PySDM 2.54__tar.gz → 2.59__tar.gz

PySDM-2.59/.codecov.yml

@@ -0,0 +1,5 @@
+coverage:
+  status:
+    project:
+      default:
+        threshold: 0.01%

{PySDM-2.54 → PySDM-2.59}/.github/workflows/readme_snippets.yml

@@ -28,7 +28,7 @@ jobs:
         run: |
           sudo ln -s `which python3` /usr/local/bin/python
           echo "PIP_INSTALL_ARGS=--break-system-packages" >> $GITHUB_ENV
-          python -m pip install --break-system-packages setuptools # Python 3.12 workaround  
+          python -m pip install --break-system-packages setuptools packaging # Python 3.12 workaround  
       - run: python -m pip install $PIP_INSTALL_ARGS -e .
       - run: python -m pip install $PIP_INSTALL_ARGS pytest-codeblocks pytest
       - run: python -m pip install $PIP_INSTALL_ARGS "pyparsing<3.0.0"  # https://github.com/matplotlib/matplotlib/issues/25204

{PySDM-2.54 → PySDM-2.59}/.github/workflows/tests+artifacts+pypi.yml

@@ -48,8 +48,7 @@ jobs:
         pip install -e ./examples
         pip install pytest-cov
         pytest --durations=10 -We tests/unit_tests --cov-report=xml --cov=PySDM
-    - if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-      uses: codecov/codecov-action@v4.1.0
+    - uses: codecov/codecov-action@v4.1.0
       with:
         fail_ci_if_error: true
         verbose: true
@@ -192,13 +191,15 @@ jobs:
           echo toml_ci_md5=$(cat pyproject.toml setup.py examples/pyproject.toml examples/setup.py tests/devops_tests/requirements.txt .github/workflows/tests+artifacts+pypi.yml \
           | python -c "import hashlib;print(hashlib.md5(open(0,'rb').read()).hexdigest())") >> $GITHUB_ENV
       - uses: actions/cache@v4
+        id: cache
         with:
           path: ${{ env.pip_user_site }}
           key: examples_pip_cache-${{ matrix.platform }}-${{ matrix.python-version }}-${{ env.toml_ci_md5 }}
+          lookup-only: true
       - if: steps.cache.outputs.cache-hit != 'true'
         run: |
           python -m pip uninstall -y jupyterlab-server # https://github.com/pypa/pip/issues/6275
-          python -m pip install -e . ./examples
+          python -m pip install -e . -e ./examples
           python -m pip install -r tests/devops_tests/requirements.txt
       - if: steps.cache.outputs.cache-hit != 'true'
         uses: actions/cache/save@v4
@@ -327,7 +328,7 @@ jobs:
           sudo ln -s `which python3` /usr/local/bin/python
           echo "PIP_INSTALL_ARGS=--break-system-packages" >> $GITHUB_ENV
           # Python 3.12 workaround  
-          python -m pip install --break-system-packages setuptools
+          python -m pip install --break-system-packages setuptools packaging
       - uses: actions/download-artifact@v3
         with:
           name: dist

{PySDM-2.54 → PySDM-2.59}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.54
+Version: 2.59
 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
 Home-page: https://github.com/open-atmos/PySDM
 Author: https://github.com/open-atmos/PySDM/graphs/contributors
@@ -74,7 +74,7 @@ Description: # PySDM
         - [de Jong, Singer et al. 2023](https://doi.org/10.21105/joss.04968) (PySDM v2).
           
         PySDM includes an extension of the SDM scheme to represent collisional breakup described in [de Jong, Mackay et al. 2023](10.5194/gmd-16-4193-2023).   
-        For a list of talks and other materials on PySDM, see the [project wiki](https://github.com/open-atmos/PySDM/wiki).
+        For a list of talks and other materials on PySDM as well as a list of published papers featuring PySDM simulations, see the [project wiki](https://github.com/open-atmos/PySDM/wiki).
         
         A [pdoc-generated](https://pdoc3.github.io/pdoc) documentation of PySDM public API is maintained at: [https://open-atmos.github.io/PySDM](https://open-atmos.github.io/PySDM) 
         
@@ -846,6 +846,8 @@ Description: # PySDM
           https://yoctoyotta1024.github.io/CLEO/
         - droplets.jl (Julia)   
           https://github.com/emmacware/droplets.jl
+        - LacmoPy (Python/Numba)    
+          https://github.com/JanKBohrer/LacmoPy/blob/master/collision/all_or_nothing.py
         
         ### non-SDM probabilistic particle-based coagulation solvers
         

{PySDM-2.54 → PySDM-2.59}/PySDM/backends/impl_numba/methods/chemistry_methods.py

@@ -62,49 +62,48 @@ class ChemistryMethods(BackendMethods):
         droplet_volume,
         multiplicity,
     ):
-        for thread_id in numba.prange(n_threads):  # pylint: disable=not-an-iterable
-            for i in range(thread_id, n_cell, n_threads):
-                cell_id = cell_order[i]
-
-                cell_start = cell_start_arg[cell_id]
-                cell_end = cell_start_arg[cell_id + 1]
-                n_sd_in_cell = cell_end - cell_start
-                if n_sd_in_cell == 0:
-                    continue
-
-                super_droplet_ids = numba.typed.List()
-                for sd_id in idx[cell_start:cell_end]:
-                    if do_chemistry_flag.data[sd_id]:
-                        super_droplet_ids.append(sd_id)
-
-                if len(super_droplet_ids) == 0:
-                    return
-
-                for key, compound in GASEOUS_COMPOUNDS.items():
-                    ChemistryMethods.dissolution_body(
-                        super_droplet_ids=super_droplet_ids,
-                        mole_amounts=mole_amounts[key].data,
-                        env_mixing_ratio=env_mixing_ratio[compound][
-                            cell_id : cell_id + 1
-                        ],
-                        henrysConstant=self.HENRY_CONST.HENRY_CONST[compound].at(
-                            env_T[cell_id]
-                        ),
-                        env_p=env_p[cell_id],
-                        env_T=env_T[cell_id],
-                        env_rho_d=env_rho_d[cell_id],
-                        timestep=timestep,
-                        dv=dv,
-                        droplet_volume=droplet_volume.data,
-                        multiplicity=multiplicity.data,
-                        system_type=system_type,
-                        specific_gravity=self.specific_gravities[compound],
-                        alpha=MASS_ACCOMMODATION_COEFFICIENTS[compound],
-                        diffusion_const=DIFFUSION_CONST[compound],
-                        dissociation_factor=dissociation_factors[compound].data,
-                        radius=self.formulae.trivia.radius,
-                        const=self.formulae.constants,
-                    )
+        assert n_cell == 1
+        assert n_threads == 1
+        for i in range(n_cell):
+            cell_id = cell_order[i]
+
+            cell_start = cell_start_arg[cell_id]
+            cell_end = cell_start_arg[cell_id + 1]
+            n_sd_in_cell = cell_end - cell_start
+            if n_sd_in_cell == 0:
+                continue
+
+            super_droplet_ids = numba.typed.List()
+            for sd_id in idx[cell_start:cell_end]:
+                if do_chemistry_flag.data[sd_id]:
+                    super_droplet_ids.append(sd_id)
+
+            if len(super_droplet_ids) == 0:
+                return
+
+            for key, compound in GASEOUS_COMPOUNDS.items():
+                ChemistryMethods.dissolution_body(
+                    super_droplet_ids=super_droplet_ids,
+                    mole_amounts=mole_amounts[key].data,
+                    env_mixing_ratio=env_mixing_ratio[compound][cell_id : cell_id + 1],
+                    henrysConstant=self.HENRY_CONST.HENRY_CONST[compound].at(
+                        env_T[cell_id]
+                    ),
+                    env_p=env_p[cell_id],
+                    env_T=env_T[cell_id],
+                    env_rho_d=env_rho_d[cell_id],
+                    timestep=timestep,
+                    dv=dv,
+                    droplet_volume=droplet_volume.data,
+                    multiplicity=multiplicity.data,
+                    system_type=system_type,
+                    specific_gravity=self.specific_gravities[compound],
+                    alpha=MASS_ACCOMMODATION_COEFFICIENTS[compound],
+                    diffusion_const=DIFFUSION_CONST[compound],
+                    dissociation_factor=dissociation_factors[compound].data,
+                    radius=self.formulae.trivia.radius,
+                    const=self.formulae.constants,
+                )
 
     @staticmethod
     @numba.njit(**{**conf.JIT_FLAGS, **{"parallel": False}})

{PySDM-2.54 → PySDM-2.59}/PySDM/exporters/netcdf_exporter_1d.py

@@ -75,7 +75,9 @@ class NetCDFExporter_1d:  # pylint: disable=too-few-public-methods,too-many-inst
                 )
 
             n_dimensions = len(instance.shape)
-            if n_dimensions == 1:
+            if n_dimensions == 0:
+                dimensions = ("time",)
+            elif n_dimensions == 1:
                 dimensions = ("height", "time")
             elif n_dimensions == 2:
                 dim_name = name.replace(" ", "_") + "_bin_index"
@@ -94,7 +96,9 @@ class NetCDFExporter_1d:  # pylint: disable=too-few-public-methods,too-many-inst
     def _write_variables(self):
         for var in self.simulator.particulator.products.keys():
             n_dimensions = len(self.simulator.particulator.products[var].shape)
-            if n_dimensions == 1:
+            if n_dimensions == 0:
+                self.vars[var][:] = self.data[var][:]
+            elif n_dimensions == 1:
                 self.vars[var][:, :] = self.data[var][-self.nz_export :, :]
             elif n_dimensions == 2:
                 if self.n_save_spec == 0:

{PySDM-2.54 → PySDM-2.59}/PySDM/physics/isotope_ratio_evolution/__init__.py

@@ -3,3 +3,4 @@
 from PySDM.impl.null_physics_class import Null
 from .merlivat_and_jouzel_1979 import MerlivatAndJouzel1979
 from .rayleigh_distillation import RayleighDistillation
+from .gedzelman_and_arnold_1994 import GedzelmanAndArnold1994

PySDM-2.59/PySDM/physics/isotope_ratio_evolution/gedzelman_and_arnold_1994.py

@@ -0,0 +1,18 @@
+"""
+eqs. (22) and (23) in [Gedzelman & Arnold 1994](https://doi.org/10.1029/93JD03518)
+"""
+
+
+# pylint: disable=too-few-public-methods
+class GedzelmanAndArnold1994:
+    def __init__(self, _):
+        pass
+
+    # pylint: disable=too-many-arguments
+    @staticmethod
+    def zero_dR_condition(
+        _, diff_rat, iso_ratio_x, iso_ratio_r, iso_ratio_v, b, alpha_w
+    ):
+        return (diff_rat * iso_ratio_x - iso_ratio_r / alpha_w) / (
+            diff_rat * iso_ratio_x - (1 + b) * iso_ratio_v + b * iso_ratio_r / alpha_w
+        )

{PySDM-2.54 → PySDM-2.59}/PySDM.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.54
+Version: 2.59
 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
 Home-page: https://github.com/open-atmos/PySDM
 Author: https://github.com/open-atmos/PySDM/graphs/contributors
@@ -74,7 +74,7 @@ Description: # PySDM
         - [de Jong, Singer et al. 2023](https://doi.org/10.21105/joss.04968) (PySDM v2).
           
         PySDM includes an extension of the SDM scheme to represent collisional breakup described in [de Jong, Mackay et al. 2023](10.5194/gmd-16-4193-2023).   
-        For a list of talks and other materials on PySDM, see the [project wiki](https://github.com/open-atmos/PySDM/wiki).
+        For a list of talks and other materials on PySDM as well as a list of published papers featuring PySDM simulations, see the [project wiki](https://github.com/open-atmos/PySDM/wiki).
         
         A [pdoc-generated](https://pdoc3.github.io/pdoc) documentation of PySDM public API is maintained at: [https://open-atmos.github.io/PySDM](https://open-atmos.github.io/PySDM) 
         
@@ -846,6 +846,8 @@ Description: # PySDM
           https://yoctoyotta1024.github.io/CLEO/
         - droplets.jl (Julia)   
           https://github.com/emmacware/droplets.jl
+        - LacmoPy (Python/Numba)    
+          https://github.com/JanKBohrer/LacmoPy/blob/master/collision/all_or_nothing.py
         
         ### non-SDM probabilistic particle-based coagulation solvers
         

{PySDM-2.54 → PySDM-2.59}/PySDM.egg-info/SOURCES.txt

@@ -1,4 +1,5 @@
 .appveyor.yml
+.codecov.yml
 .gitignore
 .gitmodules
 .pre-commit-config.yaml
@@ -285,6 +286,7 @@ PySDM/physics/isotope_meteoric_water_line_excess/__init__.py
 PySDM/physics/isotope_meteoric_water_line_excess/barkan_and_luz_2007.py
 PySDM/physics/isotope_meteoric_water_line_excess/dansgaard_1964.py
 PySDM/physics/isotope_ratio_evolution/__init__.py
+PySDM/physics/isotope_ratio_evolution/gedzelman_and_arnold_1994.py
 PySDM/physics/isotope_ratio_evolution/merlivat_and_jouzel_1979.py
 PySDM/physics/isotope_ratio_evolution/rayleigh_distillation.py
 PySDM/physics/isotope_relaxation_timescale/__init__.py

{PySDM-2.54 → PySDM-2.59}/PySDM.egg-info/requires.txt

@@ -11,7 +11,7 @@ pyevtk
 matplotlib
 pytest
 pytest-timeout
-PyPartMC==1.2.0
+PyPartMC==1.3.0
 pyrcel
 jupyter-core<5.0.0
 ipywidgets!=8.0.3

{PySDM-2.54 → PySDM-2.59}/README.md

@@ -63,7 +63,7 @@ For an overview of PySDM features (and the preferred way to cite PySDM in papers
 - [de Jong, Singer et al. 2023](https://doi.org/10.21105/joss.04968) (PySDM v2).
   
 PySDM includes an extension of the SDM scheme to represent collisional breakup described in [de Jong, Mackay et al. 2023](10.5194/gmd-16-4193-2023).   
-For a list of talks and other materials on PySDM, see the [project wiki](https://github.com/open-atmos/PySDM/wiki).
+For a list of talks and other materials on PySDM as well as a list of published papers featuring PySDM simulations, see the [project wiki](https://github.com/open-atmos/PySDM/wiki).
 
 A [pdoc-generated](https://pdoc3.github.io/pdoc) documentation of PySDM public API is maintained at: [https://open-atmos.github.io/PySDM](https://open-atmos.github.io/PySDM) 
 
@@ -835,6 +835,8 @@ licence: [GPL v3](https://www.gnu.org/licenses/gpl-3.0.html)
   https://yoctoyotta1024.github.io/CLEO/
 - droplets.jl (Julia)   
   https://github.com/emmacware/droplets.jl
+- LacmoPy (Python/Numba)    
+  https://github.com/JanKBohrer/LacmoPy/blob/master/collision/all_or_nothing.py
 
 ### non-SDM probabilistic particle-based coagulation solvers