tortoize/pyproject.toml at trunk · diff-use/tortoize · GitHub

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[build-system]
requires = [
    "scikit-build-core>=0.11",
    "pybind11>=3.0",
]
build-backend = "scikit_build_core.build"

[project]
name = "py_tortoize"
version = "0.1.0"
description = "Python bindings and scripts for PDB-REDO/tortoize"
authors = [{name = "Marcus D. Collins", email = "marcus.collins@astera.org"}]
requires-python = ">= 3.12, < 3.13"
dependencies = [
    "gemmi", "loguru"
]

[tool.scikit-build]
minimum-version = "build-system.requires"
build-dir = "build/{wheel_tag}"
ninja.make-fallback = true
cmake.args = [
    "-DPython3_EXECUTABLE=$ENV{PREFIX}/bin/python",
    "-DPython3_ROOT_DIR=$ENV{PREFIX}",
    "-DPython3_FIND_STRATEGY=LOCATION",
]

[tool.pixi.activation.env]
PYTHONNOUSERSITE = "1"

[tool.pixi.workspace]
channels = ["conda-forge"]
platforms = ["linux-64"]
preview = ["pixi-build"]

[tool.pixi.dependencies]
python = "3.12.*"
pip = "*"
cmake = "*"
ninja = "*"
zlib = "*"
gsl = "*"
pkg-config = "*"
# Compilers:
c-compiler = "*"
cxx-compiler = "*"  # recommended by ChatGPT to force a consistent compiler for all libs
nlohmann_json = "*"
catch2 = "*"
py_tortoize = {path = "."}

#[tool.pixi.pypi-dependencies]
# This is left here commented as a warning to not include this, as it fails to install properly.
#py_tortoize = { path = ".", editable = false }


[tool.pixi.environments]
analysis = {features = ["analysis"]}

[tool.pixi.package]
name = "py_tortoize"
version = "0.1.0"

[tool.pixi.tasks.crawl]
cmd = "python src/py_tortoize/scan_and_collect_results.py --parent-directory {{parentdir}} --output-file-prefix {{output_prefix}} --target-file-pattern {{pattern}}"
default-environment = "analysis"
args = [
    "parentdir",  # top level directory to crawl for result files
    # the filename prefix for the residue-level and protein-level output files
    {"arg" = "output_prefix", "default" = "tortoize_output"},
    # the pattern to search for structure files.
    {"arg" = "pattern", "default" = "refined.cif"}
]

[tool.pixi.package.build]
backend = { name = "pixi-build-cmake", version = "0.*" }

[tool.pixi.package.build.config]
# FIXME: there must be some more general way to specify all of this...
extra-args = [
    "-DCMAKE_BUILD_TYPE=Release",
    "-DLINUX_FLAG=ON",
    "-DPython3_EXECUTABLE=$PREFIX/bin/python",
    "-DPython3_ROOT_DIR=$PREFIX",
    "-DPython3_FIND_STRATEGY=LOCATION"
]

[tool.pixi.package.host-dependencies]
cmake = "3.25.*"
pybind11 = "*"
python = "3.12.*"
pcre2 = "*"
nlohmann_json = "*"
catch2 = "*"

[tool.pixi.package.build-dependencies]
cmake = "3.25.*"
pybind11 = "*"
python = "3.12.*"
pcre2 = "*"
nlohmann_json = "*"
catch2 = "*"

[dependency-groups]
analysis = [
    "polars",
    "mdtraj",
    "marimo",
    "matplotlib",
    "seaborn",
    "pandas",
    "pyzmq",
    "ipython",
    "scikit-learn"
]
test = ["pytest"]