgwas = ">=1.2.2"
pathlib-abc = ">=0.5.2"
plotly = ">=6.5.2"
polars = ">=1.41.0, <2"
py3-wget = ">=1.0.13"
pytest = ">=8.4.2"
requests = ">=2.32.5"
ruff = ">=0.13.2"
structlog = ">=25.4.0"
tqdm = ">=4.67.1"
typeguard = ">=4.4.4,<5"
types-networkx = ">=3.5.0.20251001"
types-requests = ">=2.32.4.20250913"
types-tqdm = ">=4.67.0.20250809"
universal-pathlib = ">=0.3.4"
xarray = ">=2026.4,<2027"
xxhash = ">=3.6.0"
ibis-framework = { version = ">=12,<13", extras = ["duckdb", "examples"] }
scikit-learn = ">=1.7.2,<2"
gdown = ">=6.1,<7"
mkdocs-gen-files = ">=0.6.1,<0.7"
mkdocs-literate-nav = "*"
mkdocs-api-autonav = ">=0.4.0,<0.5"
mkdocs-material = ">=9.7.1,<10"
mkdocstrings = ">=0.30.1,<0.31"
tabulate = ">=0.10,<0.11"
mkdocs-bibtex = ">=4.4.0,<5"
statsmodels = ">=0.14.5"
gget = ">=0.30.3,<0.31"
openpyxl = ">=3.1.5,<4"
scipy-stubs = ">=1.17.0.0,<2"
adjusttext = ">=0.8,<0.9"
seaborn = ">=0.13.2,<0.14"
textalloc = ">=1.2.1,<2"
types-seaborn = ">=0.13.2.20251221,<0.14"
rpy2 = ">=3.6.4,<4"
uniprot-id-mapper = ">=1.1.4,<2"
forestplot = ">=0.4.1,<0.5"
zepid = ">=0.9.1,<0.10"
synapseclient = ">=4.11.0,<5"
import-linter = ">=2.9,<3"
pyreadr = ">=0.5.4,<0.6"
pygenometracks = ">=3.9,<4"
pybedtools = ">=0.12.0,<0.13"
tomli-w = "*"
upsetplot = ">=0.9.0,<0.10"
pypng = ">=0.20220715.0,<0.20220716"
mkdocs-glightbox = ">=0.5.2,<0.6"
mkdocs-macros-plugin = ">=1.3.0,<2"
frozendict = ">=2.4.7,<3"
mkdocs-git-committers-plugin-2 = ">=2.5.0,<3"
pytest-testmon = ">=2.2.0,<3"
mkdocs-awesome-nav = ">=3.3.0, <4"

[tool.ty.environment]
python = ".pixi/envs/default"

[tool.pixi.feature.download.dependencies]
aria2 = { channel = "conda-forge" }

[tool.pixi.environments]
default = ["analysis"]

download-env = ["download"]