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Unverified Commit bc3d9992 authored by Thorsten Hater's avatar Thorsten Hater
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python/stubs/arbor/__init__.pyi
+ 166
− 7
View file @ bc3d9992
...@@ -134,11 +134,170 @@ from arbor._arbor import units ...@@ -134,11 +134,170 @@ from arbor._arbor import units
from arbor._arbor import voltage_process from arbor._arbor import voltage_process
from arbor._arbor import write_component from arbor._arbor import write_component
from . import _arbor from . import _arbor
__all__ = ['ArbFileNotFoundError', 'ArbValueError', 'MechCatItemIterator', 'MechCatKeyIterator', 'MechCatValueIterator', 'allen_catalogue', 'asc_color', 'asc_marker', 'asc_marker_set', 'asc_metadata', 'asc_spine', 'axial_resistivity', 'backend', 'bbp_catalogue', 'benchmark_cell', 'build_catalogue', 'cable', 'cable_cell', 'cable_component', 'cable_global_properties', 'cable_probe_axial_current', 'cable_probe_density_state', 'cable_probe_density_state_cell', 'cable_probe_ion_current_cell', 'cable_probe_ion_current_density', 'cable_probe_ion_diff_concentration', 'cable_probe_ion_diff_concentration_cell', 'cable_probe_ion_ext_concentration', 'cable_probe_ion_ext_concentration_cell', 'cable_probe_ion_int_concentration', 'cable_probe_ion_int_concentration_cell', 'cable_probe_membrane_voltage', 'cable_probe_membrane_voltage_cell', 'cable_probe_point_info', 'cable_probe_point_state', 'cable_probe_point_state_cell', 'cable_probe_stimulus_current_cell', 'cable_probe_total_current_cell', 'cable_probe_total_ion_current_cell', 'cable_probe_total_ion_current_density', 'catalogue', 'cell_address', 'cell_cv_data', 'cell_global_label', 'cell_kind', 'cell_local_label', 'cell_member', 'component_meta_data', 'config', 'connection', 'context', 'cv_data', 'cv_policy', 'cv_policy_every_segment', 'cv_policy_explicit', 'cv_policy_fixed_per_branch', 'cv_policy_max_extent', 'cv_policy_single', 'decor', 'default_catalogue', 'density', 'domain_decomposition', 'env', 'event_generator', 'explicit_schedule', 'ext_concentration', 'extent', 'gap_junction_connection', 'group_description', 'iclamp', 'int_concentration', 'intersect_region', 'ion_data', 'ion_dependency', 'ion_diffusivity', 'ion_settings', 'isometry', 'junction', 'label_dict', 'lif_cell', 'lif_probe_metadata', 'lif_probe_voltage', 'load_asc', 'load_catalogue', 'load_component', 'load_swc_arbor', 'load_swc_neuron', 'loaded_morphology', 'location', 'mechanism', 'mechanism_field', 'mechanism_info', 'membrane_capacitance', 'membrane_potential', 'meter_manager', 'meter_report', 'mnpos', 'modcc', 'morphology', 'morphology_provider', 'mpoint', 'msegment', 'neuroml', 'neuron_cable_properties', 'nml_metadata', 'partition_by_group', 'partition_hint', 'partition_load_balance', 'place_pwlin', 'poisson_schedule', 'print_config', 'probe', 'proc_allocation', 'profiler_initialize', 'profiler_summary', 'recipe', 'regular_schedule', 'reversal_potential', 'reversal_potential_method', 'scaled_mechanism', 'schedule_base', 'segment_tree', 'selection_policy', 'simulation', 'single_cell_model', 'spike', 'spike_recording', 'spike_source_cell', 'stochastic_catalogue', 'swc_metadata', 'synapse', 'temperature', 'threshold_detector', 'trace', 'units', 'voltage_process', 'write_component']
def build_catalogue(): __all__ = [
... "ArbFileNotFoundError",
def modcc(): "ArbValueError",
... "MechCatItemIterator",
__config__: dict = {'mpi': False, 'mpi4py': False, 'gpu': None, 'vectorize': True, 'profiling': True, 'neuroml': True, 'bundled': True, 'version': '0.9.1-dev', 'source': '2024-04-11T13:13:43+02:00 8dac3a25b35f3e73f7ad50c27bd06d018e10bb6f modified', 'build_config': 'RELEASE', 'arch': 'native', 'prefix': '/usr/local', 'python_lib_path': '/opt/homebrew/lib/python3.12/site-packages', 'binary_path': 'bin', 'lib_path': 'lib', 'data_path': 'share', 'CXX': '/opt/homebrew/bin/clang++', 'pybind-version': '2.11.1', 'timestamp': 'Apr 11 2024 20:38:51'} "MechCatKeyIterator",
__version__: str = '0.9.1-dev' "MechCatValueIterator",
"allen_catalogue",
"asc_color",
"asc_marker",
"asc_marker_set",
"asc_metadata",
"asc_spine",
"axial_resistivity",
"backend",
"bbp_catalogue",
"benchmark_cell",
"build_catalogue",
"cable",
"cable_cell",
"cable_component",
"cable_global_properties",
"cable_probe_axial_current",
"cable_probe_density_state",
"cable_probe_density_state_cell",
"cable_probe_ion_current_cell",
"cable_probe_ion_current_density",
"cable_probe_ion_diff_concentration",
"cable_probe_ion_diff_concentration_cell",
"cable_probe_ion_ext_concentration",
"cable_probe_ion_ext_concentration_cell",
"cable_probe_ion_int_concentration",
"cable_probe_ion_int_concentration_cell",
"cable_probe_membrane_voltage",
"cable_probe_membrane_voltage_cell",
"cable_probe_point_info",
"cable_probe_point_state",
"cable_probe_point_state_cell",
"cable_probe_stimulus_current_cell",
"cable_probe_total_current_cell",
"cable_probe_total_ion_current_cell",
"cable_probe_total_ion_current_density",
"catalogue",
"cell_address",
"cell_cv_data",
"cell_global_label",
"cell_kind",
"cell_local_label",
"cell_member",
"component_meta_data",
"config",
"connection",
"context",
"cv_data",
"cv_policy",
"cv_policy_every_segment",
"cv_policy_explicit",
"cv_policy_fixed_per_branch",
"cv_policy_max_extent",
"cv_policy_single",
"decor",
"default_catalogue",
"density",
"domain_decomposition",
"env",
"event_generator",
"explicit_schedule",
"ext_concentration",
"extent",
"gap_junction_connection",
"group_description",
"iclamp",
"int_concentration",
"intersect_region",
"ion_data",
"ion_dependency",
"ion_diffusivity",
"ion_settings",
"isometry",
"junction",
"label_dict",
"lif_cell",
"lif_probe_metadata",
"lif_probe_voltage",
"load_asc",
"load_catalogue",
"load_component",
"load_swc_arbor",
"load_swc_neuron",
"loaded_morphology",
"location",
"mechanism",
"mechanism_field",
"mechanism_info",
"membrane_capacitance",
"membrane_potential",
"meter_manager",
"meter_report",
"mnpos",
"modcc",
"morphology",
"morphology_provider",
"mpoint",
"msegment",
"neuroml",
"neuron_cable_properties",
"nml_metadata",
"partition_by_group",
"partition_hint",
"partition_load_balance",
"place_pwlin",
"poisson_schedule",
"print_config",
"probe",
"proc_allocation",
"profiler_initialize",
"profiler_summary",
"recipe",
"regular_schedule",
"reversal_potential",
"reversal_potential_method",
"scaled_mechanism",
"schedule_base",
"segment_tree",
"selection_policy",
"simulation",
"single_cell_model",
"spike",
"spike_recording",
"spike_source_cell",
"stochastic_catalogue",
"swc_metadata",
"synapse",
"temperature",
"threshold_detector",
"trace",
"units",
"voltage_process",
"write_component",
]
def build_catalogue(): ...
def modcc(): ...
__config__: dict = {
"mpi": False,
"mpi4py": False,
"gpu": None,
"vectorize": True,
"profiling": True,
"neuroml": True,
"bundled": True,
"version": "0.9.1-dev",
"source": "2024-04-11T13:13:43+02:00 8dac3a25b35f3e73f7ad50c27bd06d018e10bb6f modified",
"build_config": "RELEASE",
"arch": "native",
"prefix": "/usr/local",
"python_lib_path": "/opt/homebrew/lib/python3.12/site-packages",
"binary_path": "bin",
"lib_path": "lib",
"data_path": "share",
"CXX": "/opt/homebrew/bin/clang++",
"pybind-version": "2.11.1",
"timestamp": "Apr 11 2024 20:38:51",
}
__version__: str = "0.9.1-dev"
mnpos: int = 4294967295 mnpos: int = 4294967295
python/stubs/arbor/_arbor/__init__.pyi
+ 1225
− 729
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This diff is collapsed.
python/stubs/arbor/_arbor/env.pyi
+ 16
− 1
View file @ bc3d9992
""" """
Wrappers for arborenv. Wrappers for arborenv.
""" """
from __future__ import annotations from __future__ import annotations
import arbor._arbor import arbor._arbor
import typing import typing
__all__ = ['default_allocation', 'default_concurrency', 'default_gpu', 'find_private_gpu', 'get_env_num_threads', 'thread_concurrency']
__all__ = [
"default_allocation",
"default_concurrency",
"default_gpu",
"find_private_gpu",
"get_env_num_threads",
"thread_concurrency",
]
def default_allocation() -> arbor._arbor.proc_allocation: def default_allocation() -> arbor._arbor.proc_allocation:
""" """
Attempts to detect the number of locally available CPU cores. Returns 1 if unable to detect the number of cores. Use with caution in combination with MPI. Attempts to detect the number of locally available CPU cores. Returns 1 if unable to detect the number of cores. Use with caution in combination with MPI.
""" """
def default_concurrency() -> arbor._arbor.proc_allocation: def default_concurrency() -> arbor._arbor.proc_allocation:
""" """
Returns number of threads to use from get_env_num_threads(), or else from thread_concurrency() if get_env_num_threads() returns zero. Returns number of threads to use from get_env_num_threads(), or else from thread_concurrency() if get_env_num_threads() returns zero.
""" """
def default_gpu() -> int | None: def default_gpu() -> int | None:
""" """
Determine GPU id to use from the ARBENV_GPU_ID environment variable, or from the first available GPU id of those detected. Determine GPU id to use from the ARBENV_GPU_ID environment variable, or from the first available GPU id of those detected.
""" """
def find_private_gpu(arg0: typing.Any) -> None: def find_private_gpu(arg0: typing.Any) -> None:
""" """
Identify a private GPU id per node, only available if built with GPU and MPI. Identify a private GPU id per node, only available if built with GPU and MPI.
mpi: The MPI communicator. mpi: The MPI communicator.
""" """
def get_env_num_threads() -> int: def get_env_num_threads() -> int:
""" """
Retrieve user-specified number of threads to use from the environment variable ARBENV_NUM_THREADS. Retrieve user-specified number of threads to use from the environment variable ARBENV_NUM_THREADS.
""" """
def thread_concurrency() -> int: def thread_concurrency() -> int:
""" """
Attempts to detect the number of locally available CPU cores. Returns 1 if unable to detect the number of cores. Use with caution in combination with MPI. Attempts to detect the number of locally available CPU cores. Returns 1 if unable to detect the number of cores. Use with caution in combination with MPI.
......
python/stubs/arbor/_arbor/units.pyi
+ 89
− 46
View file @ bc3d9992
""" """
Units and quantities for driving the user interface. Units and quantities for driving the user interface.
""" """
from __future__ import annotations from __future__ import annotations
import typing import typing
__all__ = ['A', 'C', 'Celsius', 'F', 'Hz', 'Kelvin', 'M', 'MOhm', 'Ohm', 'S', 'V', 'cm', 'cm2', 'deg', 'giga', 'kHz', 'kOhm', 'kilo', 'm', 'm2', 'mA', 'mM', 'mS', 'mV', 'mega', 'micro', 'milli', 'mm', 'mm2', 'mol', 'ms', 'nA', 'nF', 'nano', 'nil', 'nm', 'nm2', 'ns', 'pA', 'pF', 'pico', 'quantity', 'rad', 's', 'uA', 'uF', 'uS', 'um', 'um2', 'unit', 'us']
__all__ = [
"A",
"C",
"Celsius",
"F",
"Hz",
"Kelvin",
"M",
"MOhm",
"Ohm",
"S",
"V",
"cm",
"cm2",
"deg",
"giga",
"kHz",
"kOhm",
"kilo",
"m",
"m2",
"mA",
"mM",
"mS",
"mV",
"mega",
"micro",
"milli",
"mm",
"mm2",
"mol",
"ms",
"nA",
"nF",
"nano",
"nil",
"nm",
"nm2",
"ns",
"pA",
"pF",
"pico",
"quantity",
"rad",
"s",
"uA",
"uF",
"uS",
"um",
"um2",
"unit",
"us",
]
class quantity: class quantity:
""" """
A quantity, comprising a magnitude and a unit. A quantity, comprising a magnitude and a unit.
""" """
__hash__: typing.ClassVar[None] = None __hash__: typing.ClassVar[None] = None
def __add__(self, arg0: quantity) -> quantity: def __add__(self, arg0: quantity) -> quantity: ...
... def __eq__(self, arg0: quantity) -> bool: ...
def __eq__(self, arg0: quantity) -> bool:
...
@typing.overload @typing.overload
def __mul__(self, arg0: quantity) -> quantity: def __mul__(self, arg0: quantity) -> quantity: ...
...
@typing.overload @typing.overload
def __mul__(self, arg0: float) -> quantity: def __mul__(self, arg0: float) -> quantity: ...
...
@typing.overload @typing.overload
def __mul__(self, arg0: unit) -> quantity: def __mul__(self, arg0: unit) -> quantity: ...
... def __ne__(self, arg0: quantity) -> bool: ...
def __ne__(self, arg0: quantity) -> bool: def __pow__(self: unit, arg0: int) -> unit: ...
...
def __pow__(self: unit, arg0: int) -> unit:
...
def __repr__(self) -> str: def __repr__(self) -> str:
""" """
Convert quantity to string. Convert quantity to string.
""" """
def __rmul__(self, arg0: float) -> quantity:
... def __rmul__(self, arg0: float) -> quantity: ...
def __rtruediv__(self, arg0: float) -> quantity: def __rtruediv__(self, arg0: float) -> quantity: ...
...
def __str__(self) -> str: def __str__(self) -> str:
""" """
Convert quantity to string. Convert quantity to string.
""" """
def __sub__(self, arg0: quantity) -> quantity:
... def __sub__(self, arg0: quantity) -> quantity: ...
@typing.overload @typing.overload
def __truediv__(self, arg0: quantity) -> quantity: def __truediv__(self, arg0: quantity) -> quantity: ...
...
@typing.overload @typing.overload
def __truediv__(self, arg0: float) -> quantity: def __truediv__(self, arg0: float) -> quantity: ...
...
@typing.overload @typing.overload
def __truediv__(self, arg0: unit) -> quantity: def __truediv__(self, arg0: unit) -> quantity: ...
...
def value_as(self, unit: unit) -> float: def value_as(self, unit: unit) -> float:
""" """
Convert quantity to given unit and return magnitude. Convert quantity to given unit and return magnitude.
""" """
@property @property
def units(self) -> unit: def units(self) -> unit:
""" """
Return units. Return units.
""" """
@property @property
def value(self) -> float: def value(self) -> float:
""" """
Return magnitude. Return magnitude.
""" """
class unit: class unit:
""" """
A unit. A unit.
""" """
__hash__: typing.ClassVar[None] = None __hash__: typing.ClassVar[None] = None
def __eq__(self, arg0: unit) -> bool: def __eq__(self, arg0: unit) -> bool: ...
...
@typing.overload @typing.overload
def __mul__(self, arg0: unit) -> unit: def __mul__(self, arg0: unit) -> unit: ...
...
@typing.overload @typing.overload
def __mul__(self, arg0: float) -> quantity: def __mul__(self, arg0: float) -> quantity: ...
... def __ne__(self, arg0: unit) -> bool: ...
def __ne__(self, arg0: unit) -> bool: def __pow__(self, arg0: int) -> unit: ...
...
def __pow__(self, arg0: int) -> unit:
...
def __repr__(self) -> str: def __repr__(self) -> str:
""" """
Convert unit to string. Convert unit to string.
""" """
def __rmul__(self, arg0: float) -> quantity:
... def __rmul__(self, arg0: float) -> quantity: ...
def __rtruediv__(self, arg0: float) -> quantity: def __rtruediv__(self, arg0: float) -> quantity: ...
...
def __str__(self) -> str: def __str__(self) -> str:
""" """
Convert unit to string. Convert unit to string.
""" """
@typing.overload @typing.overload
def __truediv__(self, arg0: unit) -> unit: def __truediv__(self, arg0: unit) -> unit: ...
...
@typing.overload @typing.overload
def __truediv__(self, arg0: float) -> quantity: def __truediv__(self, arg0: float) -> quantity: ...
...
A: unit # value = A A: unit # value = A
C: unit # value = C C: unit # value = C
Celsius: unit # value = °C Celsius: unit # value = °C
...@@ -132,7 +175,7 @@ ms: unit # value = ms ...@@ -132,7 +175,7 @@ ms: unit # value = ms
nA: unit # value = nA nA: unit # value = nA
nF: unit # value = nF nF: unit # value = nF
nano: unit # value = 1e-09 nano: unit # value = 1e-09
nil: unit # value = nil: unit # value =
nm: unit # value = nm nm: unit # value = nm
nm2: unit # value = nm^2 nm2: unit # value = nm^2
ns: unit # value = ns ns: unit # value = ns
......
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