NumPy compatibility fixes (deprecated API elements) + Python 3.12 com…

…patibility fixes (setuptools, etc) + upper Python version bump for CI to 3.12 (#1402)

.github/workflows/tests+artifacts+pypi.yml

@@ -67,7 +67,7 @@ jobs:
           persist-credentials: false
       - uses: actions/[email protected]
         with:
-          python-version: 3.9
+          python-version: "3.12"
       - run: |
           pip install pdoc nbformat
           pip install -e .
@@ -131,7 +131,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
-        python-version: ["3.9", "3.11"]
+        python-version: ["3.9", "3.12"]
         test-suite: ["unit_tests/!(dynamics)", "unit_tests/dynamics/!(condensation)", "unit_tests/dynamics/condensation", "smoke_tests/no_env", "smoke_tests/box", "smoke_tests/parcel_a", "smoke_tests/parcel_b", "smoke_tests/parcel_c", "smoke_tests/kinematic_1d", "smoke_tests/kinematic_2d", "tutorials_tests"]
         exclude:
           - platform: "macos-14"
@@ -197,7 +197,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-24.04, macos-13, windows-latest]
-        python-version: ["3.9", "3.11"]
+        python-version: ["3.9", "3.12"]
     runs-on: ${{ matrix.platform }}
     steps:
       - uses: actions/[email protected]
@@ -233,7 +233,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-24.04, macos-13, windows-latest]
-        python-version: ["3.9", "3.11"]
+        python-version: ["3.9", "3.12"]
         test-suite: [ "chemistry_freezing_isotopes", "condensation_a", "condensation_b", "coagulation", "breakup", "multi-process_a", "multi-process_b"]
       fail-fast: false
     runs-on: ${{ matrix.platform }}
@@ -318,15 +318,19 @@ jobs:
           fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
       - uses: actions/[email protected]
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - run: pip install twine build
 
       - run: |
           unset CI
           cd ${{ matrix.packages-dir }}
           python -m build 2>&1 | tee build.log
-          exit `fgrep -i warning build.log | grep -v impl_numba/warnings.py | grep -v "no previously-included files matching" | wc -l`
+          exit `fgrep -i warning build.log | grep -v impl_numba/warnings.py \
+            | grep -v "no previously-included files matching" \
+            | grep -v "version of {dist_name} already set" \
+            | grep -v -E "UserWarning: version of PySDM(-examples)? already set" \
+            | wc -l`
           twine check --strict dist/*
 
       - uses: actions/upload-artifact@v4
@@ -338,7 +342,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
-        python-version: ["3.9", "3.11"]
+        python-version: ["3.9", "3.12"]
         exclude:
           - platform: macos-14
             python-version: "3.9"

examples/PySDM_examples/Kreidenweis_et_al_2003/simulation.py

@@ -114,7 +114,7 @@ def __init__(self, settings, products=None):
                 key="S_VI",
                 dry_radius_bins_edges=settings.dry_radius_bins_edges,
                 name="dm_S_VI/dlog_10(dry diameter)",
-                unit='ug / m^3"',
+                unit="ug / m^3",
             ),
         )
 

examples/PySDM_examples/Srivastava_1982/simulation.py

@@ -70,7 +70,7 @@ def run_convergence_analysis(self, x, seeds):
                     if step != 0:
                         particulator.run(steps=1)
                     for prod in self.settings.prods:
-                        self.simulation_res[n_sd][prod][seed][step] = (
+                        (self.simulation_res[n_sd][prod][seed][step],) = (
                             particulator.products[prod].get()
                         )
 

examples/PySDM_examples/deJong_Azimi/simulation_0D.py

@@ -48,9 +48,9 @@ def run_box(settings, backend_class=CPU):
     for i, step in enumerate(settings.steps):
         particulator.run(step - particulator.n_steps)
         y[i] = particulator.products["dv/dlnr"].get()[0]
-        mom[i, 0] = particulator.products["M0"].get()
-        mom[i, 1] = particulator.products["M1"].get()
-        mom[i, 2] = particulator.products["M2"].get()
+        (mom[i, 0],) = particulator.products["M0"].get()
+        (mom[i, 1],) = particulator.products["M1"].get()
+        (mom[i, 2],) = particulator.products["M2"].get()
 
     return namedtuple("_", ("radius_bins_left_edges", "dv_dlnr", "moments"))(
         radius_bins_left_edges=settings.radius_bins_edges[:-1], dv_dlnr=y, moments=mom

examples/PySDM_examples/deJong_Mackay_et_al_2023/simulation_0D.py

@@ -79,11 +79,11 @@ def run_box_breakup(
         core.run(step - core.n_steps)
         y[i] = core.products["dv/dlnr"].get()[0]
         if return_nv:
-            y2[i] = core.products["N(v)"].get()[0]
-        rates[i, 0] = core.products["cr"].get()
-        rates[i, 1] = core.products["crd"].get()
-        rates[i, 2] = core.products["cor"].get()
-        rates[i, 3] = core.products["br"].get()
+            (y2[i],) = core.products["N(v)"].get()
+        (rates[i, 0],) = core.products["cr"].get()
+        (rates[i, 1],) = core.products["crd"].get()
+        (rates[i, 2],) = core.products["cor"].get()
+        (rates[i, 3],) = core.products["br"].get()
 
     x = (settings.radius_bins_edges[:-1] / si.micrometres,)[0]
 
@@ -124,10 +124,10 @@ def run_box_NObreakup(settings, steps=None, backend_class=CPU):
     # run
     for i, step in enumerate(steps):
         core.run(step - core.n_steps)
-        y[i] = core.products["dv/dlnr"].get()[0]
-        rates[i, 0] = core.products["cr"].get()
-        rates[i, 1] = core.products["crd"].get()
-        rates[i, 2] = core.products["cor"].get()
+        (y[i],) = core.products["dv/dlnr"].get()
+        (rates[i, 0],) = core.products["cr"].get()
+        (rates[i, 1],) = core.products["crd"].get()
+        (rates[i, 2],) = core.products["cor"].get()
 
     x = (settings.radius_bins_edges[:-1] / si.micrometres,)[0]
 

examples/PySDM_examples/seeding/simulation.py

@@ -90,7 +90,10 @@ def run(self):
                 data[data == 0] = np.nan
                 attr.append(data)
             for key, prod in output["products"].items():
-                prod.append(float(self.particulator.products[key].get()))
+                value = self.particulator.products[key].get()
+                if not isinstance(value, float):
+                    (value,) = value
+                prod.append(float(value))
         for out in ("attributes", "products"):
             for key, val in output[out].items():
                 output[out][key] = np.array(val)

examples/pyproject.toml

@@ -1,5 +1,5 @@
 [tool.setuptools_scm]
+root = ".."
 
-# TODO #1200
 [build-system]
-requires = ['setuptools==56.0.0', 'setuptools-scm==6.0.1']
+requires = ['setuptools==75.3.0', 'setuptools-scm==8.1.0']

examples/setup.py

@@ -26,7 +26,6 @@ def get_long_description():
     use_scm_version={
         "local_scheme": lambda _: "",
         "version_scheme": "post-release",
-        "root": "..",
     },
     install_requires=[
         "PySDM",

pyproject.toml

@@ -3,6 +3,5 @@ profile = "black"
 
 [tool.setuptools_scm]
 
-# TODO #1200
 [build-system]
-requires = ['setuptools==56.0.0', 'setuptools-scm==6.0.1']
+requires = ['setuptools==75.3.0', 'setuptools-scm==8.1.0']

setup.py

@@ -79,8 +79,8 @@ def get_long_description():
             "matplotlib",
             "pytest",
             "pytest-timeout",
-            "PyPartMC==1.3.6",
         ]
+        + (["PyPartMC==1.3.6"] if sys.version_info < (3, 12) else [])  # TODO #1410
         + (
             [
                 "pywinpty" + ("==0.5.7" if CI else ""),

tests/smoke_tests/box/partmc/test_dry_wet_equilibration.py

@@ -3,6 +3,7 @@
 
 # pylint: disable=missing-function-docstring,no-member
 import platform
+import sys
 from collections import namedtuple
 
 import numpy as np
@@ -16,7 +17,7 @@
 from PySDM.initialisation.spectra import Lognormal
 from PySDM.physics import si
 
-if platform.architecture()[0] == "64bit":
+if platform.architecture()[0] == "64bit" and sys.version_info < (3, 12):  # TODO #1410
     import PyPartMC
 
 linestyles = {"PyPartMC": "dashed", "PySDM": "dotted"}
@@ -74,7 +75,8 @@ def pypartmc(dry_diam, temp, rel_humid, kpa):
 
 
 @pytest.mark.skipif(
-    platform.architecture()[0] != "64bit", reason="binary package availability"
+    platform.architecture()[0] != "64bit" or sys.version_info >= (3, 12),
+    reason="binary package availability",  # TODO #1410
 )
 @pytest.mark.parametrize("kappa", (0.1, 1))
 @pytest.mark.parametrize("temperature", (300 * si.K,))

tests/smoke_tests/kinematic_2d/arabas_et_al_2015/test_adaptive_displacement.py

@@ -70,6 +70,6 @@ def test_adaptive_displacement(rtol, plot=False):
     # Assert
     if rtol is not None:
         assert 1 < simulation.particulator.dynamics["Displacement"]._n_substeps < 50
-    assert np.count_nonzero(sd_count) == np.product(settings.grid)
+    assert np.count_nonzero(sd_count) == np.prod(settings.grid)
     assert np.std(sd_count) < settings.n_sd_per_gridbox / 2.5
     assert np.max(sd_count) < 2.5 * settings.n_sd_per_gridbox

tests/smoke_tests/no_env/lamb_et_al_2017/test_fig_4.py

@@ -40,7 +40,7 @@ def test_values_match(notebook_local_variables, T, alpha_i_2H, paper):
         plot_x = notebook_local_variables["T"]
         plot_y = notebook_local_variables["alphas"][paper]
         eps = 5e-1
-        index = np.where(abs(plot_x - T) < eps)
+        ((index,),) = np.where(abs(plot_x - T) < eps)
         np.testing.assert_approx_equal(
             actual=plot_y[index], desired=alpha_i_2H, significant=3
         )

tests/smoke_tests/no_env/pierchala_et_al_2022/test_fig_3.py

@@ -36,7 +36,7 @@ class TestFig3:
         ),
     )
     def test_top_left_panel(notebook_local_variables, isotope, F, enrichment):
-        index = np.where(notebook_local_variables["F"] == F)
+        ((index,),) = np.where(notebook_local_variables["F"] == F)
         np.testing.assert_approx_equal(
             actual=notebook_local_variables["enrichments"][isotope][index],
             desired=enrichment,
@@ -54,7 +54,7 @@ def test_top_left_panel(notebook_local_variables, isotope, F, enrichment):
         ),
     )
     def test_bottom_left_panel(notebook_local_variables, label, F, excess):
-        index = np.where(notebook_local_variables["F"] == F)
+        ((index,),) = np.where(notebook_local_variables["F"] == F)
         excesses = notebook_local_variables["excess"]
         deltas = notebook_local_variables["deltas"]
         np.testing.assert_approx_equal(
@@ -73,7 +73,7 @@ def test_bottom_left_panel(notebook_local_variables, label, F, excess):
     )
     def test_top_right_panel(notebook_local_variables, delta_18O, delta_2H):
         eps = 0.01 * PER_MILLE
-        index = np.where(
+        ((index,),) = np.where(
             abs(notebook_local_variables["deltas"]["18O"] - delta_18O) < eps
         )
         np.testing.assert_approx_equal(
@@ -92,7 +92,7 @@ def test_gmvl(notebook_local_variables, delta_18O, delta_2H):
         eps = 0.1 * PER_MILLE
         x = np.linspace(-10 * PER_MILLE, 10 * PER_MILLE, 100)
         y = x * cd.CRAIG_1961_SLOPE_COEFF + cd.CRAIG_1961_INTERCEPT_COEFF
-        index = np.where(abs(x - delta_18O) < eps)
+        ((index,),) = np.where(abs(x - delta_18O) < eps)
         np.testing.assert_approx_equal(actual=y[index], desired=delta_2H, significant=3)
 
     @staticmethod
@@ -108,7 +108,7 @@ def test_gmvl(notebook_local_variables, delta_18O, delta_2H):
     def test_bottom_right_panel(notebook_local_variables, label, delta_18O, excess):
         eps = 0.1 * PER_MILLE
         deltas = notebook_local_variables["deltas"]
-        index = np.where(abs(deltas["18O"] - delta_18O) < eps)
+        ((index,),) = np.where(abs(deltas["18O"] - delta_18O) < eps)
         excesses = notebook_local_variables["excess"]
         np.testing.assert_approx_equal(
             actual={

tests/smoke_tests/no_env/pierchala_et_al_2022/test_fig_4.py

@@ -38,7 +38,7 @@ class TestFig4:
     def test_top_panel(notebook_local_variables, RH, delta_18O, delta_2H):
         deltas_per_rh = notebook_local_variables["deltas_per_rh"]
         eps = 0.5 * PER_MILLE
-        index = np.where(abs(deltas_per_rh[RH]["18O"] - delta_18O) < eps)
+        ((index,),) = np.where(abs(deltas_per_rh[RH]["18O"] - delta_18O) < eps)
         np.testing.assert_approx_equal(
             actual=delta_2H, desired=deltas_per_rh[RH]["2H"][index], significant=3
         )
@@ -58,7 +58,7 @@ def test_top_panel(notebook_local_variables, RH, delta_18O, delta_2H):
     def test_bottom_panel(notebook_local_variables, RH, delta_18O, excess_17O):
         deltas_per_rh = notebook_local_variables["deltas_per_rh"]
         eps = 0.5 * PER_MILLE
-        index = np.where(abs(deltas_per_rh[RH]["18O"] - delta_18O) < eps)
+        ((index,),) = np.where(abs(deltas_per_rh[RH]["18O"] - delta_18O) < eps)
         np.testing.assert_approx_equal(
             actual=notebook_local_variables[
                 "formulae"

tests/smoke_tests/parcel_b/arabas_and_shima_2017/test_conservation.py

@@ -47,7 +47,7 @@ def test_water_mass_conservation(settings_idx, mass_of_dry_air, scheme, coord):
     output = simulation.run()
 
     # Assert
-    total_water_mixing_ratio = simulation.particulator.environment[
+    (total_water_mixing_ratio,) = simulation.particulator.environment[
         "water_vapour_mixing_ratio"
     ].to_ndarray() + liquid_water_mixing_ratio(simulation)
     np.testing.assert_approx_equal(
@@ -77,4 +77,4 @@ def test_energy_conservation(settings_idx, mass_of_dry_air, coord):
     simulation.run()
 
     # Assert
-    np.testing.assert_approx_equal(thd0.to_ndarray(), env["thd"].to_ndarray())
+    np.testing.assert_array_almost_equal(thd0.to_ndarray(), env["thd"].to_ndarray())

tests/smoke_tests/parcel_b/arabas_and_shima_2017/test_initialisation.py

@@ -13,9 +13,8 @@ class TestInitialisation:
     @staticmethod
     def simulation_test(var, expected, setup):
         simulation = Simulation(setup)
-        np.testing.assert_approx_equal(
-            simulation.particulator.environment[var].to_ndarray(), expected
-        )
+        (actual,) = simulation.particulator.environment[var].to_ndarray()
+        np.testing.assert_approx_equal(actual=actual, desired=expected)
 
     @staticmethod
     @pytest.mark.parametrize("settings_idx", range(len(setups)))

tests/unit_tests/attributes/test_isotopes.py

@@ -85,15 +85,16 @@ def test_delta_attribute(backend_class, isotope, heavier_water_specific_content)
         particulator = builder.build(attributes=attributes)
 
         # act
-        delta = particulator.attributes[f"delta_{isotope}"].to_ndarray()
+        (delta,) = particulator.attributes[f"delta_{isotope}"].to_ndarray()
 
         # assert
-        n_heavy_isotope = attributes[f"moles_{isotope}"][0]
-        n_light_water = (
+        ((n_heavy_isotope,),) = attributes[f"moles_{isotope}"]
+        (n_light_water,) = (
             (1 - heavier_water_specific_content)
             * attributes["water mass"]
             / (constants_defaults.M_1H * 2 + constants_defaults.M_16O)
         )
+        print(delta, n_heavy_isotope, n_light_water)
         if isotope[-1] == "O":
             n_light_isotope = n_light_water
         elif isotope[-1] == "H":

tests/unit_tests/backends/test_freezing_methods.py

@@ -91,8 +91,9 @@ def test_freeze_singular(backend_class):
         particulator.run(steps=steps)
 
         # assert
+        (qi,) = particulator.products["qi"].get()
         np.testing.assert_approx_equal(
-            actual=np.asarray(particulator.products["qi"].get()),
+            actual=qi,
             desired=n_sd * multiplicity * water_mass / dv,
             significant=7,
         )

tests/unit_tests/dynamics/collisions/test_efficiencies.py

@@ -101,7 +101,7 @@ def test_efficiency_dist(sut, backend_class=CPU, plot=False):
                     )
                     particulator.attributes.mark_updated("water mass")
                     sut(eff, is_first_in_pair)
-                    res[i, j] = eff.data
+                    (res[i, j],) = eff.data
 
         # plot
         pyplot.colorbar(

tests/unit_tests/dynamics/collisions/test_fragmentations.py

@@ -413,7 +413,7 @@ def test_fragmentation_nf_and_frag_mass_equals(  # TODO #987
         sut(nf, frag_mass, u01, is_first_in_pair)
 
         # Assert
-        np.testing.assert_approx_equal(nf.to_ndarray(), expected_nf)
+        np.testing.assert_array_almost_equal(nf.to_ndarray(), expected_nf)
         np.testing.assert_array_almost_equal(
             [expected_frag_mass], frag_mass.to_ndarray()
         )

tests/unit_tests/dynamics/test_seeding.py

@@ -64,7 +64,10 @@ def simulation(*, dynamics):
                 if step != 0:
                     particulator.run(steps=1)
                 for key, val in products.items():
-                    val.append(float(particulator.products[key].get()))
+                    value = particulator.products[key].get()
+                    if not isinstance(value, float):
+                        (value,) = value
+                    val.append(float(value))
             for key in products:
                 products[key] = np.array(products[key])
             return products

tests/unit_tests/dynamics/test_terminal_velocity.py

@@ -80,7 +80,7 @@ def test_terminal_velocity_boundary_values(
 
     # act
     with context:
-        v_term = particulator.attributes["terminal velocity"].to_ndarray()
+        (v_term,) = particulator.attributes["terminal velocity"].to_ndarray()
 
         # assert
         np.testing.assert_approx_equal(v_term, expected_v_term)

tests/unit_tests/impl/test_moments.py

@@ -56,7 +56,7 @@ def test_moment_0d(backend_class):
         particulator.moments(
             moment_0=moment_0, moments=moments, specs={"temperature": (2,)}
         )
-        discr_mean_T_squared = moments[0, slice(0, 1)].to_ndarray()
+        (discr_mean_T_squared,) = moments[0, slice(0, 1)].to_ndarray()
 
         # Assert
         assert abs(discr_zero - 1) / 1 < 1e-3