Cleanup package building

.github/workflows/test_benchmark_collection_models.yml

@@ -28,10 +28,6 @@ jobs:
         sudo apt-get update \
           && sudo apt-get install -y swig libatlas-base-dev
 
-    - name: pip
-      run: |
-        pip3 install --upgrade --user wheel \
-          && pip3 install --upgrade --user setuptools
     - run: pip3 install pytest shyaml
 
     - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH
@@ -40,7 +36,7 @@ jobs:
     # install AMICI
     - name: Create AMICI sdist
       run: |
-        cd python/sdist && /usr/bin/python3 setup.py sdist
+        pip3 install build && cd python/sdist && python3 -m build --sdist
     - name: Install AMICI sdist
       run: |
         AMICI_PARALLEL_COMPILE=2 pip3 install -v --user \

.github/workflows/test_doc.yml

@@ -74,10 +74,6 @@ jobs:
         run: |
           sudo scripts/downloadAndBuildSwig.sh
 
-      - name: pip
-        run: |
-          pip3 install setuptools
-
       - name: sphinx
         run: |
           scripts/run-sphinx.sh

.github/workflows/test_install.yml

@@ -37,10 +37,6 @@ jobs:
       run: |
         scripts/buildCpputest.sh
 
-    - name: pip
-      run: |
-        pip3 install numpy
-
     - name: Build AMICI
       run: |
         scripts/buildAmici.sh

.github/workflows/test_performance.yml

@@ -28,10 +28,6 @@ jobs:
       run: |
         sudo apt-get update \
           && sudo apt-get install -y swig libatlas-base-dev
-    - name: pip
-      run: |
-        pip3 install --upgrade --user wheel \
-          && pip3 install --upgrade --user setuptools
     - run: pip3 install petab shyaml
 
     - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH

.github/workflows/test_petab_test_suite.yml

@@ -35,10 +35,6 @@ jobs:
             libatlas-base-dev \
             python3-venv
 
-      - name: pip
-        run: |
-          pip3 install --upgrade --user wheel \
-            && pip3 install --upgrade --user setuptools
       - run: pip3 install pytest shyaml pytest-cov pysb petab
 
       - name: Build BNGL

.github/workflows/test_python_ver_matrix.yml

@@ -45,11 +45,6 @@ jobs:
           libatlas-base-dev \
           libhdf5-serial-dev \
           libboost-math-dev
-    - name: pip
-      run: |
-        pip3 install --upgrade --user wheel \
-          && pip3 install --upgrade --user setuptools
-
 
     # install AMICI
     - name: Build BNGL

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -29,7 +29,7 @@ jobs:
     - name: apt
       run: |
         sudo apt-get update \
-          && sudo apt-get install -y swig3.0 libatlas-base-dev
+          && sudo apt-get install -y swig4.0 libatlas-base-dev
     - run: AMICI_PARALLEL_COMPILE=2 ./scripts/installAmiciSource.sh
     - run: AMICI_PARALLEL_COMPILE=2 ./scripts/run-SBMLTestsuite.sh
 

python/CMakeLists.txt

@@ -30,7 +30,8 @@ add_custom_target(python-wheel
 add_custom_target(python-sdist
     COMMENT "Creating sdist for AMICI base python package"
     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/sdist
-    COMMAND ${Python3_EXECUTABLE} setup.py sdist --dist-dir=${CMAKE_CURRENT_BINARY_DIR}
+    COMMAND ${Python3_EXECUTABLE} -m pip install build
+    COMMAND ${Python3_EXECUTABLE} -m build --sdist --outdir=${CMAKE_CURRENT_BINARY_DIR}
 )
 
 

python/sdist/pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=40.6.3", "wheel", "numpy"]
+build-backend = "setuptools.build_meta"

python/sdist/setup.cfg

@@ -0,0 +1,62 @@
+[metadata]
+name = amici
+description = Advanced multi-language Interface to CVODES and IDAS
+version = file: amici/version.txt
+license = BSD 3-Clause License
+url = https://github.com/AMICI-dev/AMICI
+keywords = differential equations, simulation, ode, cvodes, systems biology, sensitivity analysis, sbml, pysb, petab
+author = Fabian Froehlich, Jan Hasenauer, Daniel Weindl and Paul Stapor
+author_email = fabian_froehlich@hms.harvard.edu
+project_urls =
+    Bug Reports = https://github.com/AMICI-dev/AMICI/issues
+    Source = https://github.com/AMICI-dev/AMICI
+    Documentation = https://amici.readthedocs.io/en/latest/
+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
+
+[options]
+packages = find:
+package_dir =
+    amici = amici
+python_requires = >=3.6
+install_requires =
+    sympy>=1.7.1
+    python-libsbml
+    h5py
+    pandas
+    pkgconfig
+    wurlitzer
+    toposort
+include_package_data = True
+zip_safe = False
+
+[options.extras_require]
+petab = petab>=0.1.11
+pysb = pysb>=1.11.0
+
+[options.package_data]
+amici =
+    amici/include/amici/*
+    src/*template*
+    swig/*
+    libs/*
+    setup.py.template
+
+[options.exclude_package_data]
+* =
+    README.txt
+
+
+[options.entry_points]
+
+; amici_import_petab.py is kept for backwards compatibility
+console_scripts =
+    amici_import_petab = amici.petab_import:main
+    amici_import_petab.py = amici.petab_import:main

python/sdist/setup.py

@@ -5,59 +5,22 @@
 
 This file expects to be run from within its directory.
 
-Requires:
+Non-python-package requirements:
 - swig3.0
-- setuptools
-- pkgconfig python+executables
-- hdf5 libraries and headers
+- Optional: hdf5 libraries and headers
 """
 
 import os
-import subprocess
 import sys
 
-import setup_clibs  # Must run from within containing directory
-
-from distutils import log
-
-
-def try_install(package: str) -> None:
-    """Try installing the given package using pip. Exit on error."""
-
-    log.info(f"Missing required package {package}. Trying to install...")
-    errno = subprocess.call([sys.executable, "-m", "pip", "install", package])
-    if errno:
-        log.error(f"Failed trying to install {package}. "
-                  "Please install manually before installing AMICI.")
-        raise SystemExit(errno)
-
-    import importlib
-    importlib.invalidate_caches()
-    globals()[package] = importlib.import_module(package)
-
-
-try:
-    # Required for numpy include directory, and for importing anything from
-    # the `amici` package. Therefore, try before any amici import.
-    import numpy as np
-except ImportError:
-    # We need numpy, but setup_requires fires too late
-    try_install('numpy')
-    # retry
-    import numpy as np
-
-try:
-    # Required for customizing installation, but setup_requires fires too late
-    from setuptools import find_packages, setup, Extension
-except ImportError:
-    try_install('setuptools')
-    from setuptools import find_packages, setup, Extension
-
-# Add current directory to path, as we need some modules from the AMICI
+# Add containing directory to path, as we need some modules from the AMICI
 # package already for installation
-sys.path.insert(0, os.getcwd())
+sys.path.insert(0, os.path.dirname(__file__))
+
+import numpy as np
+import setup_clibs  # Must run from within containing directory
+from setuptools import find_packages, setup, Extension
 
-from amici import __version__
 from amici.custom_commands import (
     AmiciInstall, AmiciBuildCLib, AmiciDevelop,
     AmiciInstallLib, AmiciBuildExt, AmiciSDist)
@@ -69,11 +32,6 @@ def try_install(package: str) -> None:
     add_openmp_flags,
 )
 
-# Python version check. We need >= 3.6 due to e.g. f-strings
-if sys.version_info < (3, 6):
-    sys.exit('amici requires at least Python version 3.6')
-
-
 def main():
     # Extra compiler flags
     cxx_flags = []
@@ -171,7 +129,6 @@ def main():
 
     # Install
     setup(
-        name='amici',
         cmdclass={
             'install': AmiciInstall,
             'sdist': AmiciSDist,
@@ -180,63 +137,10 @@ def main():
             'install_lib': AmiciInstallLib,
             'develop': AmiciDevelop,
         },
-        version=__version__,
-        description='Advanced multi-language Interface to CVODES and IDAS',
         long_description=long_description,
         long_description_content_type="text/markdown",
-        url='https://github.com/AMICI-dev/AMICI',
-        author='Fabian Froehlich, Jan Hasenauer, Daniel Weindl and '
-               'Paul Stapor',
-        author_email='fabian_froehlich@hms.harvard.edu',
-        license='BSD',
         libraries=[libamici, libsundials, libsuitesparse],
         ext_modules=[amici_module],
-        packages=find_packages(),
-        package_dir={'amici': 'amici'},
-        entry_points={
-            'console_scripts': [
-                'amici_import_petab = amici.petab_import:main',
-                # for backwards compatibility
-                'amici_import_petab.py = amici.petab_import:main'
-            ]
-        },
-        install_requires=['sympy>=1.7.1',
-                          'python-libsbml',
-                          'h5py',
-                          'pandas',
-                          'pkgconfig',
-                          'wurlitzer',
-                          'toposort'],
-        setup_requires=['setuptools>=40.6.3'],
-        python_requires='>=3.6',
-        extras_require={
-            'petab': ['petab>=0.1.11'],
-            'pysb': ['pysb>=1.11.0']
-        },
-        package_data={
-            'amici': ['amici/include/amici/*',
-                      'src/*template*',
-                      'swig/*',
-                      'libs/*',
-                      'setup.py.template',
-                      ],
-        },
-        zip_safe=False,
-        include_package_data=True,
-        exclude_package_data={
-            '': ['README.txt'],
-        },
-        test_suite="tests",
-        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',
-        ],
     )
 
 

scripts/buildDependencies.sh

@@ -11,4 +11,3 @@ script_path=$(cd "$script_path" && pwd)
 "${script_path}/buildSundials.sh"
 "${script_path}/buildCpputest.sh"
 "${script_path}/buildBNGL.sh"
-pip3 install numpy

scripts/buildSdist.sh

@@ -7,8 +7,7 @@ set -e
 script_path=$(dirname "$BASH_SOURCE")
 amici_path=$(cd "$script_path/.." && pwd)
 
-pip3 install --upgrade --user wheel
-pip3 install --upgrade --user setuptools
+pip3 install build
 
 cd "${amici_path}/python/sdist"
-python3 setup.py sdist
+python -m build --sdist

scripts/installAmiciArchive.sh

@@ -32,6 +32,5 @@ else
     source ${AMICI_PATH}/build/venvArchive/bin/activate
 fi
 
-pip install --upgrade pip setuptools pkgconfig wheel
 pip install $(ls -t ${AMICI_PATH}/build/python/amici-*.tar.gz | head -1)
 deactivate

scripts/installAmiciSource.sh

@@ -27,9 +27,8 @@ else
     source ${AMICI_PATH}/build/venv/bin/activate
 fi
 
-# install wheel separately to prevent build_wheel fail in next step
-pip install --upgrade wheel
-pip install --upgrade pip setuptools pkgconfig scipy matplotlib coverage pytest pytest-cov
+pip install --upgrade pip pkgconfig scipy matplotlib coverage pytest pytest-cov
 pip install git+https://github.com/pysb/pysb # pin to develop to fix sympy compatibility
+
 pip install --verbose -e ${AMICI_PATH}/python/sdist[petab]
 deactivate