pixi.toml

[project]
authors = ["Durrant Lab <durrantj@pitt.edu>"]
channels = ["conda-forge"]
description = "Open-source tool to generate 3D-ready small molecules for virtual screening"
name = "gypsum_dl"
platforms = ["linux-64", "osx-64", "win-64", "osx-arm64"]

[pypi-dependencies]
gypsum_dl = { path = ".", editable = true }
molvs = ">=0.1.1, <1"
dimorphite-dl = ">=2.0.1, <3"

[tasks]

[dependencies]
python = ">=3.10,<3.14"
loguru = ">=0.7.2,<1"
numpy = ">=2.0.0,<3"
scipy = ">=1.15.1,<2"
rdkit = ">=2024.9.4,<2027"
mpi4py = ">=4.0.1,<5"

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


[feature.dev.dependencies]
ruff = ">=0.7.2,<1"
isort = ">=5.13.2,<6"
mypy = ">=1.13.0,<2"
twine = ">=5.1.1,<6"
pytest = ">=8.3.3,<9"
pytest-cov = ">=6.0.0,<7"
coverage = ">=7.6.4,<8"
pip = ">=24.3.1,<25"
setuptools = ">=75.3.0,<76"
types-pyyaml = ">=6.0.12.20240917,<7"
scalene = ">=1.5.41,<2"
basedpyright = ">=1.29.1,<2"

[feature.dev.tasks]
mdlint = { cmd = ["markdownlint-cli2", '"**/*.{md,markdown}"', "--fix", "--config", ".markdownlint.yaml", "||", "true"] }
isort = { cmd = ["isort", "--settings-path", ".isort.cfg", "./gypsum_dl", "./tests", "||", "true"] }
ruff = { cmd = ["ruff", "format", "--config", ".ruff.toml", "./gypsum_dl", "./tests", "||", "true"] }
format = { depends-on = ["mdlint", "isort", "ruff"] }
tests = { cmd = [
    "PYTHONPATH=.",
    "pytest",
    "-c",
    ".pytest.ini",
    "--cov='gypsum_dl'",
    "--cov-report=xml",
    "--junit-xml=report.xml",
    "--failed-first",
]}
profile = { cmd = [
    "PYTHONPATH=.",
    "scalene",
    "-m",
    "pytest",
    "-c",
    ".pytest.ini",
    "--cov='gypsum_dl'",
    "--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"
setuptools-scm = ">=8.0.0"

[feature.docs.dependencies]
mkdocs = ">=1.6.1,<2"
mkdocs-material = ">=9.5.44,<10"
pymdown-extensions = ">=10.12,<11"
mkdocs-table-reader-plugin = ">=3.1.0,<4"
mkdocstrings = ">=0.26.2,<0.27"
mkdocstrings-python = ">=1.12.2,<2"
mkdocs-gen-files = ">=0.4.0,<1"
mkdocs-macros-plugin = ">=1.3.7,<2"
mkdocs-jupyter = ">=0.25.0,<1"
mkdocs-glightbox = ">=0.4.0,<1"
mkdocs-git-revision-date-localized-plugin = ">=1.2.9,<2"
mkdocs-autorefs = ">=1.2.0,<2"

[feature.docs.pypi-dependencies]
material-plausible-plugin = ">=0.2.0,<1"
mkdocs-awesome-pages-plugin = ">=2.9.3,<3"

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