PySDM 2.85__tar.gz → 2.86__tar.gz

{pysdm-2.85 → pysdm-2.86}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.85
+Version: 2.86
 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
@@ -75,7 +75,7 @@ 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. 
 
-There is a growing set of example Jupyter notebooks exemplifying how to perform 
+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 
   a list of examples and links to the notebooks (which can be either executed or viewed 
@@ -134,7 +134,7 @@ Conda users may use ``pip`` as well, see the [Installing non-conda packages](htt
 For development purposes, we suggest cloning the repository and installing it using ``pip -e``.
 Test-time dependencies can be installed with ``pip -e .[tests]``.
 
-PySDM examples constitute the [``PySDM-examples``](https://github.com/open-atmos/PySDM-examples) package.
+PySDM examples constitute the [``PySDM-examples``](https://github.com/open-atmos/PySDM/blob/main/examples) package.
 The examples have additional dependencies listed in [``PySDM_examples`` package ``setup.py``](https://github.com/open-atmos/PySDM/blob/main/examples/setup.py) file.
 Running the example Jupyter notebooks requires the ``PySDM_examples`` package to be installed.
 The suggested install and launch steps are:
@@ -189,7 +189,8 @@ To run all pre-commit hooks, run `pre-commit run --all-files`.
 The `.pre-commit-config.yaml` file can be modified in case new hooks are to be added or
   existing ones need to be altered.  
 
-Further hints addressed at PySDM developers are maintained in the [open-atmos/python-dev-hints Wiki](https://github.com/open-atmos/python-dev-hints/wiki).
+Further hints addressed at PySDM developers are maintained in the [open-atmos/python-dev-hints Wiki](https://github.com/open-atmos/python-dev-hints/wiki)
+  and in [PySDM HOWTOs](https://github.com/open-atmos/PySDM/tree/main/examples/PySDM_examples/_HOWTOS).
 
 Issues regarding any incorrect, unintuitive or undocumented bahaviour of
 PySDM are best to be reported on the [GitHub issue tracker](https://github.com/open-atmos/PySDM/issues/new).

{pysdm-2.85 → pysdm-2.86}/PySDM/physics/dimensional_analysis.py

@@ -1,12 +1,12 @@
 """
-A context manager (for use with the `with` statement)
-for use in unit tests which disables Numba and enables Pint
+A context manager (for use with the `with` statement) which
+enables Pint physical-units checks and disables Numba in `PySDM.formulae.Formulae`
 """
 
 from importlib import reload
 
 from PySDM import formulae
-
+from PySDM import physics
 from . import constants, constants_defaults
 from .impl import flag
 
@@ -17,9 +17,11 @@ class DimensionalAnalysis:
         reload(constants)
         reload(constants_defaults)
         reload(formulae)
+        reload(physics)
 
     def __exit__(*_):  # pylint: disable=no-method-argument,no-self-argument
         flag.DIMENSIONAL_ANALYSIS = False
         reload(constants)
         reload(constants_defaults)
         reload(formulae)
+        reload(physics)

{pysdm-2.85 → pysdm-2.86}/PySDM.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.85
+Version: 2.86
 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
@@ -75,7 +75,7 @@ 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. 
 
-There is a growing set of example Jupyter notebooks exemplifying how to perform 
+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 
   a list of examples and links to the notebooks (which can be either executed or viewed 
@@ -134,7 +134,7 @@ Conda users may use ``pip`` as well, see the [Installing non-conda packages](htt
 For development purposes, we suggest cloning the repository and installing it using ``pip -e``.
 Test-time dependencies can be installed with ``pip -e .[tests]``.
 
-PySDM examples constitute the [``PySDM-examples``](https://github.com/open-atmos/PySDM-examples) package.
+PySDM examples constitute the [``PySDM-examples``](https://github.com/open-atmos/PySDM/blob/main/examples) package.
 The examples have additional dependencies listed in [``PySDM_examples`` package ``setup.py``](https://github.com/open-atmos/PySDM/blob/main/examples/setup.py) file.
 Running the example Jupyter notebooks requires the ``PySDM_examples`` package to be installed.
 The suggested install and launch steps are:
@@ -189,7 +189,8 @@ To run all pre-commit hooks, run `pre-commit run --all-files`.
 The `.pre-commit-config.yaml` file can be modified in case new hooks are to be added or
   existing ones need to be altered.  
 
-Further hints addressed at PySDM developers are maintained in the [open-atmos/python-dev-hints Wiki](https://github.com/open-atmos/python-dev-hints/wiki).
+Further hints addressed at PySDM developers are maintained in the [open-atmos/python-dev-hints Wiki](https://github.com/open-atmos/python-dev-hints/wiki)
+  and in [PySDM HOWTOs](https://github.com/open-atmos/PySDM/tree/main/examples/PySDM_examples/_HOWTOS).
 
 Issues regarding any incorrect, unintuitive or undocumented bahaviour of
 PySDM are best to be reported on the [GitHub issue tracker](https://github.com/open-atmos/PySDM/issues/new).

{pysdm-2.85 → pysdm-2.86}/PySDM.egg-info/SOURCES.txt

@@ -411,8 +411,11 @@ 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/markdown/pysdm_landing.md
+docs/templates/README.md
 docs/templates/custom.css
 docs/templates/index.html.jinja2
+docs/templates/syntax-highlighting.css
+docs/templates/theme.css
 examples/MANIFEST.in
 examples/README.md
 examples/pyproject.toml
@@ -606,6 +609,7 @@ examples/PySDM_examples/Yang_et_al_2018/__init__.py
 examples/PySDM_examples/Yang_et_al_2018/fig_2.ipynb
 examples/PySDM_examples/Yang_et_al_2018/settings.py
 examples/PySDM_examples/Yang_et_al_2018/simulation.py
+examples/PySDM_examples/_HOWTOs/dimensional_analysis.ipynb
 examples/PySDM_examples/deJong_Azimi/__init__.py
 examples/PySDM_examples/deJong_Azimi/box.ipynb
 examples/PySDM_examples/deJong_Azimi/cloudy_data.py

{pysdm-2.85 → pysdm-2.86}/README.md

@@ -35,7 +35,7 @@ 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. 
 
-There is a growing set of example Jupyter notebooks exemplifying how to perform 
+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 
   a list of examples and links to the notebooks (which can be either executed or viewed 
@@ -94,7 +94,7 @@ Conda users may use ``pip`` as well, see the [Installing non-conda packages](htt
 For development purposes, we suggest cloning the repository and installing it using ``pip -e``.
 Test-time dependencies can be installed with ``pip -e .[tests]``.
 
-PySDM examples constitute the [``PySDM-examples``](https://github.com/open-atmos/PySDM-examples) package.
+PySDM examples constitute the [``PySDM-examples``](https://github.com/open-atmos/PySDM/blob/main/examples) package.
 The examples have additional dependencies listed in [``PySDM_examples`` package ``setup.py``](https://github.com/open-atmos/PySDM/blob/main/examples/setup.py) file.
 Running the example Jupyter notebooks requires the ``PySDM_examples`` package to be installed.
 The suggested install and launch steps are:
@@ -149,7 +149,8 @@ To run all pre-commit hooks, run `pre-commit run --all-files`.
 The `.pre-commit-config.yaml` file can be modified in case new hooks are to be added or
   existing ones need to be altered.  
 
-Further hints addressed at PySDM developers are maintained in the [open-atmos/python-dev-hints Wiki](https://github.com/open-atmos/python-dev-hints/wiki).
+Further hints addressed at PySDM developers are maintained in the [open-atmos/python-dev-hints Wiki](https://github.com/open-atmos/python-dev-hints/wiki)
+  and in [PySDM HOWTOs](https://github.com/open-atmos/PySDM/tree/main/examples/PySDM_examples/_HOWTOS).
 
 Issues regarding any incorrect, unintuitive or undocumented bahaviour of
 PySDM are best to be reported on the [GitHub issue tracker](https://github.com/open-atmos/PySDM/issues/new).

pysdm-2.86/docs/templates/README.md

@@ -0,0 +1 @@
+dark mode .css from https://github.com/mitmproxy/pdoc/tree/main/examples/dark-mode

pysdm-2.86/docs/templates/custom.css

@@ -0,0 +1,9 @@
+img {
+    max-width: 100%;
+}
+
+mark {
+    background-color: #859bed;
+    color: black;
+}
+

{pysdm-2.85 → pysdm-2.86}/docs/templates/index.html.jinja2

@@ -91,7 +91,8 @@
         <pre><code>git clone https://github.com/open-atmos/PySDM.git
 pip install -e PySDM[tests] -e PySDM/examples[tests]
 pytest PySDM</code></pre>
-        <p>(the above should be a viable way to set up development environment for PySDM, see also our <a href="https://github.com/open-atmos/python-dev-hints/wiki">Python dev hints Wiki</a> for further information)</p>
+        <p>(the above should be a viable way to set up development environment for PySDM, see also our <a href="https://github.com/open-atmos/python-dev-hints/wiki">Python dev hints Wiki</a> 
+          and <a href="https://github.com/open-atmos/PySDM/tree/main/examples/PySDM_examples/_HOWTOS">PySDM HOWTOs</a> for further information)</p>
         <p>
             PySDM-examples is also available on PyPI and can be installed using pip:
         </p>

pysdm-2.86/docs/templates/syntax-highlighting.css

@@ -0,0 +1,80 @@
+/* monokai color scheme, see pdoc/template/README.md */
+pre { line-height: 125%; }
+span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 20px; }
+.pdoc-code .hll { background-color: #49483e }
+.pdoc-code { background: #272822; color: #f8f8f2 }
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pysdm-2.86/docs/templates/theme.css

@@ -0,0 +1,20 @@
+:root {
+    --pdoc-background: #212529;
+}
+
+.pdoc {
+    --text: #f7f7f7;
+    --muted: #9d9d9d;
+    --link: #58a6ff;
+    --link-hover: #3989ff;
+    --code: #333;
+    --active: #555;
+
+    --accent: #343434;
+    --accent2: #555;
+
+    --nav-hover: rgba(0, 0, 0, 0.1);
+    --name: #77C1FF;
+    --def: #0cdd0c;
+    --annotation: #00c037;
+}

{pysdm-2.85 → pysdm-2.86}/examples/PySDM_examples/Arabas_et_al_2015/settings.py

@@ -1,12 +1,8 @@
 from typing import Iterable
 
-import numpy as np
 from PySDM_examples.Morrison_and_Grabowski_2007.strato_cumulus import StratoCumulus
 
 from PySDM import Formulae
-from PySDM.dynamics.collisions.breakup_efficiencies import ConstEb
-from PySDM.dynamics.collisions.breakup_fragmentations import Gaussian
-from PySDM.dynamics.collisions.coalescence_efficiencies import ConstEc
 from PySDM.physics import si
 
 
@@ -39,12 +35,3 @@ class Settings(StratoCumulus):
         self.simulation_time = 90 * si.minute
         self.dt = 5 * si.second
         self.spin_up_time = 1 * si.hour
-
-        # additional breakup dynamics
-        mu_r = 10 * si.um
-        mu = 4 / 3 * np.pi * mu_r**3
-        sigma = mu / 2.5
-        vmin = mu / 1000
-        self.coalescence_efficiency = ConstEc(Ec=0.95)
-        self.breakup_efficiency = ConstEb(Eb=1.0)
-        self.breakup_fragmentation = Gaussian(mu=mu, sigma=sigma, vmin=vmin, nfmax=10)

pysdm-2.86/examples/PySDM_examples/_HOWTOs/dimensional_analysis.ipynb

@@ -0,0 +1,175 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "c1925b9647eb39e9",
+   "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/howtos/units.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/howtos/units.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/howtos/units.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "57a5c59c4cb8a1ec",
+   "metadata": {},
+   "source": [
+    "### PySDM dimensional analysis HOWTO\n",
+    "- PySDM depends on the [Pint](https://pint.readthedocs.io/en/stable/) package which offers dimensional analysis (physical units checks) of Python code \n",
+    "- this improves code readibility with expressions such as `p = 1000 * si.hPa`\n",
+    "- using [Pint](https://pint.readthedocs.io/en/stable/), `si` is an instance of [`pint.UnitRegistry`](https://pint.readthedocs.io/en/stable/api/base.html#pint.UnitRegistry) \n",
+    "- however, for performance reasons, by default PySDM uses a custom drop-in-replacement [`FakeUnitRegistry`](https://open-atmos.github.io/PySDM/PySDM/physics/impl/fake_unit_registry.html#FakeUnitRegistry)\n",
+    "- this way, we keep the readibility advantage, while not incurring any performance overhead\n",
+    "- moreover, this makes the code potentially Numba JIT-compilable!\n",
+    "- we also provide a way to leverage the dimensional analysis benefit for testing purposes\n",
+    "- to this end, the test code can use the [`DimensionalAnalysis`](https://open-atmos.github.io/PySDM/PySDM/physics/dimensional_analysis.html#DimensionalAnalysis) context manager\n",
+    "- code below demonstrate how a single unit-equipped function can be used with and without unit checks "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "97dab670c5cf8d8b",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-12-04T13:27:07.009798Z",
+     "start_time": "2024-12-04T13:27:07.003077Z"
+    }
+   },
+   "outputs": [],
+   "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')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "19a8f1dc-a5ea-461b-9019-50d25dfa7bc6",
+   "metadata": {},
+   "source": [
+    "#### sample physics-related code"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "6ea31783d8e0e849",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-12-04T13:27:08.240983Z",
+     "start_time": "2024-12-04T13:27:07.013763Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "from PySDM import physics\n",
+    "\n",
+    "def code():\n",
+    "    si = physics.si\n",
+    "\n",
+    "    p = 1000 * si.hPa\n",
+    "    T = 300 * si.K\n",
+    "    R = 286 * si.J / si.K / si.kg\n",
+    "\n",
+    "    rho = p / R / T\n",
+    "    return rho"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "183bcca3-5546-4676-a6bc-de3a1dd76ccb",
+   "metadata": {},
+   "source": [
+    "#### sample unit-unaware usage (default)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "287ae3f109f11bb6",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-12-04T13:27:08.341648Z",
+     "start_time": "2024-12-04T13:27:08.339564Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "1.2\n"
+     ]
+    }
+   ],
+   "source": [
+    "result_unit_unaware = code()\n",
+    "print(f\"{result_unit_unaware:.2g}\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "da1669cf-653b-4138-9ff9-8fac303ad8c4",
+   "metadata": {},
+   "source": [
+    "#### sample unit-aware usage (e.g., for testing)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "85bf8e7bc2ca98a",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-12-04T13:27:08.671915Z",
+     "start_time": "2024-12-04T13:27:08.402327Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "0.012 hectopascal * kilogram / joule\n",
+      "1.2 kilogram / meter ** 3\n"
+     ]
+    }
+   ],
+   "source": [
+    "from PySDM.physics.dimensional_analysis import DimensionalAnalysis\n",
+    "\n",
+    "with DimensionalAnalysis():\n",
+    "    result_unit_aware = code()\n",
+    "\n",
+    "assert result_unit_aware.check(\"[mass] / [volume]\")\n",
+    "print(f\"{result_unit_aware:.2g}\")\n",
+    "print(f\"{result_unit_aware.to_base_units():.2g}\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{pysdm-2.85 → pysdm-2.86}/tests/examples_tests/conftest.py

@@ -61,6 +61,7 @@ TEST_SUITES = {
         "Morrison_and_Grabowski_2007",
         "Szumowski_et_al_1998",
         "utils",
+        "_HOWTOs",
     ],
 }
 

pysdm-2.85/docs/templates/custom.css

@@ -1,3 +0,0 @@
-img {
-    max-width: 100%;
-}