PySDM 2.78__tar.gz → 2.80__tar.gz

{PySDM-2.78 → PySDM-2.80}/.github/workflows/readme_snippets.yml

@@ -16,32 +16,20 @@ jobs:
   python:
     strategy:
       matrix:
-        platform: [ubuntu-latest, macos-12, macos-14, windows-latest]
+        platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
     runs-on: ${{ matrix.platform }}
     steps:
       - uses: actions/checkout@v4.1.6
-      - if: matrix.platform != 'macos-14'
-        uses: actions/setup-python@v5.0.0
+      - uses: actions/setup-python@v5.0.0
         with:
-          python-version: 3.9
-      - 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 packaging # Python 3.12 workaround  
+          python-version: "3.10"
       - 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()"
+          python -c "import os,pytest_codeblocks; code=pytest_codeblocks.extract_from_file('docs/markdown/pysdm_landing.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: |
+      - run: |
           python -We readme.py
           sed -i -e 's/CPU/GPU/g' readme.py
           python -We readme.py
@@ -60,10 +48,10 @@ jobs:
       - uses: actions/checkout@v4.1.6
       - uses: actions/setup-python@v5.0.0
         with:
-          python-version: 3.9
+          python-version: "3.10"
       - run: pip install -e .
       - run: pip install pytest-codeblocks pytest
-      - run: python -c "import pytest_codeblocks; code=pytest_codeblocks.extract_from_file('README.md'); f=open('readme.jl', 'w'); f.writelines(block.code for block in code if block.syntax=='Julia'); f.close()"
+      - run: python -c "import pytest_codeblocks; code=pytest_codeblocks.extract_from_file('docs/markdown/pysdm_landing.md'); f=open('readme.jl', 'w'); f.writelines(block.code for block in code if block.syntax=='Julia'); f.close()"
       - uses: julia-actions/setup-julia@v1.9.6
       - run: cat -n readme.jl
       - run: julia readme.jl
@@ -79,7 +67,7 @@ jobs:
           python-version: 3.8
       - run: pip install -e .
       - run: pip install pytest-codeblocks pytest
-      - run: python -c "import pytest_codeblocks; code=pytest_codeblocks.extract_from_file('README.md'); f=open('readme.m', 'w'); f.writelines(block.code for block in code if block.syntax=='Matlab'); f.close()"
+      - 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:

{PySDM-2.78 → PySDM-2.80}/.github/workflows/tests+artifacts+pypi.yml

@@ -40,7 +40,7 @@ jobs:
       with:
         submodules: recursive
         fetch-depth: 0
-    - uses: actions/setup-python@master
+    - uses: actions/setup-python@v5.0.0
       with:
         python-version: 3.9
     - name: Generate coverage report
@@ -58,7 +58,7 @@ jobs:
   pdoc:
     strategy:
       matrix:
-        platform: [ubuntu-latest, macos-12, windows-latest]
+        platform: [ubuntu-latest, macos-13, windows-latest]
     runs-on: ${{ matrix.platform }}
     steps:
       - uses: actions/checkout@v4.1.6
@@ -69,10 +69,18 @@ jobs:
         with:
           python-version: 3.9
       - run: |
-          pip install pdoc
+          pip install pdoc nbformat
           pip install -e .
           pip install -e examples
-          PDOC_ALLOW_EXEC=1 python -We -m pdoc -o html PySDM examples/PySDM_examples -t pdoc_templates
+          
+          python - <<EOF
+          import glob, nbformat
+          for notebook_path in glob.glob('examples/PySDM_examples/*/*.ipynb'):
+            with open(notebook_path, encoding="utf8") as fin:
+              with open(notebook_path + ".badges.md", 'w') as fout:
+                fout.write(nbformat.read(fin, nbformat.NO_CONVERT).cells[0].source)
+          EOF
+          PDOC_ALLOW_EXEC=1 python -We -m pdoc -o html PySDM examples/PySDM_examples -t docs/templates --math --mermaid
       - if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' }}
         uses: JamesIves/github-pages-deploy-action@4.1.1
         with:
@@ -86,7 +94,7 @@ jobs:
     - uses: actions/checkout@v4.1.6
       with:
         submodules: recursive
-        fetch-depth: 0 
+        fetch-depth: 0
     - name: Set up Python 3.9
       uses: actions/setup-python@v5.0.0
       with:
@@ -114,7 +122,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4.1.6
       - uses: notiz-dev/github-action-json-property@release
-        with: 
+        with:
           path: '.zenodo.json'
           prop_path: 'creators'
 
@@ -122,12 +130,23 @@ jobs:
     needs: [pdoc, nojit_and_codecov, zenodo_json]
     strategy:
       matrix:
-        platform: [ubuntu-latest, macos-12, windows-latest]
+        platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
         python-version: ["3.9", "3.11"]
         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:
+          - platform: "macos-14"
+            python-version: "3.9"
           - test-suite: "devops_tests"
             python-version: "3.9"
+          # TODO #1406
+          - platform: "macos-14"
+            test-suite: "smoke_tests/box"
+          - platform: "macos-14"
+            test-suite: "smoke_tests/parcel_a"
+          - platform: "macos-14"
+            test-suite: "smoke_tests/kinematic_2d"
+          - platform: "macos-14"
+            test-suite: "unit_tests/!(dynamics)"
       fail-fast: false
     runs-on: ${{ matrix.platform }}
     timeout-minutes: ${{ startsWith(matrix.platform, 'windows-') && 40 || 25 }}
@@ -148,11 +167,13 @@ jobs:
       - if: startsWith(matrix.test-suite, 'smoke_tests') || matrix.test-suite == 'tutorials_tests'
         run: pip install -e ./examples
 
-      - run: pip install -e .[tests] # incl. ensuring that the previous pip did not overwrite the package
+      # incl. ensuring that the previous pip did not overwrite the package
+      - run: |
+          pip install --only-binary :all: -e .[tests]
 
       # install devops_tests for tutorials_tests
       - if: matrix.test-suite == 'tutorials_tests'
-        run: pip install -r tests/devops_tests/requirements.txt 
+        run: pip install -r tests/devops_tests/requirements.txt
 
       # https://github.com/numba/numba/issues/6350#issuecomment-728174860
       - if: startsWith(matrix.platform, 'ubuntu-')
@@ -175,7 +196,7 @@ jobs:
     needs: [nojit_and_codecov]
     strategy:
       matrix:
-        platform: [ubuntu-22.04, macos-12, windows-latest]
+        platform: [ubuntu-24.04, macos-13, windows-latest]
         python-version: ["3.9", "3.11"]
     runs-on: ${{ matrix.platform }}
     steps:
@@ -183,7 +204,7 @@ jobs:
         with:
           submodules: recursive
           fetch-depth: 0
-      - uses: actions/setup-python@v1
+      - uses: actions/setup-python@v5.0.0
         with:
           python-version: ${{ matrix.python-version }}
       - run: |
@@ -211,12 +232,12 @@ jobs:
     needs: [examples-setup]
     strategy:
       matrix:
-        platform: [ubuntu-22.04, macos-12, windows-latest]
+        platform: [ubuntu-24.04, macos-13, windows-latest]
         python-version: ["3.9", "3.11"]
         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: ${{ startsWith(matrix.platform, 'windows-') && 65 || 50 }}
+    timeout-minutes: ${{ !startsWith(matrix.platform, 'ubuntu-') && 65 || 50 }}
     steps:
       - uses: actions/checkout@v4.1.6
         with:
@@ -242,16 +263,29 @@ jobs:
       - if: startsWith(matrix.platform, 'ubuntu-')
         run: echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV
 
-      - if: startsWith(matrix.platform, 'ubuntu-')
+      - if: startsWith(matrix.platform, 'ubuntu-') && matrix.test-suite == 'multi-process_a'
         run: |
-          sudo apt-get update
-          sudo apt-get install python3-paraview
-      - if: startsWith(matrix.platform, 'macos-')
+          sudo apt-get install libegl1 libopengl0 ghostscript
+          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
+          
+      - if: startsWith(matrix.platform, 'macos-') && matrix.test-suite == 'multi-process_a'
         run: |
           brew install --cask paraview
           echo `dirname /Applications/ParaView-*.app/Contents/bin/pvpython | head -1` >> $GITHUB_PATH
-      - if: matrix.platform != 'windows-latest'
-        run: pvpython --version
+          brew install ghostscript
+
+      - if: startsWith(matrix.platform, 'windows-') && matrix.test-suite == 'multi-process_a'
+        run: |
+          curl "https://www.paraview.org/paraview-downloads/download.php?submit=Download&version=v5.13&type=binary&os=Windows&downloadFile=ParaView-5.13.1-Windows-Python3.10-msvc2017-AMD64.msi" -o paraview.msi
+          msiexec //i paraview.msi //quiet //qn //norestart 
+          echo "C:\\Program Files\\ParaView 5.13.1\\bin\\" >> $GITHUB_PATH
+
+      - if: matrix.test-suite == 'multi-process_a'
+        run: |
+          pvpython --version
+          pvpython -c "from paraview import simple"
 
       - env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -266,7 +300,7 @@ jobs:
         with:
           submodules: recursive
           fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
-      - run: pip install -r tests/devops_tests/requirements.txt
+      - run: pip install -r tests/devops_tests/requirements.txt "flexparser<0.4"
       - env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: pytest --durations=10 -v -s -We -p no:unraisableexception -k "not test_run_notebooks" tests/devops_tests
@@ -303,37 +337,22 @@ jobs:
   pkg_install_check:
     strategy:
       matrix:
-        platform: [ubuntu-latest, macos-12, macos-14, windows-latest]
-        python-version: ["3.9", "3.11", "system"]
+        platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
+        python-version: ["3.9", "3.11"]
         exclude:
-          - platform: ubuntu-latest
-            python-version: system
-          - platform: macos-12
-            python-version: system
-          - platform: windows-latest
-            python-version: system
           - platform: macos-14
             python-version: "3.9"
-          - platform: macos-14
-            python-version: "3.11"
     runs-on: ${{ matrix.platform }}
     needs: [package]
     steps:
-      - if: matrix.platform != 'macos-14'
-        uses: actions/setup-python@v5.0.0
+      - 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 packaging
       - uses: actions/download-artifact@v4
         with:
           pattern: dist-*
           merge-multiple: true
-          path: dist     
+          path: dist
       - 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__)"
@@ -351,12 +370,14 @@ jobs:
           path: dist
 
       - if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-        uses: pypa/gh-action-pypi-publish@unstable/v1
+        uses: pypa/gh-action-pypi-publish@release/v1.12
         with:
+          attestations: false
           repository_url: https://test.pypi.org/legacy/
           packages-dir: dist
 
       - if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@unstable/v1
+        uses: pypa/gh-action-pypi-publish@release/v1.12
         with:
+          attestations: false
           packages-dir: dist

{PySDM-2.78 → PySDM-2.80}/.zenodo.json

@@ -58,6 +58,11 @@
       "name": "Mackay, J. Ben",
       "orcid": "0000-0001-8677-3562"
     },
+    {
+      "affiliation": "AGH University of Krakow, Poland",
+      "name": "Magnuszewski, Paweł",
+      "orcid": "0009-0007-9269-6795"
+    },
     {
       "affiliation": "California Institute of Technology, Pasadena, CA, USA",
       "name": "Mints, Mikhail"

PySDM-2.80/PKG-INFO

@@ -0,0 +1,194 @@
+Metadata-Version: 2.1
+Name: PySDM
+Version: 2.80
+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
+Author-email: sylwester.arabas@agh.edu.pl
+License: GPL-3.0
+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
+Description: # <img src="https://raw.githubusercontent.com/open-atmos/PySDM/main/.github/pysdm_logo.png" width=100 height=146 alt="pysdm logo">
+        
+        [![Python 3](https://img.shields.io/static/v1?label=Python&logo=Python&color=3776AB&message=3)](https://www.python.org/)
+        [![LLVM](https://img.shields.io/static/v1?label=LLVM&logo=LLVM&color=gold&message=Numba)](https://numba.pydata.org)
+        [![CUDA](https://img.shields.io/static/v1?label=CUDA&logo=nVidia&color=87ce3e&message=ThrustRTC)](https://pypi.org/project/ThrustRTC/)
+        [![Linux OK](https://img.shields.io/static/v1?label=Linux&logo=Linux&color=yellow&message=%E2%9C%93)](https://en.wikipedia.org/wiki/Linux)
+        [![macOS OK](https://img.shields.io/static/v1?label=macOS&logo=Apple&color=silver&message=%E2%9C%93)](https://en.wikipedia.org/wiki/macOS)
+        [![Windows OK](https://img.shields.io/static/v1?label=Windows&logo=Windows&color=white&message=%E2%9C%93)](https://en.wikipedia.org/wiki/Windows)
+        [![Jupyter](https://img.shields.io/static/v1?label=Jupyter&logo=Jupyter&color=f37626&message=%E2%9C%93)](https://jupyter.org/)
+        [![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://github.com/open-atmos/PySDM/graphs/commit-activity)
+        [![OpenHub](https://www.openhub.net/p/atmos-cloud-sim-uj-PySDM/widgets/project_thin_badge?format=gif)](https://www.openhub.net/p/atmos-cloud-sim-uj-PySDM)
+        [![status](https://joss.theoj.org/papers/62cad07440b941f73f57d187df1aa6e9/status.svg)](https://joss.theoj.org/papers/62cad07440b941f73f57d187df1aa6e9)
+        [![DOI](https://zenodo.org/badge/199064632.svg)](https://zenodo.org/badge/latestdoi/199064632)    
+        [![EU Funding](https://img.shields.io/static/v1?label=EU%20Funding%20by&color=103069&message=FNP&logoWidth=25&logo=image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAC4AAAAeCAYAAABTwyyaAAAEzklEQVRYw9WYS2yUVRiGn3P5ZzozpZ3aUsrNgoKlKBINmkhpCCwwxIAhsDCpBBIWhmCMMYTEhSJ4i9EgBnSBEm81MRrFBhNXEuUSMCopiRWLQqEGLNgr085M5//POS46NNYFzHQ6qGc1i5nzP/P973m/9ztCrf7A8T9csiibCocUbvTzfxLcAcaM3cY3imXz25lT3Y34G7gQYAKV3+bFAHcATlBTPogJNADG92iY28FHW97kyPbnuW/W7xgzAhukQ9xe04PJeOT0HkQRwK0TlEeGWb/kOO9v3kdD3a8YK9GhDMfa6mg9fxunOm/lWPtcpDI4K7n/jnN8+uQbrFrUSiwU/DtSEUB/MsKKBT+zYslJqiYNgVE4JwhHkzy86wlWvrKVWDSZ/YFjZlU39yw4y/rGoyQGowWB67zl4QQue+jssMdXrQvZ/00jyeHwqCgDKwnsiJjSvkYAxsG5K9WsenYbJdqAtAjhCIxCSZt/4fK1w5A2WCvxrUAKCHwNVoA2aGmvq11jJQQapEXrgMBKqmJJugejKGWLIxXrBPFoigfv/omd675gRkU/xgqUDlAhH3UDaAAlLSqUQekAYyVTyhLs3tDMsvntlIYzOFcEcOcEGd9jx9oDbGs6QO0t/Tijxi9S4bhzxiWaVh5m94Zm0n7oui4ybo0raUlcncQnxx+g+WgDF/vLoYDmoqSl/dJUnt7XRCoTZjij0Z6Pc2LiNS4EBBkNvoeOJXN+yPWWSZeANOhwJq/98nKVwNdoL8B5AROxBKBL0gjh8DMhdCh3eJnrA0yqhLpplwmyup6IajvAOIGfKGVx3VmCRGnOMpe5QAdG0bT8CAeeep0d6z6nqjSJnQiZWEllLMWrmz6k+fE9rGk8MVqYgsGv5ZH2i1Opr+9kajzB5d74hKQ+KS3d/WVMLhtgdu1lriRiOR/4nDVunaR24x7qp3UV5Cb/fJvC83nv26W81LIK58SYNFmwq4hsGx/5BwKlzYRma2NUthgOJSew4i7ru9nJYCQF5tApb2yvjiDQKJV/IfJKh0o6qssSLKv/jcAoRKHQQzE2Lj2OMV5OkWFc4MZIpsev8uXWXRx6ZicbGk8QZLxxgwe+x/rlR3h3816+f2E7lbEU+ZDn3vKVpePCdFovzCISHqbl5EIoQOteKMPB1rto65zNyfOz+KOrGl06lHPQyi/WOohH0/T0l1MZH6A3GUEKl7Pmr2la6wBrBWWRDP2DUcqjKVKBGom9RZmABAykwnglafpSJSPQvsfiOR0EQ7ExVmazA8cY6N4K1iw6RdAXRwi4mgrheT5Dvs4LeuS81a15Ll/3dQisFVSVpnj7sf1sX/sZvhAc+6UOrQyBVUQ8gx/orFmDsZqtaw/y1qZ9zKjp5vDpenyjcNe+cLNmTiUdf/bEOddVQ0VpgsOn54ET+EYxvWKALSu+5tGG76it7MNaiZKGQ23zCIcMfUMxBnrjN3fmHHvCAlp+vJcXWx6itqoXpAEnUNLx8iMfo5Xh1i17R3PJYCpC2cZ3qK3sQ8WGEDDuXlAQuFKGHzpmopXhTNfk0bmxs7uC1w6uJul79AxFkMIiBJy5UoUWjrZLU5DCFdTARDHuDqVw+OkSwI0MCEW4gtNF2BPrBCo8fKNbtILWX9aUDqFqHnn7AAAAAElFTkSuQmCC)](https://www.fnp.org.pl/en/)
+        [![PL Funding](https://img.shields.io/static/v1?label=PL%20Funding%20by&color=d21132&message=NCN&logoWidth=25&logo=image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABQAAAANCAYAAACpUE5eAAAABmJLR0QA/wD/AP+gvaeTAAAAKUlEQVQ4jWP8////fwYqAiZqGjZqIHUAy4dJS6lqIOMdEZvRZDPcDQQAb3cIaY1Sbi4AAAAASUVORK5CYII=)](https://www.ncn.gov.pl/?language=en)
+        [![US Funding](https://img.shields.io/static/v1?label=US%20DOE%20Funding%20by&color=267c32&message=ASR&logoWidth=25&logo=image/png;base64,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)](https://asr.science.energy.gov/)
+        
+        [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html)
+        
+        [![Github Actions Build Status](https://github.com/open-atmos/PySDM/workflows/tests+artifacts+pypi/badge.svg?branch=main)](https://github.com/open-atmos/PySDM/actions)
+        [![Appveyor Build status](http://ci.appveyor.com/api/projects/status/github/open-atmos/PySDM?branch=main&svg=true)](https://ci.appveyor.com/project/slayoo/pysdm/branch/main)
+        [![Coverage Status](https://codecov.io/gh/open-atmos/PySDM/branch/main/graph/badge.svg)](https://app.codecov.io/gh/open-atmos/PySDM)    
+        [![PyPI version](https://badge.fury.io/py/PySDM.svg)](https://pypi.org/project/PySDM)
+        [![API docs](https://shields.mitmproxy.org/badge/docs-pdoc.dev-brightgreen.svg)](https://open-atmos.github.io/PySDM/)
+        
+        PySDM is a package for simulating the dynamics of population of particles. 
+        It is intended to serve as a building block for simulation systems modelling
+          fluid flows involving a dispersed phase,
+          with PySDM being responsible for representation of the dispersed phase.
+        Currently, the development is focused on atmospheric cloud physics
+          applications, in particular on modelling the dynamics of particles immersed in moist air 
+          using the particle-based (a.k.a. super-droplet) approach 
+          to represent aerosol/cloud/rain microphysics.
+        The package features a Pythonic high-performance implementation of the 
+          Super-Droplet Method (SDM) Monte-Carlo algorithm for representing collisional growth 
+          ([Shima et al. 2009](https://rmets.onlinelibrary.wiley.com/doi/abs/10.1002/qj.441)), hence the name. 
+        
+        There is a growing set of example Jupyter notebooks exemplifying how to perform 
+          various types of calculations and simulations using PySDM.
+        Most of the example notebooks reproduce results and plot from literature, see below for 
+          a list of examples and links to the notebooks (which can be either executed or viewed 
+          "in the cloud").
+        
+        There are also a growing set of [tutorials](https://github.com/open-atmos/PySDM/tree/main/tutorials), also in the form of Jupyter notebooks.
+        These tutorials are intended for teaching purposes and include short explanations of cloud microphysical 
+          concepts paired with widgets for running interactive simulations using PySDM.
+        Each tutorial also comes with a set of questions at the end that can be used as homework problems.
+        Like the examples, these tutorials can be executed or viewed "in the cloud" making it an especially 
+          easy way for students to get started.
+        
+        PySDM has two alternative parallel number-crunching backends 
+          available: multi-threaded CPU backend based on [Numba](http://numba.pydata.org/) 
+          and GPU-resident backend built on top of [ThrustRTC](https://pypi.org/project/ThrustRTC/).
+        The [`Numba`](https://open-atmos.github.io/PySDM/PySDM/backends/numba.html) backend (aliased ``CPU``) features multi-threaded parallelism for 
+          multi-core CPUs, it uses the just-in-time compilation technique based on the LLVM infrastructure.
+        The [`ThrustRTC`](https://open-atmos.github.io/PySDM/PySDM/backends/thrust_rtc.html) backend (aliased ``GPU``) offers GPU-resident operation of PySDM
+          leveraging the [SIMT](https://en.wikipedia.org/wiki/Single_instruction,_multiple_threads) 
+          parallelisation model. 
+        Using the ``GPU`` backend requires nVidia hardware and [CUDA driver](https://developer.nvidia.com/cuda-downloads).
+        
+        For an overview of PySDM features (and the preferred way to cite PySDM in papers), please refer to our JOSS papers:
+        - [Bartman et al. 2022](https://doi.org/10.21105/joss.03219) (PySDM v1).
+        - [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 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://pdoc.dev/) documentation of PySDM public API is maintained at: [https://open-atmos.github.io/PySDM](https://open-atmos.github.io/PySDM) 
+        
+        ## Example Jupyter notebooks (reproducing results from literature):
+        
+        See [PySDM-examples README](https://github.com/open-atmos/PySDM/blob/main/examples/README.md).
+        
+        ![animation](https://github.com/open-atmos/PySDM/wiki/files/kinematic_2D_example.gif)
+        
+        ## Dependencies and Installation
+        
+        PySDM dependencies are: [Numpy](https://numpy.org/), [Numba](http://numba.pydata.org/), [SciPy](https://scipy.org/), 
+        [Pint](https://pint.readthedocs.io/), [chempy](https://pypi.org/project/chempy/), 
+        [pyevtk](https://pypi.org/project/pyevtk/),
+        [ThrustRTC](https://fynv.github.io/ThrustRTC/) and [CURandRTC](https://github.com/fynv/CURandRTC).
+        
+        To install PySDM using ``pip``, use: ``pip install PySDM`` 
+        (or ``pip install git+https://github.com/open-atmos/PySDM.git`` to get updates
+        beyond the latest release).
+        
+        Conda users may use ``pip`` as well, see the [Installing non-conda packages](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-pkgs.html#installing-non-conda-packages) section in the conda docs. Dependencies of PySDM are available at the following conda channels:
+        - numba: [numba](https://anaconda.org/numba/numba)
+        - conda-forge: [pyevtk](https://anaconda.org/conda-forge/pyevtk), [pint](https://anaconda.org/conda-forge/pint) and []()
+        - fyplus: [ThrustRTC](https://anaconda.org/fyplus/thrustrtc), [CURandRTC](https://anaconda.org/fyplus/curandrtc)
+        - bjodah: [chempy](https://anaconda.org/bjodah/chempy)
+        - nvidia: [cudatoolkit](https://anaconda.org/nvidia/cudatoolkit)
+        
+        For development purposes, we suggest cloning the repository and installing it using ``pip -e``.
+        Test-time dependencies can be installed with ``pip -e .[tests]``.
+        
+        PySDM examples constitute the [``PySDM-examples``](https://github.com/open-atmos/PySDM-examples) package.
+        The examples have additional dependencies listed in [``PySDM_examples`` package ``setup.py``](https://github.com/open-atmos/PySDM/blob/main/examples/setup.py) file.
+        Running the example Jupyter notebooks requires the ``PySDM_examples`` package to be installed.
+        The suggested install and launch steps are:
+        ```
+        git clone https://github.com/open-atmos/PySDM.git
+        pip install -e PySDM
+        pip install -e PySDM/examples
+        jupyter-notebook PySDM/examples/PySDM_examples
+        ```
+        Alternatively, one can also install the examples package from pypi.org by 
+        using ``pip install PySDM-examples`` (note that this does not apply to notebooks itself,
+        only the supporting .py files).
+        
+        ## Contributing, reporting issues, seeking support 
+        
+        #### Our technologicial stack:   
+        [![Python 3](https://img.shields.io/static/v1?label=+&logo=Python&color=darkred&message=Python)](https://www.python.org/)
+        [![Numba](https://img.shields.io/static/v1?label=+&logo=Numba&color=orange&message=Numba)](https://numba.pydata.org)
+        [![LLVM](https://img.shields.io/static/v1?label=+&logo=LLVM&color=gold&message=LLVM)](https://llvm.org)
+        [![CUDA](https://img.shields.io/static/v1?label=+&logo=nVidia&color=darkgreen&message=ThrustRTC/CUDA)](https://pypi.org/project/ThrustRTC/)
+        [![NumPy](https://img.shields.io/static/v1?label=+&logo=numpy&color=blue&message=NumPy)](https://numpy.org/)
+        [![pytest](https://img.shields.io/static/v1?label=+&logo=pytest&color=purple&message=pytest)](https://pytest.org/)   
+        [![Colab](https://img.shields.io/static/v1?label=+&logo=googlecolab&color=darkred&message=Colab)](https://colab.research.google.com/)
+        [![Codecov](https://img.shields.io/static/v1?label=+&logo=codecov&color=orange&message=Codecov)](https://codecov.io/)
+        [![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:///)
+        
+        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
+        from the continuous integration setup which automates execution of tests 
+        with the newly added code. 
+        
+        Code contributions are assumed to imply transfer of copyright.
+        Should there be a need to make an exception, please indicate it when creating
+        a pull request or contributing code in any other way. In any case, 
+        the license of the contributed code must be compatible with GPL v3.
+        
+        Developing the code, we follow [The Way of Python](https://www.python.org/dev/peps/pep-0020/) and 
+        the [KISS principle](https://en.wikipedia.org/wiki/KISS_principle).
+        The codebase has greatly benefited from [PyCharm code inspections](https://www.jetbrains.com/help/pycharm/code-inspection.html)
+        and [Pylint](https://pylint.org), [Black](https://black.readthedocs.io/en/stable/) and [isort](https://pycqa.github.io/isort/)
+        code analysis (which are all part of the CI workflows).
+        
+        We also use [pre-commit hooks](https://pre-commit.com). 
+        In our case, the hooks modify files and re-format them.
+        The pre-commit hooks can be run locally, and then the resultant changes need to be staged before committing.
+        To set up the hooks locally, install pre-commit via `pip install pre-commit` and
+        set up the git hooks via `pre-commit install` (this needs to be done every time you clone the project).
+        To run all pre-commit hooks, run `pre-commit run --all-files`.
+        The `.pre-commit-config.yaml` file can be modified in case new hooks are to be added or
+          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).
+        
+        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).
+        Feature requests are recorded in the "Ideas..." [PySDM wiki page](https://github.com/open-atmos/PySDM/wiki/Ideas-for-new-features-and-examples).
+        
+        We encourage to use the [GitHub Discussions](https://github.com/open-atmos/PySDM/discussions) feature
+        (rather than the issue tracker) for seeking support in understanding, using and extending PySDM code.
+        
+        We look forward to your contributions and feedback.
+        
+        ## Licensing:
+        
+        copyright: [Jagiellonian University](https://en.uj.edu.pl/en) (2019-2023) & [AGH University of Krakow](https://agh.edu.pl/en) (2023-...)    
+        licence: [GPL v3](https://www.gnu.org/licenses/gpl-3.0.html)
+        
+          
+        
+Keywords: physics-simulation,monte-carlo-simulation,gpu-computing,atmospheric-modelling,particle-system,numba,thrust,nvrtc,pint,atmospheric-physics
+Platform: UNKNOWN
+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
+Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Software Development :: Libraries
+Description-Content-Type: text/markdown
+Provides-Extra: tests

PySDM-2.80/PySDM/__init__.py

@@ -0,0 +1,20 @@
+# pylint:disable=invalid-name
+"""
+.. include:: ../docs/markdown/pysdm_landing.md
+"""
+
+from importlib.metadata import PackageNotFoundError, version
+
+from PySDM.attributes.impl.attribute_registry import register_attribute
+
+from . import attributes
+from . import environments, exporters, products
+from .builder import Builder
+from .formulae import Formulae
+from .particulator import Particulator
+
+try:
+    __version__ = version(__name__)
+except PackageNotFoundError:
+    # package is not installed
+    pass

{PySDM-2.78 → PySDM-2.80}/PySDM/attributes/ice/cooling_rate.py

@@ -21,6 +21,9 @@ class CoolingRate(DerivedAttribute):
         builder.particulator.observers.append(self)
 
     def notify(self):
+        """triggers update to ensure recalculation is done before
+        overwriting `self.prev_T` with current temperature"""
+        self.update()
         cell_id = self.particulator.attributes["cell id"]
         self.prev_T[:] = self.particulator.environment["T"][cell_id]
 

{PySDM-2.78 → PySDM-2.80}/PySDM/backends/numba.py

@@ -43,9 +43,10 @@ class Numba(  # pylint: disable=too-many-ancestors,duplicate-code
 
         parallel_default = True
         if platform.machine() == "arm64":
-            warnings.warn(
-                "Disabling Numba threading due to ARM64 CPU (atomics do not work yet)"
-            )
+            if "CI" not in os.environ:
+                warnings.warn(
+                    "Disabling Numba threading due to ARM64 CPU (atomics do not work yet)"
+                )
             parallel_default = False  # TODO #1183 - atomics don't work on ARM64!
 
         try: