python-loader/pyproject.toml at master · PhysiCell-Tools/python-loader · GitHub

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#####
# a hatchling based setup module.
#
# see:
# https://packaging.python.org/en/latest/
# https://packaging.python.org/en/latest/tutorials/packaging-projects/
# https://hatch.pypa.io/latest/
#
# find files with traling spaces:
# find . -type f -exec egrep -l " +$" {} \;
#
# releasing a next version on pypi:
# 0. vim pcdl/VERSION.py  # increase version number in file
# 1. git add pcdl/VERSION.py
# 2. python3 man/scarab.py
# 3. git status
# 4. git commit -m'@ physicell data loader : next release.'
# 5. git tag -a v0.0.0 -m'version 0.0.0'
# 6. rm -r dist
# 7. python3 -c "import pcdl; pcdl.uninstall_data()"
# 8. python3 -m build --sdist  # make source distribution
# 9. python3 -m build --wheel  # make binary distribution python wheel
# 10. twine upload dist/* --verbose
# 11. git push origin
# 12. git push --tag
#
# releasing a next version on bioconda:
# 13. vim bioconda-recipes/recipes/pcdl/meta.yaml  # update version and content
# 14. git bioconda-recipes pull request
# 15. cp -r ../bioconda-recipes/recipes/pcdl jakku/biocondarecipes_recipes/
# 16. git add jakku/biocondarecipes_recipes/pcdl/meta.yaml
# 17. git commit -m'@ jakku : bioconda next release.'
# 18. git push origin
#
# releasing a next version on galaxy:
# https://planemo.readthedocs.io/en/latest/index.html
# https://docs.galaxyproject.org/en/latest/dev/schema.html
# cd tools-iuc/tools/pcdl/
# planemo lint
# planemo test
# planemo serve
#
# 19. vim tools-iuc/tools/pcdl/pcdl_macros.xml  # update version
# 20. git tools-iuc pull request
# 21. cp -r ../tools-iuc/tools/pcdl jakku/toolsiuc_tools/
# 22. git add jakku/toolsiuc_tools/pcdl/pcdl_macros.xml
# 23. git commit -m'@ jakku : galaxy next release.'
# 24. git push origin
#####


[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"


[project]
# name of the project
# pip install pcdl
# import pcdl
name = "pcdl"
dynamic = ["version"]

description = "physicell data loader (pcdl) provides a platform independent, python3 based, pip installable interface to load output, generated with the PhysiCell agent based modeling framework, into python3."
readme = "README.md"

requires-python = ">=3.11, <4"

license = "BSD-3-Clause"
#license-files = {paths = ["LICENSE"]}

authors = [
  {name="Elmar Bucher", email="epbucher@iu.edu"}
]
maintainers = [
  {name="Elmar Bucher", email="epbucher@iu.edu"}
]

keywords = [
    "analysis",
    "data",
    "physicell",
    "python3",
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Programming Language :: Python :: 3 :: Only",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]

# bue 2024-12-06: enforcing some versions
# light weight
dependencies = [
    "matplotlib",
    "numpy",
    "pandas>=2.2.2",  # numpy 2.0 comatible
    "scipy>=1.13.0",  # numpy 2.0 compatible
]

[project.optional-dependencies]
# bioconda galaxy
jakku = [
    "anndata>=0.10.8",  # numpy 2.0 compatible
    "requests",
    "vtk",
]
# heavy weight
full = [
    "pcdl[jakku]",
    "bioio>=2.0.0",
    "bioio-ome-tiff",
    "geopandas>=0.14",  # spatialdata 0.7.3 compatible
    "networkx",
    "neuroglancer",
    "scikit-image>=0.24.0",
    "shapely>=2.0.1",  # spatialdata 0.7.3 compatible
    "spatialdata>=0.7.3",
]


[project.scripts]
# special thanks to Miguel Ponce-de-Leon who introduced me to entry point scripts!
# metadata
pcdl_get_version = "pcdl.commandline:get_version"
pcdl_get_unit_dict = "pcdl.commandline:get_unit_dict"
# substrate
pcdl_get_substrate_list = "pcdl.commandline:get_substrate_list"
pcdl_get_conc_attribute = "pcdl.commandline:get_conc_attribute"
pcdl_get_conc_df = "pcdl.commandline:get_conc_df"
pcdl_plot_contour = "pcdl.commandline:plot_contour"
pcdl_make_conc_vtk = "pcdl.commandline:make_conc_vtk"
# cell agent
pcdl_get_celltype_list = "pcdl.commandline:get_celltype_list"
pcdl_get_cell_attribute_list = "pcdl.commandline:get_cell_attribute_list"
pcdl_get_cell_attribute = "pcdl.commandline:get_cell_attribute"
pcdl_get_cell_df = "pcdl.commandline:get_cell_df"
pcdl_get_anndata = "pcdl.commandline:get_anndata"
pcdl_make_graph_gml = "pcdl.commandline:make_graph_gml"
pcdl_plot_scatter = "pcdl.commandline:plot_scatter"
pcdl_make_cell_vtk = "pcdl.commandline:make_cell_vtk"
# substrate and cell agent
pcdl_get_muspan = "pcdl.commandline:get_muspan"
pcdl_get_spatialdata = "pcdl.commandline:get_spatialdata"
pcdl_plot_timeseries = "pcdl.commandline:plot_timeseries"
pcdl_make_ome_tiff = "pcdl.commandline:make_ome_tiff"
pcdl_render_neuroglancer = "pcdl.commandline:render_neuroglancer"
# making movies
pcdl_make_gif = "pcdl.commandline:make_gif"
pcdl_make_movie = "pcdl.commandline:make_movie"


[project.urls]
"Homepage lab" = "http://www.mathcancer.org/"
"Homepage project" = "http://physicell.org/"
Hompage = "https://github.com/elmbeech/physicelldataloader"
Documentation = "https://github.com/elmbeech/physicelldataloader/tree/master/man"
Issues = "https://github.com/elmbeech/physicelldataloader/issues"
Source = "https://github.com/elmbeech/physicelldataloader"
#DOI = "https://"


[tool.hatch.version]
path = "pcdl/VERSION.py"


[tool.hatch.build.targets.sdist]
include = [
    "/man",
    "/pcdl",
    "/test",
]
exclude = [
    "/output_2d.tar.gz",
    "/output_3d.tar.gz",
    "/.pytest_cache",
]