Python 3.13 compatibility: CI jobs; alternative implementation of clock(); use numdifftools instead of discontinued scipy.misc.derivative (#553)

Co-authored-by: Sylwester Arabas <[email protected]>

Author: Sfonxu

.github/workflows/tests.yml

@@ -33,10 +33,10 @@ jobs:
       with:
         submodules: recursive
         fetch-depth: 0
-    - name: Set up Python 3.9
+    - name: Set up Python
       uses: actions/[email protected]
       with:
-        python-version: 3.9
+        python-version: 3.11
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -79,17 +79,21 @@ jobs:
 
   nojit_and_codecov:
     needs: [ precommit, pylint, zenodo_json, devops ]
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.13"]
     runs-on: ubuntu-latest
     env:
       NUMBA_DISABLE_JIT: 1
+      PYTHON: ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@master
         with:
           submodules: recursive
           fetch-depth: 0
       - uses: actions/[email protected]
         with:
-          python-version: 3.9
+          python-version: ${{ matrix.python-version }}
       - name: Generate coverage report
         run: |
           pip install -e .[tests] -e ./examples
@@ -98,6 +102,7 @@ jobs:
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
         with:
+          env_vars: PYTHON
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true
           verbose: true
@@ -108,7 +113,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.9", "3.13"]
         exclude:
           - platform: macos-14
             python-version: "3.9"
@@ -148,7 +153,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.9", "3.13"]
       fail-fast: false
     runs-on: ${{ matrix.platform }}
     steps:
@@ -185,7 +190,7 @@ jobs:
           NUMBA_OPT: 1
         run: python -m pytest --durations=10 -p no:unraisableexception -We tests/devops_tests/test_notebooks.py
 
-      - if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12'}}
+      - if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.13'}}
         run: |
           mkdir -p /home/runner/work/_temp/_github_home/figures
           rm /tmp/pytest-of-runner/pytest-current/test_run_notebooks_examples_Pycurrent
@@ -199,7 +204,7 @@ jobs:
       #   with:
       #     limit-access-to-actor: true
 
-      - if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12'}}
+      - if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.13'}}
         uses: eine/tip@master
         with:
           token: ${{ secrets.GITHUB_TOKEN }}

PyMPDATA/impl/clock.py

@@ -2,7 +2,25 @@
 no time unit guaranteed, returned value only for relative time measurements"""
 
 import ctypes
+import sys
 
-clock = ctypes.pythonapi._PyTime_GetSystemClock  # pylint:disable=protected-access
-clock.argtypes = []
-clock.restype = ctypes.c_int64
+import numba
+import numpy as np
+
+if sys.version_info < (3, 13):
+    clock = ctypes.pythonapi._PyTime_GetSystemClock  # pylint:disable=protected-access
+    clock.argtypes = []
+    clock.restype = ctypes.c_int64
+else:
+    clock_impl = ctypes.pythonapi.PyTime_Time
+    clock_impl.argtypes = [ctypes.c_void_p]
+    clock_impl.restype = ctypes.c_int64
+
+    assert ctypes.c_time_t == ctypes.c_int64  # pylint: disable=no-member
+
+    @numba.jit("int64()", nopython=True)
+    def clock():
+        """Numba-JITable version of clock function for Python > 3.12"""
+        result = np.empty(shape=(1,), dtype=np.int64)
+        clock_impl(result.ctypes)
+        return result[0]

examples/PyMPDATA_examples/Shipway_and_Hill_2012/settings.py

@@ -1,11 +1,11 @@
 from typing import Optional
 
 import numpy as np
+from numdifftools import Derivative
 from PyMPDATA_examples.Olesik_et_al_2022.settings import ksi_1 as default_ksi_1
 from pystrict import strict
 from scipy.integrate import solve_ivp
 from scipy.interpolate import interp1d
-from scipy.misc import derivative
 
 from . import formulae
 from .arakawa_c import arakawa_c
@@ -53,7 +53,7 @@ def drhod_dz(z, rhod):
             drhod_dz = formulae.drho_dz(const.g, p, T, self.qv(z), const.lv)
             if not apprx_drhod_dz:  # to resolve issue #335
                 qv = self.qv(z)
-                dqv_dz = derivative(self.qv, z)
+                dqv_dz = Derivative(self.qv)(z)
                 drhod_dz = drhod_dz / (1 + qv) - rhod * dqv_dz / (1 + qv)
             return drhod_dz
 

examples/setup.py

@@ -29,13 +29,14 @@ def get_long_description():
         "open-atmos-jupyter-utils",
         "pystrict",
         "matplotlib",
-        "ipywidgets" + "<8.0.3" if CI else "",
+        "ipywidgets" + "==8.1.7" if CI else "",
         "scipy",
         "pint",
         "joblib",
         "sympy",
         "imageio",
         "meshio",
+        "numdifftools",
     ],
     author="https://github.com/open-atmos/PyMPDATA/graphs/contributors",
     license="GPL-3.0",

setup.py

@@ -35,7 +35,7 @@ def get_long_description():
                 10: "==0.58.1",
                 11: "==0.58.1",
                 12: "==0.59.1",
-                13: "==0.59.1",
+                13: "==0.61.2",
             }[sys.version_info.minor]
             if CI and not _32bit
             else ""
@@ -48,7 +48,7 @@ def get_long_description():
                 10: "==1.24.4",
                 11: "==1.24.4",
                 12: "==1.26.4",
-                13: "==1.26.4",
+                13: "==2.2.5",
             }[sys.version_info.minor]
             if CI
             else ""
@@ -67,14 +67,15 @@ def get_long_description():
                     10: "==1.10.1",
                     11: "==1.10.1",
                     12: "==1.13.0",
-                    13: "==1.13.0",
+                    13: "==1.15.3",
                 }[sys.version_info.minor]
                 if CI and not _32bit
                 else ""
             ),
             "jupyter-core" + ("<5.0.0" if CI else ""),
-            "ipywidgets" + ("!=8.0.3" if CI else ""),
-            "ipykernel" + ("<6.22.0" if CI else ""),
+            "jupyter_client" + ("==8.6.3" if CI else ""),
+            "ipywidgets" + ("==8.1.7" if CI else ""),
+            "ipykernel" + ("==7.0.0a1" if CI else ""),
             "ghapi",
             "pytest",
             "pytest-benchmark",