PySDM 2.118__tar.gz → 2.120__tar.gz

{pysdm-2.118 → pysdm-2.120}/.github/workflows/pdoc.yml

@@ -26,6 +26,10 @@ jobs:
       - uses: actions/setup-python@v5.0.0
         with:
           python-version: "3.12"
+
+      - name: exclude pvpython scripts
+        run: rm examples/PySDM_examples/utils/pvanim.py
+
       - run: pip install pdoc nbformat gitpython
       - run: pip install -e .
       - run: pip install -e examples

{pysdm-2.118 → pysdm-2.120}/.github/workflows/readme_snippets.yml

@@ -65,14 +65,14 @@ jobs:
       - uses: actions/checkout@v4.1.6
       - uses: actions/setup-python@v5.0.0
         with:
-          python-version: 3.8
+          python-version: 3.9
       - run: pip install -e .
       - run: pip install pytest-codeblocks pytest
       - run: python -c "import pytest_codeblocks; code=pytest_codeblocks.extract_from_file('docs/markdown/pysdm_landing.md'); f=open('readme.m', 'w'); f.writelines(block.code for block in code if block.syntax=='Matlab'); f.close()"
       - run: cat -n readme.m
       - uses: matlab-actions/setup-matlab@v2.1.0
         with:
-          release: R2021a
+          release: R2022a
       - uses: matlab-actions/run-command@v2.1.0
         with:
           command: readme

{pysdm-2.118 → pysdm-2.120}/.github/workflows/tests.yml

@@ -4,6 +4,13 @@ defaults:
   run:
     shell: bash
 
+env:
+  # arbitrarily selected runs for generating animation
+  anim_python-version: '3.12'
+  anim_test-suite: 'multi-process_a'
+  # common options for pytest
+  pytest_options: "--durations=10 -v -s -We -p no:unraisableexception"
+        
 on:
   push:
     branches: [ main ]
@@ -67,7 +74,7 @@ jobs:
       - run: pip install -r tests/devops_tests/requirements.txt
       - env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: pytest --durations=10 -v -s -We -p no:unraisableexception -k "not test_run_notebooks" tests/devops_tests
+        run: pytest  ${{ env.pytest_options }} -k "not test_run_notebooks" tests/devops_tests
 
   zenodo_json:
     runs-on: ubuntu-24.04
@@ -96,7 +103,7 @@ jobs:
         pip install -e .[tests]
         pip install -e ./examples
         pip install pytest-cov
-        pytest --durations=10 -We tests/unit_tests --cov-report=xml --cov=PySDM
+        pytest ${{ env.pytest_options }} tests/unit_tests --cov-report=xml --cov=PySDM
     - uses: codecov/codecov-action@v4.5.0
       with:
         fail_ci_if_error: true
@@ -164,12 +171,7 @@ jobs:
           NUMBA_OPT: 1
         run: |
           shopt -s extglob
-          pytest --durations=10 --timeout=900 --timeout_method=thread -p no:unraisableexception -We tests/${{ matrix.test-suite }}
-
-#       - if: ${{ failure() }}
-#         uses: mxschmitt/action-tmate@v3
-#         with:
-#           limit-access-to-actor: true
+          pytest ${{ env.pytest_options }} --timeout=900 --timeout_method=thread tests/${{ matrix.test-suite }}
 
   examples-setup:
     needs: [nojit_and_codecov]
@@ -245,7 +247,7 @@ jobs:
       - if: startsWith(matrix.platform, 'ubuntu-') && (matrix.test-suite == 'multi-process_a' || matrix.test-suite == 'multi-process_b')
         run: |
           sudo apt-get update
-          sudo apt-get install libegl1 libopengl0 ghostscript
+          sudo apt-get install libegl1 libopengl0 ghostscript ffmpeg
           wget -nv "https://paraview.org/paraview-downloads/download.php?submit=Download&version=v5.13&type=binary&os=Linux&downloadFile=ParaView-5.13.1-egl-MPI-Linux-Python3.10-x86_64.tar.gz" -O paraview.tar.gz
           tar xzf paraview.tar.gz
           echo `pwd`/`dirname ParaView*/bin/pvpython` >> $GITHUB_PATH
@@ -254,7 +256,7 @@ jobs:
         run: |
           brew install --cask paraview
           echo `dirname /Applications/ParaView-*.app/Contents/bin/pvpython | head -1` >> $GITHUB_PATH
-          brew install ghostscript
+          brew install ghostscript ffmpeg
 
       - if: startsWith(matrix.platform, 'windows-') && (matrix.test-suite == 'multi-process_a' || matrix.test-suite == 'multi-process_b')
         run: |
@@ -268,11 +270,45 @@ jobs:
           pvpython -c "from paraview import simple"
 
       - run: |
-          python -m pytest --durations=10 -v -p no:unraisableexception -We tests/examples_tests/test_tests_completeness.py
+          python -m pytest ${{ env.pytest_options }} tests/examples_tests/test_tests_completeness.py
 
-       # TODO #1207
+      # TODO #1207
       - if: startsWith(matrix.platform, 'macos-13')
-        run: python -m pytest --durations=10 -v -p no:unraisableexception -We 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" --suite ${{ matrix.test-suite }}
 
       - if: ( ! startsWith(matrix.platform, 'macos-13') )
-        run: python -m pytest --durations=10 -v -p no:unraisableexception -We tests/examples_tests/test_run* --suite ${{ matrix.test-suite }}
+        run: python -m pytest ${{ env.pytest_options }} --basetemp=/tmp/pytest tests/examples_tests/test_run* --suite ${{ matrix.test-suite }}
+        
+      - if: ( ! startsWith(matrix.platform, 'windows-') ) && matrix.test-suite == env.anim_test-suite && matrix.python-version == env.anim_python-version
+        run: |
+          set -x
+          mkdir -p $HOME/work/_temp/_github_home/figures
+          rm /tmp/pytest/test_run_notebooks_*current
+          ls /tmp/pytest/test_run_notebooks_*/
+          ls /tmp/pytest/test_run_notebooks_*/output/
+          ffmpeg -i /tmp/pytest/test_run_notebooks_*/output/docs_intro_animation.ogv $HOME/work/_temp/_github_home/figures/docs_intro_animation_${{ matrix.platform }}.mp4
+          mv /tmp/pytest/test_run_notebooks_*/output/last_animation_frame.pdf $HOME/work/_temp/_github_home/figures/last_animation_frame_${{ matrix.platform }}.pdf
+          ls $HOME/work/_temp/_github_home/figures
+
+      - name: animation movie upload
+        if: ( ! startsWith(matrix.platform, 'windows-') ) && matrix.test-suite == env.anim_test-suite && matrix.python-version == env.anim_python-version
+        uses: actions/upload-artifact@v4
+        with:
+          name: animation-movie
+          if-no-files-found: error
+          path: ~/work/_temp/_github_home/figures/*.mp4
+
+      - name: animation frame upload
+        if: ( ! startsWith(matrix.platform, 'windows-') ) && matrix.test-suite == env.anim_test-suite && matrix.python-version == env.anim_python-version
+        uses: actions/upload-artifact@v4
+        with:
+          name: animation-frame
+          if-no-files-found: error
+          path: ~/work/_temp/_github_home/figures/*.pdf
+
+      - name: tip release upload
+        if: github.ref == 'refs/heads/main' && ( ! startsWith(matrix.platform, 'windows-') ) && matrix.test-suite == env.anim_test-suite && matrix.python-version == env.anim_python-version
+        uses: eine/tip@master
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          files: /*(home|Users)/runner/work/_temp/_github_home/figures/*.mp4

{pysdm-2.118 → pysdm-2.120}/.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 files: '.py'
 exclude: '.git'
-default_stages: [commit]
+default_stages: [pre-commit]
 
 repos:
   - repo: https://github.com/psf/black

{pysdm-2.118 → pysdm-2.120}/PKG-INFO

@@ -1,16 +1,15 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pysdm
-Version: 2.118
+Version: 2.120
 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: GPL-3.0
+License-Expression: GPL-3.0-only
 Project-URL: Tracker, https://github.com/open-atmos/PySDM/issues
 Project-URL: Documentation, https://open-atmos.github.io/PySDM
 Project-URL: Source, https://github.com/open-atmos/PySDM
 Keywords: physics-simulation,monte-carlo-simulation,gpu-computing,atmospheric-modelling,particle-system,numba,thrust,nvrtc,pint,atmospheric-physics
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering
@@ -38,6 +37,9 @@ Requires-Dist: open-atmos-jupyter-utils>=v1.2.0; extra == "tests"
 Requires-Dist: pyrcel; extra == "tests"
 Requires-Dist: jupyter-core<5.0.0; extra == "tests"
 Requires-Dist: ipywidgets!=8.0.3; extra == "tests"
+Dynamic: license-file
+Dynamic: provides-extra
+Dynamic: requires-dist
 
 # <img src="https://raw.githubusercontent.com/open-atmos/PySDM/main/docs/logos/pysdm_logo.svg" width=100 height=146 alt="pysdm logo">
 

{pysdm-2.118 → pysdm-2.120}/docs/templates/index.html.jinja2

@@ -32,7 +32,7 @@
         <h2>What is PySDM?</h2>
         <p>
             <video controls style="float:right; width:40%">
-                <source src="https://github.com/open-atmos/PySDM/wiki/files/animation_save.mp4" type="video/mp4">
+                <source src="https://github.com/open-atmos/PySDM/releases/download/tip/docs_intro_animation_ubuntu-24.04.mp4" type="video/mp4">
                 Your browser does not support the video tag.
             </video>
             PySDM is a package for simulating the <mark>dynamics of population of particles undergoing diffusional and collisional growth (and breakage)</mark>.

{pysdm-2.118 → pysdm-2.120}/examples/PySDM_examples/Bolin_1958/table_1.ipynb

@@ -14,10 +14,13 @@
    "cell_type": "markdown",
    "id": "bb84c52c57a729ec",
    "metadata": {},
-   "source": "### based on Table 1 from B.Bolin 1958 \"On the use of tritium as a tracer for water in nature\" (https://digitallibrary.un.org/record/3892725)"
+   "source": [
+    "### based on Table 1 from B.Bolin 1958 \"On the use of tritium as a tracer for water in nature\" (https://digitallibrary.un.org/record/3892725)"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 1,
    "id": "5e4e58050cc01f64",
    "metadata": {
     "ExecuteTime": {
@@ -25,18 +28,18 @@
      "start_time": "2024-12-05T21:30:20.209298Z"
     }
    },
+   "outputs": [],
    "source": [
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
     "    !pip --quiet install open-atmos-jupyter-utils\n",
     "    from open_atmos_jupyter_utils import pip_install_on_colab\n",
     "    pip_install_on_colab('PySDM-examples')"
-   ],
-   "outputs": [],
-   "execution_count": 1
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 8,
    "id": "95f360dc62f373f9",
    "metadata": {
     "ExecuteTime": {
@@ -44,17 +47,18 @@
      "start_time": "2024-12-05T21:30:20.218383Z"
     }
    },
+   "outputs": [],
    "source": [
     "import numpy as np\n",
     "import pandas\n",
     "from PySDM.physics import in_unit, si\n",
-    "from PySDM import Formulae"
-   ],
-   "outputs": [],
-   "execution_count": 2
+    "from PySDM import Formulae\n",
+    "from IPython.display import display"
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": 3,
    "id": "e29a92d6680c4e51",
    "metadata": {
     "ExecuteTime": {
@@ -62,92 +66,24 @@
      "start_time": "2024-12-05T21:30:21.687254Z"
     }
    },
-   "source": "radii = np.asarray([0.005, 0.01, 0.025, 0.05, 0.075, 0.1, 0.15, 0.20]) * si.cm",
    "outputs": [],
-   "execution_count": 3
+   "source": [
+    "radii = np.asarray([0.005, 0.01, 0.025, 0.05, 0.075, 0.1, 0.15, 0.20]) * si.cm"
+   ]
   },
   {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "314f42c310883cfa",
    "metadata": {
     "ExecuteTime": {
      "end_time": "2024-12-05T21:30:24.420354Z",
      "start_time": "2024-12-05T21:30:21.698737Z"
     }
    },
-   "cell_type": "code",
-   "source": [
-    "formulae = Formulae(\n",
-    "    terminal_velocity='RogersYau',\n",
-    "    drop_growth='Mason1951',\n",
-    "    diffusion_thermics='Neglect',\n",
-    "    saturation_vapour_pressure='AugustRocheMagnus',\n",
-    "    ventilation='Froessling1938',\n",
-    "    particle_shape_and_density='LiquidSpheres',\n",
-    "    air_dynamic_viscosity='ZografosEtAl1987',\n",
-    "    constants={'BOLIN_ISOTOPE_TIMESCALE_COEFF_C1': 1.63},\n",
-    "    isotope_relaxation_timescale='Bolin1958',\n",
-    ")\n",
-    "const = formulae.constants\n",
-    "any_non_zero_value = 44.\n",
-    "temperature = const.T0 + 10 * si.K\n",
-    "pressure = const.p_STP\n",
-    "pvs = formulae.saturation_vapour_pressure.pvs_water(temperature)\n",
-    "v_term = formulae.terminal_velocity.v_term(radii)\n",
-    "eta_air=formulae.air_dynamic_viscosity.eta_air(temperature)\n",
-    "D=formulae.diffusion_thermics.D(T=temperature, p=pressure)\n",
-    "\n",
-    "air_density = pressure/const.Rd/temperature\n",
-    "assert abs(air_density - 1)/air_density <.3\n",
-    "Re = formulae.particle_shape_and_density.reynolds_number(\n",
-    "     radius=radii,\n",
-    "     velocity_wrt_air=v_term,\n",
-    "     dynamic_viscosity=eta_air,\n",
-    "     density=air_density,\n",
-    ")\n",
-    "Sc = formulae.trivia.air_schmidt_number(\n",
-    "    dynamic_viscosity=eta_air, \n",
-    "    diffusivity=D, \n",
-    "    density=air_density,\n",
-    ")\n",
-    "F = formulae.ventilation.ventilation_coefficient(sqrt_re_times_cbrt_sc=Re**(1/2) * Sc**(1/3))\n",
-    "\n",
-    "r_dr_dt = formulae.drop_growth.r_dr_dt(\n",
-    "    RH_eq=1,\n",
-    "    T=temperature,\n",
-    "    RH=0,\n",
-    "    lv=0,\n",
-    "    pvs=pvs,\n",
-    "    D=D,\n",
-    "    K=any_non_zero_value,\n",
-    "    ventilation_factor=F\n",
-    ")\n",
-    "adjustment_time = formulae.isotope_relaxation_timescale.tau(radius = radii, r_dr_dt = r_dr_dt)\n",
-    "\n",
-    "\n",
-    "pandas.options.display.float_format = '{:>,.2g}'.format\n",
-    "data = pandas.DataFrame({\n",
-    "    'radius [cm]': in_unit(radii, si.cm),\n",
-    "    'adjustment time [s]': adjustment_time,\n",
-    "    'terminal velocity [m/s]': v_term,\n",
-    "    'distance [m]': v_term * adjustment_time,\n",
-    "})\n",
-    "\n",
-    "data # pylint: disable=pointless-statement"
-   ],
-   "id": "314f42c310883cfa",
    "outputs": [
     {
      "data": {
-      "text/plain": [
-       "   radius [cm]  adjustment time [s]  terminal velocity [m/s]  distance [m]\n",
-       "0        0.005                  1.7                      0.4          0.69\n",
-       "1         0.01                  5.4                      0.8           4.3\n",
-       "2        0.025                   20                        2            40\n",
-       "3         0.05                   48                        4       1.9e+02\n",
-       "4        0.075                   81                      5.5       4.4e+02\n",
-       "5          0.1              1.2e+02                      6.4       7.6e+02\n",
-       "6         0.15                2e+02                      7.8       1.6e+03\n",
-       "7          0.2                3e+02                        9       2.7e+03"
-      ],
       "text/html": [
        "<div>\n",
        "<style scoped>\n",
@@ -233,14 +169,90 @@
        "  </tbody>\n",
        "</table>\n",
        "</div>"
+      ],
+      "text/plain": [
+       "   radius [cm]  adjustment time [s]  terminal velocity [m/s]  distance [m]\n",
+       "0        0.005                  1.7                      0.4          0.69\n",
+       "1         0.01                  5.4                      0.8           4.3\n",
+       "2        0.025                   20                        2            40\n",
+       "3         0.05                   48                        4       1.9e+02\n",
+       "4        0.075                   81                      5.5       4.4e+02\n",
+       "5          0.1              1.2e+02                      6.4       7.6e+02\n",
+       "6         0.15                2e+02                      7.8       1.6e+03\n",
+       "7          0.2                3e+02                        9       2.7e+03"
       ]
      },
-     "execution_count": 4,
      "metadata": {},
-     "output_type": "execute_result"
+     "output_type": "display_data"
     }
    ],
-   "execution_count": 4
+   "source": [
+    "formulae = Formulae(\n",
+    "    terminal_velocity='RogersYau',\n",
+    "    drop_growth='Mason1951',\n",
+    "    diffusion_thermics='Neglect',\n",
+    "    saturation_vapour_pressure='AugustRocheMagnus',\n",
+    "    ventilation='Froessling1938',\n",
+    "    particle_shape_and_density='LiquidSpheres',\n",
+    "    air_dynamic_viscosity='ZografosEtAl1987',\n",
+    "    constants={'BOLIN_ISOTOPE_TIMESCALE_COEFF_C1': 1.63},\n",
+    "    isotope_relaxation_timescale='Bolin1958',\n",
+    ")\n",
+    "const = formulae.constants\n",
+    "any_non_zero_value = 44.\n",
+    "temperature = const.T0 + 10 * si.K\n",
+    "pressure = const.p_STP\n",
+    "pvs = formulae.saturation_vapour_pressure.pvs_water(temperature)\n",
+    "v_term = formulae.terminal_velocity.v_term(radii)\n",
+    "eta_air=formulae.air_dynamic_viscosity.eta_air(temperature)\n",
+    "D=formulae.diffusion_thermics.D(T=temperature, p=pressure)\n",
+    "\n",
+    "air_density = pressure/const.Rd/temperature\n",
+    "assert abs(air_density - 1)/air_density <.3\n",
+    "Re = formulae.particle_shape_and_density.reynolds_number(\n",
+    "     radius=radii,\n",
+    "     velocity_wrt_air=v_term,\n",
+    "     dynamic_viscosity=eta_air,\n",
+    "     density=air_density,\n",
+    ")\n",
+    "Sc = formulae.trivia.air_schmidt_number(\n",
+    "    dynamic_viscosity=eta_air, \n",
+    "    diffusivity=D, \n",
+    "    density=air_density,\n",
+    ")\n",
+    "F = formulae.ventilation.ventilation_coefficient(sqrt_re_times_cbrt_sc=Re**(1/2) * Sc**(1/3))\n",
+    "\n",
+    "r_dr_dt = formulae.drop_growth.r_dr_dt(\n",
+    "    RH_eq=1,\n",
+    "    T=temperature,\n",
+    "    RH=0,\n",
+    "    lv=0,\n",
+    "    pvs=pvs,\n",
+    "    D=D,\n",
+    "    K=any_non_zero_value,\n",
+    "    ventilation_factor=F\n",
+    ")\n",
+    "adjustment_time = formulae.isotope_relaxation_timescale.tau(radius = radii, r_dr_dt = r_dr_dt)\n",
+    "\n",
+    "\n",
+    "pandas.options.display.float_format = '{:>,.2g}'.format\n",
+    "data = pandas.DataFrame({\n",
+    "    'radius [cm]': in_unit(radii, si.cm),\n",
+    "    'adjustment time [s]': adjustment_time,\n",
+    "    'terminal velocity [m/s]': v_term,\n",
+    "    'distance [m]': v_term * adjustment_time,\n",
+    "})\n",
+    "\n",
+    "display(data)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0bef57bc-7e19-4a3f-8f77-6ec762e8f236",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -259,7 +271,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.6"
+   "version": "3.9.2"
   }
  },
  "nbformat": 4,

{pysdm-2.118 → pysdm-2.120}/examples/PySDM_examples/Pyrcel/simulation.py

@@ -91,7 +91,9 @@ class Simulation(BasicSimulation):
                 attr[drop_id].append(attr_data[drop_id])
         super()._save(output)
 
-    def run(self):
+    def run(self, observers=()):
+        for observer in observers:
+            self.particulator.observers.append(observer)
         output_products = super()._run(
             self.settings.nt, self.settings.steps_per_output_interval
         )