PySDM 2.70__tar.gz → 2.72__tar.gz

{PySDM-2.70 → PySDM-2.72}/.github/workflows/tests+artifacts+pypi.yml

@@ -69,11 +69,10 @@ jobs:
         with:
           python-version: 3.9
       - run: |
-          pip install pdoc3
+          pip install pdoc
           pip install -e .
           pip install -e examples
-          python -We -m pdoc --html PySDM examples/PySDM_examples
-          python -We .github/workflows/pdoc_index_workaround.py
+          PDOC_ALLOW_EXEC=1 python -We -m pdoc -o html PySDM examples/PySDM_examples -t pdoc_templates
       - if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' }}
         uses: JamesIves/github-pages-deploy-action@4.1.1
         with:

{PySDM-2.70 → PySDM-2.72}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.70
+Version: 2.72
 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
@@ -32,7 +32,7 @@ Description: # PySDM
         [![Appveyor Build status](http://ci.appveyor.com/api/projects/status/github/open-atmos/PySDM?branch=main&svg=true)](https://ci.appveyor.com/project/slayoo/pysdm/branch/main)
         [![Coverage Status](https://codecov.io/gh/open-atmos/PySDM/branch/main/graph/badge.svg)](https://app.codecov.io/gh/open-atmos/PySDM)    
         [![PyPI version](https://badge.fury.io/py/PySDM.svg)](https://pypi.org/project/PySDM)
-        [![API docs](https://img.shields.io/badge/API_docs-pdoc3-blue.svg)](https://open-atmos.github.io/PySDM/)
+        [![API docs](https://shields.mitmproxy.org/badge/docs-pdoc.dev-brightgreen.svg)](https://open-atmos.github.io/PySDM/)
         
         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
@@ -62,9 +62,9 @@ Description: # PySDM
         PySDM has two alternative parallel number-crunching backends 
           available: multi-threaded CPU backend based on [Numba](http://numba.pydata.org/) 
           and GPU-resident backend built on top of [ThrustRTC](https://pypi.org/project/ThrustRTC/).
-        The [`Numba`](https://open-atmos.github.io/PySDM/PySDM/backends/numba/numba.html) backend (aliased ``CPU``) features multi-threaded parallelism for 
+        The [`Numba`](https://open-atmos.github.io/PySDM/PySDM/backends/numba.html) backend (aliased ``CPU``) features multi-threaded parallelism for 
           multi-core CPUs, it uses the just-in-time compilation technique based on the LLVM infrastructure.
-        The [`ThrustRTC`](https://open-atmos.github.io/PySDM/PySDM/backends/thrustRTC/thrustRTC.html) backend (aliased ``GPU``) offers GPU-resident operation of PySDM
+        The [`ThrustRTC`](https://open-atmos.github.io/PySDM/PySDM/backends/thrust_rtc.html) backend (aliased ``GPU``) offers GPU-resident operation of PySDM
           leveraging the [SIMT](https://en.wikipedia.org/wiki/Single_instruction,_multiple_threads) 
           parallelisation model. 
         Using the ``GPU`` backend requires nVidia hardware and [CUDA driver](https://developer.nvidia.com/cuda-downloads).
@@ -76,7 +76,7 @@ Description: # PySDM
         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://pdoc3.github.io/pdoc) documentation of PySDM public API is maintained at: [https://open-atmos.github.io/PySDM](https://open-atmos.github.io/PySDM) 
+        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):
         
@@ -186,8 +186,8 @@ Description: # PySDM
           listings provide sample code roughly reproducing the 
           Figure 2 from [Shima et al. 2009 paper](http://doi.org/10.1002/qj.441)
           using PySDM from Python, Julia and Matlab.
-        It is a [`Coalescence`](https://open-atmos.github.io/PySDM/PySDM/dynamics/coalescence.html)-only set-up in which the initial particle size 
-          spectrum is [`Exponential`](https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra.html#PySDM.initialisation.spectra.Exponential) and is deterministically sampled to match
+        It is a [`Coalescence`](https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/sollision.html#Coalescence)-only set-up in which the initial particle size 
+          spectrum is [`Exponential`](https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra/exponential.html#Exponential) and is deterministically sampled to match
           the condition of each super-droplet having equal initial multiplicity:
         <details>
         <summary>Julia (click to expand)</summary>
@@ -241,9 +241,9 @@ Description: # PySDM
         ```
         </details>
         
-        The key element of the PySDM interface is the [``Particulator``](https://open-atmos.github.io/PySDM/PySDM/particulator.html) 
+        The key element of the PySDM interface is the [``Particulator``](https://open-atmos.github.io/PySDM/PySDM/particulator.html#Particulator) 
           class instances of which are used to manage the system state and control the simulation.
-        Instantiation of the [``Particulator``](https://open-atmos.github.io/PySDM/PySDM/particulator.html) class is handled by the [``Builder``](https://open-atmos.github.io/PySDM/PySDM/builder.html)
+        Instantiation of the [``Particulator``](https://open-atmos.github.io/PySDM/PySDM/particulator.html#Particulator) class is handled by the [``Builder``](https://open-atmos.github.io/PySDM/PySDM/builder.html#Builder)
           as exemplified below:
         <details>
         <summary>Julia (click to expand)</summary>
@@ -313,18 +313,18 @@ Description: # PySDM
         The ``backend`` argument may be set to ``CPU`` or ``GPU``
           what translates to choosing the multi-threaded backend or the 
           GPU-resident computation mode, respectively.
-        The employed [`Box`](https://open-atmos.github.io/PySDM/PySDM/environments/box.html) environment corresponds to a zero-dimensional framework
+        The employed [`Box`](https://open-atmos.github.io/PySDM/PySDM/environments/box.html#Box) environment corresponds to a zero-dimensional framework
           (particle positions are not considered).
         The vectors of particle multiplicities ``n`` and particle volumes ``v`` are
           used to initialise super-droplet attributes.
-        The [`Coalescence`](https://open-atmos.github.io/PySDM/PySDM/dynamics/coalescence.html)
+        The [`Coalescence`](https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision.html#Coalescence)
           Monte-Carlo algorithm (Super Droplet Method) is registered as the only
           dynamic in the system.
-        Finally, the [`build()`](https://open-atmos.github.io/PySDM/PySDM/builder.html#PySDM.builder.Builder.build) method is used to obtain an instance
-          of [`Particulator`](https://open-atmos.github.io/PySDM/PySDM/particulator.html#PySDM.particulator.Particulator) which can then be used to control time-stepping and
+        Finally, the [`build()`](https://open-atmos.github.io/PySDM/PySDM/builder.html#Builder.build) method is used to obtain an instance
+          of [`Particulator`](https://open-atmos.github.io/PySDM/PySDM/particulator.html#Particulator) which can then be used to control time-stepping and
           access simulation state.
         
-        The [`run(nt)`](https://open-atmos.github.io/PySDM/PySDM/particulator.html#PySDM.particuparticulatorr.Particulator.run) method advances the simulation by ``nt`` timesteps.
+        The [`run(nt)`](https://open-atmos.github.io/PySDM/PySDM/particulator.html#Particulator.run) method advances the simulation by ``nt`` timesteps.
         In the listing below, its usage is interleaved with plotting logic
           which displays a histogram of particle mass distribution 
           at selected timesteps:
@@ -441,16 +441,16 @@ Description: # PySDM
             SPECTRUM_INIT["ParticleVolumeVersusRadiusLogarithmSpectrum.__init__()"] -->|instantiates| SPECTRUM
             SPECTRUM[":ParticleVolumeVersusRadiusLogarithmSpectrum"] -->|added as element of| PRODUCTS
         
-            click COAL "https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision.html"
+            click COAL "https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision.html#Coalescence"
             click BUILDER_INSTANCE "https://open-atmos.github.io/PySDM/PySDM/builder.html"
             click BUILDER_INIT "https://open-atmos.github.io/PySDM/PySDM/builder.html"
             click BUILDER_ADD_DYN "https://open-atmos.github.io/PySDM/PySDM/builder.html"
-            click ENV_INIT "https://open-atmos.github.io/PySDM/PySDM/environments/index.html"
-            click ENV "https://open-atmos.github.io/PySDM/PySDM/environments/index.html"
-            click KERNEL_INIT "https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision_kernels/index.html"
-            click KERNEL "https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision_kernels/index.html"
-            click EXP_INIT "https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra/index.html"
-            click IS "https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra/index.html"
+            click ENV_INIT "https://open-atmos.github.io/PySDM/PySDM/environments.html"
+            click ENV "https://open-atmos.github.io/PySDM/PySDM/environments.html"
+            click KERNEL_INIT "https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision_kernels.html"
+            click KERNEL "https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision_kernels.html"
+            click EXP_INIT "https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra.html"
+            click IS "https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra.html"
             click CM_INIT "https://open-atmos.github.io/PySDM/PySDM/initialisation/sampling/spectral_sampling.html"
             click CM_INSTANCE "https://open-atmos.github.io/PySDM/PySDM/initialisation/sampling/spectral_sampling.html"
             click SAMPLE "https://open-atmos.github.io/PySDM/PySDM/initialisation/sampling/spectral_sampling.html"
@@ -466,7 +466,7 @@ Description: # PySDM
         
         In the following example, a condensation-only setup is used with the adiabatic 
         [`Parcel`](https://open-atmos.github.io/PySDM/PySDM/environments/parcel.html) environment.
-        An initial [`Lognormal`](https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra.html#PySDM.initialisation.spectra.Lognormal)
+        An initial [`Lognormal`](https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra/lognormal.html#Lognormal)
         spectrum of dry aerosol particles is first initialised to equilibrium wet size for the given
         initial humidity. 
         Subsequent particle growth due to [`Condensation`](https://open-atmos.github.io/PySDM/PySDM/dynamics/condensation.html) of water vapour (coupled with the release of latent heat)
@@ -476,7 +476,7 @@ Description: # PySDM
         and depict the evolution of 
         [`PeakSupersaturation`](https://open-atmos.github.io/PySDM/PySDM/products/condensation/peak_supersaturation.html), 
         [`EffectiveRadius`](https://open-atmos.github.io/PySDM/PySDM/products/size_spectral/effective_radius.html), 
-        [`ParticleConcentration`](https://open-atmos.github.io/PySDM/PySDM/products/size_spectral/particle_concentration.html#PySDM.products.particles_concentration.ParticleConcentration) 
+        [`ParticleConcentration`](https://open-atmos.github.io/PySDM/PySDM/products/size_spectral/particle_concentration.html#ParticleConcentration) 
         and the 
         [`WaterMixingRatio `](https://open-atmos.github.io/PySDM/PySDM/products/size_spectral/water_mixing_ratio.html).
         

{PySDM-2.70 → PySDM-2.72}/PySDM/builder.py

@@ -121,8 +121,8 @@ class Builder:
             self._resolve_attribute(attr_name)
         self.req_attr_names = None
 
-        for dynamic in self.particulator.dynamics.values():
-            dynamic.register(self)
+        for key, dynamic in self.particulator.dynamics.items():
+            self.particulator.dynamics[key] = dynamic.instantiate(builder=self)
 
         single_buffer_for_all_products = np.empty(self.particulator.mesh.grid)
         for product in products:

{PySDM-2.70 → PySDM-2.72}/PySDM/dynamics/ambient_thermodynamics.py

@@ -2,7 +2,10 @@
 environment-sync triggering class
 """
 
+from PySDM.dynamics.impl import register_dynamic
 
+
+@register_dynamic()
 class AmbientThermodynamics:
     def __init__(self):
         self.particulator = None

{PySDM-2.70 → PySDM-2.72}/PySDM/dynamics/aqueous_chemistry.py

@@ -13,12 +13,14 @@ from PySDM.dynamics.impl.chemistry_utils import (
     M,
     SpecificGravities,
 )
+from PySDM.dynamics.impl import register_dynamic
 
 DEFAULTS = namedtuple("_", ("pH_min", "pH_max", "pH_rtol", "ionic_strength_threshold"))(
     pH_min=-1.0, pH_max=14.0, pH_rtol=1e-6, ionic_strength_threshold=0.02 * M
 )
 
 
+@register_dynamic()
 class AqueousChemistry:  # pylint: disable=too-many-instance-attributes
     def __init__(
         self,

{PySDM-2.70 → PySDM-2.72}/PySDM/dynamics/collisions/collision.py

@@ -23,6 +23,7 @@ from PySDM.dynamics.impl.random_generator_optimizer_nopair import (
     RandomGeneratorOptimizerNoPair,
 )
 from PySDM.physics import si
+from PySDM.dynamics.impl import register_dynamic
 
 # pylint: disable=too-many-lines
 
@@ -36,6 +37,7 @@ DEFAULTS = namedtuple(
 )
 
 
+@register_dynamic()
 class Collision:  # pylint: disable=too-many-instance-attributes
     def __init__(
         self,
@@ -288,6 +290,7 @@ class Collision:  # pylint: disable=too-many-instance-attributes
         )
 
 
+@register_dynamic()
 class Coalescence(Collision):
     def __init__(
         self,
@@ -316,6 +319,7 @@ class Coalescence(Collision):
         )
 
 
+@register_dynamic()
 class Breakup(Collision):
     def __init__(
         self,

{PySDM-2.70 → PySDM-2.72}/PySDM/dynamics/condensation.py

@@ -7,7 +7,8 @@ from collections import namedtuple
 
 import numpy as np
 
-from ..physics import si
+from PySDM.physics import si
+from PySDM.dynamics.impl import register_dynamic
 
 DEFAULTS = namedtuple("_", ("rtol_x", "rtol_thd", "cond_range", "schedule"))(
     rtol_x=1e-6,
@@ -17,6 +18,7 @@ DEFAULTS = namedtuple("_", ("rtol_x", "rtol_thd", "cond_range", "schedule"))(
 )
 
 
+@register_dynamic()
 class Condensation:  # pylint: disable=too-many-instance-attributes
     def __init__(
         self,

{PySDM-2.70 → PySDM-2.72}/PySDM/dynamics/displacement.py

@@ -11,9 +11,12 @@ from collections import namedtuple
 
 import numpy as np
 
+from PySDM.dynamics.impl import register_dynamic
+
 DEFAULTS = namedtuple("_", ("rtol", "adaptive"))(rtol=1e-2, adaptive=True)
 
 
+@register_dynamic()
 class Displacement:  # pylint: disable=too-many-instance-attributes
     def __init__(
         self,

PySDM-2.72/PySDM/dynamics/eulerian_advection.py

@@ -0,0 +1,22 @@
+"""
+wrapper class for triggering integration in the Eulerian advection solver
+"""
+
+from PySDM.dynamics.impl import register_dynamic
+
+
+@register_dynamic()
+class EulerianAdvection:
+    def __init__(self, solvers):
+        self.solvers = solvers
+        self.particulator = None
+
+    def register(self, builder):
+        self.particulator = builder.particulator
+
+    def __call__(self):
+        for field in ("water_vapour_mixing_ratio", "thd"):
+            self.particulator.environment.get_predicted(field).download(
+                getattr(self.particulator.environment, f"get_{field}")(), reshape=True
+            )
+        self.solvers(self.particulator.dynamics["Displacement"])

{PySDM-2.70 → PySDM-2.72}/PySDM/dynamics/freezing.py

@@ -7,8 +7,10 @@ from PySDM.backends.impl_common.freezing_attributes import (
     TimeDependentAttributes,
 )
 from PySDM.physics.heterogeneous_ice_nucleation_rate import Null
+from PySDM.dynamics.impl import register_dynamic
 
 
+@register_dynamic()
 class Freezing:
     def __init__(self, *, singular=True, record_freezing_temperature=False, thaw=False):
         assert not (record_freezing_temperature and singular)

{PySDM-2.70 → PySDM-2.72}/PySDM/dynamics/impl/__init__.py

@@ -1 +1,3 @@
 """ stuff not intended to be imported from user code """
+
+from .register_dynamic import register_dynamic

PySDM-2.72/PySDM/dynamics/impl/register_dynamic.py

@@ -0,0 +1,21 @@
+""" decorator for dynamics classes
+ensuring that their instances can be re-used with multiple builders """
+
+from copy import deepcopy
+
+
+def _instantiate(self, *, builder):
+    copy = deepcopy(self)
+    copy.register(builder=builder)
+    return copy
+
+
+def register_dynamic():
+    def decorator(cls):
+        if hasattr(cls, "instantiate"):
+            assert cls.instantiate is _instantiate
+        else:
+            setattr(cls, "instantiate", _instantiate)
+        return cls
+
+    return decorator

{PySDM-2.70 → PySDM-2.72}/PySDM/dynamics/isotopic_fractionation.py

@@ -4,11 +4,13 @@ requires condensation dynamic to be registered (and run beforehand)
 """
 
 from PySDM.dynamics.condensation import Condensation
+from PySDM.dynamics.impl import register_dynamic
 
 LIGHT_ISOTOPES = ("1H", "16O")
 HEAVY_ISOTOPES = ("2H", "3H", "17O", "18O")
 
 
+@register_dynamic()
 class IsotopicFractionation:
     def __init__(self, isotopes: tuple = HEAVY_ISOTOPES):
         self.isotopes = isotopes

{PySDM-2.70 → PySDM-2.72}/PySDM/dynamics/relaxed_velocity.py

@@ -6,8 +6,10 @@ towards the terminal velocity
 
 from PySDM.attributes.impl.attribute import Attribute
 from PySDM.particulator import Particulator
+from PySDM.dynamics.impl import register_dynamic
 
 
+@register_dynamic()
 class RelaxedVelocity:  # pylint: disable=too-many-instance-attributes
     """
     A dynamic which updates the fall momentum according to a relaxation timescale

{PySDM-2.70 → PySDM-2.72}/PySDM/environments/impl/moist.py

@@ -44,21 +44,21 @@ class Moist:
             result[var] = self.particulator.Storage.empty((self.mesh.n_cell,), float)
         return result
 
-    def __getitem__(self, index):
-        """returns a Storage representing the variable (field) at a given index or
-        otherwise a NaN-filled Storage if the index is not found (in order to simplify
+    def __getitem__(self, key: str):
+        """returns a Storage representing the variable (field) at a given key or
+        otherwise a NaN-filled Storage if the key is not found (in order to simplify
         generic code which uses optional variables, e.g. air viscosity, etc.)"""
-        if index in self._values["current"]:
-            return self._values["current"][index]
+        if key in self._values["current"]:
+            return self._values["current"][key]
         return self._nan_field
 
-    def get_predicted(self, index):
+    def get_predicted(self, key: str):
         if self._values["predicted"] is None:
             raise AssertionError(
                 "It seems the AmbientThermodynamics dynamic was not added"
                 " when building particulator"
             )
-        return self._values["predicted"][index]
+        return self._values["predicted"][key]
 
     def _recalculate_temperature_pressure_relative_humidity(self, target):
         self.particulator.backend.temperature_pressure_rh(

{PySDM-2.70 → PySDM-2.72}/PySDM/environments/kinematic_1d.py

@@ -26,7 +26,7 @@ class Kinematic1D(Moist):
         self._tmp["rhod"] = rhod
 
     def get_water_vapour_mixing_ratio(self) -> np.ndarray:
-        return self.particulator.dynamics["EulerianAdvection"].solvers.advectee.get()
+        return self.particulator.dynamics["EulerianAdvection"].solvers.advectee
 
     def get_thd(self) -> np.ndarray:
         return self.thd0
@@ -61,9 +61,7 @@ class Kinematic1D(Moist):
                 v_wet, n_per_kg = spectral_discretisation.sample(
                     backend=self.particulator.backend, n_sd=self.particulator.n_sd
                 )
-                # attributes["dry volume"] = v_wet
                 attributes["volume"] = v_wet
-                # attributes["kappa times dry volume"] = attributes["dry volume"] * kappa
             else:
                 r_dry, n_per_kg = spectral_discretisation.sample(
                     backend=self.particulator.backend, n_sd=self.particulator.n_sd

{PySDM-2.70 → PySDM-2.72}/PySDM/environments/kinematic_2d.py

@@ -85,16 +85,12 @@ class Kinematic2D(Moist):
         return attributes
 
     def get_thd(self):
-        return (
-            self.particulator.dynamics["EulerianAdvection"].solvers["th"].advectee.get()
-        )
+        return self.particulator.dynamics["EulerianAdvection"].solvers["th"]
 
     def get_water_vapour_mixing_ratio(self):
-        return (
-            self.particulator.dynamics["EulerianAdvection"]
-            .solvers["water_vapour_mixing_ratio"]
-            .advectee.get()
-        )
+        return self.particulator.dynamics["EulerianAdvection"].solvers[
+            "water_vapour_mixing_ratio"
+        ]
 
     def sync(self):
         self.particulator.dynamics["EulerianAdvection"].solvers.wait()

{PySDM-2.70 → PySDM-2.72}/PySDM.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.70
+Version: 2.72
 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
@@ -32,7 +32,7 @@ Description: # PySDM
         [![Appveyor Build status](http://ci.appveyor.com/api/projects/status/github/open-atmos/PySDM?branch=main&svg=true)](https://ci.appveyor.com/project/slayoo/pysdm/branch/main)
         [![Coverage Status](https://codecov.io/gh/open-atmos/PySDM/branch/main/graph/badge.svg)](https://app.codecov.io/gh/open-atmos/PySDM)    
         [![PyPI version](https://badge.fury.io/py/PySDM.svg)](https://pypi.org/project/PySDM)
-        [![API docs](https://img.shields.io/badge/API_docs-pdoc3-blue.svg)](https://open-atmos.github.io/PySDM/)
+        [![API docs](https://shields.mitmproxy.org/badge/docs-pdoc.dev-brightgreen.svg)](https://open-atmos.github.io/PySDM/)
         
         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
@@ -62,9 +62,9 @@ Description: # PySDM
         PySDM has two alternative parallel number-crunching backends 
           available: multi-threaded CPU backend based on [Numba](http://numba.pydata.org/) 
           and GPU-resident backend built on top of [ThrustRTC](https://pypi.org/project/ThrustRTC/).
-        The [`Numba`](https://open-atmos.github.io/PySDM/PySDM/backends/numba/numba.html) backend (aliased ``CPU``) features multi-threaded parallelism for 
+        The [`Numba`](https://open-atmos.github.io/PySDM/PySDM/backends/numba.html) backend (aliased ``CPU``) features multi-threaded parallelism for 
           multi-core CPUs, it uses the just-in-time compilation technique based on the LLVM infrastructure.
-        The [`ThrustRTC`](https://open-atmos.github.io/PySDM/PySDM/backends/thrustRTC/thrustRTC.html) backend (aliased ``GPU``) offers GPU-resident operation of PySDM
+        The [`ThrustRTC`](https://open-atmos.github.io/PySDM/PySDM/backends/thrust_rtc.html) backend (aliased ``GPU``) offers GPU-resident operation of PySDM
           leveraging the [SIMT](https://en.wikipedia.org/wiki/Single_instruction,_multiple_threads) 
           parallelisation model. 
         Using the ``GPU`` backend requires nVidia hardware and [CUDA driver](https://developer.nvidia.com/cuda-downloads).
@@ -76,7 +76,7 @@ Description: # PySDM
         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://pdoc3.github.io/pdoc) documentation of PySDM public API is maintained at: [https://open-atmos.github.io/PySDM](https://open-atmos.github.io/PySDM) 
+        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):
         
@@ -186,8 +186,8 @@ Description: # PySDM
           listings provide sample code roughly reproducing the 
           Figure 2 from [Shima et al. 2009 paper](http://doi.org/10.1002/qj.441)
           using PySDM from Python, Julia and Matlab.
-        It is a [`Coalescence`](https://open-atmos.github.io/PySDM/PySDM/dynamics/coalescence.html)-only set-up in which the initial particle size 
-          spectrum is [`Exponential`](https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra.html#PySDM.initialisation.spectra.Exponential) and is deterministically sampled to match
+        It is a [`Coalescence`](https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/sollision.html#Coalescence)-only set-up in which the initial particle size 
+          spectrum is [`Exponential`](https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra/exponential.html#Exponential) and is deterministically sampled to match
           the condition of each super-droplet having equal initial multiplicity:
         <details>
         <summary>Julia (click to expand)</summary>
@@ -241,9 +241,9 @@ Description: # PySDM
         ```
         </details>
         
-        The key element of the PySDM interface is the [``Particulator``](https://open-atmos.github.io/PySDM/PySDM/particulator.html) 
+        The key element of the PySDM interface is the [``Particulator``](https://open-atmos.github.io/PySDM/PySDM/particulator.html#Particulator) 
           class instances of which are used to manage the system state and control the simulation.
-        Instantiation of the [``Particulator``](https://open-atmos.github.io/PySDM/PySDM/particulator.html) class is handled by the [``Builder``](https://open-atmos.github.io/PySDM/PySDM/builder.html)
+        Instantiation of the [``Particulator``](https://open-atmos.github.io/PySDM/PySDM/particulator.html#Particulator) class is handled by the [``Builder``](https://open-atmos.github.io/PySDM/PySDM/builder.html#Builder)
           as exemplified below:
         <details>
         <summary>Julia (click to expand)</summary>
@@ -313,18 +313,18 @@ Description: # PySDM
         The ``backend`` argument may be set to ``CPU`` or ``GPU``
           what translates to choosing the multi-threaded backend or the 
           GPU-resident computation mode, respectively.
-        The employed [`Box`](https://open-atmos.github.io/PySDM/PySDM/environments/box.html) environment corresponds to a zero-dimensional framework
+        The employed [`Box`](https://open-atmos.github.io/PySDM/PySDM/environments/box.html#Box) environment corresponds to a zero-dimensional framework
           (particle positions are not considered).
         The vectors of particle multiplicities ``n`` and particle volumes ``v`` are
           used to initialise super-droplet attributes.
-        The [`Coalescence`](https://open-atmos.github.io/PySDM/PySDM/dynamics/coalescence.html)
+        The [`Coalescence`](https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision.html#Coalescence)
           Monte-Carlo algorithm (Super Droplet Method) is registered as the only
           dynamic in the system.
-        Finally, the [`build()`](https://open-atmos.github.io/PySDM/PySDM/builder.html#PySDM.builder.Builder.build) method is used to obtain an instance
-          of [`Particulator`](https://open-atmos.github.io/PySDM/PySDM/particulator.html#PySDM.particulator.Particulator) which can then be used to control time-stepping and
+        Finally, the [`build()`](https://open-atmos.github.io/PySDM/PySDM/builder.html#Builder.build) method is used to obtain an instance
+          of [`Particulator`](https://open-atmos.github.io/PySDM/PySDM/particulator.html#Particulator) which can then be used to control time-stepping and
           access simulation state.
         
-        The [`run(nt)`](https://open-atmos.github.io/PySDM/PySDM/particulator.html#PySDM.particuparticulatorr.Particulator.run) method advances the simulation by ``nt`` timesteps.
+        The [`run(nt)`](https://open-atmos.github.io/PySDM/PySDM/particulator.html#Particulator.run) method advances the simulation by ``nt`` timesteps.
         In the listing below, its usage is interleaved with plotting logic
           which displays a histogram of particle mass distribution 
           at selected timesteps:
@@ -441,16 +441,16 @@ Description: # PySDM
             SPECTRUM_INIT["ParticleVolumeVersusRadiusLogarithmSpectrum.__init__()"] -->|instantiates| SPECTRUM
             SPECTRUM[":ParticleVolumeVersusRadiusLogarithmSpectrum"] -->|added as element of| PRODUCTS
         
-            click COAL "https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision.html"
+            click COAL "https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision.html#Coalescence"
             click BUILDER_INSTANCE "https://open-atmos.github.io/PySDM/PySDM/builder.html"
             click BUILDER_INIT "https://open-atmos.github.io/PySDM/PySDM/builder.html"
             click BUILDER_ADD_DYN "https://open-atmos.github.io/PySDM/PySDM/builder.html"
-            click ENV_INIT "https://open-atmos.github.io/PySDM/PySDM/environments/index.html"
-            click ENV "https://open-atmos.github.io/PySDM/PySDM/environments/index.html"
-            click KERNEL_INIT "https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision_kernels/index.html"
-            click KERNEL "https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision_kernels/index.html"
-            click EXP_INIT "https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra/index.html"
-            click IS "https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra/index.html"
+            click ENV_INIT "https://open-atmos.github.io/PySDM/PySDM/environments.html"
+            click ENV "https://open-atmos.github.io/PySDM/PySDM/environments.html"
+            click KERNEL_INIT "https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision_kernels.html"
+            click KERNEL "https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision_kernels.html"
+            click EXP_INIT "https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra.html"
+            click IS "https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra.html"
             click CM_INIT "https://open-atmos.github.io/PySDM/PySDM/initialisation/sampling/spectral_sampling.html"
             click CM_INSTANCE "https://open-atmos.github.io/PySDM/PySDM/initialisation/sampling/spectral_sampling.html"
             click SAMPLE "https://open-atmos.github.io/PySDM/PySDM/initialisation/sampling/spectral_sampling.html"
@@ -466,7 +466,7 @@ Description: # PySDM
         
         In the following example, a condensation-only setup is used with the adiabatic 
         [`Parcel`](https://open-atmos.github.io/PySDM/PySDM/environments/parcel.html) environment.
-        An initial [`Lognormal`](https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra.html#PySDM.initialisation.spectra.Lognormal)
+        An initial [`Lognormal`](https://open-atmos.github.io/PySDM/PySDM/initialisation/spectra/lognormal.html#Lognormal)
         spectrum of dry aerosol particles is first initialised to equilibrium wet size for the given
         initial humidity. 
         Subsequent particle growth due to [`Condensation`](https://open-atmos.github.io/PySDM/PySDM/dynamics/condensation.html) of water vapour (coupled with the release of latent heat)
@@ -476,7 +476,7 @@ Description: # PySDM
         and depict the evolution of 
         [`PeakSupersaturation`](https://open-atmos.github.io/PySDM/PySDM/products/condensation/peak_supersaturation.html), 
         [`EffectiveRadius`](https://open-atmos.github.io/PySDM/PySDM/products/size_spectral/effective_radius.html), 
-        [`ParticleConcentration`](https://open-atmos.github.io/PySDM/PySDM/products/size_spectral/particle_concentration.html#PySDM.products.particles_concentration.ParticleConcentration) 
+        [`ParticleConcentration`](https://open-atmos.github.io/PySDM/PySDM/products/size_spectral/particle_concentration.html#ParticleConcentration) 
         and the 
         [`WaterMixingRatio `](https://open-atmos.github.io/PySDM/PySDM/products/size_spectral/water_mixing_ratio.html).
         

{PySDM-2.70 → PySDM-2.72}/PySDM.egg-info/SOURCES.txt

@@ -15,7 +15,6 @@ setup.py
 .github/workflows/cancel.yml
 .github/workflows/joss.yml
 .github/workflows/joss_paper.yml
-.github/workflows/pdoc_index_workaround.py
 .github/workflows/readme_snippets.yml
 .github/workflows/stale.yml
 .github/workflows/tests+artifacts+pypi.yml
@@ -177,6 +176,7 @@ PySDM/dynamics/impl/__init__.py
 PySDM/dynamics/impl/chemistry_utils.py
 PySDM/dynamics/impl/random_generator_optimizer.py
 PySDM/dynamics/impl/random_generator_optimizer_nopair.py
+PySDM/dynamics/impl/register_dynamic.py
 PySDM/dynamics/terminal_velocity/__init__.py
 PySDM/dynamics/terminal_velocity/gunn_and_kinzer.py
 PySDM/dynamics/terminal_velocity/power_series.py
@@ -632,6 +632,7 @@ paper/paper.md
 paper/paperv1.md
 paper/readme.pdf
 paper/test.pdf
+pdoc_templates/index.html.jinja2
 tests/__init__.py
 tests/examples_tests/__init__.py
 tests/examples_tests/conftest.py
@@ -776,6 +777,7 @@ tests/unit_tests/backends/storage/test_index.py
 tests/unit_tests/backends/storage/test_setitem.py
 tests/unit_tests/dynamics/__init__.py
 tests/unit_tests/dynamics/test_eulerian_advection.py
+tests/unit_tests/dynamics/test_impl_register_dynamic.py
 tests/unit_tests/dynamics/test_isotopic_fractionation.py
 tests/unit_tests/dynamics/test_relaxed_velocity.py
 tests/unit_tests/dynamics/test_terminal_velocity.py