[Python] Fix Numpy 2.0 compatibility issues

.github/workflows/main.yml

@@ -454,8 +454,10 @@ jobs:
           find samples/python -type f -iname "*.py" \
           -exec sh -c 'for n; do echo "$n" | tee -a results.txt && python3 "$n" >> results.txt || exit 1; done' sh {} +
         env:
-          # The ignore setting here is due to a new warning introduced in Matplotlib==3.6.0
-          PYTHONWARNINGS: "error,ignore:warn_name_set_on_empty_Forward::pyparsing,ignore:datetime.datetime.utcfromtimestamp:DeprecationWarning:"
+          # The pyparsing ignore setting is due to a new warning introduced in Matplotlib==3.6.0
+          # @todo: Remove the trapz-related ignore when dropping support for NumPy 1.x
+          #     and replacing np.trapz with np.trapezoid
+          PYTHONWARNINGS: "error,ignore:warn_name_set_on_empty_Forward::pyparsing,ignore:datetime.datetime.utcfromtimestamp:DeprecationWarning:,ignore:`trapz`:DeprecationWarning"
           MPLBACKEND: Agg
       - name: Save the results file for inspection
         uses: actions/upload-artifact@v4

samples/python/onedim/flame_speed_convergence_analysis.py

@@ -305,10 +305,10 @@ def analyze_errors(grids, speeds, true_speed):
     and compare these with our estimated errors.
     This will show if our estimates are reasonable, or conservative, or too optimistic.
     """
-    true_speed_estimates = np.full_like(speeds, np.NaN)
-    total_percent_error_estimates = np.full_like(speeds, np.NaN)
-    actual_extrapolated_percent_errors = np.full_like(speeds, np.NaN)
-    actual_raw_percent_errors = np.full_like(speeds, np.NaN)
+    true_speed_estimates = np.full_like(speeds, np.nan)
+    total_percent_error_estimates = np.full_like(speeds, np.nan)
+    actual_extrapolated_percent_errors = np.full_like(speeds, np.nan)
+    actual_raw_percent_errors = np.full_like(speeds, np.nan)
     for i in range(3, len(grids)):
         print(grids[: i + 1])
         true_speed_estimate, total_percent_error_estimate = extrapolate_uncertainty(

site_scons/buildutils.py

@@ -972,9 +972,9 @@ def compare_profiles(
         "pos. err"
     ))
     header.append(f"{10*'-'}  -----  {14*'-'}  {14*'-'}  {9*'-'}  {9*'-'}  {9*'-'}")
-    ref_ptp = reference.ptp(axis=1)
+    ref_ptp = np.ptp(reference, axis=1)
     ref_max = np.abs(reference).max(axis=1)
-    sample_ptp = sample.ptp(axis=1)
+    sample_ptp = np.ptp(sample, axis=1)
     sample_max = np.abs(sample).max(axis=1)
     scale = np.maximum(
         np.maximum(ref_ptp[1:], ref_max[1:]),

test/python/test_onedim.py

@@ -470,11 +470,11 @@ def test_unity_lewis(self):
         self.sim.transport_model = 'unity-Lewis-number'
         self.sim.set_refine_criteria(ratio=3.0, slope=0.08, curve=0.12)
         self.sim.solve(loglevel=0, auto=True)
-        dh_unity_lewis = self.sim.enthalpy_mass.ptp()
+        dh_unity_lewis = np.ptp(self.sim.enthalpy_mass)
 
         self.sim.transport_model = 'mixture-averaged'
         self.sim.solve(loglevel=0)
-        dh_mix = self.sim.enthalpy_mass.ptp()
+        dh_mix = np.ptp(self.sim.enthalpy_mass)
 
         # deviation of enthalpy should be much lower for unity Le model (tends
         # towards zero as grid is refined)

test/python/test_reaction.py

@@ -1841,7 +1841,7 @@ def test_interface_adjacent(self):
 class InterfaceReactionTests(ReactionTests):
     # test suite for surface reaction expressions
 
-    _value = np.NAN # reference value
+    _value = np.nan # reference value
     _coverage_deps = None
 
     @classmethod

test/python/test_reactor.py

@@ -2383,7 +2383,9 @@ def calc_dtdh(self, species):
         return dtdp
 
     # See https://github.com/Cantera/enhancements/issues/55
+    # @todo: replace np.trapz with np.trapezoid when dropping support for NumPy 1.x
     @unittest.skip("Integration of sensitivity ODEs is unreliable")
+    @pytest.mark.filterwarnings("ignore:`trapz` is deprecated")
     def test_ignition_delay_sensitivity(self):
         species = ('H2', 'H', 'O2', 'H2O2', 'H2O', 'OH', 'HO2')
         dtigdh_cvodes = self.calc_dtdh(species)

test/python/test_thermo.py

@@ -1208,6 +1208,8 @@ def test_isotropic_velocity_electron_energy_distribution(self):
                                (ct.avogadro * ct.electron_charge))
         self.assertNear(mean_electron_energy, self.phase.mean_electron_energy)
 
+    # @todo: replace np.trapz with np.trapezoid when dropping support for NumPy 1.x
+    @pytest.mark.filterwarnings("ignore:`trapz` is deprecated")
     def test_discretized_electron_energy_distribution(self):
         levels = np.array([0.0, 1.0, 10.0])
         dist = np.array([0.0, 0.9, 0.01])

test/python/utilities.py

@@ -181,10 +181,10 @@ def compareProfiles(reference, sample, rtol=1e-5, atol=1e-12, xtol=1e-5):
     bad = []
     template = '{0:9.4e}  {1: 3d}   {2:14.7e}  {3:14.7e}  {4:9.3e}  {5:9.3e}  {6:9.3e}'
     for i in range(1, nVars):
-        scale = max(max(abs(reference[i])), reference[i].ptp(),
-                    max(abs(sample[i])), sample[i].ptp())
+        scale = max(max(abs(reference[i])), np.ptp(reference[i]),
+                    max(abs(sample[i])), np.ptp(sample[i]))
         slope = np.zeros(nTimes)
-        slope[1:] = np.diff(reference[i]) / np.diff(reference[0]) * reference[0].ptp()
+        slope[1:] = np.diff(reference[i]) / np.diff(reference[0]) * np.ptp(reference[0])
 
         comp = np.interp(reference[0], sample[0], sample[i])
         for j in range(nTimes):