pixi.toml

[workspace]
name = "bioconda-utils"
version = "0.0.0"
platforms = ["linux-64", "osx-64"]
channels = ["conda-forge", "bioconda"]

[dependencies]
# pinnings
conda-forge-pinning = "==2026.01.07.13.16.30"

# basics
python = "3.13.*"
setuptools = "81.*"
setuptools-scm = ">=8"
conda = "26.3.*"
conda-libmamba-solver = "26.3.*"
conda-build = "26.3.*"
conda-index = "0.10.*"
conda-package-streaming = "0.12.*"
mamba = "2.5.*"

# CLI
typer = "0.26.*"
# Logging
colorlog = "6.*"
tqdm = "4.67.*"  # Progress monitor
yaspin = "3.*"
# Recipe YAML parsing
"ruamel.yaml" = "0.18.*"
pyaml = "26.2.*"  # Faster YAML parser (deprecate?)
networkx = "3.6.*"  # (networkx>3.3 needs python>=3.10)
pandas = "3.0.*"
# Avoid large mkl package (pulled in by pandas)
libblas = { version = "*", build = "*openblas" }
boltons = "25.0.*"
jsonschema = "4.26.*"  # JSON schema verification
jinja2 = "3.1.*"

# anaconda_upload
anaconda-client = "1.14.*"
# mulled test and container build
galaxy-tool-util = "25.*"
involucro = "1.1.*"
# docker upload
skopeo = "1.22.*"
# find/xargs copy built packages from container
findutils = "*"
# well - git
git = "2.*"

# hosters - special regex not supported by RE
regex = "2026.*"

# asyncio
aiohttp = "3.13.*"  # HTTP lib; pinning to reflect dependabot alert
aiohttp-jinja2 = "*"  # jinja2 renderer for aiohttp.web
aiohttp-session = "*"
aiohttp-security = "*"
aiofiles = "25.*"  # async open
aioftp = "0.27.*"  # FTP lib
backoff = "2.2.*"  # retrying of failed API calls
cachetools = "7.0.*"  # request caching (NEEDED?)

# client API wrappers
gitpython = "3.1.*"  # githandler
gidgethub = "5.*"  # githubhandler
pyjwt = ">=2.4.0"  # githubhandler (JWT signing), needs >=2.4.0, CVE-2022-29217

# bioconductor-skeleton
beautifulsoup4 = "4.*"
# The bioconductor skeleton needs this
requests = "2.33.*"

# merge handling
pygithub = "*"

# caching
diskcache = "5.*"
platformdirs = "4.*"

# build failure output
tabulate = "0.10.*"

# resource reporting for builds
psutil = "*"

[feature.test.dependencies]
pip = "*"
pytest = ">=3.3"
pytest-cov = "*"

[feature.dev.dependencies]
ty = "*"
ruff = "*"
"go-shfmt" = "*"
shellcheck = "*"
just = "*"

[environments]
default = ["test"]
dev = ["test", "dev"]

[tasks.format]
cmd = "ruff format ."
default-environment = "dev"
description = "Format Python files"

[tasks.install]
cmd = "python -m pip install --no-deps --no-build-isolation ."
default-environment = "dev"
description = "Build and install bioconda-utils into the Pixi environment"

[tasks.global-install]
cmd = """
mkdir -p ~/.local/bin
ln -sf "$CONDA_PREFIX/bin/bioconda-utils" ~/.local/bin/bioconda-utils
"""
depends-on = ["install"]
default-environment = "dev"
description = "Make the Pixi-installed CLI available in ~/.local/bin"

[tasks.regenerate-requirements]
cmd = "python scripts/generate-requirements-txt.py"
description = "Regenerate the shipped conda requirements file"

[tasks.check-requirements]
cmd = "python scripts/generate-requirements-txt.py --check"
description = "Check that the shipped conda requirements file is current"

[tasks.check]
cmd = "ruff check . && ty check ."
depends-on = ["check-requirements"]
default-environment = "dev"
description = "Run fast Python static checks"

[tasks.test]
cmd = "pytest"
depends-on = ["install"]
default-environment = "dev"
description = "Run the full test suite (slow)"

[tasks.shfmt]
cmd = "shfmt"
default-environment = "dev"
description = "Run shfmt with arguments supplied by the caller"

[tasks.shellcheck]
cmd = "shellcheck"
default-environment = "dev"
description = "Run ShellCheck with arguments supplied by the caller"