PySDM 2.119__tar.gz → 2.120__tar.gz

{pysdm-2.119 → 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-2.119 → 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-2.119 → 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-2.119 → pysdm-2.120}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysdm
-Version: 2.119
+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-Expression: GPL-3.0-only

{pysdm-2.119 → 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-2.120/examples/PySDM_examples/_HOWTOs/paraview_hello_world.ipynb

@@ -0,0 +1,320 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "a491199946368a38",
+   "metadata": {},
+   "source": [
+    "[![preview notebook](https://img.shields.io/static/v1?label=render%20on&logo=github&color=87ce3e&message=GitHub)](https://github.com/open-atmos/PySDM/blob/main/examples/PySDM_examples/_HOWTOs/paraview_hello_world.ipynb)\n",
+    "[![launch on mybinder.org](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PySDM.git/main?urlpath=lab/tree/examples/PySDM_examples/_HOWTOs/paraview_hello_world.ipynb)\n",
+    "[![launch on Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PySDM/blob/main/examples/PySDM_examples/_HOWTOs/paraview_hello_world.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "35dba30bf42bd326",
+   "metadata": {},
+   "source": [
+    "### TODO #1417 add description\n",
+    "### TODO #1490 fix installation on binder\n",
+    "For more informations about Paraview please refere to [Paraview documentation](https://docs.paraview.org/en/latest/Tutorials/SelfDirectedTutorial/)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "id": "93289adf665b5c7f",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-05-09T08:27:59.767037Z",
+     "start_time": "2025-05-09T08:27:59.763173Z"
+    }
+   },
+   "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",
+   "id": "e3537b5faa81e11f",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-05-09T08:28:06.258130Z",
+     "start_time": "2025-05-09T08:28:00.353771Z"
+    }
+   },
+   "source": [
+    "import os\n",
+    "import subprocess\n",
+    "SUBPROCESS_ENV = os.environ.copy()\n",
+    "\n",
+    "if 'google.colab' in sys.modules:\n",
+    "    !apt-get install -qq ghostscript\n",
+    "    !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\n",
+    "    !tar xzf paraview.tar.gz\n",
+    "    SUBPROCESS_ENV['PATH'] += ':' + subprocess.check_output(['bash', '-c', \"echo `pwd`/`dirname ParaView*/bin/pvpython`\"], text=True)[:-1]\n",
+    "    \n",
+    "    # check if Ghostscript's ps2pdf works\n",
+    "    assert subprocess.check_call(['type', 'ps2pdf'], shell=True) == 0\n",
+    "    \n",
+    "# check if Paraview's pvpython works\n",
+    "assert subprocess.check_call(['pvpython', '--version'], env=SUBPROCESS_ENV) == 0\n",
+    "assert subprocess.check_call(['pvpython', '-c', 'import paraview'], env=SUBPROCESS_ENV) == 0"
+   ],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "paraview version 5.13.1\n"
+     ]
+    }
+   ],
+   "execution_count": 2
+  },
+  {
+   "cell_type": "code",
+   "id": "ee889545",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-05-09T08:28:08.607057Z",
+     "start_time": "2025-05-09T08:28:06.263583Z"
+    }
+   },
+   "source": [
+    "from PySDM_examples.Arabas_et_al_2015 import Settings, SpinUp\n",
+    "from PySDM_examples.Szumowski_et_al_1998 import Simulation, Storage\n",
+    "from PySDM.exporters import VTKExporter\n",
+    "from PySDM_examples.utils import ProgBarController\n",
+    "from PySDM import products as PySDM_products\n",
+    "import PySDM_examples\n",
+    "import glob\n",
+    "import platform\n",
+    "import pathlib"
+   ],
+   "outputs": [],
+   "execution_count": 3
+  },
+  {
+   "cell_type": "code",
+   "id": "f0d2581f",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-05-09T08:28:08.617918Z",
+     "start_time": "2025-05-09T08:28:08.615072Z"
+    }
+   },
+   "source": [
+    "products = [\n",
+    "    PySDM_products.EffectiveRadius(unit='um'),\n",
+    "    PySDM_products.FlowVelocityComponent(component = 0, name = 'cx'),\n",
+    "    PySDM_products.FlowVelocityComponent(component = 1, name = 'cy')\n",
+    "]"
+   ],
+   "outputs": [],
+   "execution_count": 4
+  },
+  {
+   "cell_type": "markdown",
+   "id": "25232d9f",
+   "metadata": {},
+   "source": [
+    "##### 1. run a simulations saving output to VTK files"
+   ]
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "settings = Settings()\n",
+    "storage = Storage()\n",
+    "simulation = Simulation(settings, storage, SpinUp=SpinUp)\n",
+    "simulation.reinit(products)\n",
+    "\n",
+    "vtk_exporter = VTKExporter(path='.')    \n",
+    "\n",
+    "simulation.run(ProgBarController(\"progress:\"), vtk_exporter=vtk_exporter)\n",
+    "vtk_exporter.write_pvd()"
+   ],
+   "id": "c7634bb25cdbbe46"
+  },
+  {
+   "cell_type": "markdown",
+   "id": "066f9c18",
+   "metadata": {},
+   "source": "#### 2. execute ``PySDM_examples/utils/pvanim.py`` script using `pvpython`"
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-05-09T08:52:00.913288Z",
+     "start_time": "2025-05-09T08:51:55.311337Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "pvanim = pathlib.Path(PySDM_examples.__file__).parent / \"utils\" / \"pvanim.py\"\n",
+    "result = subprocess.run([\"pvpython\", str(pvanim), '--help'], check=True, env=SUBPROCESS_ENV)"
+   ],
+   "id": "154ce67d9a84a51d",
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "usage: pvanim.py [-h] [--multiplicity_preset MULTIPLICITY_PRESET]\n",
+      "                 [--multiplicity_logscale]\n",
+      "                 [--effectiveradius_preset EFFECTIVERADIUS_PRESET]\n",
+      "                 [--effectiveradius_logscale]\n",
+      "                 [--effectiveradius_nan_color EFFECTIVERADIUS_NAN_COLOR EFFECTIVERADIUS_NAN_COLOR EFFECTIVERADIUS_NAN_COLOR]\n",
+      "                 [--sd_products_opacity SD_PRODUCTS_OPACITY]\n",
+      "                 [--calculator1_opacity CALCULATOR1_OPACITY]\n",
+      "                 [--sd_attributes_opacity SD_ATTRIBUTES_OPACITY]\n",
+      "                 [--animationframename ANIMATIONFRAMENAME]\n",
+      "                 [--animationname ANIMATIONNAME] [--framerate FRAMERATE]\n",
+      "                 product_path attributes_path output_path\n",
+      "\n",
+      "positional arguments:\n",
+      "  product_path          path to pvd products file\n",
+      "  attributes_path       path to pvd attributes file\n",
+      "  output_path           path where to write output files\n",
+      "\n",
+      "options:\n",
+      "  -h, --help            show this help message and exit\n",
+      "  --multiplicity_preset MULTIPLICITY_PRESET\n",
+      "                        Preset for multiplicity (default: Inferno\n",
+      "                        (matplotlib))\n",
+      "  --multiplicity_logscale\n",
+      "                        Use log scale for multiplicity (default: True)\n",
+      "  --effectiveradius_preset EFFECTIVERADIUS_PRESET\n",
+      "                        Preset for effectiveradius (default: Black, Blue and\n",
+      "                        White)\n",
+      "  --effectiveradius_logscale\n",
+      "                        Use log scale for effectiveradius (default: True)\n",
+      "  --effectiveradius_nan_color EFFECTIVERADIUS_NAN_COLOR EFFECTIVERADIUS_NAN_COLOR EFFECTIVERADIUS_NAN_COLOR\n",
+      "                        Nan color in RGB format for effectiveradius (default:\n",
+      "                        [0.666, 0.333, 1.0])\n",
+      "  --sd_products_opacity SD_PRODUCTS_OPACITY\n",
+      "                        Opacity for sd_products (default: 0.9)\n",
+      "  --calculator1_opacity CALCULATOR1_OPACITY\n",
+      "                        Opacity for calculator1 (default: 0.19)\n",
+      "  --sd_attributes_opacity SD_ATTRIBUTES_OPACITY\n",
+      "                        Opacity for sd_attributes (default: 0.77)\n",
+      "  --animationframename ANIMATIONFRAMENAME\n",
+      "                        Name of the file with animation last frame (default:\n",
+      "                        None)\n",
+      "  --animationname ANIMATIONNAME\n",
+      "                        Name of the file with animation (default: None)\n",
+      "  --framerate FRAMERATE\n",
+      "                        Number of frame rates. (default: 15)\n"
+     ]
+    }
+   ],
+   "execution_count": 10
+  },
+  {
+   "cell_type": "code",
+   "id": "23e0cf61",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-05-09T08:27:54.021909Z",
+     "start_time": "2025-05-09T08:25:42.918680Z"
+    }
+   },
+   "source": [
+    "product = pathlib.Path(\"./output/sd_products.pvd\").absolute()\n",
+    "attributes = pathlib.Path(\"./output/sd_attributes.pvd\").absolute()\n",
+    "\n",
+    "try:\n",
+    "    result = subprocess.run(\n",
+    "        [\n",
+    "            \"pvpython\",\n",
+    "            \"--force-offscreen-rendering\",\n",
+    "            str(pvanim),\n",
+    "            str(product),\n",
+    "            str(attributes),\n",
+    "            str(pathlib.Path('./output').absolute()),\n",
+    "            \"--animationname\", \"docs_intro_animation.ogv\",\n",
+    "            \"--animationframename\", \"last_animation_frame.pdf\"\n",
+    "        ],\n",
+    "        check=platform.system() != \"Windows\",\n",
+    "        capture_output=True,\n",
+    "        text=True,\n",
+    "        env=SUBPROCESS_ENV,\n",
+    "    )\n",
+    "except subprocess.CalledProcessError as e:\n",
+    "    print(e.stderr)\n",
+    "    assert False"
+   ],
+   "outputs": [],
+   "execution_count": 13
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8a95f135",
+   "metadata": {},
+   "source": [
+    "#### 3. reduce file size for generated pdf files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "id": "3e170fdc",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-05-09T08:27:54.022827Z",
+     "start_time": "2025-05-09T08:26:10.268239Z"
+    }
+   },
+   "source": [
+    "if platform.system() != 'Windows':\n",
+    "    for file in glob.glob('output/anim_frame_*.pdf'):\n",
+    "        subprocess.run(['ps2pdf', file, file+'_'], capture_output=True, check=True)\n",
+    "        subprocess.run(['mv', file+'_', file], check=True)"
+   ],
+   "outputs": [],
+   "execution_count": 14
+  },
+  {
+   "cell_type": "code",
+   "id": "9d3e4a35",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-05-09T08:27:54.022911Z",
+     "start_time": "2025-05-09T08:26:10.277448Z"
+    }
+   },
+   "source": [],
+   "outputs": [],
+   "execution_count": null
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "base",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}