PySDM 3.0.0rc5__tar.gz → 3.0.0rc6__tar.gz

{pysdm-3.0.0rc5 → pysdm-3.0.0rc6}/.github/workflows/tests.yml

@@ -54,10 +54,14 @@ jobs:
   
 
   nojit_and_codecov:
-    needs: [pylint]
-    runs-on: ubuntu-24.04
+    strategy:
+      matrix:
+        platform: [ ubuntu-24.04, macos-13, macos-14, windows-latest ]
+        python-version: [ "3.9", "3.12" ]
+    runs-on: ${{ matrix.platform }}
     env:
       NUMBA_DISABLE_JIT: 1
+      PYTHON: ${{ matrix.python-version }}
     steps:
     - uses: actions/checkout@v4.1.6
       with:
@@ -65,7 +69,7 @@ jobs:
         fetch-depth: 0
     - uses: actions/setup-python@v5.0.0
       with:
-        python-version: 3.9
+        python-version: ${{ matrix.python-version }}
     - name: Generate coverage report
       run: |
         pip install -e .[tests]
@@ -77,19 +81,16 @@ jobs:
         fail_ci_if_error: true
         verbose: true
         token: ${{ secrets.CODECOV_TOKEN }}
+        env_vars: PYTHON,RUNNER_OS
 
   tests:
-    needs: [nojit_and_codecov]
+    needs: [pylint,nojit_and_codecov]
     strategy:
       matrix:
-        platform: [ubuntu-24.04, macos-13, macos-14, windows-latest]
-        python-version: ["3.9", "3.12"]
+        platform: [ubuntu-24.04, macos-14, windows-latest]
+        python-version: ["3.12"]
         test-suite: ["unit_tests/!(dynamics)", "unit_tests/dynamics/!(condensation|collisions)", "unit_tests/dynamics/condensation", "unit_tests/dynamics/collisions","smoke_tests/no_env", "smoke_tests/box", "smoke_tests/parcel_a", "smoke_tests/parcel_b", "smoke_tests/parcel_c", "smoke_tests/parcel_d", "smoke_tests/kinematic_1d", "smoke_tests/kinematic_2d", "tutorials_tests"]
         exclude:
-          - platform: "macos-14"
-            python-version: "3.9"
-          - test-suite: "devops_tests"
-            python-version: "3.9"
           # TODO #1406
           - platform: "macos-14"
             test-suite: "smoke_tests/box"
@@ -142,11 +143,11 @@ jobs:
           pytest ${{ env.pytest_options }} --timeout=900 --timeout_method=thread tests/${{ matrix.test-suite }}
 
   examples-setup:
-    needs: [nojit_and_codecov]
+    needs: [pylint,nojit_and_codecov]
     strategy:
       matrix:
         platform: [ubuntu-24.04, macos-14, windows-latest]
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.12"]
     runs-on: ${{ matrix.platform }}
     steps:
       - uses: actions/checkout@v4.1.6
@@ -187,7 +188,7 @@ jobs:
         test-suite: [ "isotopes_chemistry_extraterrestrial", "coagulation_freezing", "condensation_a", "condensation_b", "condensation_c", "multi-process_a", "multi-process_b", "multi-process_c_breakup", "multi-process_d", "multi-process_e"]
       fail-fast: true
     runs-on: ${{ matrix.platform }}
-    timeout-minutes: ${{ startsWith(matrix.platform, 'windows-') && 35 || 20 }}
+    timeout-minutes: ${{ startsWith(matrix.platform, 'windows-') && 28 || 17 }}
     steps:
       - uses: actions/checkout@v4.1.6
         with:

{pysdm-3.0.0rc5 → pysdm-3.0.0rc6}/.pre-commit-config.yaml

@@ -21,3 +21,10 @@ repos:
       - id: debug-statements
       - id: check-json
         files: '.json'
+
+  - repo: https://github.com/lk16/detect-missing-init
+    rev: v0.1.6
+    hooks:
+    - id: detect-missing-init
+      args: ['--create', "--track", "--python-folders", "tests,PySDM,examples/PySDM_examples"]
+

{pysdm-3.0.0rc5/pysdm.egg-info → pysdm-3.0.0rc6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysdm
-Version: 3.0.0rc5
+Version: 3.0.0rc6
 Summary: Pythonic particle-based (super-droplet) warm-rain/aqueous-chemistry cloud microphysics package with box, parcel & 1D/2D prescribed-flow examples in Python, Julia and Matlab
 Author-email: "https://github.com/open-atmos/PySDM/graphs/contributors" <sylwester.arabas@agh.edu.pl>
 License-Expression: GPL-3.0-only

pysdm-3.0.0rc6/PySDM/physics/isotope_relaxation_timescale/bolin_1958.py

@@ -0,0 +1,14 @@
+"""Bolin number"""
+
+import numpy as np
+
+
+class Bolin1958:  # pylint: disable=too-few-public-methods
+    """Implementation of timescale used by Bolin 1958"""
+
+    def __init__(self, const):
+        assert np.isfinite(const.BOLIN_ISOTOPE_TIMESCALE_COEFF_C1)
+
+    @staticmethod
+    def bolin_number(const):
+        return const.BOLIN_ISOTOPE_TIMESCALE_COEFF_C1

{pysdm-3.0.0rc5 → pysdm-3.0.0rc6}/PySDM/physics/trivia.py

@@ -161,3 +161,10 @@ class Trivia:  # pylint: disable=too-many-public-methods
         process with a constant rate `r`
         """
         return np.exp(-r * dt)
+
+    @staticmethod
+    def tau(Bo, dm_dt_over_m):
+        """
+        see text above Table 1 [Bolin 1958](https://digitallibrary.un.org/record/3892725)
+        """
+        return 1 / Bo / dm_dt_over_m

{pysdm-3.0.0rc5 → pysdm-3.0.0rc6}/docs/bibliography.json

@@ -682,10 +682,10 @@
   },
   "https://digitallibrary.un.org/record/3892725": {
     "usages": [
-      "PySDM/physics/isotope_relaxation_timescale/bolin_1958.py",
       "PySDM/physics/constants_defaults.py",
-      "examples/PySDM_examples/Bolin_1958/table_1.ipynb",
+      "PySDM/physics/trivia.py",
       "examples/PySDM_examples/Bolin_1958/__init__.py",
+      "examples/PySDM_examples/Bolin_1958/table_1.ipynb",
       "examples/PySDM_examples/Zaba_et_al/timescales_comparison.ipynb"
     ],
     "label": "Bolin 1958 (Proc. 2nd UN Intl Conf. Peaceful Uses of Atomic Energy)",

{pysdm-3.0.0rc5 → pysdm-3.0.0rc6}/examples/PySDM_examples/Bolin_1958/table_1.ipynb

@@ -23,8 +23,8 @@
    "id": "5e4e58050cc01f64",
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-06-27T18:55:07.411745Z",
-     "start_time": "2025-06-27T18:55:07.401377Z"
+     "end_time": "2025-08-12T13:56:32.855405Z",
+     "start_time": "2025-08-12T13:56:32.851730Z"
     }
    },
    "source": [
@@ -35,15 +35,15 @@
     "    pip_install_on_colab('PySDM-examples')"
    ],
    "outputs": [],
-   "execution_count": 5
+   "execution_count": 1
   },
   {
    "cell_type": "code",
    "id": "95f360dc62f373f9",
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-06-27T18:55:08.148769Z",
-     "start_time": "2025-06-27T18:55:08.144342Z"
+     "end_time": "2025-08-12T13:56:35.553021Z",
+     "start_time": "2025-08-12T13:56:32.868658Z"
     }
    },
    "source": [
@@ -54,13 +54,13 @@
     "from IPython.display import display"
    ],
    "outputs": [],
-   "execution_count": 6
+   "execution_count": 2
   },
   {
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-06-27T18:55:08.549521Z",
-     "start_time": "2025-06-27T18:55:08.517457Z"
+     "end_time": "2025-08-12T13:56:38.312522Z",
+     "start_time": "2025-08-12T13:56:35.612041Z"
     }
    },
    "cell_type": "code",
@@ -110,15 +110,15 @@
    ],
    "id": "4a8c2bd612c892f2",
    "outputs": [],
-   "execution_count": 7
+   "execution_count": 3
   },
   {
    "cell_type": "code",
    "id": "340812de267c4290",
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-06-27T19:04:24.139475Z",
-     "start_time": "2025-06-27T19:04:24.120075Z"
+     "end_time": "2025-08-12T13:56:38.762219Z",
+     "start_time": "2025-08-12T13:56:38.345299Z"
     }
    },
    "source": [
@@ -141,7 +141,8 @@
     "    Fk=Fk,\n",
     "    Fd=Fd,\n",
     ")\n",
-    "adjustment_time = formulae.isotope_relaxation_timescale.tau(\n",
+    "adjustment_time = formulae.trivia.tau(\n",
+    "    Bo=formulae.isotope_relaxation_timescale.bolin_number(),\n",
     "    dm_dt_over_m=(\n",
     "        formulae.particle_shape_and_density.dm_dt_over_m(\n",
     "            radii,\n",
@@ -265,15 +266,15 @@
      "output_type": "display_data"
     }
    ],
-   "execution_count": 14
+   "execution_count": 4
   },
   {
    "cell_type": "code",
    "id": "0bef57bc-7e19-4a3f-8f77-6ec762e8f236",
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2025-06-27T18:41:40.340143Z",
-     "start_time": "2025-06-03T21:24:22.478342Z"
+     "end_time": "2025-08-12T13:56:38.799723Z",
+     "start_time": "2025-08-12T13:56:38.798348Z"
     }
    },
    "source": [],

{pysdm-3.0.0rc5 → pysdm-3.0.0rc6/pysdm.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysdm
-Version: 3.0.0rc5
+Version: 3.0.0rc6
 Summary: Pythonic particle-based (super-droplet) warm-rain/aqueous-chemistry cloud microphysics package with box, parcel & 1D/2D prescribed-flow examples in Python, Julia and Matlab
 Author-email: "https://github.com/open-atmos/PySDM/graphs/contributors" <sylwester.arabas@agh.edu.pl>
 License-Expression: GPL-3.0-only

{pysdm-3.0.0rc5 → pysdm-3.0.0rc6}/pysdm.egg-info/SOURCES.txt

@@ -712,6 +712,7 @@ tests/examples_tests/test_run_notebooks.py
 tests/examples_tests/test_tests_completeness.py
 tests/smoke_tests/__init__.py
 tests/smoke_tests/conftest.py
+tests/smoke_tests/box/__init__.py
 tests/smoke_tests/box/alpert_and_knopf_2016/__init__.py
 tests/smoke_tests/box/alpert_and_knopf_2016/test_ak16_fig_1.py
 tests/smoke_tests/box/alpert_and_knopf_2016/test_frozen_fraction.py
@@ -724,6 +725,7 @@ tests/smoke_tests/box/dejong_and_mackay_et_al_2023/test_collision.py
 tests/smoke_tests/box/dejong_and_mackay_et_al_2023/test_fig_6.py
 tests/smoke_tests/box/dejong_and_mackay_et_al_2023/test_fig_7.py
 tests/smoke_tests/box/dejong_and_mackay_et_al_2023/test_fig_8.py
+tests/smoke_tests/box/dejong_azimi/__init__.py
 tests/smoke_tests/box/dejong_azimi/test_box.py
 tests/smoke_tests/box/partmc/__init__.py
 tests/smoke_tests/box/partmc/test_dry_wet_equilibration.py
@@ -734,6 +736,7 @@ tests/smoke_tests/box/srivastava_1982/__init__.py
 tests/smoke_tests/box/srivastava_1982/test_eq_10.py
 tests/smoke_tests/box/srivastava_1982/test_eq_13.py
 tests/smoke_tests/box/srivastava_1982/test_equations.py
+tests/smoke_tests/kinematic_1d/__init__.py
 tests/smoke_tests/kinematic_1d/deJong_Azimi/__init__.py
 tests/smoke_tests/kinematic_1d/deJong_Azimi/test_few_steps.py
 tests/smoke_tests/kinematic_1d/deJong_Azimi/test_initial_condition.py
@@ -742,6 +745,7 @@ tests/smoke_tests/kinematic_1d/shipway_and_hill_2012/test_1d_exporters.py
 tests/smoke_tests/kinematic_1d/shipway_and_hill_2012/test_few_steps.py
 tests/smoke_tests/kinematic_1d/shipway_and_hill_2012/test_initial_condition.py
 tests/smoke_tests/kinematic_1d/shipway_and_hill_2012/test_settings.py
+tests/smoke_tests/kinematic_2d/__init__.py
 tests/smoke_tests/kinematic_2d/arabas_et_al_2015/__init__.py
 tests/smoke_tests/kinematic_2d/arabas_et_al_2015/dummy_storage.py
 tests/smoke_tests/kinematic_2d/arabas_et_al_2015/test_adaptive_displacement.py
@@ -778,6 +782,7 @@ tests/smoke_tests/no_env/toon_et_al_1980/__init__.py
 tests/smoke_tests/no_env/toon_et_al_1980/test_fig_1.py
 tests/smoke_tests/no_env/zaba_et_al/__init__.py
 tests/smoke_tests/no_env/zaba_et_al/test_global_meteoric_water_line.py
+tests/smoke_tests/parcel_a/__init__.py
 tests/smoke_tests/parcel_a/lowe_et_al_2019/__init__.py
 tests/smoke_tests/parcel_a/lowe_et_al_2019/conftest.py
 tests/smoke_tests/parcel_a/lowe_et_al_2019/test_dz_sensitivity.py
@@ -795,6 +800,7 @@ tests/smoke_tests/parcel_b/arabas_and_shima_2017/test_displacement.py
 tests/smoke_tests/parcel_b/arabas_and_shima_2017/test_event_rates.py
 tests/smoke_tests/parcel_b/arabas_and_shima_2017/test_initialisation.py
 tests/smoke_tests/parcel_b/arabas_and_shima_2017/test_vs_scipy.py
+tests/smoke_tests/parcel_c/__init__.py
 tests/smoke_tests/parcel_c/abade_and_albuquerque_2024/__init__.py
 tests/smoke_tests/parcel_c/abade_and_albuquerque_2024/test_fig_2.py
 tests/smoke_tests/parcel_c/abdul_razzak_ghan_2000/__init__.py
@@ -825,6 +831,7 @@ tests/smoke_tests/parcel_d/kreidenweis_et_al_2003/test_spectrum_at_t_0.py
 tests/smoke_tests/parcel_d/kreidenweis_et_al_2003/test_table_3.py
 tests/smoke_tests/parcel_d/niedermeier_et_al_2013/__init__.py
 tests/smoke_tests/parcel_d/niedermeier_et_al_2013/test_temperature_profile.py
+tests/smoke_tests/parcel_d/rogers_1975/__init__.py
 tests/smoke_tests/parcel_d/rogers_1975/test_fig_1.py
 tests/smoke_tests/parcel_d/rozanski_and_sonntag_1982/__init__.py
 tests/smoke_tests/parcel_d/rozanski_and_sonntag_1982/test_figs_4_5_6.py
@@ -890,6 +897,7 @@ tests/unit_tests/dynamics/collisions/test_kernels.py
 tests/unit_tests/dynamics/collisions/test_sdm_breakup.py
 tests/unit_tests/dynamics/collisions/test_sdm_multi_cell.py
 tests/unit_tests/dynamics/collisions/test_sdm_single_cell.py
+tests/unit_tests/dynamics/condensation/__init__.py
 tests/unit_tests/dynamics/condensation/test_diagnostics.py
 tests/unit_tests/dynamics/condensation/test_parcel_sanity_checks.py
 tests/unit_tests/dynamics/condensation/test_ventilation.py

{pysdm-3.0.0rc5 → pysdm-3.0.0rc6}/tests/examples_tests/conftest.py

@@ -2,6 +2,81 @@
 import os
 import pathlib
 import re
+import ast
+import importlib
+import inspect
+import pkgutil
+
+
+from .. import smoke_tests
+
+
+class NotebookVarExtractor(ast.NodeVisitor):
+    def __init__(self):
+        self.paths = []
+
+    def visit_Call(self, node):
+        if isinstance(node.func, ast.Name) and node.func.id == "notebook_vars":
+            for arg in node.args:
+                self._maybe_add_path_expr(arg)
+            for kw in node.keywords:
+                self._maybe_add_path_expr(kw.value)
+        self.generic_visit(node)
+
+    def _maybe_add_path_expr(self, expr):
+        """Extract a path-like expression string from AST."""
+        expr_str = ast.unparse(expr)
+        if "Path(" in expr_str:
+            self.paths.append(expr_str)
+
+
+def extract_path_expressions_from_module(mod):
+    try:
+        source = inspect.getsource(mod)
+    except (OSError, TypeError):
+        return []
+
+    tree = ast.parse(source)
+    extractor = NotebookVarExtractor()
+    extractor.visit(tree)
+
+    return extractor.paths
+
+
+def evaluate_path_expr(expr_str, module_globals):
+    """Evaluate the path expression using the module's globals."""
+    local_ctx = {"Path": pathlib.Path}
+    value = eval(expr_str, {**module_globals, **local_ctx})  # pylint: disable=eval-used
+    return value.resolve() if isinstance(value, pathlib.Path) else None
+
+
+def iter_submodule_names(module):
+    """Yield names of all submodules recursively without importing."""
+    if not hasattr(module, "__path__"):
+        return
+    for _, name, _ in pkgutil.walk_packages(module.__path__, module.__name__ + "."):
+        yield name
+
+
+def find_modules_using_notebook_vars(module):
+    names = []
+    for name in iter_submodule_names(module):
+        filepath = importlib.util.find_spec(name).origin
+        with open(filepath, "r", encoding="utf-8") as f:
+            source = f.read()
+        if "notebook_vars" in source:
+            names.append(name)
+    return names
+
+
+SMOKE_TEST_COVERED_PATHS = []
+for mod_name in find_modules_using_notebook_vars(smoke_tests):
+    submodule = importlib.import_module(mod_name)
+    exprs = extract_path_expressions_from_module(submodule)
+    for path_expr in exprs:
+        submodule_path = evaluate_path_expr(path_expr, vars(submodule))
+        if submodule_path:
+            SMOKE_TEST_COVERED_PATHS.append(submodule_path)
 
 
 # https://stackoverflow.com/questions/7012921/recursive-grep-using-python
@@ -119,8 +194,14 @@ def pytest_generate_tests(metafunc):
         .joinpath("PySDM_examples")
     )
     if "notebook_filename" in metafunc.fixturenames:
-        notebook_paths = findfiles(pysdm_examples_abs_path, r".*\.(ipynb)$")
-        selected_paths = get_selected_test_paths(suite_name, notebook_paths)
+        notebook_paths = [
+            path
+            for path in findfiles(pysdm_examples_abs_path, r".*\.ipynb$")
+            if ".ipynb_checkpoints" not in str(path)
+        ]
+        selected_paths = set(get_selected_test_paths(suite_name, notebook_paths)) - set(
+            SMOKE_TEST_COVERED_PATHS
+        )
         metafunc.parametrize(
             "notebook_filename",
             selected_paths,

{pysdm-3.0.0rc5 → pysdm-3.0.0rc6}/tests/unit_tests/physics/test_isotope_relaxation_timescale.py

@@ -58,18 +58,15 @@ def test_unit_and_magnitude(paper, iso):
         assert 0 * si.s < result.to_base_units() < 10 * si.s
 
 
-def test_bolin_tritium_formula_unit():
+def test_bolin_number_unit():
     with DimensionalAnalysis():
         # arrange
         si = constants_defaults.si
-        formulae = Formulae(
-            isotope_relaxation_timescale="Bolin1958",
-            constants={"BOLIN_ISOTOPE_TIMESCALE_COEFF_C1": 1 * si.dimensionless},
-        )
-        tau = formulae.isotope_relaxation_timescale.tau
+        sut = isotope_relaxation_timescale.bolin_1958.Bolin1958.bolin_number
+        formulae = Formulae()
 
         # act
-        sut = tau(dm_dt_over_m=1 / si.s)
+        value = sut(formulae.constants)
 
         # assert
-        assert sut.check("[time]")
+        assert value.check(si.dimensionless)

{pysdm-3.0.0rc5 → pysdm-3.0.0rc6}/tests/unit_tests/physics/test_trivia.py

@@ -3,7 +3,7 @@ import numpy as np
 import pytest
 from scipy.special import erfinv  # pylint: disable=no-name-in-module
 
-from PySDM import Formulae
+from PySDM import Formulae, physics
 from PySDM.physics.dimensional_analysis import DimensionalAnalysis
 from PySDM.physics import constants_defaults
 
@@ -113,3 +113,18 @@ class TestTrivia:
 
         # assert
         assert temperature_in_kelvin == temperature_in_celsius + 273.15
+
+    @staticmethod
+    @pytest.mark.parametrize(
+        "bolin_number, dm_dt_over_m, expected_tau",
+        ((1, 2, 0.5), (2, 1, 0.5), (2, 2, 0.25)),
+    )
+    def test_tau(bolin_number, dm_dt_over_m, expected_tau):
+        # arrange
+        sut = physics.trivia.Trivia.tau
+
+        # act
+        value = sut(Bo=bolin_number, dm_dt_over_m=dm_dt_over_m)
+
+        # assert
+        np.testing.assert_almost_equal(actual=value, desired=expected_tau)

pysdm-3.0.0rc5/PySDM/physics/isotope_relaxation_timescale/bolin_1958.py

@@ -1,15 +0,0 @@
-"""Timescale derived for tritium with assumption of zero ambient concentration - see text above
-Table 1 [Bolin 1958](https://digitallibrary.un.org/record/3892725)"""
-
-import numpy as np
-
-
-class Bolin1958:  # pylint: disable=too-few-public-methods
-    """Implementation of timescale used by Bolin 1958"""
-
-    def __init__(self, const):
-        assert np.isfinite(const.BOLIN_ISOTOPE_TIMESCALE_COEFF_C1)
-
-    @staticmethod
-    def tau(const, dm_dt_over_m):
-        return 1 / (const.BOLIN_ISOTOPE_TIMESCALE_COEFF_C1 * dm_dt_over_m)