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manual updates
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@rieder
rieder committed Sep 17, 2024
1 parent 185cf8f commit fffb834
Showing 1 changed file with 47 additions and 54 deletions.
101 changes: 47 additions & 54 deletions src/amuse/datamodel/incode_storage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,10 +80,11 @@
:py:class:`InCodeGridAttributeStorage`
Subclass of AbstractInCodeAttributeStorage, manages grids
"""

import numpy
import inspect

from amuse.support.methods import AbstractCodeMethodWrapper
from amuse.units import nbody_system
from amuse.units import units
Expand All @@ -92,9 +93,6 @@
from amuse.support.core import late
from amuse.support import exceptions

import numpy
import inspect

from amuse.datamodel import parameters
from amuse.datamodel import base
from amuse.datamodel import Particles, ParticlesSuperset
Expand Down Expand Up @@ -178,7 +176,7 @@ def check_arguments(self, storage, attributes_to_return, *indices):
"getter method {0} cannot handle arrays".format(self.method)
)
elif self.method_is_code:
if not self.method.legacy_specification is None:
if self.method.legacy_specification is not None:
if not (
self.method.legacy_specification.can_handle_array
or self.method.legacy_specification.must_handle_array
Expand Down Expand Up @@ -398,13 +396,13 @@ def convert_attributes_and_values_to_list_and_keyword_arguments(
for index, x in enumerate(list_arguments):
if x is not_set_marker:
name_of_attribute = self.attribute_names[index]
if not name_of_attribute in self.optional_attribute_names:
if name_of_attribute not in self.optional_attribute_names:
missing_attributes.append(name_of_attribute)
else:
default_argument_found = True
elif default_argument_found:
name_of_attribute = self.attribute_names[index]
if not name_of_attribute in self.optional_attribute_names:
if name_of_attribute not in self.optional_attribute_names:
raise exceptions.AmuseException(
"Optional before required arguments"
)
Expand Down Expand Up @@ -520,14 +518,12 @@ def set_attribute_values_async(self, storage, attributes, values, *indices):

class NewParticleMethod(ParticleSetAttributesMethod):
"""
Instances wrap a method to create particles. The method may
take attributes values to set initial values on
the created particles.
Instances wrap a method to create particles. The method may take attributes
values to set initial values on the created particles.
The new particle functions work a lot like
the set attribute methods, only the new particle
function is supposed to return an array
of the indices of the created particles.
The new particle functions work a lot like the set attribute methods, only
the new particle function is supposed to return an array of the indices of
the created particles.
.. code-block:: python
Expand All @@ -549,7 +545,7 @@ def add_entities(self, attributes, values):
return indices


class ParticleQueryMethod(object):
class ParticleQueryMethod:
"""
Instances wrap a function that can take one or more arguments
and returns an index (or a list of indices, if the arguments are
Expand Down Expand Up @@ -598,19 +594,18 @@ def apply_for_superset(self, particles, *args, **kwargs):
return ParticlesSuperset(subset_results)


class ParticleSpecificSelectMethod(object):
class ParticleSpecificSelectMethod:
"""
Instances wrap a function that can take a particle index
and returns one or more indices
(but a limited and fixed number of indices). This method is most
useful to return links between particles (subparticles or
nearest neighbors)
Instances wrap a function that can take a particle index and returns one or
more indices (but a limited and fixed number of indices). This method is
most useful to return links between particles (subparticles or nearest
neighbors)
.. code-block:: python
output_index = instance.get_nearest_neigbord(input_index)
output_index = instance.get_nearest_neighbor(input_index)
The idex or indices are converted to a particle subset.
The index or indices are converted to a particle subset.
"""

def __init__(self, method, names=(), public_name=None):
Expand Down Expand Up @@ -640,22 +635,22 @@ def apply_on_all(self, particles):

return result

def apply_on_one(self, set, particle):
index = set._private.attribute_storage.get_indices_of(particle.key)
def apply_on_one(self, particleset, particle):
index = particleset._private.attribute_storage.get_indices_of(particle.key)

result = self.method(index)

keys = set._private.attribute_storage._get_keys_for_indices_in_the_code(result)
keys = particleset._private.attribute_storage._get_keys_for_indices_in_the_code(result)

result = []
return particle.as_set()._subset(keys)


class ParticleMethod(AbstractCodeMethodWrapper):
"""
Instances wrap a function that returns quanties given particle
indices and optional arguments. Instances have a lot in common
with attribute getters, but can take extra arguments.
Instances wrap a function that returns quantities given particle indices
and optional arguments. Instances have a lot in common with attribute
getters, but can take extra arguments.
.. code-block:: python
Expand All @@ -673,13 +668,13 @@ def apply_on_all(self, particles, *list_arguments, **keyword_arguments):
)
return self.method(all_indices, *list_arguments, **keyword_arguments)

def apply_on_one(self, set, particle, *list_arguments, **keyword_arguments):
def apply_on_one(self, particleset, particle, *list_arguments, **keyword_arguments):
storage = particle.particles_set._private.attribute_storage
index = storage.get_indices_of([particle.key])
return self.method(index[0], *list_arguments, **keyword_arguments)


class ParticleSetSelectSubsetMethod(object):
class ParticleSetSelectSubsetMethod:
"""
Generic method to query and retrieve particles from the
set. This selection can have up to tree stages:
Expand Down Expand Up @@ -720,7 +715,7 @@ def __init__(

def apply_on_all(self, particles, *list_arguments, **keyword_arguments):
query_identifiers = None
if not self.set_query_arguments_method is None:
if self.set_query_arguments_method is not None:
query_identifiers = self.set_query_arguments_method(
*list_arguments, **keyword_arguments
)
Expand All @@ -730,7 +725,7 @@ def apply_on_all(self, particles, *list_arguments, **keyword_arguments):
elif not hasattr(query_identifiers, "__iter__"):
query_identifiers = (query_identifiers,)

if not self.get_number_of_particles_in_set_method is None:
if self.get_number_of_particles_in_set_method is not None:
number_of_particles_in_set = self.get_number_of_particles_in_set_method(
*query_identifiers
)
Expand All @@ -747,7 +742,7 @@ def apply_on_all(self, particles, *list_arguments, **keyword_arguments):
return particles._subset(keys)


class ParticlesAddedUpdateMethod(object):
class ParticlesAddedUpdateMethod:
def __init__(
self,
get_number_of_particles_added_method=None,
Expand All @@ -758,7 +753,7 @@ def __init__(

def apply_on_all(self, particles, *list_arguments, **keyword_arguments):
query_identifiers = None
if not self.set_query_arguments_method is None:
if self.set_query_arguments_method is not None:
query_identifiers = self.set_query_arguments_method(
*list_arguments, **keyword_arguments
)
Expand All @@ -768,7 +763,7 @@ def apply_on_all(self, particles, *list_arguments, **keyword_arguments):
elif not hasattr(query_identifiers, "__iter__"):
query_identifiers = (query_identifiers,)

if not self.get_number_of_particles_in_set_method is None:
if self.get_number_of_particles_in_set_method is not None:
number_of_particles_in_set = self.get_number_of_particles_in_set_method(
*query_identifiers
)
Expand All @@ -785,7 +780,7 @@ def apply_on_all(self, particles, *list_arguments, **keyword_arguments):
return particles._subset(keys)


class ParticleGetIndexMethod(object):
class ParticleGetIndexMethod:
"""
Instances return the index of a particle in the code
"""
Expand All @@ -805,10 +800,9 @@ def get_attribute_values(self, storage, attributes_to_return, *indices):

class AbstractInCodeAttributeStorage(base.AttributeStorage):
"""
Abstract base storage for incode attribute storage.
It provides functions to handle getters and setters of
attributes but not for creating or deleting of particles as
this differs between grids and particle sets.
Abstract base storage for incode attribute storage. It provides functions
to handle getters and setters of attributes but not for creating or
deleting of particles as this differs between grids and particle sets.
"""

Expand Down Expand Up @@ -870,7 +864,7 @@ def select_getters_for(self, attributes):

if set_of_attributes:
raise exceptions.AmuseException(
"Do not have attributes {0}".format(sorted(set_of_attributes))
f"Do not have attributes {sorted(set_of_attributes)}"
)

return result
Expand Down Expand Up @@ -961,7 +955,7 @@ def add_particles_to_store(self, keys, attributes=[], values=[]):
index = 0
for key in keys:
if key in self.mapping_from_particle_key_to_index_in_the_code:
raise Exception("particle with same key added twice: {0}".format(key))
raise Exception(f"particle with same key added twice: {key}")
self.mapping_from_particle_key_to_index_in_the_code[key] = indices[index]
self.mapping_from_index_in_the_code_to_particle_key[indices[index]] = key
index = index + 1
Expand Down Expand Up @@ -1422,17 +1416,16 @@ def get_defined_settable_attribute_names(self):
return sorted(self.writable_attributes)


class ParticleSpecificSelectSubsetMethod(object):
class ParticleSpecificSelectSubsetMethod:
"""
Instances wrap a function that can take a particle index, plus a list
offset and returns one index. This method is most
useful to return links between particles (subparticles or
nearest neighbors). Instances also need a function to get
the number of links.
offset and returns one index. This method is most useful to return links
between particles (subparticles or nearest neighbors). Instances also need
a function to get the number of links.
.. code-block:: python
output_index = instance.get_nearest_neigbors(index_of_the_particle, input_index)
output_index = instance.get_nearest_neighbors(index_of_the_particle, input_index)
The index or indices are converted to a particle subset.
"""
Expand All @@ -1451,14 +1444,14 @@ def apply_on_all(self, particles):
"Getting all links to other particles from all particles in a set is not implemented yet"
)

def apply_on_one(self, set, particle):
from_indices = set._private.attribute_storage.get_indices_of(
def apply_on_one(self, particleset, particle):
from_indices = particleset._private.attribute_storage.get_indices_of(
[
particle.key,
]
)

if not self.get_number_of_particles_in_set_method is None:
if self.get_number_of_particles_in_set_method is not None:
number_of_particles_in_set = self.get_number_of_particles_in_set_method(
from_indices
)[0]
Expand All @@ -1470,6 +1463,6 @@ def apply_on_one(self, set, particle):
index = self.method()
indices = [index]

keys = set._private.attribute_storage._get_keys_for_indices_in_the_code(indices)
keys = particleset._private.attribute_storage._get_keys_for_indices_in_the_code(indices)

return particle.as_set()._subset(keys)

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