PySDM 2.87__tar.gz → 2.89__tar.gz

pysdm-2.89/.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-2.89/.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-2.87/.github/workflows/tests+artifacts+pypi.yml → pysdm-2.89/.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:
@@ -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-2.87 → pysdm-2.89}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.87
+Version: 2.89
 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

{pysdm-2.87 → pysdm-2.89}/PySDM/exporters/vtk_exporter.py

@@ -134,7 +134,7 @@ class VTKExporter:
 
                 if isinstance(v, np.ndarray):
                     if v.shape == particulator.mesh.grid:
-                        payload[k] = v[:, :, np.newaxis]
+                        payload[k] = v[:, :, np.newaxis].copy()
                     else:
                         if self.verbose:
                             print(

{pysdm-2.87 → pysdm-2.89}/PySDM/physics/impl/fake_unit_registry.py

@@ -12,7 +12,7 @@ def _fake(si_unit):
 class FakeUnitRegistry:  # pylint: disable=too-few-public-methods
     def __init__(self, si):
         self.dimensionless = 1.0
-        for prefix in ("nano", "micro", "milli", "centi", "", "hecto", "kilo"):
+        for prefix in ("nano", "micro", "milli", "centi", "deci", "", "hecto", "kilo"):
             for unit in (
                 "bar",
                 "metre",
@@ -34,7 +34,7 @@ class FakeUnitRegistry:  # pylint: disable=too-few-public-methods
                     prefix + unit + "s", _fake(si.__getattr__(prefix + unit + "s"))
                 )
 
-        for prefix in ("n", "u", "m", "c", "", "h", "k"):
+        for prefix in ("n", "u", "m", "c", "d", "", "h", "k"):
             for unit in (
                 "b",
                 "m",

{pysdm-2.87 → pysdm-2.89}/PySDM.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.87
+Version: 2.89
 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

{pysdm-2.87 → pysdm-2.89}/PySDM.egg-info/SOURCES.txt

@@ -17,9 +17,11 @@ setup.py
 .github/workflows/cancel.yml
 .github/workflows/joss.yml
 .github/workflows/joss_paper.yml
+.github/workflows/pdoc.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
@@ -827,6 +829,8 @@ tests/unit_tests/dynamics/displacement/test_courant_product.py
 tests/unit_tests/dynamics/displacement/test_sedimentation.py
 tests/unit_tests/environments/__init__.py
 tests/unit_tests/environments/test_impl.py
+tests/unit_tests/exporters/__init__.py
+tests/unit_tests/exporters/test_vtk_exporter.py
 tests/unit_tests/impl/__init__.py
 tests/unit_tests/impl/test_camel_case.py
 tests/unit_tests/impl/test_mesh.py
@@ -848,6 +852,7 @@ tests/unit_tests/physics/test_bulk_phase_partitioning.py
 tests/unit_tests/physics/test_constants.py
 tests/unit_tests/physics/test_dimensional_analysis.py
 tests/unit_tests/physics/test_drop_growth.py
+tests/unit_tests/physics/test_fake_unit_registry.py
 tests/unit_tests/physics/test_formulae.py
 tests/unit_tests/physics/test_fragmentation_functions.py
 tests/unit_tests/physics/test_freezing_temperature_spectra.py

{pysdm-2.87 → pysdm-2.89}/examples/PySDM_examples/Bolin_1958/table_1.ipynb

@@ -5,9 +5,9 @@
    "id": "e3f1edc815e974f4",
    "metadata": {},
    "source": [
-    "[![preview notebook](https://img.shields.io/static/v1?label=render%20on&logo=github&color=87ce3e&message=GitHub)](https://github.com/open-atmos/devops_tests/blob/main/test_files/template.ipynb)\n",
-    "[![launch on mybinder.org](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/open-atmos/devops_tests.git/main?urlpath=lab/tree/test_files/template.ipynb)\n",
-    "[![launch on Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/open-atmos/devops_tests/blob/main/test_files/template.ipynb)"
+    "[![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)\n"
    ]
   },
   {

{pysdm-2.87 → pysdm-2.89}/examples/docs/pysdm_examples_landing.md

@@ -121,5 +121,6 @@ The box environment is also featured in the <a href="https://open-atmos.github.i
   - `PySDM_examples.Pierchala_et_al_2022`: reproducing model plots for a <mark>triple-isotope</mark> lab study, including <mark>kinetic fractionation</mark>
 - isotopic relaxation timescale:
   - `PySDM_examples.Miyake_et_al_1968`: incl. comparison of different <mark>ventilation</mark> parameterisations
+  - `PySDM_examples.Bolin_1958`
 - below-cloud <mark>kinetic fractionation</mark>:
   - `PySDM_examples.Gedzelman_and_Arnold_1994`

{pysdm-2.87 → pysdm-2.89}/tests/examples_tests/test_tests_completeness.py

@@ -45,7 +45,7 @@ def test_all_test_suites_are_on_ci():
         .parent.parent.parent.absolute()
         .joinpath(".github")
         .joinpath("workflows")
-        .joinpath("tests+artifacts+pypi.yml")
+        .joinpath("tests.yml")
     )
     with open(workflow_file_path, "r", encoding="utf8") as workflow_file:
         d = yaml.safe_load(workflow_file)

pysdm-2.89/tests/unit_tests/exporters/test_vtk_exporter.py

@@ -0,0 +1,57 @@
+""" checks for VTK exporter """
+
+from collections import namedtuple
+
+import numpy as np
+
+from PySDM.exporters import VTKExporter
+
+
+def test_vtk_exporter_copies_product_data(tmp_path):
+    """note: since VTK files contain unencoded binary data, we cannot use XML parsers;
+    not to introduce a new dependency to PySDM, we read the binary data with NumPy"""
+    # arrange
+    productc_filename = tmp_path / "prod"
+    sut = VTKExporter(products_filename=productc_filename)
+
+    grid = (1, 1)
+    arr = np.zeros(shape=grid, dtype=float)
+
+    incr = 666
+
+    def plusplus(arr):
+        arr += incr
+        return arr
+
+    prod = namedtuple(typename="MockProductA", field_names=("get",))(
+        get=lambda: plusplus(arr)
+    )
+
+    particulator = namedtuple(
+        typename="MockParticulator", field_names=("products", "n_steps", "dt", "mesh")
+    )(
+        n_steps=1,
+        products={
+            "a": prod,
+            "b": prod,
+        },
+        dt=0,
+        mesh=namedtuple(typename="MockMesh", field_names=("dimension", "grid", "size"))(
+            dimension=2,
+            grid=grid,
+            size=(1, 1),
+        ),
+    )
+
+    # act
+    sut.export_products(particulator)
+
+    # assert
+    offsets = (113, 129)
+    with open(str(productc_filename) + "_num0000000001.vts", mode="rb") as vtk:
+        binary_data = vtk.readlines()[14]
+        for i, off in enumerate(offsets):
+            assert (
+                np.frombuffer(binary_data[off : off + 8], dtype=np.float64)
+                == (i + 1) * incr
+            )

pysdm-2.89/tests/unit_tests/physics/test_fake_unit_registry.py

@@ -0,0 +1,15 @@
+""" checks for SI units conversions in FakeUnitRegistry """
+
+from PySDM.physics import si
+
+
+class TestFakeUnitRegistry:
+    @staticmethod
+    def test_d():
+        """a check for the 'd' prefix"""
+        assert 44 * si.dm == 440 * si.cm
+
+    @staticmethod
+    def test_deci():
+        """a check for the 'deci' prefix"""
+        assert 44 * si.decimetre == 440 * si.centimetre