setup.cfg -> pyproject.toml (#2408)

Let's reduce the number of package configuration files...

.github/workflows/deploy_release.yml

@@ -39,7 +39,7 @@ jobs:
     - name: Remove direct dependencies from setup.cfg
       # Remove any "git+https"-based dependencies that are not supported
       #  by PyPI and are only required for testing.
-      run: sed -i '/git+https/d' python/sdist/setup.cfg
+      run: sed -i '/git+https/d' python/sdist/pyproject.toml
 
     - name: sdist
       run: scripts/buildSdist.sh

python/sdist/amici/custom_commands.py

@@ -17,13 +17,17 @@
 class AmiciInstall(install):
     """Custom `install` command to handle extra arguments"""
 
-    print("running AmiciInstall")
-
     # Passing --no-clibs allows to install the Python-only part of AMICI
     user_options = install.user_options + [
         ("no-clibs", None, "Don't build AMICI C++ extension"),
     ]
 
+    def run(self):
+        """Setuptools entry-point"""
+        print(f"running {self.__class__.__name__}")
+
+        super().run()
+
     def initialize_options(self):
         super().initialize_options()
         self.no_clibs = False

python/sdist/pyproject.toml

@@ -1,6 +1,8 @@
+# https://packaging.python.org/en/latest/guides/writing-pyproject-toml/
+# https://setuptools.pypa.io/en/latest/userguide/index.html
 [build-system]
 requires = [
-    "setuptools>=40.6.3",
+    "setuptools>=61",
     "wheel",
     # oldest-supported-numpy helps us to pin numpy here to the lowest supported
     # version to have ABI-compatibility with the numpy version in the runtime
@@ -13,6 +15,112 @@ requires = [
 ]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "amici"
+dynamic = ["version"]
+description = "Advanced multi-language Interface to CVODES and IDAS"
+requires-python = ">=3.9"
+dependencies = [
+    "cmake-build-extension==0.5.1",
+    "sympy>=1.9",
+    "numpy>=1.19.3; python_version=='3.9'",
+    "numpy>=1.21.4; python_version>='3.10'",
+    "numpy>=1.23.2; python_version=='3.11'",
+    "numpy; python_version>='3.12'",
+    "python-libsbml",
+    "pandas>=2.0.2",
+    "pyarrow",
+    "wurlitzer",
+    "toposort",
+    "setuptools>=48",
+    "mpmath",
+]
+license = {text = "BSD 3-Clause License"}
+authors = [
+    {name = "Fabian Froehlich", email = "[email protected]"},
+    {name = "Daniel Weindl", email = "[email protected]"},
+    {name = "Jan Hasenauer"},
+    {name = "AMICI contributors"},
+]
+maintainers = [
+    {name = "Fabian Froehlich", email = "[email protected]"},
+    {name = "Daniel Weindl", email = "[email protected]"},
+]
+readme = "README.md"
+keywords =["differential equations", "simulation", "ode", "cvodes",
+    "systems biology", "sensitivity analysis", "sbml", "pysb", "petab"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS :: MacOS X",
+    "Programming Language :: Python",
+    "Programming Language :: C++",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+[project.optional-dependencies]
+# Don't include any URLs here - they are not supported by PyPI:
+#  HTTPError: 400 Bad Request from https://upload.pypi.org/legacy/
+#  Invalid value for requires_dist. Error: Can't have direct dependency: ...
+petab = ["petab>=0.2.9"]
+pysb = ["pysb>=1.13.1"]
+test = [
+    "benchmark_models_petab @ git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python",
+    "h5py",
+    "pytest",
+    "pytest-cov",
+    "pytest-rerunfailures",
+    "coverage",
+    "shyaml",
+    "antimony>=2.13",
+    # see https://github.com/sys-bio/antimony/issues/92
+    #  unsupported x86_64 / x86_64h
+    "antimony!=2.14; platform_system=='Darwin' and platform_machine in 'x86_64h'",
+    "scipy",
+    "pooch"
+]
+vis =[
+    "matplotlib",
+    "seaborn",
+]
+examples =[
+    "jupyter",
+    "scipy",
+]
+
+[project.scripts]
+# amici_import_petab.py is kept for backwards compatibility
+amici_import_petab = "amici.petab.cli.import_petab:_main"
+"amici_import_petab.py" = "amici.petab.cli.import_petab:_main"
+
+[project.urls]
+Homepage = "https://github.com/AMICI-dev/AMICI"
+Documentation = "https://amici.readthedocs.io/en/latest/"
+Repository = "https://github.com/AMICI-dev/AMICI.git"
+"Bug Tracker" = "https://github.com/AMICI-dev/AMICI/issues"
+
+# TODO: consider using setuptools_scm
+#[tool.setuptools_scm]
+## https://setuptools-scm.readthedocs.io/en/latest/
+#root = "../.."
+
+[tool.setuptools.package-data]
+amici = [
+    "amici/include/amici/*",
+    "src/*template*",
+    "swig/*",
+    "libs/*",
+    "setup.py.template",
+]
+
+[tool.setuptools.exclude-package-data]
+"*" = ["README.txt"]
+
+[tool.setuptools.dynamic]
+version = {attr = "amici.__version__"}
+
 [tool.black]
 line-length = 79
 

python/sdist/setup.py

@@ -158,14 +158,6 @@ def get_extensions():
 
 
 def main():
-    # Readme as long package description to go on PyPi
-    # (https://pypi.org/project/amici/)
-    with open(
-        os.path.join(os.path.dirname(__file__), "README.md"),
-        encoding="utf-8",
-    ) as fh:
-        long_description = fh.read()
-
     ext_modules = get_extensions()
 
     # handle parallel building
@@ -185,8 +177,6 @@ def main():
             "develop": AmiciDevelop,
             "build_py": AmiciBuildPy,
         },
-        long_description=long_description,
-        long_description_content_type="text/markdown",
         ext_modules=ext_modules,
     )