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Clean up dependencies Include optional "dev" component Update README.md with badges Test minimal setup.py Neuter - for now - sample C extension
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| @@ -1,3 +1,9 @@ | ||
| # MASER - Measles Simulation for ERadication | ||
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| Spatial measles models implemented with the LASER toolkit. | ||
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| [](https://pypi.org/project/laser-measles/) | ||
|  | ||
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|  | ||
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@@ -8,9 +8,9 @@ version = "0.5.0" | |
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| dependencies = [ | ||
| "click", | ||
| "laser-core @ git+https://github.com/InstituteforDiseaseModeling/[email protected]", | ||
| "numpy>=1.26.4,<2.0.0", | ||
| "numba>=0.59.1", | ||
| "laser-core==0.1.1", | ||
| # "numpy>=1.26.4,<2.0.0", # use laser-core version | ||
| # "numba~=0.59.1", # use laser-core version | ||
| "tqdm", | ||
| "geopandas", | ||
| "pandas", | ||
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@@ -51,6 +51,10 @@ classifiers = [ | |
| "Topic :: Utilities", | ||
| ] | ||
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| [project.optional-dependencies] | ||
| dev = ["tox", "uv"] | ||
| # docs = ["sphinx", "sphinx-rtd-theme"] | ||
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| [project.urls] | ||
| Homepage = "https://example.com" | ||
| Documentation = "https://laser-measles.readthedocs.io/en/latest/" | ||
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| @@ -1,107 +1,66 @@ | ||
| #!/usr/bin/env python | ||
| import os | ||
| import platform | ||
| import re | ||
| from pathlib import Path | ||
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| from setuptools import Extension | ||
| from setuptools import find_packages | ||
| from setuptools import setup | ||
| from setuptools.dist import Distribution | ||
| import setuptools | ||
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| # Enable code coverage for C code: we cannot use CFLAGS=-coverage in tox.ini, since that may mess with compiling | ||
| # dependencies (e.g. numpy). Therefore, we set SETUPPY_CFLAGS=-coverage in tox.ini and copy it to CFLAGS here (after | ||
| # deps have been safely installed). | ||
| if "TOX_ENV_NAME" in os.environ and os.environ.get("SETUPPY_EXT_COVERAGE") == "yes" and platform.system() == "Linux": | ||
| CFLAGS = os.environ["CFLAGS"] = "-fprofile-arcs -ftest-coverage" | ||
| LFLAGS = os.environ["LFLAGS"] = "-lgcov" | ||
| else: | ||
| CFLAGS = "" | ||
| LFLAGS = "" | ||
| if __name__ == "__main__": | ||
| setuptools.setup() | ||
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| class BinaryDistribution(Distribution): | ||
| """ | ||
| Distribution which almost always forces a binary package with platform name | ||
| """ | ||
| # import os | ||
| # import platform | ||
| # import re | ||
| # from pathlib import Path | ||
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| def has_ext_modules(self): | ||
| return super().has_ext_modules() or not os.environ.get("SETUPPY_ALLOW_PURE") | ||
| # from setuptools import Extension | ||
| # from setuptools import find_packages | ||
| # from setuptools import setup | ||
| # from setuptools.dist import Distribution | ||
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| # # Enable code coverage for C code: we cannot use CFLAGS=-coverage in tox.ini, since that may mess with compiling | ||
| # # dependencies (e.g. numpy). Therefore, we set SETUPPY_CFLAGS=-coverage in tox.ini and copy it to CFLAGS here (after | ||
| # # deps have been safely installed). | ||
| # if "TOX_ENV_NAME" in os.environ and os.environ.get("SETUPPY_EXT_COVERAGE") == "yes" and platform.system() == "Linux": | ||
| # CFLAGS = os.environ["CFLAGS"] = "-fprofile-arcs -ftest-coverage" | ||
| # LFLAGS = os.environ["LFLAGS"] = "-lgcov" | ||
| # else: | ||
| # CFLAGS = "" | ||
| # LFLAGS = "" | ||
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| def read(*names, **kwargs): | ||
| with Path(__file__).parent.joinpath(*names).open(encoding=kwargs.get("encoding", "utf8")) as fh: | ||
| return fh.read() | ||
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| # class BinaryDistribution(Distribution): | ||
| # """ | ||
| # Distribution which almost always forces a binary package with platform name | ||
| # """ | ||
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| setup( | ||
| # name="laser-measles", | ||
| # version="0.5.0", | ||
| # license="MIT", | ||
| # description="Spatial models of measles implemented with the LASER toolkit.", | ||
| long_description="{}\n{}".format( | ||
| re.compile("^.. start-badges.*^.. end-badges", re.M | re.S).sub("", read("README.rst")), | ||
| re.sub(":[a-z]+:`~?(.*?)`", r"``\1``", read("CHANGELOG.rst")), | ||
| ), | ||
| # author="Christopher Lorton", | ||
| # author_email="[email protected]", | ||
| url="https://github.com/InstituteforDiseaseModeling/laser-measles", | ||
| packages=find_packages("src"), | ||
| package_dir={"": "src"}, | ||
| py_modules=[path.stem for path in Path("src").glob("*.py")], | ||
| include_package_data=True, | ||
| zip_safe=False, | ||
| # classifiers=[ | ||
| # # complete classifier list: http://pypi.python.org/pypi?%3Aaction=list_classifiers | ||
| # "Development Status :: 5 - Production/Stable", | ||
| # "Intended Audience :: Developers", | ||
| # "License :: OSI Approved :: MIT License", | ||
| # "Operating System :: Unix", | ||
| # "Operating System :: POSIX", | ||
| # "Operating System :: Microsoft :: Windows", | ||
| # "Programming Language :: Python", | ||
| # "Programming Language :: Python :: 3", | ||
| # "Programming Language :: Python :: 3 :: Only", | ||
| # "Programming Language :: Python :: 3.8", | ||
| # "Programming Language :: Python :: 3.9", | ||
| # "Programming Language :: Python :: 3.10", | ||
| # "Programming Language :: Python :: 3.11", | ||
| # "Programming Language :: Python :: 3.12", | ||
| # "Programming Language :: Python :: Implementation :: CPython", | ||
| # "Topic :: Utilities", | ||
| # ], | ||
| # project_urls={ | ||
| # "Documentation": "https://laser-measles.readthedocs.io/en/latest/", | ||
| # "Changelog": "https://laser-measles.readthedocs.io/en/latest/changelog.html", | ||
| # "Issue Tracker": "https://github.com/InstituteforDiseaseModeling/laser-measles/issues", | ||
| # }, | ||
| # keywords=[ | ||
| # # eg: "keyword1", "keyword2", "keyword3", | ||
| # ], | ||
| # python_requires=">=3.8", | ||
| # install_requires=[ | ||
| # "click", | ||
| # # eg: "aspectlib==1.1.1", "six>=1.7", | ||
| # ], | ||
| extras_require={ | ||
| # eg: | ||
| # "rst": ["docutils>=0.11"], | ||
| # ":python_version=='3.8'": ["backports.zoneinfo"], | ||
| }, | ||
| # entry_points={ | ||
| # "console_scripts": [ | ||
| # "laser-measles = laser_measles.cli:run", | ||
| # ] | ||
| # }, | ||
| ext_modules=[ | ||
| Extension( | ||
| str(path.relative_to("src").with_suffix("")).replace(os.sep, "."), | ||
| sources=[str(path)], | ||
| extra_compile_args=CFLAGS.split(), | ||
| extra_link_args=LFLAGS.split(), | ||
| include_dirs=[str(path.parent)], | ||
| ) | ||
| for path in Path("src").glob("**/*.c") | ||
| ], | ||
| distclass=BinaryDistribution, | ||
| ) | ||
| # def has_ext_modules(self): | ||
| # return super().has_ext_modules() or not os.environ.get("SETUPPY_ALLOW_PURE") | ||
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| # def read(*names, **kwargs): | ||
| # with Path(__file__).parent.joinpath(*names).open(encoding=kwargs.get("encoding", "utf8")) as fh: | ||
| # return fh.read() | ||
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| # setup( | ||
| # long_description="{}\n{}".format( | ||
| # re.compile("^.. start-badges.*^.. end-badges", re.M | re.S).sub("", read("README.rst")), | ||
| # re.sub(":[a-z]+:`~?(.*?)`", r"``\1``", read("CHANGELOG.rst")), | ||
| # ), | ||
| # url="https://github.com/InstituteforDiseaseModeling/laser-measles", | ||
| # packages=find_packages("src"), | ||
| # package_dir={"": "src"}, | ||
| # py_modules=[path.stem for path in Path("src").glob("*.py")], | ||
| # include_package_data=True, | ||
| # zip_safe=False, | ||
| # ext_modules=[ | ||
| # Extension( | ||
| # str(path.relative_to("src").with_suffix("")).replace(os.sep, "."), | ||
| # sources=[str(path)], | ||
| # extra_compile_args=CFLAGS.split(), | ||
| # extra_link_args=LFLAGS.split(), | ||
| # include_dirs=[str(path.parent)], | ||
| # ) | ||
| # for path in Path("src").glob("**/*.c") | ||
| # ], | ||
| # distclass=BinaryDistribution, | ||
| # ) |
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