PySDM 2.50__tar.gz → 2.53__tar.gz

{PySDM-2.50 → PySDM-2.53}/.github/workflows/readme_snippets.yml

@@ -14,22 +14,40 @@ on:
 
 jobs:
   python:
-    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, macos-12, macos-14, windows-latest]
+    runs-on: ${{ matrix.platform }}
     steps:
       - uses: actions/checkout@v4.1.1
-      - uses: actions/setup-python@v5.0.0
+      - if: matrix.platform != 'macos-14'
+        uses: actions/setup-python@v5.0.0
         with:
           python-version: 3.9
-      - run: pip install -e .[tests]
-      - run: pip install pytest-codeblocks pytest
-      - run: pip install "pyparsing<3.0.0"  # https://github.com/matplotlib/matplotlib/issues/25204
-      - run: python -c "import pytest_codeblocks; code=pytest_codeblocks.extract_from_file('README.md'); f=open('readme.py', 'w'); f.writelines(block.code for block in code if block.syntax=='Python'); f.close()"
-      - run: python -We readme.py
-      - run: sed -i 's/CPU/GPU/g' readme.py
-      - run: python -We readme.py
+      - if: matrix.platform == 'macos-14'
+        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  
+      - 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
+      - run: |
+          python -c "import os,pytest_codeblocks; code=pytest_codeblocks.extract_from_file('README.md'); f=open('readme.py', 'w', encoding='utf-8'); f.write('# coding: utf-8'+os.linesep); f.writelines(block.code for block in code if block.syntax=='Python'); f.close()"
+      - run: cat -n readme.py
+      - if: matrix.platform == 'macos-14'
+        run: |
+          python readme.py
+          sed -i -e 's/CPU/GPU/g' readme.py
+          python readme.py
+      - if: matrix.platform != 'macos-14'
+        run: |
+          python -We readme.py
+          sed -i -e 's/CPU/GPU/g' readme.py
+          python -We readme.py
       
       - name: artefacts
-        if: github.ref == 'refs/heads/main'
+        if: github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest'
         uses: eine/tip@master
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
@@ -49,7 +67,7 @@ jobs:
       - uses: julia-actions/setup-julia@v1.9.6
       - run: cat -n readme.jl
       - run: julia readme.jl
-      - run: sed -i 's/CPU/GPU/g' readme.jl
+      - run: sed -i -e 's/CPU/GPU/g' readme.jl
       - run: julia readme.jl
 
   matlab:
@@ -69,7 +87,7 @@ jobs:
       - uses: matlab-actions/run-command@v2.1.0
         with:
           command: readme
-      - run: sed -i 's/CPU/GPU/g' readme.m
+      - run: sed -i -e 's/CPU/GPU/g' readme.m
       - uses: matlab-actions/run-command@v2.1.0
         with:
           command: readme

{PySDM-2.50 → PySDM-2.53}/.github/workflows/tests+artifacts+pypi.yml

@@ -58,7 +58,7 @@ jobs:
   pdoc:
     strategy:
       matrix:
-        platform: [ubuntu-latest, macos-latest, windows-latest]
+        platform: [ubuntu-latest, macos-12, windows-latest]
     runs-on: ${{ matrix.platform }}
     steps:
       - uses: actions/checkout@v4.1.1
@@ -126,13 +126,13 @@ jobs:
       matrix:
         platform: [ubuntu-latest, macos-12, windows-latest]
         python-version: ["3.8", "3.11"]
-        test-suite: ["unit_tests", "smoke_tests/no_env", "smoke_tests/box", "smoke_tests/parcel", "smoke_tests/kinematic_1d", "smoke_tests/kinematic_2d", "tutorials_tests"]
+        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:
           - test-suite: "devops_tests"
             python-version: "3.8"
       fail-fast: false
     runs-on: ${{ matrix.platform }}
-    timeout-minutes: 100
+    timeout-minutes: 40
     steps:
       - uses: actions/checkout@v4.1.1
         with:
@@ -142,47 +142,80 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - run: |
-          pip install -e .
+      - run: pip install -e .
 
       # sanity check if we do not depend on something from tests extras
-      - run: |
-          python -We -c "import PySDM"
+      - run: python -We -c "import PySDM"
 
-      - run: |
-          pip install -e ./examples
-          pip install -e .[tests]
+      - if: startsWith(matrix.test-suite, 'smoke_tests') || matrix.test-suite == 'tutorials_tests'
+        run: pip install -e ./examples
 
-      # ensure previous pip did not overwrite the package
-      - run: |
-          pip install -e .
-
-      # https://github.com/numba/numba/issues/6350#issuecomment-728174860
-      - if: startsWith(matrix.platform, 'ubuntu-')
-        run: echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV
+      - run: pip install -e .[tests] # incl. ensuring that the previous pip did not overwrite the package
 
       # install devops_tests for tutorials_tests
       - if: matrix.test-suite == 'tutorials_tests'
         run: pip install -r tests/devops_tests/requirements.txt 
 
-      - env:
+      # https://github.com/numba/numba/issues/6350#issuecomment-728174860
+      - if: startsWith(matrix.platform, 'ubuntu-')
+        run: echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV
+
+      - name: Run pytest
+        env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: pytest --durations=10 --timeout=900 --timeout_method=thread -p no:unraisableexception -We tests/${{ matrix.test-suite }}
+          NUMBA_OPT: 1
+        run: |
+          shopt -s extglob
+          pytest --durations=10 --timeout=900 --timeout_method=thread -p no:unraisableexception -We tests/${{ matrix.test-suite }}
 
 #       - if: ${{ failure() }}
 #         uses: mxschmitt/action-tmate@v3
 #         with:
 #           limit-access-to-actor: true
 
+  examples-setup:
+    strategy:
+      matrix:
+        platform: [ubuntu-22.04, macos-12, windows-latest]
+        python-version: ["3.8", "3.11"]
+    runs-on: ${{ matrix.platform }}
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - run: |
+          echo pip_user_site=$(python -c "import sysconfig; print(sysconfig.get_path('purelib'))") >> $GITHUB_ENV
+          echo toml_ci_md5=$(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
+        with:
+          path: ${{ env.pip_user_site }}
+          key: examples_pip_cache-${{ matrix.platform }}-${{ matrix.python-version }}-${{ env.toml_ci_md5 }}
+      - 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 -r tests/devops_tests/requirements.txt
+      - if: steps.cache.outputs.cache-hit != 'true'
+        uses: actions/cache/save@v4
+        with:
+          path: ${{ env.pip_user_site }}
+          key: examples_pip_cache-${{ matrix.platform }}-${{ matrix.python-version }}-${{ env.toml_ci_md5 }}
+
   examples:
-    needs: [pylint, precommit]
+    needs: [pylint, precommit, examples-setup]
     strategy:
       matrix:
         platform: [ubuntu-22.04, macos-12, windows-latest]
         python-version: ["3.8", "3.11"]
-        test-suite: [ "aqueous_chemistry", "freezing", "condensation", "coagulation", "breakup", "multi-process", "isotopes"]
+        test-suite: [ "chemistry_freezing_isotopes", "condensation_a", "condensation_b", "coagulation", "breakup", "multi-process_a", "multi-process_b"]
       fail-fast: false
     runs-on: ${{ matrix.platform }}
+    timeout-minutes: 50
     steps:
       - uses: actions/checkout@v4.1.1
         with:
@@ -192,10 +225,17 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - run: |
-          python -m pip install --upgrade --user pip
+          echo pip_user_site=$(python -c "import sysconfig; print(sysconfig.get_path('purelib'))") >> $GITHUB_ENV
+          echo toml_ci_md5=$(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
       - run: |
-          python -m pip install -e . ./examples
-          python -m pip install -r tests/devops_tests/requirements.txt
+          rm -rf $pip_user_site
+      - id: cache
+        uses: actions/cache/restore@v4
+        with:
+          fail-on-cache-miss: true
+          path: ${{ env.pip_user_site }}
+          key: examples_pip_cache-${{ matrix.platform }}-${{ matrix.python-version }}-${{ env.toml_ci_md5 }}
 
       # https://github.com/numba/numba/issues/6350#issuecomment-728174860
       - if: startsWith(matrix.platform, 'ubuntu-')
@@ -262,19 +302,37 @@ jobs:
   pkg_install_check:
     strategy:
       matrix:
-        platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.11"]
+        platform: [ubuntu-latest, macos-12, macos-14, windows-latest]
+        python-version: ["3.8", "3.11", "system"]
+        exclude:
+          - platform: ubuntu-latest
+            python-version: system
+          - platform: macos-12
+            python-version: system
+          - platform: windows-latest
+            python-version: system
+          - platform: macos-14
+            python-version: "3.8"
+          - platform: macos-14
+            python-version: "3.11"
     runs-on: ${{ matrix.platform }}
     needs: [package]
     steps:
-      - uses: actions/setup-python@v5.0.0
+      - if: matrix.platform != 'macos-14'
+        uses: actions/setup-python@v5.0.0
         with:
           python-version: ${{ matrix.python-version }}
+      - if: matrix.platform == 'macos-14'
+        run: |
+          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
       - uses: actions/download-artifact@v3
         with:
           name: dist
           path: dist     
-      - run: pip install dist/*.whl
+      - run: python -m pip install $PIP_INSTALL_ARGS dist/*.whl
       - run: python -c "import PySDM; print(PySDM.__version__)"
       - run: python -c "import PySDM_examples; print(PySDM_examples.__version__)"
 

{PySDM-2.50 → PySDM-2.53}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.50
+Version: 2.53
 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

{PySDM-2.50 → PySDM-2.53}/PySDM/formulae.py

@@ -34,7 +34,7 @@ class Formulae:  # pylint: disable=too-few-public-methods,too-many-instance-attr
         saturation_vapour_pressure: str = "FlatauWalkoCotton",
         latent_heat: str = "Kirchhoff",
         hygroscopicity: str = "KappaKoehlerLeadingTerms",
-        drop_growth: str = "MaxwellMason",
+        drop_growth: str = "Mason1971",
         surface_tension: str = "Constant",
         diffusion_kinetics: str = "FuchsSutugin",
         diffusion_thermics: str = "Neglect",

{PySDM-2.50 → PySDM-2.53}/PySDM/initialisation/spectra/lognormal.py

@@ -12,6 +12,9 @@ from PySDM.initialisation.impl.spectrum import Spectrum
 
 class Lognormal(Spectrum):
     def __init__(self, norm_factor: float, m_mode: float, s_geom: float):
+        """`norm_factor=1` corresponds to standard normalised probability density,
+        other settings allow to express, e.g., size or mass distributions;
+        `m_mode` is the median value, `s_geom` is the geometric standard deviation"""
         super().__init__(lognorm, (math.log(s_geom), 0, m_mode), norm_factor)
 
     @property

{PySDM-2.50 → PySDM-2.53}/PySDM/physics/constants_defaults.py

@@ -312,7 +312,7 @@ asymmetry_g = 0.85  # forward scattering from cloud droplets
 
 """ TODO #1266 """
 diffussion_thermics_D_G11_A = 1e-5 * si.m**2 / si.s
-diffussion_thermics_D_G11_B = 0.15 / si.K
+diffussion_thermics_D_G11_B = 0.015 / si.K
 diffussion_thermics_D_G11_C = -1.9
 
 diffussion_thermics_K_G11_A = 1.5e-11 * si.W / si.m / si.K**4
@@ -386,3 +386,20 @@ def compute_derived_values(c: dict):
     c["water_molar_volume"] = c["Mv"] / c["rho_w"]
     c["rho_STP"] = c["p_STP"] / c["Rd"] / c["T_STP"]
     c["H_u"] = c["M"] / c["p_STP"]
+
+
+W76W_G0 = -2.9912729e3 * si.K**2
+W76W_G1 = -6.0170128e3 * si.K
+W76W_G2 = 1.887643854e1
+W76W_G3 = -2.8354721e-2 * si.K**-1
+W76W_G4 = 1.7838301e-5 * si.K**-2
+W76W_G5 = -8.4150417e-10 * si.K**-3
+W76W_G6 = 4.4412543e-13 * si.K**-4
+W76W_G7 = 2.858487
+W76W_G8 = 1 * si.Pa
+
+B80W_G0 = 6.112 * si.hPa
+B80W_G1 = 17.67 * si.dimensionless
+B80W_G2 = 243.5 * si.K
+
+one_kelvin = 1 * si.K

{PySDM-2.50 → PySDM-2.53}/PySDM/physics/diffusion_kinetics/__init__.py

@@ -6,4 +6,3 @@ from .fuchs_sutugin import FuchsSutugin
 from .lowe_et_al_2019 import LoweEtAl2019
 from .neglect import Neglect
 from .grabowski_et_al_2011 import GrabowskiEtAl2011
-from .jensen_and_nugent_2017 import JensenAndNugent2017

{PySDM-2.50 → PySDM-2.53}/PySDM/physics/diffusion_thermics/grabowski_et_al_2011.py

@@ -9,12 +9,14 @@ class GrabowskiEtAl2011:
 
     @staticmethod
     def D(const, T, p):  # pylint: disable=unused-argument
+        """eq (10)"""
         return const.diffussion_thermics_D_G11_A * (
             const.diffussion_thermics_D_G11_B * T + const.diffussion_thermics_D_G11_C
         )
 
     @staticmethod
     def K(const, T, p):  # pylint: disable=unused-argument
+        """eq (12)"""
         return (
             const.diffussion_thermics_K_G11_A * T**3
             + const.diffussion_thermics_K_G11_B * T**2

{PySDM-2.50 → PySDM-2.53}/PySDM/physics/drop_growth/__init__.py

@@ -2,4 +2,5 @@
 Formulation of the coupled heat-moisture diffusion problem
 """
 
-from .maxwell_mason import MaxwellMason
+from .mason_1951 import Mason1951
+from .mason_1971 import Mason1971

PySDM-2.53/PySDM/physics/drop_growth/mason_1951.py

@@ -0,0 +1,23 @@
+"""
+single-equation approximation of the vapour and heat diffusion problem
+as derived in [Mason 1951](https://doi.org/10.1088/0370-1301/64/9/307)
+(note that Mason's work did not include the ventilation factor, it
+is included here for code maintainability - to reduce duplication at the
+calling scopes; it is not ignored and is used as a multiplicative factor
+in the same way as in `PySDM.physics.drop_growth.mason_1971.Mason1971`)
+"""
+
+
+class Mason1951:  # pylint: disable=too-few-public-methods
+    def __init__(self, _):
+        pass
+
+    # pylint: disable=too-many-arguments
+    @staticmethod
+    def r_dr_dt(const, RH_eq, T, RH, lv, pvs, D, K, ventilation_factor):
+        return (
+            ventilation_factor
+            * (RH - RH_eq)
+            / const.rho_w
+            / (const.Rv * T / D / pvs + lv**2 / K / T**2 / const.Rv)
+        )

PySDM-2.50/PySDM/physics/drop_growth/maxwell_mason.py → PySDM-2.53/PySDM/physics/drop_growth/mason_1971.py

@@ -1,9 +1,11 @@
 """
 single-equation approximation of the vapour and heat diffusion problem
+as given in eq. 3.11 in [Mason 1971](https://archive.org/details/physicsofclouds0000maso)
+(see also discussion of the ventilation effect on page 125)
 """
 
 
-class MaxwellMason:  # pylint: disable=too-few-public-methods
+class Mason1971:  # pylint: disable=too-few-public-methods
     def __init__(self, _):
         pass
 
@@ -13,8 +15,6 @@ class MaxwellMason:  # pylint: disable=too-few-public-methods
         return (
             ventilation_factor
             * (RH - RH_eq)
-            / (
-                const.rho_w * const.Rv * T / D / pvs
-                + const.rho_w * lv / K / T * (lv / const.Rv / T - 1)
-            )
+            / const.rho_w
+            / (const.Rv * T / D / pvs + lv / K / T * (lv / T / const.Rv - 1))
         )

{PySDM-2.50 → PySDM-2.53}/PySDM/physics/impl/fake_unit_registry.py

@@ -14,6 +14,7 @@ class FakeUnitRegistry:  # pylint: disable=too-few-public-methods
         self.dimensionless = 1.0
         for prefix in ("nano", "micro", "milli", "centi", "", "hecto", "kilo"):
             for unit in (
+                "bar",
                 "metre",
                 "gram",
                 "hertz",
@@ -35,6 +36,7 @@ class FakeUnitRegistry:  # pylint: disable=too-few-public-methods
 
         for prefix in ("n", "u", "m", "c", "", "h", "k"):
             for unit in (
+                "b",
                 "m",
                 "g",
                 "Hz",
@@ -47,7 +49,7 @@ class FakeUnitRegistry:  # pylint: disable=too-few-public-methods
                 "Pa",
                 "l",
                 "h",
-                "bar",
+                "bar",  # note: "b" is barn !!!
                 "N",
                 "W",
             ):

{PySDM-2.50 → PySDM-2.53}/PySDM/physics/saturation_vapour_pressure/__init__.py

@@ -6,3 +6,5 @@ from .august_roche_magnus import AugustRocheMagnus
 from .flatau_walko_cotton import FlatauWalkoCotton
 from .lowe1977 import Lowe1977
 from .murphy_koop_2005 import MurphyKoop2005
+from .wexler_1976 import Wexler1976
+from .bolton_1980 import Bolton1980

PySDM-2.53/PySDM/physics/saturation_vapour_pressure/bolton_1980.py

@@ -0,0 +1,20 @@
+"""
+[Bolton 1980](https://doi.org/10.1175/1520-0493(1980)108<1046:TCOEPT>2.0.CO;2)
+"""
+
+import numpy as np
+
+
+class Bolton1980:
+    def __init__(self, _):
+        pass
+
+    @staticmethod
+    def pvs_Celsius(const, T):
+        """valid for -30 <= T <= 35 C, eq (10)"""
+        return const.B80W_G0 * np.exp((const.B80W_G1 * T) / (T + const.B80W_G2))
+
+    @staticmethod
+    def ice_Celsius(const, T):
+        """NaN with unit of pressure and correct dimension"""
+        return np.nan * T / const.B80W_G2 * const.B80W_G0

PySDM-2.53/PySDM/physics/saturation_vapour_pressure/wexler_1976.py

@@ -0,0 +1,31 @@
+"""
+[Wexler 1976](https://nvlpubs.nist.gov/nistpubs/jres/80A/jresv80An5-6p775_A1b.pdf)
+"""
+
+import numpy as np
+
+
+class Wexler1976:
+    def __init__(self, _):
+        pass
+
+    @staticmethod
+    def pvs_Celsius(const, T):
+        return (
+            np.exp(
+                const.W76W_G0 / (T + const.T0) ** 2
+                + const.W76W_G1 / (T + const.T0)
+                + const.W76W_G2
+                + const.W76W_G3 * (T + const.T0)
+                + const.W76W_G4 * (T + const.T0) ** 2
+                + const.W76W_G5 * (T + const.T0) ** 3
+                + const.W76W_G6 * (T + const.T0) ** 4
+                + const.W76W_G7 * np.log((T + const.T0) / const.one_kelvin)
+            )
+            * const.W76W_G8
+        )
+
+    @staticmethod
+    def ice_Celsius(const, T):
+        """NaN with unit of pressure and correct dimension"""
+        return np.nan * T / const.B80W_G2 * const.B80W_G0

{PySDM-2.50 → PySDM-2.53}/PySDM.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.50
+Version: 2.53
 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