PySDM 2.88__tar.gz → 2.90__tar.gz

pysdm-2.90/.github/workflows/pdoc.yml

@@ -0,0 +1,47 @@
+name: pdoc
+
+defaults:
+  run:
+    shell: bash
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  schedule:
+    - cron: '0 13 * * 4'
+
+jobs:
+  pdoc:
+    strategy:
+      matrix:
+        platform: [ ubuntu-latest, macos-13, windows-latest ]
+    runs-on: ${{ matrix.platform }}
+    steps:
+      - uses: actions/checkout@v4.1.6
+        with:
+          submodules: recursive
+          persist-credentials: false
+      - uses: actions/setup-python@v5.0.0
+        with:
+          python-version: "3.12"
+      - run: |
+          pip install pdoc nbformat
+          pip install -e .
+          pip install -e examples
+
+          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:
+          branch: pdoc
+          folder: html
+          clean: true

pysdm-2.90/.github/workflows/projects.yml

@@ -0,0 +1,19 @@
+name: Add new issues and pull requests to project board
+
+on:
+  issues:
+    types:
+      - opened
+  pull_request:
+    types:
+      - opened
+
+jobs:
+  add-to-project:
+    name: Add to project
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/add-to-project@v1.0.2
+        with:
+          project-url: https://github.com/orgs/open-atmos/projects/6
+          github-token: ${{ secrets.ADD_TO_PROJECT_PAT }}

pysdm-2.90/.github/workflows/pypi.yml

@@ -0,0 +1,97 @@
+name: pypi
+
+defaults:
+  run:
+    shell: bash
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  schedule:
+    - cron: '0 13 * * 4'
+  release:
+    types: [published]
+
+jobs:
+  package:
+    strategy:
+      matrix:
+        packages-dir: [ ".", "examples" ]
+      fail-fast: false
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4.1.6
+        with:
+          submodules: recursive
+          fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
+      - uses: actions/setup-python@v5.0.0
+        with:
+          python-version: "3.12"
+
+      - run: pip install twine build
+
+      - run: |
+          unset CI
+          cd ${{ matrix.packages-dir }}
+          python -m build 2>&1 | tee build.log
+          exit `fgrep -i warning build.log | grep -v impl_numba/warnings.py \
+            | grep -v "no previously-included files matching" \
+            | grep -v "version of {dist_name} already set" \
+            | grep -v -E "UserWarning: version of PySDM(-examples)? already set" \
+            | wc -l`
+          twine check --strict dist/*
+
+      - uses: actions/upload-artifact@v4
+        with:
+          path: ${{ matrix.packages-dir }}/dist
+          name: dist-${{ matrix.packages-dir }}
+
+  pkg_install_check:
+    strategy:
+      matrix:
+        platform: [ ubuntu-latest, macos-13, macos-14, windows-latest ]
+        python-version: [ "3.9", "3.12" ]
+        exclude:
+          - platform: macos-14
+            python-version: "3.9"
+    runs-on: ${{ matrix.platform }}
+    needs: [ package ]
+    steps:
+      - uses: actions/setup-python@v5.0.0
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: dist-*
+          merge-multiple: true
+          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__)"
+
+  publish:
+    runs-on: ubuntu-latest
+    needs: [ package, pkg_install_check ]
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: dist-*
+          merge-multiple: true
+          path: dist
+
+      - if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        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@release/v1.12
+        with:
+          attestations: false
+          packages-dir: dist

pysdm-2.88/.github/workflows/tests+artifacts+pypi.yml → pysdm-2.90/.github/workflows/tests.yml

@@ -1,4 +1,4 @@
-name: tests+artifacts+pypi
+name: tests
 
 defaults:
   run:
@@ -11,8 +11,6 @@ on:
     branches: [ main ]
   schedule:
     - cron: '0 13 * * 4'
-  release:
-    types: [published]
 
 jobs:
   precommit:
@@ -30,64 +28,6 @@ jobs:
       - if: ${{ failure() }}
         run: git diff
 
-  nojit_and_codecov:
-    needs: [precommit, pylint, devops]
-    runs-on: ubuntu-latest
-    env:
-      NUMBA_DISABLE_JIT: 1
-    steps:
-    - uses: actions/checkout@v4.1.6
-      with:
-        submodules: recursive
-        fetch-depth: 0
-    - uses: actions/setup-python@v5.0.0
-      with:
-        python-version: 3.9
-    - name: Generate coverage report
-      run: |
-        pip install -e .[tests]
-        pip install -e ./examples
-        pip install pytest-cov
-        pytest --durations=10 -We tests/unit_tests --cov-report=xml --cov=PySDM
-    - uses: codecov/codecov-action@v4.5.0
-      with:
-        fail_ci_if_error: true
-        verbose: true
-        token: ${{ secrets.CODECOV_TOKEN }}
-
-  pdoc:
-    strategy:
-      matrix:
-        platform: [ubuntu-latest, macos-13, windows-latest]
-    runs-on: ${{ matrix.platform }}
-    steps:
-      - uses: actions/checkout@v4.1.6
-        with:
-          submodules: recursive
-          persist-credentials: false
-      - uses: actions/setup-python@v5.0.0
-        with:
-          python-version: "3.12"
-      - run: |
-          pip install pdoc nbformat
-          pip install -e .
-          pip install -e examples
-          
-          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:
-          BRANCH: pdoc
-          FOLDER: html
-          CLEAN: true
-
   pylint:
     runs-on: ubuntu-latest
     steps:
@@ -117,6 +57,18 @@ jobs:
         # TODO #682
         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
+    steps:
+      - uses: actions/checkout@v4.1.6
+        with:
+          submodules: recursive
+          fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
+      - 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
+
   zenodo_json:
     runs-on: ubuntu-latest
     steps:
@@ -126,8 +78,33 @@ jobs:
           path: '.zenodo.json'
           prop_path: 'creators'
 
+  nojit_and_codecov:
+    needs: [precommit, pylint, devops, zenodo_json]
+    runs-on: ubuntu-latest
+    env:
+      NUMBA_DISABLE_JIT: 1
+    steps:
+    - uses: actions/checkout@v4.1.6
+      with:
+        submodules: recursive
+        fetch-depth: 0
+    - uses: actions/setup-python@v5.0.0
+      with:
+        python-version: 3.9
+    - name: Generate coverage report
+      run: |
+        pip install -e .[tests]
+        pip install -e ./examples
+        pip install pytest-cov
+        pytest --durations=10 -We tests/unit_tests --cov-report=xml --cov=PySDM
+    - uses: codecov/codecov-action@v4.5.0
+      with:
+        fail_ci_if_error: true
+        verbose: true
+        token: ${{ secrets.CODECOV_TOKEN }}
+
   tests:
-    needs: [pdoc, nojit_and_codecov, zenodo_json]
+    needs: [nojit_and_codecov]
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
@@ -149,7 +126,7 @@ jobs:
             test-suite: "unit_tests/!(dynamics)"
       fail-fast: false
     runs-on: ${{ matrix.platform }}
-    timeout-minutes: ${{ startsWith(matrix.platform, 'windows-') && 40 || 25 }}
+    timeout-minutes: ${{ startsWith(matrix.platform, 'windows-') && 40 || 40 }}
     steps:
       - uses: actions/checkout@v4.1.6
         with:
@@ -209,7 +186,7 @@ jobs:
           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 \
+          echo toml_ci_md5=$(cat pyproject.toml setup.py examples/pyproject.toml examples/setup.py tests/devops_tests/requirements.txt .github/workflows/tests.yml \
           | python -c "import hashlib;print(hashlib.md5(open(0,'rb').read()).hexdigest())") >> $GITHUB_ENV
       - uses: actions/cache@v4
         id: cache
@@ -248,7 +225,7 @@ jobs:
           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 \
+          echo toml_ci_md5=$(cat pyproject.toml setup.py examples/pyproject.toml examples/setup.py tests/devops_tests/requirements.txt .github/workflows/tests.yml \
           | python -c "import hashlib;print(hashlib.md5(open(0,'rb').read()).hexdigest())") >> $GITHUB_ENV
       - run: |
           rm -rf $pip_user_site
@@ -292,96 +269,3 @@ jobs:
         run: |
           python -m pytest --durations=10 -v -p no:unraisableexception -We tests/examples_tests/test_tests_completeness.py
           python -m pytest --durations=10 -v -p no:unraisableexception -We tests/examples_tests/test_run* --suite ${{ matrix.test-suite }}
-
-  devops:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4.1.6
-        with:
-          submodules: recursive
-          fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
-      - 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
-
-  package:
-    strategy:
-      matrix:
-        packages-dir: [".", "examples"]
-      fail-fast: false
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4.1.6
-        with:
-          submodules: recursive
-          fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
-      - uses: actions/setup-python@v5.0.0
-        with:
-          python-version: "3.12"
-
-      - run: pip install twine build
-
-      - run: |
-          unset CI
-          cd ${{ matrix.packages-dir }}
-          python -m build 2>&1 | tee build.log
-          exit `fgrep -i warning build.log | grep -v impl_numba/warnings.py \
-            | grep -v "no previously-included files matching" \
-            | grep -v "version of {dist_name} already set" \
-            | grep -v -E "UserWarning: version of PySDM(-examples)? already set" \
-            | wc -l`
-          twine check --strict dist/*
-
-      - uses: actions/upload-artifact@v4
-        with:
-          path: ${{ matrix.packages-dir }}/dist
-          name: dist-${{ matrix.packages-dir }}
-
-  pkg_install_check:
-    strategy:
-      matrix:
-        platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
-        python-version: ["3.9", "3.12"]
-        exclude:
-          - platform: macos-14
-            python-version: "3.9"
-    runs-on: ${{ matrix.platform }}
-    needs: [package]
-    steps:
-      - uses: actions/setup-python@v5.0.0
-        with:
-          python-version: ${{ matrix.python-version }}
-      - uses: actions/download-artifact@v4
-        with:
-          pattern: dist-*
-          merge-multiple: true
-          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__)"
-
-  publish:
-    runs-on: ubuntu-latest
-    needs: [tests, examples, package, pkg_install_check]
-    permissions:
-      id-token: write
-    steps:
-      - uses: actions/download-artifact@v4
-        with:
-          pattern: dist-*
-          merge-multiple: true
-          path: dist
-
-      - if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-        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@release/v1.12
-        with:
-          attestations: false
-          packages-dir: dist

{pysdm-2.88 → pysdm-2.90}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.88
+Version: 2.90
 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
@@ -38,7 +38,7 @@ Requires-Dist: pyrcel; extra == "tests"
 Requires-Dist: jupyter-core<5.0.0; extra == "tests"
 Requires-Dist: ipywidgets!=8.0.3; extra == "tests"
 
-# <img src="https://raw.githubusercontent.com/open-atmos/PySDM/main/.github/pysdm_logo.png" width=100 height=146 alt="pysdm logo">
+# <img src="https://raw.githubusercontent.com/open-atmos/PySDM/main/docs/logos/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)
@@ -75,6 +75,8 @@ 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. 
 
+PySDM documentation is maintained at: [https://open-atmos.github.io/PySDM](https://open-atmos.github.io/PySDM) 
+
 There is a growing set of [example Jupyter notebooks](https://open-atmos.github.io/PySDM/PySDM_examples.html) 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 
@@ -105,14 +107,6 @@ For an overview of PySDM features (and the preferred way to cite PySDM in papers
 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/), 

{pysdm-2.88 → pysdm-2.90}/PySDM.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.88
+Version: 2.90
 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
@@ -38,7 +38,7 @@ Requires-Dist: pyrcel; extra == "tests"
 Requires-Dist: jupyter-core<5.0.0; extra == "tests"
 Requires-Dist: ipywidgets!=8.0.3; extra == "tests"
 
-# <img src="https://raw.githubusercontent.com/open-atmos/PySDM/main/.github/pysdm_logo.png" width=100 height=146 alt="pysdm logo">
+# <img src="https://raw.githubusercontent.com/open-atmos/PySDM/main/docs/logos/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)
@@ -75,6 +75,8 @@ 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. 
 
+PySDM documentation is maintained at: [https://open-atmos.github.io/PySDM](https://open-atmos.github.io/PySDM) 
+
 There is a growing set of [example Jupyter notebooks](https://open-atmos.github.io/PySDM/PySDM_examples.html) 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 
@@ -105,14 +107,6 @@ For an overview of PySDM features (and the preferred way to cite PySDM in papers
 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/), 

{pysdm-2.88 → pysdm-2.90}/PySDM.egg-info/SOURCES.txt

@@ -12,14 +12,15 @@ setup.py
 .binder/postBuild
 .binder/requirements.txt
 .github/dependabot.yml
-.github/pysdm_logo.png
-.github/pysdm_logo.svg
 .github/workflows/cancel.yml
 .github/workflows/joss.yml
 .github/workflows/joss_paper.yml
+.github/workflows/pdoc.yml
+.github/workflows/projects.yml
+.github/workflows/pypi.yml
 .github/workflows/readme_snippets.yml
 .github/workflows/stale.yml
-.github/workflows/tests+artifacts+pypi.yml
+.github/workflows/tests.yml
 PySDM/__init__.py
 PySDM/builder.py
 PySDM/formulae.py
@@ -411,6 +412,8 @@ PySDM/products/size_spectral/size_standard_deviation.py
 PySDM/products/size_spectral/total_particle_concentration.py
 PySDM/products/size_spectral/total_particle_specific_concentration.py
 PySDM/products/size_spectral/water_mixing_ratio.py
+docs/logos/pysdm_logo.png
+docs/logos/pysdm_logo.svg
 docs/markdown/pysdm_landing.md
 docs/templates/README.md
 docs/templates/custom.css

{pysdm-2.88 → pysdm-2.90}/README.md

@@ -1,4 +1,4 @@
-# <img src="https://raw.githubusercontent.com/open-atmos/PySDM/main/.github/pysdm_logo.svg" width=100 height=146 alt="pysdm logo">
+# <img src="https://raw.githubusercontent.com/open-atmos/PySDM/main/docs/logos/pysdm_logo.svg" 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)
@@ -35,6 +35,8 @@ 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. 
 
+PySDM documentation is maintained at: [https://open-atmos.github.io/PySDM](https://open-atmos.github.io/PySDM) 
+
 There is a growing set of [example Jupyter notebooks](https://open-atmos.github.io/PySDM/PySDM_examples.html) 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 
@@ -65,14 +67,6 @@ For an overview of PySDM features (and the preferred way to cite PySDM in papers
 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/), 

{pysdm-2.88/.github → pysdm-2.90/docs/logos}/pysdm_logo.svg

@@ -1 +1 @@
-<?xml version="1.0" encoding="UTF-8"?><svg id="Warstwa_2" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 153 222.59"><defs><style>.cls-1{fill:#13a4de;}</style></defs><g id="Warstwa_4"><g><g><path class="cls-1" d="m48.45,57.44c0,8.04-6.82,14.56-15.23,14.56s-15.23-6.52-15.23-14.56c0-14.56,15.23-33.97,15.23-33.97,0,0,15.23,19.41,15.23,33.97Z"/><path class="cls-1" d="m63,22.22c0,5.26-4.46,9.52-9.96,9.52s-9.96-4.26-9.96-9.52c0-9.52,9.96-22.22,9.96-22.22,0,0,9.96,12.7,9.96,22.22Z"/></g><path class="cls-1" d="m90,0s-45,57.6-45,100.8c0,23.86,20.15,43.2,45,43.2s45-19.34,45-43.2C135,57.6,90,0,90,0Zm29.37,131.64c-19.14,16.75-34.42,5.24-37.26-6.95-2.84-12.19,6.42-41.71,8.5-50.63s4.38-30.39-6.36-28.46-12.2,18.32-9.98,27.76c2.22,9.45,14.98,52.01-9.23,44.17-22.97-7.44-13.86-45.93-13.86-45.93,0,0-2.53,30.62,13.12,35.08,11.1,3.16,9.97-15.47,6.64-28.6-3.33-13.12-12.86-29.48-1.93-43.03,10.94-13.55,27.62-17.48,35.24-9.51,7.62,7.97-1.92,29.94-5.9,42.22s-6.42,26.66-6.74,34.82c-.32,8.17,3.88,23.62,16.36,20.47s16.08-22.73,12.4-34.06c-3.67-11.33-6.57-10.6-10.97-20.55-.91-2.06-.8-3.68-.2-4.69-.69-1.05-2.6-1.33-2.6-1.33,1.21-.26,1.17-.14,1.75-.12-.02-.22-.14-1.21-.14-1.21.6.45,1.08,1.89,1.21,2.33.58-.72,1.46-1,2.35-.74,2.09.61,5.09,2.78,5.81,3.03,1.9.67,3.8,1.45,4.82,2.38,2.87,2.62,3.31,3.95,4.34,6.3,1.77,4.05,16.99,35.94-7.37,57.25Z"/><path class="cls-1" d="m119.37,68.87s1.13.6,1.53.85.95.69,1.61,1.2c-1.38.17-2.07-.06-2.42-.38-.49-.44-.73-1.67-.73-1.67Z"/></g><g><path class="cls-1" d="m1.14,213.6c-.32,0-.58-.11-.8-.33-.22-.22-.33-.49-.33-.8v-30.81c0-.35.11-.63.33-.85.22-.22.49-.33.8-.33h12.68c2.46,0,4.61.39,6.44,1.16,1.83.77,3.25,1.94,4.26,3.5,1.01,1.56,1.51,3.51,1.51,5.84s-.5,4.32-1.51,5.85c-1.01,1.53-2.43,2.67-4.26,3.43-1.83.76-3.98,1.14-6.44,1.14h-7.05v11.07c0,.32-.1.58-.31.8-.21.22-.48.33-.83.33H1.14Zm5.54-17.46h6.91c1.83,0,3.23-.43,4.21-1.3.98-.87,1.47-2.15,1.47-3.86,0-1.58-.46-2.85-1.37-3.81s-2.35-1.44-4.31-1.44h-6.91v10.41Z"/><path class="cls-1" d="m35.07,222.59c-.25,0-.47-.09-.66-.28-.19-.19-.28-.41-.28-.66,0-.13,0-.24.02-.36.02-.11.07-.24.17-.4l3.69-8.76-9.09-21.44c-.13-.31-.19-.54-.19-.66.03-.28.14-.53.33-.73.19-.2.43-.31.71-.31h3.83c.38,0,.66.09.85.28.19.19.33.39.43.62l6.29,15.48,6.48-15.48c.09-.25.24-.47.43-.64.19-.17.47-.26.85-.26h3.79c.25,0,.48.09.69.28.2.19.31.41.31.66,0,.19-.06.44-.19.76l-13.39,31c-.13.25-.28.47-.47.64-.19.17-.47.26-.85.26h-3.74Z"/><path class="cls-1" d="m69.85,214.07c-2.93,0-5.39-.43-7.36-1.3-1.97-.87-3.47-2-4.5-3.41s-1.57-2.88-1.63-4.43c0-.28.1-.52.28-.71.19-.19.43-.28.71-.28h4.21c.41,0,.72.09.92.26.2.17.39.39.54.64.19.6.55,1.19,1.09,1.77.54.58,1.27,1.06,2.2,1.44.93.38,2.11.57,3.53.57,2.27,0,3.97-.38,5.09-1.14,1.12-.76,1.68-1.78,1.68-3.08,0-.92-.3-1.65-.9-2.2-.6-.55-1.52-1.06-2.77-1.51-1.25-.46-2.89-.94-4.95-1.44-2.37-.57-4.35-1.25-5.94-2.06-1.59-.8-2.79-1.82-3.6-3.05-.8-1.23-1.21-2.79-1.21-4.69s.5-3.45,1.49-4.87c.99-1.42,2.41-2.54,4.26-3.36,1.85-.82,4.05-1.23,6.6-1.23,2.05,0,3.86.28,5.44.83,1.58.55,2.89,1.28,3.93,2.18s1.84,1.86,2.39,2.89.84,2.03.88,3.01c0,.25-.09.48-.26.69-.17.21-.42.31-.73.31h-4.4c-.25,0-.5-.06-.76-.19-.25-.13-.46-.36-.62-.71-.19-.98-.8-1.81-1.85-2.51-1.04-.69-2.38-1.04-4.02-1.04s-3.08.31-4.12.95c-1.04.63-1.56,1.61-1.56,2.93,0,.88.26,1.62.78,2.2.52.58,1.36,1.1,2.51,1.54,1.15.44,2.67.92,4.57,1.42,2.68.6,4.87,1.29,6.58,2.08,1.7.79,2.95,1.79,3.74,3.01.79,1.22,1.18,2.75,1.18,4.61,0,2.08-.56,3.86-1.68,5.32-1.12,1.47-2.69,2.6-4.71,3.38-2.02.79-4.37,1.18-7.05,1.18Z"/><path class="cls-1" d="m89.87,213.6c-.32,0-.58-.11-.8-.33-.22-.22-.33-.49-.33-.8v-30.81c0-.35.11-.63.33-.85.22-.22.49-.33.8-.33h11.55c3.19,0,5.81.49,7.88,1.47,2.07.98,3.63,2.43,4.69,4.35,1.06,1.92,1.6,4.28,1.63,7.05.06,1.39.09,2.62.09,3.69s-.03,2.29-.09,3.64c-.06,2.93-.6,5.36-1.61,7.26-1.01,1.91-2.53,3.33-4.57,4.26-2.04.93-4.63,1.4-7.79,1.4h-11.78Zm5.44-5.44h6.11c1.77,0,3.2-.25,4.31-.76,1.1-.5,1.92-1.32,2.44-2.44.52-1.12.8-2.59.83-4.43.03-.95.05-1.77.07-2.48.02-.71.02-1.42,0-2.13-.02-.71-.04-1.52-.07-2.44-.06-2.59-.71-4.5-1.94-5.73-1.23-1.23-3.19-1.85-5.87-1.85h-5.87v22.24Z"/><path class="cls-1" d="m123.19,213.6c-.35,0-.63-.11-.85-.33-.22-.22-.33-.49-.33-.8v-30.81c0-.35.11-.63.33-.85.22-.22.5-.33.85-.33h3.74c.44,0,.77.12.99.35.22.24.36.42.43.54l9.13,17.04,9.23-17.04c.06-.13.21-.31.43-.54.22-.24.55-.35.99-.35h3.69c.35,0,.63.11.85.33s.33.5.33.85v30.81c0,.32-.11.58-.33.8-.22.22-.5.33-.85.33h-3.98c-.35,0-.62-.11-.83-.33-.21-.22-.31-.49-.31-.8v-20.49l-6.63,12.64c-.16.28-.36.53-.62.73-.25.21-.58.31-.99.31h-1.94c-.44,0-.78-.1-1.02-.31s-.43-.45-.59-.73l-6.63-12.64v20.49c0,.32-.11.58-.33.8s-.49.33-.8.33h-3.97Z"/></g></g></svg>
+<?xml version="1.0" encoding="UTF-8"?><svg id="Warstwa_2" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 153 222.59"><defs><style>.cls-1{fill:#13a4de;}</style></defs><g id="Warstwa_4"><g><g><path class="cls-1" d="m48.45,57.44c0,8.04-6.82,14.56-15.23,14.56s-15.23-6.52-15.23-14.56c0-14.56,15.23-33.97,15.23-33.97,0,0,15.23,19.41,15.23,33.97Z"/><path class="cls-1" d="m63,22.22c0,5.26-4.46,9.52-9.96,9.52s-9.96-4.26-9.96-9.52c0-9.52,9.96-22.22,9.96-22.22,0,0,9.96,12.7,9.96,22.22Z"/></g><path class="cls-1" d="m90,0s-45,57.6-45,100.8c0,23.86,20.15,43.2,45,43.2s45-19.34,45-43.2C135,57.6,90,0,90,0Zm29.37,131.64c-19.14,16.75-34.42,5.24-37.26-6.95-2.84-12.19,6.42-41.71,8.5-50.63s4.38-30.39-6.36-28.46-12.2,18.32-9.98,27.76c2.22,9.45,14.98,52.01-9.23,44.17-22.97-7.44-13.86-45.93-13.86-45.93,0,0-2.53,30.62,13.12,35.08,11.1,3.16,9.97-15.47,6.64-28.6-3.33-13.12-12.86-29.48-1.93-43.03,10.94-13.55,27.62-17.48,35.24-9.51,7.62,7.97-1.92,29.94-5.9,42.22s-6.42,26.66-6.74,34.82c-.32,8.17,3.88,23.62,16.36,20.47s16.08-22.73,12.4-34.06c-3.67-11.33-6.57-10.6-10.97-20.55-.91-2.06-.8-3.68-.2-4.69-.69-1.05-2.6-1.33-2.6-1.33,1.21-.26,1.17-.14,1.75-.12-.02-.22-.14-1.21-.14-1.21.6.45,1.08,1.89,1.21,2.33.58-.72,1.46-1,2.35-.74,2.09.61,5.09,2.78,5.81,3.03,1.9.67,3.8,1.45,4.82,2.38,2.87,2.62,3.31,3.95,4.34,6.3,1.77,4.05,16.99,35.94-7.37,57.25Z"/><path class="cls-1" d="m119.37,68.87s1.13.6,1.53.85.95.69,1.61,1.2c-1.38.17-2.07-.06-2.42-.38-.49-.44-.73-1.67-.73-1.67Z"/></g><g><path class="cls-1" d="m1.14,213.6c-.32,0-.58-.11-.8-.33-.22-.22-.33-.49-.33-.8v-30.81c0-.35.11-.63.33-.85.22-.22.49-.33.8-.33h12.68c2.46,0,4.61.39,6.44,1.16,1.83.77,3.25,1.94,4.26,3.5,1.01,1.56,1.51,3.51,1.51,5.84s-.5,4.32-1.51,5.85c-1.01,1.53-2.43,2.67-4.26,3.43-1.83.76-3.98,1.14-6.44,1.14h-7.05v11.07c0,.32-.1.58-.31.8-.21.22-.48.33-.83.33H1.14Zm5.54-17.46h6.91c1.83,0,3.23-.43,4.21-1.3.98-.87,1.47-2.15,1.47-3.86,0-1.58-.46-2.85-1.37-3.81s-2.35-1.44-4.31-1.44h-6.91v10.41Z"/><path class="cls-1" d="m35.07,222.59c-.25,0-.47-.09-.66-.28-.19-.19-.28-.41-.28-.66,0-.13,0-.24.02-.36.02-.11.07-.24.17-.4l3.69-8.76-9.09-21.44c-.13-.31-.19-.54-.19-.66.03-.28.14-.53.33-.73.19-.2.43-.31.71-.31h3.83c.38,0,.66.09.85.28.19.19.33.39.43.62l6.29,15.48,6.48-15.48c.09-.25.24-.47.43-.64.19-.17.47-.26.85-.26h3.79c.25,0,.48.09.69.28.2.19.31.41.31.66,0,.19-.06.44-.19.76l-13.39,31c-.13.25-.28.47-.47.64-.19.17-.47.26-.85.26h-3.74Z"/><path class="cls-1" d="m69.85,214.07c-2.93,0-5.39-.43-7.36-1.3-1.97-.87-3.47-2-4.5-3.41s-1.57-2.88-1.63-4.43c0-.28.1-.52.28-.71.19-.19.43-.28.71-.28h4.21c.41,0,.72.09.92.26.2.17.39.39.54.64.19.6.55,1.19,1.09,1.77.54.58,1.27,1.06,2.2,1.44.93.38,2.11.57,3.53.57,2.27,0,3.97-.38,5.09-1.14,1.12-.76,1.68-1.78,1.68-3.08,0-.92-.3-1.65-.9-2.2-.6-.55-1.52-1.06-2.77-1.51-1.25-.46-2.89-.94-4.95-1.44-2.37-.57-4.35-1.25-5.94-2.06-1.59-.8-2.79-1.82-3.6-3.05-.8-1.23-1.21-2.79-1.21-4.69s.5-3.45,1.49-4.87c.99-1.42,2.41-2.54,4.26-3.36,1.85-.82,4.05-1.23,6.6-1.23,2.05,0,3.86.28,5.44.83,1.58.55,2.89,1.28,3.93,2.18s1.84,1.86,2.39,2.89.84,2.03.88,3.01c0,.25-.09.48-.26.69-.17.21-.42.31-.73.31h-4.4c-.25,0-.5-.06-.76-.19-.25-.13-.46-.36-.62-.71-.19-.98-.8-1.81-1.85-2.51-1.04-.69-2.38-1.04-4.02-1.04s-3.08.31-4.12.95c-1.04.63-1.56,1.61-1.56,2.93,0,.88.26,1.62.78,2.2.52.58,1.36,1.1,2.51,1.54,1.15.44,2.67.92,4.57,1.42,2.68.6,4.87,1.29,6.58,2.08,1.7.79,2.95,1.79,3.74,3.01.79,1.22,1.18,2.75,1.18,4.61,0,2.08-.56,3.86-1.68,5.32-1.12,1.47-2.69,2.6-4.71,3.38-2.02.79-4.37,1.18-7.05,1.18Z"/><path class="cls-1" d="m89.87,213.6c-.32,0-.58-.11-.8-.33-.22-.22-.33-.49-.33-.8v-30.81c0-.35.11-.63.33-.85.22-.22.49-.33.8-.33h11.55c3.19,0,5.81.49,7.88,1.47,2.07.98,3.63,2.43,4.69,4.35,1.06,1.92,1.6,4.28,1.63,7.05.06,1.39.09,2.62.09,3.69s-.03,2.29-.09,3.64c-.06,2.93-.6,5.36-1.61,7.26-1.01,1.91-2.53,3.33-4.57,4.26-2.04.93-4.63,1.4-7.79,1.4h-11.78Zm5.44-5.44h6.11c1.77,0,3.2-.25,4.31-.76,1.1-.5,1.92-1.32,2.44-2.44.52-1.12.8-2.59.83-4.43.03-.95.05-1.77.07-2.48.02-.71.02-1.42,0-2.13-.02-.71-.04-1.52-.07-2.44-.06-2.59-.71-4.5-1.94-5.73-1.23-1.23-3.19-1.85-5.87-1.85h-5.87v22.24Z"/><path class="cls-1" d="m123.19,213.6c-.35,0-.63-.11-.85-.33-.22-.22-.33-.49-.33-.8v-30.81c0-.35.11-.63.33-.85.22-.22.5-.33.85-.33h3.74c.44,0,.77.12.99.35.22.24.36.42.43.54l9.13,17.04,9.23-17.04c.06-.13.21-.31.43-.54.22-.24.55-.35.99-.35h3.69c.35,0,.63.11.85.33s.33.5.33.85v30.81c0,.32-.11.58-.33.8-.22.22-.5.33-.85.33h-3.98c-.35,0-.62-.11-.83-.33-.21-.22-.31-.49-.31-.8v-20.49l-6.63,12.64c-.16.28-.36.53-.62.73-.25.21-.58.31-.99.31h-1.94c-.44,0-.78-.1-1.02-.31s-.43-.45-.59-.73l-6.63-12.64v20.49c0,.32-.11.58-.33.8s-.49.33-.8.33h-3.97Z"/></g></g></svg>

{pysdm-2.88 → pysdm-2.90}/docs/markdown/pysdm_landing.md

@@ -1,6 +1,6 @@
 # Introduction
 
-<img align="left" src="https://raw.githubusercontent.com/open-atmos/PySDM/main/.github/pysdm_logo.svg" width=150 height=219 alt="pysdm logo" style="padding-right:1em">
+<img align="left" src="https://raw.githubusercontent.com/open-atmos/PySDM/main/docs/logos/pysdm_logo.svg" width=150 height=219 alt="pysdm logo" style="padding-right:1em">
 
 PySDM offers a set of building blocks for development of atmospheric cloud
 simulation systems revolving around the particle-based microphysics modelling concept

{pysdm-2.88 → pysdm-2.90}/docs/templates/index.html.jinja2

@@ -24,25 +24,32 @@
     <main class="pdoc">
         <div style="display: flex; align-items: center;">
             <a href="https://open-atmos.github.io/PySDM/index.html">
-                <img src="https://raw.githubusercontent.com/open-atmos/PySDM/main/.github/pysdm_logo.svg" style="height:10em" alt="PySDM logo">
+                <img src="https://raw.githubusercontent.com/open-atmos/PySDM/main/docs/logos/pysdm_logo.svg" style="height:10em" alt="PySDM logo">
             </a>
             <h1 style="padding-left: 0.5em; color: #13A4DE; font-weight: normal ">Documentation</h1>
     </div>
     <div style="padding-top: 2em">
         <h2>What is PySDM?</h2>
         <p>
-            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 
-            (<a href="https://doi.org/10.1002/qj.441">Shima et al. 2009</a>), hence the name.
+            <video controls style="float:right; width:40%">
+                <source src="https://github.com/open-atmos/PySDM/wiki/files/animation_save.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>.
+            The package features a Pythonic high-performance (multi-threaded CPU &amp; CUDA GPU) implementation of the <mark>Super-Droplet Method (SDM) Monte-Carlo algorithm</mark> 
+              for representing collisional growth (<a href="https://doi.org/10.1002/qj.441">Shima et al. 2009</a>), hence the name.
+            It is intended to serve as a building block for simulation systems modelling <mark>fluid flows involving a dispersed phase</mark>,
+               with PySDM being responsible for representation of the dispersed phase.
+            Currently, the development is focused on atmospheric <mark>cloud physics applications</mark>, 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 key goal of PySDM is to enable rapid development and independent reproducibility of simulations in cloud microphysics
+              while being free from the two-language barrier commonly separating prototype and high-performance research code.
         </p>
     </div>
     <div style="padding-top: 0.5em">
         <h2>What is the difference between PySDM and PySDM-examples?</h2>
         <p>
-            PySDM is a Python package that provides the implementation of the Super-Droplet Method (SDM) Monte-Carlo algorithm.
-            It is a library that can be used in your own projects.
+            PySDM is a Python package that provides the implementation of SDM that can be used in your own projects.
         </p>
         <p>
             PySDM-examples is a Python package that provides examples of how to use PySDM.
@@ -159,7 +166,7 @@ jupyter-notebook PySDM/examples</code></pre>
         </p>
         <p>
           Development of PySDM was supported by:
-          <ul>
+          <ul style="list-style:square; margin-left:1em;">
             <li><a href="https://www.fnp.org.pl/en/">Foundation for Polish Science</a> (grant no. POIR.04.04.00-00-5E1C/18 co-financed by the European Union under the European Regional Development Fund)</li>
             <li><a href="https://ncn.gov.pl/en">Polish National Science Centre</a> (grant no. 2020/39/D/ST10/01220)</li>
             <li><a href="https://science.energy.gov">US Department of Energy</a> via the <a href="https://www.krellinst.org/csgf/">Computational Science Graduate Fellowship</a> and via the <a href="https://asr.science.energy.gov/">Atmospheric System Research Program</a> (grant no. DE-SC0021034)</li>

{pysdm-2.88 → pysdm-2.90}/examples/PySDM_examples/Bolin_1958/table_1.ipynb

@@ -7,7 +7,7 @@
    "source": [
     "[![preview notebook](https://img.shields.io/static/v1?label=render%20on&logo=github&color=87ce3e&message=GitHub)](https://github.com/open-atmos/PySDM/examples/PySDM_examples/Bolin_1958/table_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/Bolin_1958/table_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/Bolin_1958/table_1.ipynb"
+    "[![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/Bolin_1958/table_1.ipynb)\n"
    ]
   },
   {