pixi.toml

[project]
authors = [
    "OASCI <us@oasci.org>",
]
channels = ["conda-forge"]
description = "Investigating metal-sensing green fluorescent protein."
name = "metalflare"
platforms = ["linux-64"]
version = "0.0.0"
license = "Apache-2.0"
readme = "README.md"

[pypi-dependencies]
metalflare = { path = ".", editable = true }
ray = ">=2.32.0"
pdb2pqr = ">=3.6.2"

[system-requirements]
linux = "3.10.0"
libc = { family="glibc", version="2.17" }

[environments]
dev = ["dev"]
docs = ["docs"]

[tasks]

[dependencies]
python = "=3.11"
loguru = ">=0.7.2"
mdanalysis = ">=2.7.0"
jinja2 = ">=3.1.4"
zarr = ">=2.18.2"
seaborn = ">=0.13.2"
pymoo = ">=0.6.1.1"
pyarrow = ">=15.0.2"
scikit-learn = ">=1.5.1"
umap-learn = ">=0.5.6"
ipykernel = ">=6.29.5"
netcdf4 = ">=1.7.1"
jupyterlab = ">=4.2.3"
xgboost = ">=2.1.1"
"ruamel.yaml" = ">=0.18.6,<0.19"
ambertools = ">=23.6,<24"
xtb = ">=6.7.1,<7"
openbabel = ">=3.1.1,<4"
pandas = ">=2.2.3,<3"

[feature.dev.dependencies]
black = ">=23.10.0"
isort = ">=5.12.0"
pylint = ">=3.0.1"
mypy = ">=1.6.0"
bump-my-version = ">=0.11.0"
poetry-dynamic-versioning = ">=1.1.0"
pytest = ">=7.4.2"
pytest-cov = ">=4.1.0"
coverage = ">=7.3.1"
pytest-html = ">=4.0.1"
colorama = ">=0.4.6"

[feature.dev.tasks]
mdlint = { cmd = ["markdownlint-cli2", '"**/*.{md,markdown}"', "--fix", "--config", ".markdownlint.yaml", "||", "true"] }
isort = { cmd = ["isort", "--settings-path", ".isort.cfg", "./metalflare", "./tests", "||", "true"] }
black = { cmd = ["black", "--config", ".black.toml", "./metalflare", "./tests", "||", "true"] }
format = { depends-on = ["mdlint", "isort", "black"] }
tests = { cmd = [
    "PYTHONPATH=.",
    "pytest",
    "-c",
    ".pytest.ini",
    "--cov='metalflare'",
    "--cov-report=xml",
    "--junit-xml=report.xml",
    "--failed-first",
]}
coverage = { cmd = ["coverage", "report"] }
cleanup-build = { cmd = ["rm", "-rf", "./build"] }
build = { cmd = ["python3", "-m", "build"], depends-on = ["cleanup-build"]}
publish-test = { cmd = ["twine", "upload", "--repository", "testpypi", "dist/*"] }
publish = { cmd = ["twine", "upload", "dist/*"] }

[feature.dev.pypi-dependencies]
build = ">=1.2.2.post1,<2"
mypy-extensions = ">=1.0.0"

[feature.docs.dependencies]
mkdocs = ">=1.5.3"
mkdocs-material = ">=9.4.7"
pymdown-extensions = ">=10.3.1"
mkdocs-table-reader-plugin = ">=2.0.3"
mkdocstrings = ">=0.23.0"
mkdocstrings-python = ">=1.7.3"
mkdocs-glightbox = ">=0.3.6"
mkdocs-macros-plugin = ">=1.0.5"

[feature.docs.pypi-dependencies]
material-plausible-plugin = ">=0.2.0,<0.3"
mkdocs-gen-files = ">=0.5.0"
mkdocs-awesome-pages-plugin = ">=2.9.3,<3"

[feature.docs.tasks]
docs = { cmd = ["rm", "-rf", "./public/", "&&", "mkdocs", "build", "-d", "public/"] }
serve = { cmd = ["mkdocs", "serve"] }