magellanmapper/pyproject.toml at master · sanderslab/magellanmapper · GitHub

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# MagellanMapper project configuration file
# This file is used to define the build system and project metadata.

# required for building the package
[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

# specify source directory and discover packages
[tool.setuptools.packages.find]
include = ["magmap*"]

# Project metadata
[project]
name = "magellanmapper"
version = "1.7a1"
description = "3D atlas analysis and annotation"
readme = "README.md"
authors = [
    { name = "David Young", email = "david@textflex.com" }
]
license-files = ["LICENSE.txt"]
requires-python = ">=3.10"
urls = { Homepage = "https://github.com/sanderslab/magellanmapper" }

# main dependencies for the project
dependencies = [
    "scikit-image",
    "matplotlib != 3.3.0, != 3.3.1",
    "pandas",
    "PyYAML",
    "appdirs",
    "importlib-metadata >= 1.0 ; python_version < '3.8'",
    "tifffile",
    "imagecodecs",
    "dataclasses ; python_version < '3.7'",
    "brainglobe-atlasapi ; python_version >= '3.9'",
    "bg-atlasapi ; python_version < '3.9'",
    "typing_extensions",
]

# optional dependencies for the project
[project.optional-dependencies]

# optional dependencies to import files via BioFormats, which req Java 8+;
# must use pip arg `--extra-index-url https://pypi.fury.io/dd8/` to install
import = [
    "javabridge==1.0.19.post4+gbebed64 ; python_version < '3.8'",
    "javabridge==1.0.19.post9+gc8c12b4 ; python_version >= '3.8'",
    "python-bioformats==4.0.5.post2+g51eb88a ; python_version < '3.8'",
    "python-bioformats==4.0.7.post5+g52309d1 ; python_version >= '3.8'",
]

# optional dependencies for AWS interaction
aws = ["boto3", "awscli"]

# optional dependencies for Pandas
pandas_plus = ["openpyxl", "jinja2"]

# optional dependencies to build API documentation
docs = ["sphinx", "sphinx-autodoc-typehints", "myst-parser", "furo"]

# optional dependencies for Jupyter notebooks
jupyter = ["jupyterlab", "bash_kernel"]

# optional dependencies for classification
classifier = ["tensorflow"]

# optional dependencies for main GUI; note that this group is not necessary
# for the Matplotlib-based viewers (eg ROI Editor, Atlas Editor)
gui = ["PyQt5 != 5.15.8", "pyface", "traitsui"]

# optional dependencies for the 3D viewer.
3d = ["mayavi", "vtk < 9.3.0"]

#: Optional ITK and Elastix for image I/O and registration.
#: `itk` not included since it does not load properly when installed with rest
#: of dependencies. `itk-elastix` also installs a later `itk` version.
itk = ["itk-elastix==0.20"]

# optional pre-built SimpleITK with Elastix for image I/O and registration.
simplitk = [
    "simpleitk==2.0.2rc2.dev785+g8ac4f ; python_version < '3.8'",
    "simpleitk==2.3.0.dev117+g0640d ; python_version >= '3.8'",
]

# dependencies for most common tasks
most = [
    "matplotlib_scalebar",
    "pyamg",
    "magellanmapper[gui]",
    "magellanmapper[itk]",
]

# (almost) all optional dependencies;
# must use pip arg `--extra-index-url https://pypi.fury.io/dd8/` to install
# because of the `import` group
all = [
    "matplotlib_scalebar",
    "pyamg",
    "seaborn",
    "scikit-learn",
    "magellanmapper[gui]",
    "magellanmapper[docs]",
    "magellanmapper[itk]",
    "magellanmapper[import]",
    "magellanmapper[aws]",
    "magellanmapper[jupyter]",
    "magellanmapper[3d]",
]

[project.scripts]
mm = "magmap.io.load_env:launch_magmap"