Drop python3.9 support

NEP 29: > On Apr 05, 2024 drop support for Python 3.9 *Wait until after the next release.*
dweindl · Apr 3, 2024 · e48c89a · e48c89a
1 parent b28b83b
commit e48c89a
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Showing 19 changed files with 35 additions and 33 deletions.
diff --git a/.github/workflows/deploy_branch.yml b/.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 }}

diff --git a/.github/workflows/deploy_protected.yml b/.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 }}

diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -12,7 +12,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     environment:
       name: pypi

diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.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 }}

diff --git a/.github/workflows/test_doc.yml b/.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 }}

diff --git a/.github/workflows/test_install.yml b/.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 }}

diff --git a/.github/workflows/test_performance.yml b/.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 }}

diff --git a/.github/workflows/test_petab_test_suite.yml b/.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 }}

diff --git a/.github/workflows/test_pypi.yml b/.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 }}

diff --git a/.github/workflows/test_python_cplusplus.yml b/.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

diff --git a/.github/workflows/test_python_ver_matrix.yml b/.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:

diff --git a/.github/workflows/test_sbml_semantic_test_suite.yml b/.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 }}

diff --git a/.github/workflows/test_valgrind.yml b/.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"

diff --git a/.github/workflows/test_windows.yml b/.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 }}

diff --git a/documentation/gfx/amici_workflow.png b/documentation/gfx/amici_workflow.png
diff --git a/documentation/gfx/amici_workflow.svg b/documentation/gfx/amici_workflow.svg
diff --git a/documentation/python_installation.rst b/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)

diff --git a/python/sdist/amici/setup.template.py b/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,

diff --git a/python/sdist/setup.cfg b/python/sdist/setup.cfg
@@ -25,14 +25,14 @@ classifiers =
 packages = find_namespace:
 package_dir =
     amici = amici
-python_requires = >=3.9
+python_requires = >=3.10
 install_requires =
     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