Drop python3.9 support (AMICI-dev#2391)

NEP 29:

> On Apr 05, 2024 drop support for Python 3.9

.github/workflows/deploy_branch.yml

@@ -9,7 +9,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/deploy_protected.yml

@@ -36,7 +36,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/deploy_release.yml

@@ -12,7 +12,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     environment:
       name: pypi

.github/workflows/test_benchmark_collection_models.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
         extract_subexpressions: ["true", "false"]
     env:
       AMICI_EXTRACT_CSE: ${{ matrix.extract_subexpressions }}

.github/workflows/test_doc.yml

@@ -20,7 +20,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/test_install.yml

@@ -9,7 +9,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -50,7 +50,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -83,7 +83,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/test_performance.yml

@@ -23,7 +23,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/test_petab_test_suite.yml

@@ -22,7 +22,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}

.github/workflows/test_pypi.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
         os: [ubuntu-22.04, macos-latest]
 
     runs-on: ${{ matrix.os }}

.github/workflows/test_python_cplusplus.yml

@@ -15,7 +15,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
 
     steps:
     - name: Cache
@@ -117,7 +117,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.10" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -193,7 +193,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -233,7 +233,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.11"
 
     - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
@@ -282,7 +282,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.11"
 
     - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow

.github/workflows/test_python_ver_matrix.yml

@@ -25,7 +25,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12']
         experimental: [false]
 
     steps:

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -29,7 +29,7 @@ jobs:
       matrix:
         cases: ["1-250", "251-500", "501-750", "751-1000",
                 "1000-1250", "1251-"]
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/test_valgrind.yml

@@ -18,7 +18,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
 
     env:
       ENABLE_AMICI_DEBUGGING: "TRUE"
@@ -57,7 +57,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
 
     env:
       ENABLE_AMICI_DEBUGGING: "TRUE"

.github/workflows/test_windows.yml

@@ -27,7 +27,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

documentation/python_installation.rst

@@ -8,7 +8,7 @@ Short guide
 
 Installation of the AMICI Python package has the following prerequisites:
 
-* Python>=3.9
+* Python>=3.10
 * :term:`SWIG`>=3.0
 * CBLAS compatible BLAS library
   (e.g., OpenBLAS, CBLAS, Atlas, Accelerate, Intel MKL)

python/sdist/amici/setup.template.py

@@ -72,7 +72,7 @@ def get_extension() -> CMakeExtension:
     packages=find_namespace_packages(),
     install_requires=["amici==TPL_AMICI_VERSION"],
     extras_require={"wurlitzer": ["wurlitzer"]},
-    python_requires=">=3.9",
+    python_requires=">=3.10",
     package_data={},
     zip_safe=False,
     classifiers=CLASSIFIERS,

python/sdist/pyproject.toml

@@ -19,14 +19,15 @@ build-backend = "setuptools.build_meta"
 name = "amici"
 dynamic = ["version"]
 description = "Advanced multi-language Interface to CVODES and IDAS"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 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'",
+    "numpy>=1.26.2; python_version=='3.12'",
+    "numpy; python_version>='3.13'",
     "python-libsbml",
     "pandas>=2.0.2",
     "pyarrow",

python/sdist/setup.cfg

@@ -0,0 +1,91 @@
+[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 = [email protected]
+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_namespace:
+package_dir =
+    amici = amici
+python_requires = >=3.10
+install_requires =
+    cmake-build-extension==0.5.1
+    sympy>=1.9
+    numpy>=1.21.4; python_version>='3.10'
+    numpy>=1.23.2; python_version=='3.11'
+    numpy>=1.26.2; python_version=='3.12'
+    numpy; python_version>='3.13'
+    python-libsbml
+    pandas>=2.0.2
+    pyarrow
+    wurlitzer
+    toposort
+    setuptools>=48
+    mpmath
+include_package_data = True
+zip_safe = False
+
+[options.extras_require]
+# 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
+
+[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.cli.import_petab:_main
+    amici_import_petab.py = amici.petab.cli.import_petab:_main