diff --git a/.gitignore b/.gitignore index b1caaf8a8..6eb84927e 100644 --- a/.gitignore +++ b/.gitignore @@ -64,7 +64,7 @@ packrat/lib*/ dist/ SEIR.egg-info/ Outcomes.egg-info/ -venv/ +*venv*/ .venv/ # R package manuals diff --git a/flepimop/gempyor_pkg/pyproject.toml b/flepimop/gempyor_pkg/pyproject.toml index 374b58cbf..6f90e1053 100644 --- a/flepimop/gempyor_pkg/pyproject.toml +++ b/flepimop/gempyor_pkg/pyproject.toml @@ -1,6 +1,58 @@ [build-system] -requires = [ - "setuptools>=42", - "wheel" -] +requires = ["setuptools>=61.0", "wheel"] build-backend = "setuptools.build_meta" + +[project] +authors = [ + {name = "Joseph Lemaitre", email = "jo.lemaitresamra@gmail.com"}, + {name = "Joshua Kaminsky and others"}, +] +classifiers = [ + "Programming Language :: Python :: 3", + "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", + "Operating System :: OS Independent", +] +description = "Generic epidemic compartmental modeling pipelines with interventions and outcome reporting." +dependencies = [ + "click>=8.1.7", + "confuse", + "dask[dataframe]", + "emcee", + "graphviz", + "h5py", + "matplotlib", + "numba>=0.53.1", + "numpy", + "pandas", + "pyarrow", + "scipy", + "seaborn", + "sympy", + "tqdm", + "xarray", +] +name = "gempyor" +readme = "README.md" +requires-python = ">=3.10,<3.12" +version = "2.1" + +[project.optional-dependencies] +aws = ["boto3", "botocore"] +test = ["pytest", "mock"] + +[project.urls] +Homepage = "https://www.flepimop.org/" +Issues = "https://github.com/HopkinsIDD/flepiMoP/issues" + +[project.scripts] +flepimop = "gempyor.cli:cli" +flepimop-calibrate = "gempyor.calibrate:calibrate" +gempyor-simulate = "gempyor.simulate:_deprecated_simulate" + +[tool.setuptools] +package-dir = {"" = "src"} +include-package-data = false + +[tool.setuptools.packages.find] +where = ["src"] +namespaces = false diff --git a/flepimop/gempyor_pkg/setup.cfg b/flepimop/gempyor_pkg/setup.cfg deleted file mode 100644 index b79955d62..000000000 --- a/flepimop/gempyor_pkg/setup.cfg +++ /dev/null @@ -1,57 +0,0 @@ -[metadata] -name = gempyor -version = 2.1 -author = Joseph Lemaitre, Joshua kaminski and others -author_email = jo.lemaitresamra@gmail.com, jkaminsky@jhu.edu -description = General Epidemics Modeling Pipeline with Yterventions and Outcome Reporting, GEMPYOR: a large scale infectious disease dynamics model with configurable compartmental graph structure and interventions. Simulate metapopulation spread and health outcomes. -long_description = file: README.md -long_description_content_type = text/markdown -url = https://github.com/HopkinsIDD/flepiMoP -project_urls = - Bug Tracker = https://github.com/HopkinsIDD/flepiMoP/issues -classifiers = - Programming Language :: Python :: 3 - License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) - Operating System :: OS Independent - -[options] -package_dir = - = src -packages = find: -python_requires = >=3.7 -install_requires = - numba >=0.53.1 - pandas - numpy - seaborn - tqdm - matplotlib - xarray - emcee - click >= 8.1.7 - confuse - pyarrow - sympy - dask - scipy - graphviz - -# see https://stackoverflow.com/questions/58826164/dependencies-requirements-for-setting-up-testing-and-installing-a-python-lib -# installed for pip install -e ".[test]" -[options.extras_require] -test = - pytest - mock -aws = - boto3 - botocore - -[options.entry_points] -console_scripts = - flepimop = gempyor.cli:cli - gempyor-simulate = gempyor.simulate:_deprecated_simulate - flepimop-calibrate = gempyor.calibrate:calibrate - -[options.packages.find] -where = src -