PySDM 2.131__tar.gz → 3.0.0rc1__tar.gz

{pysdm-2.131 → pysdm-3.0.0rc1}/.github/workflows/pdoc.yml

@@ -16,7 +16,7 @@ jobs:
   pdoc:
     strategy:
       matrix:
-        platform: [ ubuntu-latest, macos-13, windows-latest ]
+        platform: [ ubuntu-latest, macos-latest, windows-latest ]
     runs-on: ${{ matrix.platform }}
     steps:
       - uses: actions/checkout@v4.1.6

pysdm-3.0.0rc1/.github/workflows/precommit.yml

@@ -0,0 +1,81 @@
+name: precommit, url-check and devops tests
+
+defaults:
+  run:
+    shell: bash
+
+env:
+  # common options for pytest
+  pytest_options: "--durations=10 -v -s -We -p no:unraisableexception"
+
+on:
+  push:
+    branches: [ main ]
+    paths: ['docs/**', '**.md']
+  pull_request:
+    branches: [ main ]
+  schedule:
+    - cron: '0 13 * * 4'
+
+jobs:
+  precommit:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4.1.6
+      - uses: actions/setup-python@v5.0.0
+        with:
+          python-version: 3.9
+      - run: |
+          pip install pre-commit
+          pre-commit clean
+          pre-commit autoupdate
+          pre-commit run --all-files
+      - if: ${{ failure() }}
+        run: git diff
+
+  devops:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4.1.6
+        with:
+          submodules: recursive
+          fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
+      - run: pip install -r tests/devops_tests/requirements.txt
+      - env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: pytest  ${{ env.pytest_options }} -k "not test_run_notebooks" tests/devops_tests
+
+
+  url-check:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4.1.6
+      - name: URLs-checker
+        uses: urlstechie/urlchecker-action@master
+        with:
+          # A subfolder or path to navigate to in the present or cloned repository
+          # subfolder: docs
+
+          # A comma-separated list of file types to cover in the URL checks
+          file_types: .md,.py,.json,.ipynb,.yaml,.yml,.jinja2,.toml
+
+          # Choose whether to include file with no URLs in the prints.
+          print_all: false
+
+          # Choose whether to print a more verbose end summary with files and broken URLs.
+          verbose: true
+
+          # The timeout seconds to provide to requests, defaults to 5 seconds
+          timeout: 7
+
+          # How many times to retry a failed request (each is logged, defaults to 1)
+          retry_count: 3
+
+          # A comma separated links to exclude during URL checks
+          exclude_urls: https://www.gnu.org/licenses/gpl-3.0.html,https://open-atmos.github.io/PySDM/\2/\3.html
+
+          # A comma separated patterns to exclude during URL checks
+          exclude_patterns: http://purl.org,http://www.w3.org
+
+          # A comma separated list of file patterns (direct paths work as well) to exclude
+          exclude_files: docs/generate_html.py,.github/workflows/precommit.yml

{pysdm-2.131 → pysdm-3.0.0rc1}/.github/workflows/pypi.yml

@@ -57,7 +57,7 @@ jobs:
   pkg_install_check:
     strategy:
       matrix:
-        platform: [ ubuntu-latest, macos-13, macos-14, windows-latest ]
+        platform: [ ubuntu-latest, macos-latest, windows-latest ]
         python-version: [ "3.9", "3.12" ]
         exclude:
           - platform: macos-14

{pysdm-2.131 → pysdm-3.0.0rc1}/.github/workflows/tests.yml

@@ -243,7 +243,7 @@ jobs:
 
       # TODO #1207
       - if: startsWith(matrix.platform, 'macos-13')
-        run: python -m pytest --basetemp=/tmp/pytest ${{ env.pytest_options }} tests/examples_tests/test_run* -k "not Rozanski_and_Sonntag_1982" --suite ${{ matrix.test-suite }}
+        run: python -m pytest --basetemp=/tmp/pytest ${{ env.pytest_options }} tests/examples_tests/test_run* -k "not (Rozanski_and_Sonntag_1982 or copula_hello)" --suite ${{ matrix.test-suite }}
 
       - if: ( ! startsWith(matrix.platform, 'macos-13') )
         run: python -m pytest ${{ env.pytest_options }} --basetemp=/tmp/pytest --timeout_method=thread --timeout=${{ startsWith(matrix.platform, 'windows-') && 1000 || 900 }} tests/examples_tests/test_run* --suite ${{ matrix.test-suite }}

{pysdm-2.131/pysdm.egg-info → pysdm-3.0.0rc1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysdm
-Version: 2.131
+Version: 3.0.0rc1
 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
@@ -160,7 +160,7 @@ only the supporting .py files).
 [![PyPI](https://img.shields.io/static/v1?label=+&logo=pypi&color=gold&message=PyPI)](https://pypi.org/)
 [![GithubActions](https://img.shields.io/static/v1?label=+&logo=github&color=darkgreen&message=GitHub&nbsp;Actions)](https://github.com/features/actions)
 [![Jupyter](https://img.shields.io/static/v1?label=+&logo=Jupyter&color=blue&message=Jupyter)](https://jupyter.org/)
-[![PyCharm](https://img.shields.io/static/v1?label=+&logo=pycharm&color=purple&message=PyCharm)](https:///)
+[![PyCharm](https://img.shields.io/static/v1?label=+&logo=pycharm&color=purple&message=PyCharm)](https://www.jetbrains.com/pycharm/)
 
 Submitting new code to the project, please preferably use [GitHub pull requests](https://github.com/open-atmos/PySDM/pulls) - it helps to keep record of code authorship, 
 track and archive the code review workflow and allows to benefit
@@ -188,7 +188,7 @@ The `.pre-commit-config.yaml` file can be modified in case new hooks are to be a
   existing ones need to be altered.  
 
 Further hints addressed at PySDM developers are maintained in the [open-atmos/python-dev-hints Wiki](https://github.com/open-atmos/python-dev-hints/wiki)
-  and in [PySDM HOWTOs](https://github.com/open-atmos/PySDM/tree/main/examples/PySDM_examples/_HOWTOS).
+  and in [PySDM HOWTOs](https://github.com/open-atmos/PySDM/tree/main/examples/PySDM_examples/_HOWTOs).
 
 Issues regarding any incorrect, unintuitive or undocumented bahaviour of
 PySDM are best to be reported on the [GitHub issue tracker](https://github.com/open-atmos/PySDM/issues/new).

{pysdm-2.131 → pysdm-3.0.0rc1}/PySDM/attributes/ice/freezing_temperature.py

@@ -20,7 +20,9 @@ class TemperatureOfLastFreezing(DerivedAttribute):
 
     def __init__(self, builder):
         assert "Freezing" in builder.particulator.dynamics
-        assert not builder.particulator.dynamics["Freezing"].singular
+        assert (
+            builder.particulator.dynamics["Freezing"].immersion_freezing != "singular"
+        )
         self.signed_water_mass = builder.get_attribute("signed water mass")
         self.cell_id = builder.get_attribute("cell id")
         super().__init__(

{pysdm-2.131 → pysdm-3.0.0rc1}/PySDM/backends/impl_common/freezing_attributes.py

@@ -1,5 +1,6 @@
 """
-groups of attributes used in either singular or time-dependent immersion freezing regimes
+groups of attributes used in either singular or time-dependent immersion freezing regimes,
+in threshold or time-dependent homogeneous freezing and for thaw routines
 """
 
 from collections import namedtuple
@@ -36,3 +37,14 @@ class TimeDependentHomogeneousAttributes(
     """groups attributes required in time-dependent regime for homogeneous freezing"""
 
     __slots__ = ()
+
+
+class ThresholdHomogeneousAndThawAttributes(
+    namedtuple(
+        typename="ThresholdHomogeneousAttributes",
+        field_names=("signed_water_mass"),
+    )
+):
+    """groups attributes required in time-dependent regime for homogeneous freezing"""
+
+    __slots__ = ()

{pysdm-2.131 → pysdm-3.0.0rc1}/PySDM/backends/impl_numba/atomic_operations.py

@@ -1,5 +1,5 @@
 """
-https://github.com/KatanaGraph/katana/blob/master/python/katana/numba_support/numpy_atomic.py
+https://github.com/KatanaGraph/katana/blob/master/python/katana/native_interfacing/numpy_atomic.py
 """
 
 from numba import types

{pysdm-2.131 → pysdm-3.0.0rc1}/PySDM/backends/impl_numba/methods/freezing_methods.py

@@ -14,6 +14,7 @@ from ...impl_common.freezing_attributes import (
     SingularAttributes,
     TimeDependentAttributes,
     TimeDependentHomogeneousAttributes,
+    ThresholdHomogeneousAndThawAttributes,
 )
 
 
@@ -37,25 +38,40 @@ class FreezingMethods(BackendMethods):
         return body
 
     @cached_property
-    def _freeze_singular_body(self):
+    def _thaw_instantaneous_body(self):
         _thaw = self._thaw
-        _freeze = self._freeze
         frozen_and_above_freezing_point = (
             self.formulae.trivia.frozen_and_above_freezing_point
         )
+
+        @numba.njit(**self.default_jit_flags)
+        def body(attributes, cell, temperature):
+            n_sd = len(attributes.signed_water_mass)
+            for i in numba.prange(n_sd):  # pylint: disable=not-an-iterable
+                if frozen_and_above_freezing_point(
+                    attributes.signed_water_mass[i], temperature[cell[i]]
+                ):
+                    _thaw(attributes.signed_water_mass, i)
+
+        return body
+
+    @cached_property
+    def _immersion_freezing_singular_body(self):
+        _freeze = self._freeze
         unfrozen_and_saturated = self.formulae.trivia.unfrozen_and_saturated
 
         @numba.njit(**self.default_jit_flags)
-        def body(attributes, temperature, relative_humidity, cell, thaw):
+        def body(
+            attributes,
+            temperature,
+            relative_humidity,
+            cell,
+        ):
             n_sd = len(attributes.freezing_temperature)
             for i in numba.prange(n_sd):  # pylint: disable=not-an-iterable
                 if attributes.freezing_temperature[i] == 0:
                     continue
-                if thaw and frozen_and_above_freezing_point(
-                    attributes.signed_water_mass[i], temperature[cell[i]]
-                ):
-                    _thaw(attributes.signed_water_mass, i)
-                elif (
+                if (
                     unfrozen_and_saturated(
                         attributes.signed_water_mass[i], relative_humidity[cell[i]]
                     )
@@ -66,12 +82,8 @@ class FreezingMethods(BackendMethods):
         return body
 
     @cached_property
-    def _freeze_time_dependent_body(self):
-        _thaw = self._thaw
+    def _immersion_freezing_time_dependent_body(self):
         _freeze = self._freeze
-        frozen_and_above_freezing_point = (
-            self.formulae.trivia.frozen_and_above_freezing_point
-        )
         unfrozen_and_saturated = self.formulae.trivia.unfrozen_and_saturated
         j_het = self.formulae.heterogeneous_ice_nucleation_rate.j_het
         prob_zero_events = self.formulae.trivia.poissonian_avoidance_function
@@ -83,20 +95,14 @@ class FreezingMethods(BackendMethods):
             timestep,
             cell,
             a_w_ice,
-            temperature,
             relative_humidity,
-            thaw,
         ):
             n_sd = len(attributes.signed_water_mass)
             for i in numba.prange(n_sd):  # pylint: disable=not-an-iterable
                 if attributes.immersed_surface_area[i] == 0:
                     continue
                 cell_id = cell[i]
-                if thaw and frozen_and_above_freezing_point(
-                    attributes.signed_water_mass[i], temperature[cell_id]
-                ):
-                    _thaw(attributes.signed_water_mass, i)
-                elif unfrozen_and_saturated(
+                if unfrozen_and_saturated(
                     attributes.signed_water_mass[i], relative_humidity[cell_id]
                 ):
                     rate_assuming_constant_temperature_within_dt = (
@@ -111,12 +117,8 @@ class FreezingMethods(BackendMethods):
         return body
 
     @cached_property
-    def _freeze_time_dependent_homogeneous_body(self):
-        _thaw = self._thaw
+    def _homogeneous_freezing_time_dependent_body(self):
         _freeze = self._freeze
-        frozen_and_above_freezing_point = (
-            self.formulae.trivia.frozen_and_above_freezing_point
-        )
         unfrozen_and_ice_saturated = self.formulae.trivia.unfrozen_and_ice_saturated
         j_hom = self.formulae.homogeneous_ice_nucleation_rate.j_hom
         prob_zero_events = self.formulae.trivia.poissonian_avoidance_function
@@ -136,17 +138,12 @@ class FreezingMethods(BackendMethods):
             a_w_ice,
             temperature,
             relative_humidity_ice,
-            thaw,
         ):
 
             n_sd = len(attributes.signed_water_mass)
             for i in numba.prange(n_sd):  # pylint: disable=not-an-iterable
                 cell_id = cell[i]
-                if thaw and frozen_and_above_freezing_point(
-                    attributes.signed_water_mass[i], temperature[cell_id]
-                ):
-                    _thaw(attributes.signed_water_mass, i)
-                elif unfrozen_and_ice_saturated(
+                if unfrozen_and_ice_saturated(
                     attributes.signed_water_mass[i], relative_humidity_ice[cell_id]
                 ):
                     d_a_w_ice = (relative_humidity_ice[cell_id] - 1.0) * a_w_ice[
@@ -167,10 +164,44 @@ class FreezingMethods(BackendMethods):
 
         return body
 
-    def freeze_singular(
-        self, *, attributes, temperature, relative_humidity, cell, thaw: bool
+    @cached_property
+    def _homogeneous_freezing_threshold_body(self):
+        _freeze = self._freeze
+        unfrozen_and_ice_saturated = self.formulae.trivia.unfrozen_and_ice_saturated
+        const = self.formulae.constants
+
+        @numba.njit(**self.default_jit_flags)
+        def body(attributes, cell, temperature, relative_humidity_ice):
+            n_sd = len(attributes.signed_water_mass)
+            for i in numba.prange(n_sd):  # pylint: disable=not-an-iterable
+                cell_id = cell[i]
+                if unfrozen_and_ice_saturated(
+                    attributes.signed_water_mass[i], relative_humidity_ice[cell_id]
+                ):
+                    if temperature[cell_id] <= const.HOMOGENEOUS_FREEZING_THRESHOLD:
+                        _freeze(attributes.signed_water_mass, i)
+
+        return body
+
+    def thaw_instantaneous(
+        self,
+        *,
+        attributes,
+        cell,
+        temperature,
+    ):
+        self._thaw_instantaneous_body(
+            ThresholdHomogeneousAndThawAttributes(
+                signed_water_mass=attributes.signed_water_mass.data,
+            ),
+            cell.data,
+            temperature.data,
+        )
+
+    def immersion_freezing_singular(
+        self, *, attributes, temperature, relative_humidity, cell
     ):
-        self._freeze_singular_body(
+        self._immersion_freezing_singular_body(
             SingularAttributes(
                 freezing_temperature=attributes.freezing_temperature.data,
                 signed_water_mass=attributes.signed_water_mass.data,
@@ -178,10 +209,9 @@ class FreezingMethods(BackendMethods):
             temperature.data,
             relative_humidity.data,
             cell.data,
-            thaw=thaw,
         )
 
-    def freeze_time_dependent(
+    def immersion_freezing_time_dependent(
         self,
         *,
         rand,
@@ -189,11 +219,9 @@ class FreezingMethods(BackendMethods):
         timestep,
         cell,
         a_w_ice,
-        temperature,
         relative_humidity,
-        thaw: bool,
     ):
-        self._freeze_time_dependent_body(
+        self._immersion_freezing_time_dependent_body(
             rand.data,
             TimeDependentAttributes(
                 immersed_surface_area=attributes.immersed_surface_area.data,
@@ -202,12 +230,27 @@ class FreezingMethods(BackendMethods):
             timestep,
             cell.data,
             a_w_ice.data,
-            temperature.data,
             relative_humidity.data,
-            thaw=thaw,
         )
 
-    def freeze_time_dependent_homogeneous(
+    def homogeneous_freezing_threshold(
+        self,
+        *,
+        attributes,
+        cell,
+        temperature,
+        relative_humidity_ice,
+    ):
+        self._homogeneous_freezing_threshold_body(
+            ThresholdHomogeneousAndThawAttributes(
+                signed_water_mass=attributes.signed_water_mass.data,
+            ),
+            cell.data,
+            temperature.data,
+            relative_humidity_ice.data,
+        )
+
+    def homogeneous_freezing_time_dependent(
         self,
         *,
         rand,
@@ -217,9 +260,8 @@ class FreezingMethods(BackendMethods):
         a_w_ice,
         temperature,
         relative_humidity_ice,
-        thaw: bool,
     ):
-        self._freeze_time_dependent_homogeneous_body(
+        self._homogeneous_freezing_time_dependent_body(
             rand.data,
             TimeDependentHomogeneousAttributes(
                 volume=attributes.volume.data,
@@ -230,7 +272,6 @@ class FreezingMethods(BackendMethods):
             a_w_ice.data,
             temperature.data,
             relative_humidity_ice.data,
-            thaw=thaw,
         )
 
     @cached_property