Merge branch 'main' into products-implementation

.github/workflows/projects.yml

@@ -4,7 +4,7 @@ on:
   issues:
     types:
       - opened
-  pull_request:
+  pull_request_target:
     types:
       - opened
 

.github/workflows/pypi.yml

@@ -32,7 +32,9 @@ jobs:
 
       - run: pip install twine build
 
-      - run: |
+      - name: run python -m build to generate wheel files, check for warnings
+        run: |
+          set -x
           unset CI
           cd ${{ matrix.packages-dir }}
           python -m build 2>&1 | tee build.log
@@ -41,7 +43,11 @@ jobs:
             | grep -v "version of {dist_name} already set" \
             | grep -v -E "UserWarning: version of PySDM(-examples)? already set" \
             | wc -l`
-          twine check --strict dist/*
+      - run: twine check --strict ${{ matrix.packages-dir }}/dist/*
+      - name: check if version string does not contain PyPI-incompatible + char 
+        run: |
+          set -x
+          [ `ls ${{ matrix.packages-dir }}/dist | fgrep + | tee /dev/stderr | wc -l` -ne 0 ] && exit 1 || echo OK
 
       - uses: actions/upload-artifact@v4
         with:

.github/workflows/tests.yml

@@ -14,7 +14,7 @@ on:
 
 jobs:
   precommit:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/[email protected]
       - uses: actions/[email protected]
@@ -29,7 +29,7 @@ jobs:
         run: git diff
 
   pylint:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
     - uses: actions/[email protected]
       with:
@@ -58,7 +58,7 @@ jobs:
         nbqa pylint --unsafe-load-any-extension=y --disable=fixme,duplicate-code,invalid-name,trailing-whitespace,line-too-long,missing-function-docstring,wrong-import-position,missing-module-docstring,wrong-import-order,ungrouped-imports,no-member,too-many-locals,unnecessary-lambda-assignment $(git ls-files '*.ipynb')
 
   devops:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/[email protected]
         with:
@@ -70,7 +70,7 @@ jobs:
         run: pytest --durations=10 -v -s -We -p no:unraisableexception -k "not test_run_notebooks" tests/devops_tests
 
   zenodo_json:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/[email protected]
       - uses: notiz-dev/github-action-json-property@release
@@ -80,7 +80,7 @@ jobs:
 
   nojit_and_codecov:
     needs: [precommit, pylint, devops, zenodo_json]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     env:
       NUMBA_DISABLE_JIT: 1
     steps:
@@ -107,9 +107,9 @@ jobs:
     needs: [nojit_and_codecov]
     strategy:
       matrix:
-        platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
+        platform: [ubuntu-24.04, macos-13, macos-14, windows-latest]
         python-version: ["3.9", "3.12"]
-        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"]
+        test-suite: ["unit_tests/!(dynamics)", "unit_tests/dynamics/!(collisions)", "unit_tests/dynamics/collisions", "smoke_tests/no_env", "smoke_tests/box", "smoke_tests/parcel_a", "smoke_tests/parcel_b", "smoke_tests/parcel_c", "smoke_tests/parcel_d", "smoke_tests/kinematic_1d", "smoke_tests/kinematic_2d", "tutorials_tests"]
         exclude:
           - platform: "macos-14"
             python-version: "3.9"
@@ -120,13 +120,15 @@ jobs:
             test-suite: "smoke_tests/box"
           - platform: "macos-14"
             test-suite: "smoke_tests/parcel_a"
+          - platform: "macos-14"
+            test-suite: "smoke_tests/parcel_d"
           - 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 || 40 }}
+    timeout-minutes: ${{ startsWith(matrix.platform, 'windows-') && 35 || 30 }}
     steps:
       - uses: actions/[email protected]
         with:
@@ -211,10 +213,10 @@ jobs:
       matrix:
         platform: [ubuntu-24.04, macos-13, windows-latest]
         python-version: ["3.9", "3.12"]
-        test-suite: [ "chemistry_freezing_isotopes", "condensation_a", "condensation_b", "coagulation", "breakup", "multi-process_a", "multi-process_b"]
+        test-suite: [ "chemistry_freezing", "isotopes", "condensation_a", "condensation_b", "condensation_c", "coagulation", "breakup", "multi-process_a", "multi-process_b", "multi-process_c", "multi-process_d", "multi-process_e"]
       fail-fast: false
     runs-on: ${{ matrix.platform }}
-    timeout-minutes: ${{ !startsWith(matrix.platform, 'ubuntu-') && 65 || 50 }}
+    timeout-minutes: 35
     steps:
       - uses: actions/[email protected]
         with:
@@ -240,26 +242,27 @@ jobs:
       - if: startsWith(matrix.platform, 'ubuntu-')
         run: echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV
 
-      - if: startsWith(matrix.platform, 'ubuntu-') && matrix.test-suite == 'multi-process_a'
+      - 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
           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'
+      - if: startsWith(matrix.platform, 'macos-') && (matrix.test-suite == 'multi-process_a' || matrix.test-suite == 'multi-process_b')
         run: |
           brew install --cask paraview
           echo `dirname /Applications/ParaView-*.app/Contents/bin/pvpython | head -1` >> $GITHUB_PATH
           brew install ghostscript
 
-      - if: startsWith(matrix.platform, 'windows-') && matrix.test-suite == 'multi-process_a'
+      - if: startsWith(matrix.platform, 'windows-') && (matrix.test-suite == 'multi-process_a' || matrix.test-suite == 'multi-process_b')
         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'
+      - if: matrix.test-suite == (matrix.test-suite == 'multi-process_a' || matrix.test-suite == 'multi-process_b')
         run: |
           pvpython --version
           pvpython -c "from paraview import simple"

PySDM/products/displacement/flow_velocity_component.py

@@ -1,6 +1,5 @@
 """
-reports on the maximum Courant field value for each cell (maximum of
-absolute values of Courant number on all edges of a cell)
+reports on the flow velocity
 """
 
 import numpy as np

examples/PySDM_examples/Abade_and_Albuquerque_2024/fig_2.ipynb

@@ -6,8 +6,8 @@
    "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/Abade_and_Albuquerque_2024/fig_2.ipynb)\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PySDM.git/main?urlpath=lab/tree/examples/PySDM_examples/Abade_and_Albuquerque_2024/fig_2.ipynb)\n",
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PySDM/blob/main/examples/PySDM_examples/Abade_and_Albuquerque_2024/fig_2.ipynb)"
+    "[![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/Abade_and_Albuquerque_2024/fig_2.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/Abade_and_Albuquerque_2024/fig_2.ipynb)"
    ]
   },
   {
@@ -23,18 +23,23 @@
    ]
   },
   {
-   "metadata": {},
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-12-06T10:37:52.672366Z",
+     "start_time": "2024-12-06T10:37:52.668120Z"
+    }
+   },
    "cell_type": "code",
-   "outputs": [],
-   "execution_count": null,
    "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')"
    ],
-   "id": "aa876f2db21bb522"
+   "id": "aa876f2db21bb522",
+   "outputs": [],
+   "execution_count": 1
   },
   {
    "cell_type": "code",

examples/PySDM_examples/Abdul_Razzak_Ghan_2000/fig_4_kinetic_limitations.ipynb

@@ -4,8 +4,8 @@
    "cell_type": "markdown",
    "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/Abdul_Razzak_Ghan_2000/fig_4_kinetic_limitations.ipynb)\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PySDM.git/main?urlpath=lab/tree/examples/PySDM_examples/Abdul_Razzak_Ghan_2000/fig_4_kinetic_limitations.ipynb)\n",
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PySDM/blob/main/examples/PySDM_examples/Abdul_Razzak_Ghan_2000/fig_4_kinetic_limitations.ipynb)"
+    "[![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/Abdul_Razzak_Ghan_2000/fig_4_kinetic_limitations.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/Abdul_Razzak_Ghan_2000/fig_4_kinetic_limitations.ipynb)"
    ],
    "metadata": {
     "collapsed": false
@@ -25,18 +25,23 @@
    ]
   },
   {
-   "metadata": {},
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-12-06T10:38:02.660871Z",
+     "start_time": "2024-12-06T10:38:02.649799Z"
+    }
+   },
    "cell_type": "code",
-   "outputs": [],
-   "execution_count": null,
    "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')"
    ],
-   "id": "f52cbd092d056ba6"
+   "id": "f52cbd092d056ba6",
+   "outputs": [],
+   "execution_count": 1
   },
   {
    "cell_type": "code",

examples/PySDM_examples/Abdul_Razzak_Ghan_2000/figs1-5.ipynb

@@ -6,8 +6,8 @@
    "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/Abdul_Razzak_Ghan_2000/figs1-5.ipynb)\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PySDM.git/main?urlpath=lab/tree/examples/PySDM_examples/Abdul_Razzak_Ghan_2000/figs1-5.ipynb)\n",
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PySDM/blob/main/examples/PySDM_examples/Abdul_Razzak_Ghan_2000/figs1-5.ipynb)"
+    "[![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/Abdul_Razzak_Ghan_2000/figs1-5.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/Abdul_Razzak_Ghan_2000/figs1-5.ipynb)"
    ]
   },
   {

examples/PySDM_examples/Alpert_and_Knopf_2016/fig_1.ipynb

@@ -5,8 +5,8 @@
    "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/Alpert_and_Knopf_2016/fig_1.ipynb)\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PySDM.git/main?urlpath=lab/tree/examples/PySDM_examples/Alpert_and_Knopf_2016/fig_1.ipynb)\n",
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PySDM/blob/main/examples/PySDM_examples/Alpert_and_Knopf_2016/fig_1.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/Alpert_and_Knopf_2016/fig_1.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/Alpert_and_Knopf_2016/fig_1.ipynb)"
    ]
   },
   {

examples/PySDM_examples/Alpert_and_Knopf_2016/fig_2.ipynb

@@ -10,8 +10,8 @@
    },
    "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/Alpert_and_Knopf_2016/fig_2.ipynb)\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PySDM.git/main?urlpath=lab/tree/examples/PySDM_examples/Alpert_and_Knopf_2016/fig_2.ipynb)\n",
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PySDM/blob/main/examples/PySDM_examples/Alpert_and_Knopf_2016/fig_2.ipynb)"
+    "[![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/Alpert_and_Knopf_2016/fig_2.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/Alpert_and_Knopf_2016/fig_2.ipynb)"
    ]
   },
   {

examples/PySDM_examples/Alpert_and_Knopf_2016/fig_3.ipynb

@@ -5,8 +5,8 @@
    "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/Alpert_and_Knopf_2016/fig_3.ipynb)\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PySDM.git/main?urlpath=lab/tree/examples/PySDM_examples/Alpert_and_Knopf_2016/fig_3.ipynb)\n",
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PySDM/blob/main/examples/PySDM_examples/Alpert_and_Knopf_2016/fig_3.ipynb)"
+    "[![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/Alpert_and_Knopf_2016/fig_3.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/Alpert_and_Knopf_2016/fig_3.ipynb)"
    ]
   },
   {

examples/PySDM_examples/Alpert_and_Knopf_2016/fig_4.ipynb

@@ -5,8 +5,8 @@
    "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/Alpert_and_Knopf_2016/fig_4.ipynb)\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PySDM.git/main?urlpath=lab/tree/examples/PySDM_examples/Alpert_and_Knopf_2016/fig_4.ipynb)\n",
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PySDM/blob/main/examples/PySDM_examples/Alpert_and_Knopf_2016/fig_4.ipynb)"
+    "[![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/Alpert_and_Knopf_2016/fig_4.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/Alpert_and_Knopf_2016/fig_4.ipynb)"
    ]
   },
   {

examples/PySDM_examples/Alpert_and_Knopf_2016/fig_5.ipynb

@@ -5,8 +5,8 @@
    "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/Alpert_and_Knopf_2016/fig_5.ipynb)\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PySDM.git/main?urlpath=lab/tree/examples/PySDM_examples/Alpert_and_Knopf_2016/fig_5.ipynb)\n",
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PySDM/blob/main/examples/PySDM_examples/Alpert_and_Knopf_2016/fig_5.ipynb)"
+    "[![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/Alpert_and_Knopf_2016/fig_5.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/Alpert_and_Knopf_2016/fig_5.ipynb)"
    ]
   },
   {

examples/PySDM_examples/Arabas_and_Shima_2017/fig_5.ipynb

@@ -4,9 +4,9 @@
    "cell_type": "markdown",
    "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/Arabas_and_Shima_2017/fig_5.ipynb) \n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/PySDM.git/main?urlpath=lab/tree/examples/PySDM_examples/Arabas_and_Shima_2017/fig_5.ipynb)    \n",
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/PySDM/blob/main/examples/PySDM_examples/Arabas_and_Shima_2017/fig_5.ipynb)"
+    "[![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/Arabas_and_Shima_2017/fig_5.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/Arabas_and_Shima_2017/fig_5.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/Arabas_and_Shima_2017/fig_5.ipynb)"
    ]
   },
   {