Merge github.com:slayoo/PySDM into HEAD

open-atmos · Dec 11, 2024 · 211f1f0 · 211f1f0
2 parents 95cf76e + d3ab146
commit 211f1f0
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diff --git a/.github/workflows/readme_snippets.yml b/.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/[email protected]
-      - if: matrix.platform != 'macos-14'
-        uses: actions/[email protected]
+      - uses: actions/[email protected]
         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/[email protected]
       - uses: actions/[email protected]
         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/[email protected]
       - 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/[email protected]
         with:

diff --git a/.github/workflows/tests+artifacts+pypi.yml b/.github/workflows/tests+artifacts+pypi.yml
@@ -21,7 +21,7 @@ jobs:
       - uses: actions/[email protected]
       - uses: actions/[email protected]
         with:
-          python-version: 3.8
+          python-version: 3.9
       - run: |
           pip install pre-commit
           pre-commit clean
@@ -31,7 +31,7 @@ jobs:
         run: git diff
 
   nojit_and_codecov:
-    needs: [precommit, pylint]
+    needs: [precommit, pylint, devops]
     runs-on: ubuntu-latest
     env:
       NUMBA_DISABLE_JIT: 1
@@ -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/[email protected]
@@ -67,12 +67,20 @@ jobs:
           persist-credentials: false
       - uses: actions/[email protected]
         with:
-          python-version: 3.9
+          python-version: "3.12"
       - 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/[email protected]
         with:
@@ -86,7 +94,7 @@ jobs:
     - uses: actions/[email protected]
       with:
         submodules: recursive
-        fetch-depth: 0 
+        fetch-depth: 0
     - name: Set up Python 3.9
       uses: actions/[email protected]
       with:
@@ -114,20 +122,31 @@ jobs:
     steps:
       - uses: actions/[email protected]
       - uses: notiz-dev/github-action-json-property@release
-        with: 
+        with:
           path: '.zenodo.json'
           prop_path: 'creators'
 
   tests:
     needs: [pdoc, nojit_and_codecov, zenodo_json]
     strategy:
       matrix:
-        platform: [ubuntu-latest, macos-12, windows-latest]
-        python-version: ["3.8", "3.11"]
+        platform: [ubuntu-latest, 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"]
         exclude:
+          - platform: "macos-14"
+            python-version: "3.9"
           - test-suite: "devops_tests"
-            python-version: "3.8"
+            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-')
@@ -175,15 +196,15 @@ jobs:
     needs: [nojit_and_codecov]
     strategy:
       matrix:
-        platform: [ubuntu-22.04, macos-12, windows-latest]
-        python-version: ["3.8", "3.11"]
+        platform: [ubuntu-24.04, macos-13, windows-latest]
+        python-version: ["3.9", "3.12"]
     runs-on: ${{ matrix.platform }}
     steps:
       - uses: actions/[email protected]
         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]
-        python-version: ["3.8", "3.11"]
+        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"]
       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/[email protected]
         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 }}
@@ -284,77 +318,70 @@ jobs:
           fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
       - uses: actions/[email protected]
         with:
-          python-version: "3.11"
+          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" | wc -l`
+          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@v3
+      - uses: actions/upload-artifact@v4
         with:
-          path: ${{ matrix.packages-dir}}/dist
-          name: dist
+          path: ${{ matrix.packages-dir }}/dist
+          name: dist-${{ matrix.packages-dir }}
 
   pkg_install_check:
     strategy:
       matrix:
-        platform: [ubuntu-latest, macos-12, macos-14, windows-latest]
-        python-version: ["3.8", "3.11", "system"]
+        platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
+        python-version: ["3.9", "3.12"]
         exclude:
-          - platform: ubuntu-latest
-            python-version: system
-          - platform: macos-12
-            python-version: system
-          - platform: windows-latest
-            python-version: system
           - platform: macos-14
-            python-version: "3.8"
-          - platform: macos-14
-            python-version: "3.11"
+            python-version: "3.9"
     runs-on: ${{ matrix.platform }}
     needs: [package]
     steps:
-      - if: matrix.platform != 'macos-14'
-        uses: actions/[email protected]
+      - uses: actions/[email protected]
         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@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: dist
-          path: dist     
+          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, devops, package, pkg_install_check]
+    needs: [tests, examples, package, pkg_install_check]
     permissions:
       id-token: write
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: dist
-          path: dist     
+          pattern: dist-*
+          merge-multiple: true
+          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
diff --git a/.zenodo.json b/.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"

diff --git a/PySDM/__init__.py b/PySDM/__init__.py
@@ -1,25 +1,6 @@
 # pylint:disable=invalid-name
 """
-PySDM offers a set of building blocks for development of atmospheric cloud
-simulation systems revolving around the particle-based microphysics modelling concept
-and the Super-Droplet Method algorithm ([Shima et al. 2009](https://doi.org/10.1002/qj.441))
-for numerically tackling the probabilistic representation of particle coagulation.
-
-For an overview of PySDM, see [Bartman, Arabas et al. 2021](https://arxiv.org/abs/2103.17238).
-PySDM is released under the [GNU GPL v3 license](https://www.gnu.org/licenses/gpl-3.0.en.html).
-PySDM development has been spearheaded at the Faculty of Mathematics and Computer Science,
-[Jagiellonian University in Kraków](https://en.uj.edu.pl/en) (the copyright holder).
-
-For details on PySDM dependencies and installation procedures, see project
-[README.md file](https://github.com/open-atmos/PySDM/blob/master/README.md)
-which also includes basic usage examples in **Python**, **Julia** and **Matlab**.
-
-A set of more elaborate examples engineered in Python and accompanied by Jupyter
-notebooks are maintained in the
-[PySDM-examples package](https://github.com/open-atmos/PySDM-examples).
-
-PySDM test-suite built using [pytest](https://docs.pytest.org/) is located in the
-[tests package](https://github.com/open-atmos/PySDM/tree/master/tests).
+.. include:: ../docs/markdown/pysdm_landing.md
 """
 
 from importlib.metadata import PackageNotFoundError, version