Require Python>=3.9 (#2039)

dweindl · web-flow · commit d3a92b05e6fe · 2023-05-08T12:53:15.000+02:00
see https://numpy.org/neps/nep-0029-deprecation_policy.html#drop-schedule
diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
@@ -9,7 +9,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
diff --git a/.github/workflows/deploy_protected.yml b/.github/workflows/deploy_protected.yml
@@ -21,7 +21,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     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: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
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: [ "3.8" ]
+        python-version: [ "3.9" ]
         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
@@ -21,7 +21,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     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: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -57,7 +57,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     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: [3.8]
+        python-version: [3.9]
 
     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: [3.8]
+        python-version: [3.9]
 
     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: [3.8, 3.9, '3.10']
+        python-version: [3.9, 3.9, '3.10']
         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
@@ -148,7 +148,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.9
 
     - uses: actions/checkout@v3
     - 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: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11']
         experimental: [false]
 
     steps:
diff --git a/.github/workflows/test_windows.yml b/.github/workflows/test_windows.yml
@@ -23,7 +23,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.8" ]
+        python-version: [ "3.9" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -24,4 +24,4 @@ build:
     - libatlas-base-dev
     - swig
   tools:
-    python: "3.8"
+    python: "3.9"
diff --git a/codecov.yml b/codecov.yml
@@ -1,8 +1,8 @@
 fixes:
-  - "build/venv/lib/python3.6/site-packages/::python/"
-  - "build/venv/lib/python3.7/site-packages/::python/"
-  - "build/venv/lib/python3.8/site-packages/::python/"
-  
+  - "build/venv/lib/python3.9/site-packages/::python/"
+  - "build/venv/lib/python3.10/site-packages/::python/"
+  - "build/venv/lib/python3.11/site-packages/::python/"
+
 codecov:
   require_ci_to_pass: yes
 
@@ -23,11 +23,11 @@ comment:
   layout: "reach,diff,flags,tree"
   behavior: default
   require_changes: no
-  
+
 ignore:
   - "tests/*"
   - "tests/**/*"
-  
+
 flags:
   python:
     carryforward: false
diff --git a/documentation/development.rst b/documentation/development.rst
@@ -99,7 +99,8 @@ General
 Python
 ^^^^^^
 
--  We want to be compatible with Python 3.8
+-  In terms of Python compatibility, we follow numpy's
+   `NEP 29 <https://numpy.org/neps/nep-0029-deprecation_policy.html>`__.
 
 -  For the Python code we want to follow
    `PEP8 <https://www.python.org/dev/peps/pep-0008/>`__. Although this
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
@@ -1498,7 +1498,7 @@
              id="tspan20651"
              x="-16.819941"
              y="40.732136"
-             style="stroke-width:0.264583px">&gt;= 3.8</tspan></text>
+             style="stroke-width:0.264583px">&gt;= 3.9</tspan></text>
       </g>
       <path
          style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.26499999;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-end:url(#marker21180)"
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>=3.8
+* Python>=3.9
 * :term:`SWIG`>=3.0
 * CBLAS compatible BLAS library
   (e.g., OpenBLAS, CBLAS, Atlas, Accelerate, Intel MKL)
@@ -31,7 +31,7 @@ If this does not work for you, please follow the full instructions below.
 Installation on Linux
 +++++++++++++++++++++
 
-Ubuntu 20.04
+Ubuntu 22.04
 ------------
 
 Install the AMICI dependencies via ``apt``
diff --git a/python/sdist/amici/setup.template.py b/python/sdist/amici/setup.template.py
@@ -71,7 +71,7 @@ def get_extension() -> CMakeExtension:
     packages=find_namespace_packages(),
     install_requires=['amici==TPL_AMICI_VERSION'],
     extras_require={'wurlitzer': ['wurlitzer']},
-    python_requires='>=3.8',
+    python_requires='>=3.9',
     package_data={},
     zip_safe=False,
     classifiers=CLASSIFIERS,
diff --git a/python/sdist/setup.cfg b/python/sdist/setup.cfg
@@ -25,13 +25,14 @@ classifiers =
 packages = find_namespace:
 package_dir =
     amici = amici
-python_requires = >=3.8
+python_requires = >=3.9
 install_requires =
     cmake-build-extension==0.5.1
     sympy>=1.9
-    numpy>=1.17.5; python_version=='3.8'
     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
     h5py
     pandas
diff --git a/sonar-project.properties b/sonar-project.properties
@@ -32,4 +32,4 @@ sonar.cfamily.cache.path=sonar_cache
 sonar.cpp.std=c++17
 
 sonar.python.coverage.reportPaths=build/coverage_py.xml
-sonar.python.version=3.8, 3.9, 3.10
+sonar.python.version=3.9, 3.10, 3.11
