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bump PySDM requirement (in notebooks that use it) to >=3.0.0 and adapt code to new PySDM v3 API #566

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Merged
slayoo merged 11 commits into from
Oct 17, 2026
Merged

bump PySDM requirement (in notebooks that use it) to >=3.0.0 and adapt code to new PySDM v3 API #566

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1451f70
bump PySDM requirement (in notebooks that use it) to >=3.0.0 and adap…
slayoo Oct 14, 2026
9c28deb
enforce examples dependencies for pylint workflow
slayoo Oct 15, 2026
007eaa4
bump Python version for pylint workflow (needed by JAX - a new PySDM …
slayoo Oct 15, 2026
b1a612c
fix import
slayoo Oct 15, 2026
47fcaa1
one more fix in PySDM code
slayoo Oct 15, 2026
a4d36f5
address pylint hint
slayoo Oct 15, 2026
c6eabbd
use sample_deterministic instead of obsolete init_attributes
slayoo Oct 16, 2026
30ad899
fix Particulator instantiation; drop macos-intel from run_example_not…
slayoo Oct 16, 2026
4b268ba
pylint hints
slayoo Oct 16, 2026
9b85213
run() -> advance()
slayoo Oct 17, 2026
b104833
shorter lines...
slayoo Oct 17, 2026
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4 changes: 2 additions & 2 deletions .github/workflows/buildwheels.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,7 @@ jobs:
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest, ubuntu-24.04-arm, macos-14, macos-15, macos-15-intel, windows-latest]
os: [ubuntu-latest, ubuntu-24.04-arm, macos-14, macos-15, windows-latest]

steps:
- uses: actions/checkout@v7
Expand Down Expand Up @@ -391,7 +391,7 @@ jobs:

- run: |
temp=`find dist/ -name "*cp312*.whl"`
python -m pip install $temp[examples]
python -m pip install $temp

- run: pip install pytest-codeblocks pytest
- run: mkdir readme_cpp
Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/pylint.yml
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Expand Up @@ -18,11 +18,11 @@ jobs:
fetch-depth: 0
- uses: actions/setup-python@v6
with:
python-version: 3.9
python-version: 3.14
- run: |
python -m pip install --upgrade pip
pip install pylint nbqa
pip install -e .[tests]
pip install -e .[tests,examples]
pip install -r .binder/requirements.txt
- run: pylint --unsafe-load-any-extension=y --disable=fixme,no-member,trailing-newlines,missing-module-docstring,missing-class-docstring,missing-function-docstring,unnecessary-pass $(git ls-files '*.py')
- run: nbqa pylint --unsafe-load-any-extension=y --disable=fixme,no-member,duplicate-code,wrong-import-position,ungrouped-imports,trailing-whitespace,missing-function-docstring,missing-module-docstring,unsubscriptable-object,invalid-name $(git ls-files '*.ipynb')
56 changes: 32 additions & 24 deletions examples/additive_coag_comparison.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,7 @@
"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('PyPartMC', 'PySDM','dustpy')\n",
" pip_install_on_colab('PyPartMC', 'PySDM>3.0.0','dustpy')\n",
"\n",
" # install julia if not in system\n",
" if shutil.which('julia') is None:\n",
Expand Down Expand Up @@ -287,31 +287,31 @@
" import PySDM\n",
" from PySDM.physics import si\n",
"\n",
" builder = PySDM.Builder(\n",
" settings.N_PART,\n",
" backend=PySDM.backends.CPU(override_jit_flags={\"parallel\": False}),\n",
" environment=PySDM.environments.Box(\n",
" dt=settings.DT_SEC * si.s,\n",
" dv=settings.VOLUME_M3 * si.m**3\n",
" )\n",
" backend = PySDM.backends.CPU()\n",
" box = PySDM.environments.Box(\n",
" dt=settings.DT_SEC * si.s,\n",
" dv=settings.VOLUME_M3 * si.m**3,\n",
" backend=backend,\n",
" )\n",
" trivia = builder.formulae.trivia\n",
" trivia = backend.formulae.trivia\n",
" spectrum = PySDM.initialisation.spectra.Exponential(\n",
" norm_factor=settings.NUM_CONC_PER_M3 * settings.VOLUME_M3 / si.m**3,\n",
" scale=trivia.volume(radius=settings.DIAM_AT_MEAN_VOL_M / 2 * si.m)\n",
" )\n",
" builder.add_dynamic(PySDM.dynamics.Coalescence(\n",
" collision_kernel=PySDM.dynamics.collisions.collision_kernels.Golovin(\n",
" b=settings.ADDITIVE_KERNEL_COEFF\n",
" ), adaptive=False\n",
" ))\n",
"\n",
" self.particulator = builder.build(\n",
" attributes=builder.particulator.environment.init_attributes(\n",
" spectral_discretisation=PySDM.initialisation.sampling.spectral_sampling.Logarithmic(\n",
" spectrum,\n",
" )\n",
" ),\n",
" attributes = {}\n",
" (\n",
" attributes['volume'],\n",
" attributes['multiplicity'],\n",
" ) = PySDM.initialisation.sampling.spectral_sampling.Logarithmic(\n",
" spectrum\n",
" ).sample_deterministic(\n",
" backend=backend,\n",
" n_sd=settings.N_PART,\n",
" )\n",
" self.particulator = PySDM.Particulator(\n",
" environment=box,\n",
" n_sd=settings.N_PART,\n",
" attributes=attributes,\n",
" products=(\n",
" PySDM.products.ParticleSizeSpectrumPerVolume(\n",
" radius_bins_edges=settings.RADIUS_BIN_EDGES_M,\n",
Expand All @@ -321,7 +321,14 @@
" radius_bins_edges=settings.RADIUS_BIN_EDGES_M,\n",
" name='Volume Density (1/ unit ln R)',\n",
" )\n",
" )\n",
" ),\n",
" dynamics=(\n",
" PySDM.dynamics.Coalescence(\n",
" collision_kernel=PySDM.dynamics.collisions.collision_kernels.Golovin(\n",
" b=settings.ADDITIVE_KERNEL_COEFF\n",
" ), adaptive=False\n",
" ),\n",
" ),\n",
" )\n",
" super().__init__(settings)\n",
"\n",
Expand All @@ -332,7 +339,8 @@
" 'Mass Density (kg/m^3/unit ln R)':{}}\n",
" for step in range(self.settings.N_PLOT_STEPS + 1):\n",
" if step != 0:\n",
" self.particulator.run(int(self.settings.PLOT_TIME_STEP_SEC // self.settings.DT_SEC))\n",
" n_steps = int(self.settings.PLOT_TIME_STEP_SEC // self.settings.DT_SEC)\n",
" self.particulator.advance(n_steps)\n",
" #next two lines convert from dr to dlnr\n",
" pysdm_output['Number Concentration (#/m^3/unit ln R)'][step] = (\n",
" self.particulator.products['Number Concentration (#/m^3/m)'].get()\n",
Expand Down Expand Up @@ -1070,7 +1078,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.2"
"version": "3.13.5"
}
},
"nbformat": 4,
Expand Down
51 changes: 24 additions & 27 deletions examples/lognorm_ex.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -36,9 +36,9 @@
"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('PyPartMC', 'PySDM')\n",
" pip_install_on_colab('PyPartMC', 'PySDM>=3.0.0')\n",
"elif 'JUPYTER_IMAGE' in os.environ and '.arm.gov' in os.environ['JUPYTER_IMAGE']:\n",
" !pip --quiet install PyPartMC PySDM open-atmos-jupyter-utils\n",
" !pip --quiet install PyPartMC 'PySDM>=3.0.0' open-atmos-jupyter-utils\n",
" _pypartmc_path = !pip show PyPartMC | fgrep Location | cut -f2 -d' '\n",
" sys.path.extend(_pypartmc_path if _pypartmc_path[0] not in sys.path else [])"
]
Expand All @@ -54,14 +54,13 @@
"import ipywidgets as widgets\n",
"import numpy as np\n",
"from PySDM.environments import Box\n",
"from PySDM import Builder\n",
"from PySDM.backends import CPU\n",
"from PySDM.initialisation import equilibrate_wet_radii\n",
"from PySDM.initialisation.hygroscopic_equilibrium import equilibrate_wet_radii\n",
"from matplotlib import pyplot\n",
"from IPython.display import display, clear_output\n",
"from open_atmos_jupyter_utils import show_plot\n",
"from PyPartMC import si\n",
"import PyPartMC as ppmc\n"
"import PyPartMC as ppmc"
]
},
{
Expand Down Expand Up @@ -234,16 +233,14 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 17,
"id": "4d9881b4",
"metadata": {},
"outputs": [],
"source": [
"def pysdm(dry_diameters, temp, rel_humid, kappa):\n",
" r_dry = dry_diameters / 2\n",
" builder = Builder(n_sd=0, backend=CPU())\n",
" environment = Box(dt=np.nan, dv=np.nan)\n",
" environment.register(builder)\n",
" environment = Box(dt=np.nan, dv=np.nan, backend=CPU())\n",
" environment['T'] = temp\n",
" environment['RH'] = rel_humid\n",
" kappa_times_dry_volume = kappa * (np.pi / 6) * dry_diameters**3\n",
Expand All @@ -256,7 +253,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 18,
"id": "ee131ad8",
"metadata": {},
"outputs": [],
Expand All @@ -269,14 +266,14 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 19,
"id": "56fd1c71",
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "8413898068594929b63f25b06825f179",
"model_id": "2a2407370aa24bde8fb70b9e8ec5d5ac",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -290,7 +287,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "a6ae915030f7410292141561b880b036",
"model_id": "69d5191b28fe45ed8c16fb1dce09e4a3",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -304,7 +301,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "ccef33aae7484b94bf014631e97a5ce7",
"model_id": "5b841ee13d2f414781d71e9d5ada2662",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -318,7 +315,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "210dc96de734412e969291856705b875",
"model_id": "2de009dab50a484f852ef4bc0953b394",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -332,7 +329,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "b367f53a27d14a5fa96b7c44f342877f",
"model_id": "5e013b0a4d7d4d428fdf12121f7f32d2",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -346,7 +343,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "52c9258492e24a4581b6621f148818c5",
"model_id": "43c68b80d3374c3aa17998bd2c057515",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -360,12 +357,12 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "f6339251b9dd4d819c1d00fc965e6a64",
"model_id": "dd4071d070b544b496984f5001b54d10",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"HBox(children=(Label(value='Mode 1 Geometric Mean Diameter [microns]:'), FloatSlider(value=0.9, max=10.0, min=…"
"HBox(children=(Label(value='Mode 1 Geometric Mean Diameter [microns]:'), FloatSlider(value=0.901, max=10.0, mi…"
]
},
"metadata": {},
Expand All @@ -374,7 +371,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "074657939eee416eaad66e74a0db2041",
"model_id": "2dc027992cc748719d3f979e145014c9",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -388,7 +385,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "0774b29ac6384f1eb7d9b4ba4e519a88",
"model_id": "6f697a6bb1f943d6b8c1b6866ae40481",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -402,12 +399,12 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "d31861643fad408cbdc92b9ac5a4f1ce",
"model_id": "041227f317094df7b9cb3b1b60dc5de0",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"HBox(children=(Label(value='Mode 2 Geometric Mean Diameter [microns]:'), FloatSlider(value=5.8, max=10.0, min=…"
"HBox(children=(Label(value='Mode 2 Geometric Mean Diameter [microns]:'), FloatSlider(value=5.801, max=10.0, mi…"
]
},
"metadata": {},
Expand All @@ -416,7 +413,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "df434a9a1721464b95c35ce8ee79a0cc",
"model_id": "44b2228c41c244e9b513d786025f9151",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -430,7 +427,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "fa23ee7ebb8c4defbe29892795ed986a",
"model_id": "2be546cfe3fc4125a420832b2c6ef335",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -444,7 +441,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "b709cc132b6f4d60af07434521f4abcc",
"model_id": "03ae40fabaa04509993c675ad0ad02cd",
"version_major": 2,
"version_minor": 0
},
Expand Down Expand Up @@ -549,7 +546,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.13"
"version": "3.13.5"
},
"vscode": {
"interpreter": {
Expand Down
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