diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 0f2921b72a667541f57923abe628b08b8d9eee19..c9ee4645693ac807739e1c06df9b3dc1ec546b87 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -20,11 +20,11 @@ jobs:
sudo apt-get update
sudo apt-get install -y ninja-build ccache
- name: Set up cmake
- uses: jwlawson/actions-setup-cmake@v1.13
+ uses: jwlawson/actions-setup-cmake@v2.0.0
with:
cmake-version: 3.22.x
- name: Clone w/ submodules
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
submodules: recursive
# figure out vector extensions for ccache key
diff --git a/.github/workflows/build-pip-wheels.yml b/.github/workflows/build-pip-wheels.yml
index 9370c56a19f36e5784f65d22f67cbfe7a40ae72d..9a5f9d243904ec692c6aa43732fb96bfadbd3354 100644
--- a/.github/workflows/build-pip-wheels.yml
+++ b/.github/workflows/build-pip-wheels.yml
@@ -17,7 +17,7 @@ jobs:
steps:
- name: Get Arbor
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
submodules: recursive
- name: Create unique version in pyproject.toml
@@ -38,7 +38,7 @@ jobs:
steps:
- name: Get Arbor
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
submodules: recursive
- name: Delete pyproject.toml
@@ -69,7 +69,7 @@ jobs:
- name: Get packages
run: python3 -m pip install build
- name: Get Arbor
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
submodules: recursive
- name: Delete pyproject.toml
@@ -118,7 +118,7 @@ jobs:
needs: [build_binary_wheels, build_sdist]
steps:
- name: "Clone w/ submodules"
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
fetch-depth: 0
submodules: "recursive"
diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
index 892bb704e8f8d675d87e0a573754c3cc1ded2a32..8c9a2eaf0ff00ffd85f031f31648ea6e67ab92c6 100644
--- a/.github/workflows/codeql.yml
+++ b/.github/workflows/codeql.yml
@@ -46,13 +46,13 @@ jobs:
steps:
- name: Checkout repository
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
submodules: recursive
# Initializes the CodeQL tools for scanning.
- name: Initialize CodeQL
- uses: github/codeql-action/init@v2
+ uses: github/codeql-action/init@v3
with:
languages: ${{ matrix.language }}
# If you wish to specify custom queries, you can do so here or in a config file.
@@ -81,6 +81,6 @@ jobs:
# ./location_of_script_within_repo/buildscript.sh
- name: Perform CodeQL Analysis
- uses: github/codeql-action/analyze@v2
+ uses: github/codeql-action/analyze@v3
with:
category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 0cf9fd3bd88873253bdaff86273afdac5009904b..518b0e9110f6f8938668d60577d0271404eb5ed7 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -11,9 +11,9 @@ jobs:
strategy:
fail-fast: false
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
- name: Set up Python
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
with:
python-version: '3.10'
- name: Get packages
@@ -21,7 +21,7 @@ jobs:
python -m pip install --upgrade pip
pip install flake8
- name: Clone w/ submodules
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
submodules: recursive
- name: Python Formatting
diff --git a/.github/workflows/sanitize.yml b/.github/workflows/sanitize.yml
index 8fd3c75772abf65097b68e56321e11b437e18cd3..bb172833173e75bad480c76e2ddc1648ad8985bf 100644
--- a/.github/workflows/sanitize.yml
+++ b/.github/workflows/sanitize.yml
@@ -33,11 +33,11 @@ jobs:
sudo apt-get update
sudo apt-get install -y ninja-build ccache
- name: Set up cmake
- uses: jwlawson/actions-setup-cmake@v1.13
+ uses: jwlawson/actions-setup-cmake@v2.0.0
with:
cmake-version: 3.19.x
- name: Clone w/ submodules
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
submodules: recursive
- name: Update pip
diff --git a/.github/workflows/test-docs.yaml b/.github/workflows/test-docs.yaml
index d7cac2a8b2e70e3e08f1eea6d3b9f6a8fc2f3687..3ef6683b6e4aaed4113e94bddfe92ada8218fb7d 100644
--- a/.github/workflows/test-docs.yaml
+++ b/.github/workflows/test-docs.yaml
@@ -18,17 +18,17 @@ jobs:
python-version: [3.8]
steps:
- name: Set up cmake
- uses: jwlawson/actions-setup-cmake@v1.13
+ uses: jwlawson/actions-setup-cmake@v2.0.0
with:
cmake-version: ${{ matrix.config.cmake }}
- name: Set up Python
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Update pip and setup venv
run: python -m pip install --upgrade pip && python -m venv ~/env && . ~/env/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV
- name: Clone w/ submodules
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
submodules: recursive
- name: Install Python packages
diff --git a/.github/workflows/test-matrix.yml b/.github/workflows/test-matrix.yml
index d1c4e8d0c68eecdeb1fae44b6315faf2dd234340..8878809b06bd0ff0e10dcf1b305d72fbfe507dc2 100644
--- a/.github/workflows/test-matrix.yml
+++ b/.github/workflows/test-matrix.yml
@@ -105,11 +105,11 @@ jobs:
run: |
brew install openmpi ninja ccache
- name: Set up cmake
- uses: jwlawson/actions-setup-cmake@v1.13
+ uses: jwlawson/actions-setup-cmake@v2.0.0
with:
cmake-version: ${{ matrix.config.cmake }}
- name: Set up Python
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
with:
python-version: ${{ matrix.config.py }}
- name: Update pip
@@ -117,7 +117,7 @@ jobs:
- name: Install Python packages
run: pip install numpy sphinx svgwrite sphinx-rtd-theme mpi4py pandas seaborn
- name: Clone w/ submodules
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
submodules: recursive
# figure out vector extensions for ccache key
diff --git a/.github/workflows/test-pip.yml b/.github/workflows/test-pip.yml
index df029593e91587e61df8502454f8c660606973ae..e25928f827d1cbde4de6159a327d12ab606929ec 100644
--- a/.github/workflows/test-pip.yml
+++ b/.github/workflows/test-pip.yml
@@ -17,11 +17,11 @@ jobs:
os: [ubuntu-20.04]
python-version: [3.8]
steps:
- - uses: actions/setup-python@v4
+ - uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Clone w/ submodules
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
submodules: recursive
- name: Update pip and setup venv
diff --git a/.github/workflows/test-spack.yml b/.github/workflows/test-spack.yml
index b78a3475805b2caac1d67a67ac78e31291eaa1b8..44171e6216f2f27018111ffffaef835bbf996df9 100644
--- a/.github/workflows/test-spack.yml
+++ b/.github/workflows/test-spack.yml
@@ -32,7 +32,7 @@ jobs:
sudo apt-get install -y gfortran libblas-dev
- name: clone arbor
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
path: arbor
submodules: recursive
diff --git a/README.md b/README.md
index 955b07554a353cc732a41d65701dfc43f8d9c513..d0ed6aec72cf1a7c8fe800916cfc3a1745d107b4 100644
--- a/README.md
+++ b/README.md
@@ -5,6 +5,7 @@
[](https://gitpod.io/#https://github.com/arbor-sim/arbor)
[](https://docs.arbor-sim.org/en/latest/)
[](https://gitter.im/arbor-sim/community)
+[](https://github.com/arbor-sim/arbor/actions/workflows/codeql.yml)
# Arbor Library
diff --git a/arbor/cable_cell_group.cpp b/arbor/cable_cell_group.cpp
index 559f3e9ef8ff59dee7fa8ee8958efd56d555fa5d..efa27ea0e8fdb9e15190ef1c72d4abafda2636e7 100644
--- a/arbor/cable_cell_group.cpp
+++ b/arbor/cable_cell_group.cpp
@@ -1,6 +1,3 @@
-#include <functional>
-#include <optional>
-#include <unordered_set>
#include <variant>
#include <vector>
@@ -18,8 +15,6 @@
#include "cable_cell_group.hpp"
#include "profile/profiler_macro.hpp"
#include "sampler_map.hpp"
-#include "util/filter.hpp"
-#include "util/maputil.hpp"
#include "util/partition.hpp"
#include "util/range.hpp"
#include "util/span.hpp"
@@ -215,9 +210,9 @@ void run_samples(
fvm_probe_scratch& scratch)
{
const sample_size_type n_raw_per_sample = p.raw_handles.size();
- sample_size_type n_sample = (sc.end_offset-sc.begin_offset)/n_raw_per_sample;
- arb_assert((sc.end_offset-sc.begin_offset)==n_sample*n_raw_per_sample);
- arb_assert((unsigned)n_raw_per_sample==p.weight.size());
+ sample_size_type n_sample = (sc.end_offset - sc.begin_offset)/n_raw_per_sample;
+ arb_assert((sc.end_offset - sc.begin_offset)==n_sample*n_raw_per_sample);
+ arb_assert((unsigned)n_raw_per_sample == p.weight.size());
auto& sample_ranges = std::get<std::vector<cable_sample_range>>(scratch);
sample_ranges.clear();
@@ -249,14 +244,12 @@ void run_samples(
sc.sampler({sc.probeset_id, sc.index, p.get_metadata_ptr()}, n_sample, sample_records.data());
}
-void run_samples(
- const fvm_probe_interpolated_multi& p,
- const sampler_call_info& sc,
- const arb_value_type* raw_times,
- const arb_value_type* raw_samples,
- std::vector<sample_record>& sample_records,
- fvm_probe_scratch& scratch)
-{
+void run_samples(const fvm_probe_interpolated_multi& p,
+ const sampler_call_info& sc,
+ const arb_value_type* raw_times,
+ const arb_value_type* raw_samples,
+ std::vector<sample_record>& sample_records,
+ fvm_probe_scratch& scratch) {
const sample_size_type n_raw_per_sample = p.raw_handles.size();
const sample_size_type n_interp_per_sample = n_raw_per_sample/2;
sample_size_type n_sample = (sc.end_offset-sc.begin_offset)/n_raw_per_sample;
diff --git a/arbor/communication/dry_run_context.cpp b/arbor/communication/dry_run_context.cpp
index affcd776608ded9d099362914ecd252740505f7a..9936eaabba65cae48e358e88143eacd667da643a 100644
--- a/arbor/communication/dry_run_context.cpp
+++ b/arbor/communication/dry_run_context.cpp
@@ -1,4 +1,3 @@
-#include <algorithm>
#include <string>
#include <vector>
@@ -6,12 +5,12 @@
#include "distributed_context.hpp"
#include "label_resolution.hpp"
-#include "threading/threading.hpp"
#include "util/rangeutil.hpp"
namespace arb {
struct dry_run_context_impl {
+ using count_type = typename gathered_vector<spike>::count_type;
explicit dry_run_context_impl(unsigned num_ranks, unsigned num_cells_per_tile):
num_ranks_(num_ranks), num_cells_per_tile_(num_cells_per_tile) {};
@@ -21,7 +20,6 @@ struct dry_run_context_impl {
}
gathered_vector<spike>
gather_spikes(const std::vector<spike>& local_spikes) const {
- using count_type = typename gathered_vector<spike>::count_type;
count_type local_size = local_spikes.size();
@@ -49,8 +47,6 @@ struct dry_run_context_impl {
void remote_ctrl_send_done() const {}
gathered_vector<cell_gid_type>
gather_gids(const std::vector<cell_gid_type>& local_gids) const {
- using count_type = typename gathered_vector<cell_gid_type>::count_type;
-
count_type local_size = local_gids.size();
std::vector<cell_gid_type> gathered_gids;
@@ -68,7 +64,7 @@ struct dry_run_context_impl {
std::vector<count_type> partition;
for (count_type i = 0; i <= num_ranks_; i++) {
- partition.push_back(static_cast<count_type>(i*local_size));
+ partition.push_back(i*local_size);
}
return gathered_vector<cell_gid_type>(std::move(gathered_gids), std::move(partition));
diff --git a/arbor/include/arbor/common_types.hpp b/arbor/include/arbor/common_types.hpp
index be3f4f095d3231fbefd23c11066df4857a26087e..5e57f723c26e5d6641b1c8379166175cb63198e9 100644
--- a/arbor/include/arbor/common_types.hpp
+++ b/arbor/include/arbor/common_types.hpp
@@ -138,8 +138,8 @@ using time_type = double;
constexpr time_type terminal_time = std::numeric_limits<time_type>::max();
// For holding counts and indexes into generated sample data.
-
-using sample_size_type = std::int32_t;
+using sample_index_type = std::int32_t;
+using sample_size_type = std::uint32_t;
// Enumeration for execution back-end targets, as specified in domain decompositions.
diff --git a/arbor/include/arbor/math.hpp b/arbor/include/arbor/math.hpp
index 17e12b3c2c2242e91a195f1cc8585815507ed1ff..d9483f350186b62d04b3f3d430ad2d00358a860c 100644
--- a/arbor/include/arbor/math.hpp
+++ b/arbor/include/arbor/math.hpp
@@ -101,7 +101,8 @@ template <
>
C round_up(T v, U b) {
C m = v%b;
- return v-m+signum(m)*impl::abs_if_signed(b, Signed{});
+ C sign = signum(m);
+ return v - m + sign*impl::abs_if_signed(b, Signed{});
}
// Returns 1/x if x != 0; 0 otherwise
diff --git a/arbor/include/arbor/util/hash_def.hpp b/arbor/include/arbor/util/hash_def.hpp
index 261e112948f40b95ebb6300ac850ba619d9046c2..4ea944bb3a07e69782bf13322a7788e5e73c3539 100644
--- a/arbor/include/arbor/util/hash_def.hpp
+++ b/arbor/include/arbor/util/hash_def.hpp
@@ -40,8 +40,9 @@ namespace detail {
template <typename T>
inline constexpr std::size_t internal_hash(T&& data) {
using D = std::decay_t<T>;
- constexpr std::size_t prime = 0x100000001b3;
- constexpr std::size_t offset_basis = 0xcbf29ce484222325;
+ // Due to constexpr if we might never use these.
+ [[maybe_unused]] constexpr std::size_t prime = 0x100000001b3;
+ [[maybe_unused]] constexpr std::size_t offset_basis = 0xcbf29ce484222325;
static_assert(!std::is_pointer_v<D> || std::is_same_v<D, void*> || std::is_convertible_v<T, std::string_view>,
"Pointer types except void* will not be hashed.");
if constexpr (std::is_convertible_v<T, std::string_view>) {
diff --git a/example/generators/generators.cpp b/example/generators/generators.cpp
index 858fe05e6bfb4c801dac3d17e8782d75136b342a..b0600175b957ff5806a17eb19bc0e8bb3f5bb1fc 100644
--- a/example/generators/generators.cpp
+++ b/example/generators/generators.cpp
@@ -82,8 +82,6 @@ public:
std::vector<arb::event_generator> event_generators(cell_gid_type gid) const override {
assert(gid==0); // There is only one cell in the model
- using RNG = std::mt19937_64;
-
auto hz_to_freq = [](double hz) { return hz*1e-3; };
time_type t0 = 0;
diff --git a/modcc/io/prefixbuf.cpp b/modcc/io/prefixbuf.cpp
index 6b85f907dfcbae882c7af7728fa616eabf5a31ac..78771e66025b2137bd0f3ade0df719152402fd0a 100644
--- a/modcc/io/prefixbuf.cpp
+++ b/modcc/io/prefixbuf.cpp
@@ -75,11 +75,13 @@ int indent_manip::xindex() {
static void apply_indent_prefix(std::ios& s, int index) {
if (auto pbuf = dynamic_cast<prefixbuf*>(s.rdbuf())) {
- indent_stack* stack_ptr = static_cast<indent_stack*>(s.pword(index));
- unsigned tabwidth = s.iword(index);
-
- unsigned tabs = (!stack_ptr || stack_ptr->empty())? 0: stack_ptr->top();
- pbuf->prefix = std::string(tabs*tabwidth, ' ');
+ if (auto ptr = static_cast<indent_stack*>(s.pword(index)); ptr && !ptr->empty()) {
+ unsigned n_tab = ptr->top();
+ unsigned width = s.iword(index);
+ pbuf->prefix = std::string(n_tab*width, ' ');
+ } else {
+ pbuf->prefix = std::string();
+ }
}
}
diff --git a/python/stubs/arbor/_arbor/__init__.pyi b/python/stubs/arbor/_arbor/__init__.pyi
index aabd4f3de210a0e84da571d95e2cccc55ffb9198..a0ae1484c9289fb442e6b12abc4d53bf54aae61a 100644
--- a/python/stubs/arbor/_arbor/__init__.pyi
+++ b/python/stubs/arbor/_arbor/__init__.pyi
@@ -1,6 +1,7 @@
"""
arbor: multicompartment neural network models.
"""
+
from __future__ import annotations
import typing
from . import env
@@ -164,11 +165,13 @@ class asc_morphology:
"""
The four canonical regions are labeled 'soma', 'axon', 'dend' and 'apic'.
"""
+
@property
def morphology(self) -> morphology:
"""
The cable cell morphology.
"""
+
@property
def segment_tree(self) -> segment_tree:
"""
@@ -235,6 +238,7 @@ class benchmark_cell:
Construct a benchmark cell that generates spikes on 'source_label' at regular intervals.
The cell has one source labeled 'source_label', and one target labeled 'target_label'.
"""
+
@typing.overload
def __init__(
self,
@@ -247,6 +251,7 @@ class benchmark_cell:
Construct a benchmark cell that generates spikes on 'source_label' at a sequence of user-defined times.
The cell has one source labeled 'source_label', and one target labeled 'target_label'.
"""
+
@typing.overload
def __init__(
self,
@@ -259,6 +264,7 @@ class benchmark_cell:
Construct a benchmark cell that generates spikeson 'source_label' at times defined by a Poisson sequence.
The cell has one source labeled 'source_label', and one target labeled 'target_label'.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@@ -273,11 +279,13 @@ class cable:
"""
The id of the branch on which the cable lies.
"""
+
@property
def dist(self) -> float:
"""
The relative position of the distal end of the cable on its branch ∈ [0,1].
"""
+
@property
def prox(self) -> float:
"""
@@ -297,6 +305,7 @@ class cable_cell:
"""
Construct with a morphology, decor, and label dictionary.
"""
+
@typing.overload
def __init__(
self, segment_tree: segment_tree, decor: decor, labels: label_dict | None = None
@@ -304,16 +313,19 @@ class cable_cell:
"""
Construct with a morphology derived from a segment tree, decor, and label dictionary.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
def cables(self, label: str) -> list[cable]:
"""
The cable segments of the cell morphology for a region label.
"""
+
def locations(self, label: str) -> list[location]:
"""
The locations of the cell morphology for a locset label.
"""
+
@property
def num_branches(self) -> int:
"""
@@ -328,11 +340,13 @@ class cable_component:
"""
cable-cell component.
"""
+
@property
def meta_data(self) -> component_meta_data:
"""
cable-cell component meta-data.
"""
+
@meta_data.setter
def meta_data(self, arg0: component_meta_data) -> None: ...
@@ -347,6 +361,7 @@ class cable_global_properties:
"""
Test whether all default parameters and ion species properties have been set.
"""
+
def set_ion(
self,
ion: str,
@@ -374,6 +389,7 @@ class cable_global_properties:
reversal potential is global for all compartments in the cell, and can't be
overriden locally.
"""
+
def set_property(
self,
Vm: units.quantity | None = None,
@@ -389,10 +405,12 @@ class cable_global_properties:
* tempK: temperature [Kelvin].
These values can be overridden on specific regions using the paint interface.
"""
+
def unset_ion(self, arg0: str) -> None:
"""
Remove ion species from properties.
"""
+
@property
def axial_resistivity(self) -> float | None: ...
@axial_resistivity.setter
@@ -402,6 +420,7 @@ class cable_global_properties:
"""
The mechanism catalogue.
"""
+
@catalogue.setter
def catalogue(self, arg0: catalogue) -> None: ...
@property
@@ -409,6 +428,7 @@ class cable_global_properties:
"""
Flag for enabling/disabling linear syanpse coalescing.
"""
+
@coalesce_synapses.setter
def coalesce_synapses(self, arg0: bool) -> None: ...
@property
@@ -422,6 +442,7 @@ class cable_global_properties:
"""
Return a view of all ion settings.
"""
+
@property
def membrane_capacitance(self) -> float | None: ...
@membrane_capacitance.setter
@@ -447,6 +468,7 @@ class cable_probe_point_info:
"""
Location of point process instance on cell.
"""
+
@location.setter
def location(self, arg0: location) -> None: ...
@property
@@ -454,6 +476,7 @@ class cable_probe_point_info:
"""
Number of coalesced point processes (linear synapses) associated with this instance.
"""
+
@multiplicity.setter
def multiplicity(self, arg0: int) -> None: ...
@property
@@ -461,6 +484,7 @@ class cable_probe_point_info:
"""
The target index of the point process instance on the cell.
"""
+
@target.setter
def target(self, arg0: int) -> None: ...
@@ -469,6 +493,7 @@ class catalogue:
"""
Is 'name' in the catalogue?
"""
+
def __getitem__(self, arg0: str) -> mechanism_info: ...
@typing.overload
def __init__(self) -> None: ...
@@ -478,6 +503,7 @@ class catalogue:
"""
Return an iterator over all mechanism names in this catalogues.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
def derive(
@@ -491,18 +517,22 @@ class catalogue:
"""
Import another catalogue, possibly with a prefix. Will overwrite in case of name collisions.
"""
+
def is_derived(self, name: str) -> bool:
"""
Is 'name' a derived mechanism or can it be implicitly derived?
"""
+
def items(self) -> MechCatItemIterator:
"""
Return an iterator over all (name, mechanism) tuples in this catalogues.
"""
+
def keys(self) -> MechCatKeyIterator:
"""
Return an iterator over all mechanism names in this catalogues.
"""
+
def values(self) -> MechCatValueIterator:
"""
Return an iterator over all mechanism info values in this catalogues.
@@ -523,14 +553,17 @@ class cell_cv_data:
"""
Return a list of cables representing the CV at the given index.
"""
+
def children(self, index: int) -> list[int]:
"""
Return a list of indices of the CVs representing the children of the CV at the given index.
"""
+
def parent(self, index: int) -> int:
"""
Return the index of the CV representing the parent of the CV at the given index.
"""
+
@property
def num_cv(self) -> int:
"""
@@ -552,6 +585,7 @@ class cell_global_label:
Construct a cell_global_label identifier from a gid and a label argument identifying an item on the cell.
The default round_robin policy is used for selecting one of possibly multiple items on the cell associated with the label.
"""
+
@typing.overload
def __init__(self, gid: int, label: cell_local_label) -> None:
"""
@@ -559,6 +593,7 @@ class cell_global_label:
gid: The global identifier of the cell.
label: The cell_local_label representing the label and selection policy of an item on the cell.
"""
+
@typing.overload
def __init__(self, arg0: tuple) -> None:
"""
@@ -566,6 +601,7 @@ class cell_global_label:
gid: The global identifier of the cell.
label: The cell_local_label representing the label and selection policy of an item on the cell.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -573,6 +609,7 @@ class cell_global_label:
"""
The global identifier of the cell.
"""
+
@gid.setter
def gid(self, arg0: int) -> None: ...
@property
@@ -580,6 +617,7 @@ class cell_global_label:
"""
The cell_local_label representing the label and selection policy of an item on the cell.
"""
+
@label.setter
def label(self, arg0: cell_local_label) -> None: ...
@@ -635,6 +673,7 @@ class cell_local_label:
Construct a cell_local_label identifier from a label argument identifying a group of one or more items on a cell.
The default round_robin policy is used for selecting one of possibly multiple items associated with the label.
"""
+
@typing.overload
def __init__(self, label: str, policy: selection_policy) -> None:
"""
@@ -642,6 +681,7 @@ class cell_local_label:
label: The identifier of a group of one or more items on a cell.
policy: The policy for selecting one of possibly multiple items associated with the label.
"""
+
@typing.overload
def __init__(self, arg0: tuple) -> None:
"""
@@ -649,6 +689,7 @@ class cell_local_label:
label: The identifier of a group of one or more items on a cell.
policy: The policy for selecting one of possibly multiple items associated with the label.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -656,6 +697,7 @@ class cell_local_label:
"""
The identifier of a a group of one or more items on a cell.
"""
+
@label.setter
def label(self, arg0: str) -> None: ...
@property
@@ -663,6 +705,7 @@ class cell_local_label:
"""
The policy for selecting one of possibly multiple items associated with the label.
"""
+
@policy.setter
def policy(self, arg0: selection_policy) -> None: ...
@@ -682,6 +725,7 @@ class cell_member:
gid: The global identifier of the cell.
index: The cell-local index of the item.
"""
+
@typing.overload
def __init__(self, arg0: tuple) -> None:
"""
@@ -689,6 +733,7 @@ class cell_member:
gid: The global identifier of the cell.
index: The cell-local index of the item.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -696,6 +741,7 @@ class cell_member:
"""
The global identifier of the cell.
"""
+
@gid.setter
def gid(self, arg0: int) -> None: ...
@property
@@ -703,6 +749,7 @@ class cell_member:
"""
Cell-local index of the item.
"""
+
@index.setter
def index(self, arg0: int) -> None: ...
@@ -712,6 +759,7 @@ class component_meta_data:
"""
cable-cell component version.
"""
+
@version.setter
def version(self, arg0: str) -> None: ...
@@ -735,6 +783,7 @@ class connection:
weight: The weight delivered to the target synapse (unit defined by the type of synapse target).
delay: The delay of the connection [ms].
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -742,6 +791,7 @@ class connection:
"""
The delay time of the connection [ms].
"""
+
@delay.setter
def delay(self, arg0: float) -> None: ...
@property
@@ -749,6 +799,7 @@ class connection:
"""
The destination label of the connection.
"""
+
@dest.setter
def dest(self, arg0: cell_local_label) -> None: ...
@property
@@ -756,6 +807,7 @@ class connection:
"""
The source gid and label of the connection.
"""
+
@source.setter
def source(self, arg0: cell_global_label) -> None: ...
@property
@@ -763,6 +815,7 @@ class connection:
"""
The weight of the connection.
"""
+
@weight.setter
def weight(self, arg0: float) -> None: ...
@@ -776,6 +829,7 @@ class context:
"""
Construct a local context with proc_allocation = env.default_allocation().
"""
+
@typing.overload
def __init__(
self,
@@ -796,6 +850,7 @@ class context:
bind_procs: Create process binding mask.
bind_threads: Create thread binding mask.
"""
+
@typing.overload
def __init__(
self,
@@ -810,6 +865,7 @@ class context:
mpi: The MPI communicator, None by default. Only available if arbor.__config__['mpi']==True.
inter: An MPI intercommunicator used to connect to external simulations, None by default. Only available if arbor.__config__['mpi']==True.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -817,21 +873,25 @@ class context:
"""
Whether the context has a GPU.
"""
+
@property
def has_mpi(self) -> bool:
"""
Whether the context uses MPI for distributed communication.
"""
+
@property
def rank(self) -> int:
"""
The numeric id of the local domain (equivalent to MPI rank).
"""
+
@property
def ranks(self) -> int:
"""
The number of distributed domains (equivalent to the number of MPI ranks).
"""
+
@property
def threads(self) -> int:
"""
@@ -848,6 +908,7 @@ class cv_policy:
"""
A valid CV policy expression
"""
+
def __or__(self, arg0: cv_policy) -> cv_policy: ...
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@@ -884,31 +945,37 @@ class decor:
"""
Return a view of all defaults.
"""
+
@typing.overload
def discretization(self, policy: cv_policy) -> decor:
"""
A cv_policy used to discretise the cell into compartments for simulation
"""
+
@typing.overload
def discretization(self, policy: str) -> decor:
"""
An s-expression string representing a cv_policy used to discretise the cell into compartments for simulation
"""
+
@typing.overload
def paint(self, region: str, mechanism: density) -> decor:
"""
Associate a density mechanism with a region.
"""
+
@typing.overload
def paint(self, region: str, mechanism: voltage_process) -> decor:
"""
Associate a voltage process mechanism with a region.
"""
+
@typing.overload
def paint(self, region: str, mechanism: scaled_mechanism) -> None:
"""
Associate a scaled density mechanism with a region.
"""
+
@typing.overload
def paint(
self,
@@ -926,6 +993,7 @@ class decor:
* rL: axial resistivity [Ω·cm].
* tempK: temperature [Kelvin].
"""
+
@typing.overload
def paint(
self,
@@ -945,6 +1013,7 @@ class decor:
* method: mechanism for calculating reversal potential.
* diff: diffusivity [m^2/s].
"""
+
def paintings(
self,
) -> list[
@@ -966,32 +1035,38 @@ class decor:
"""
Return a view of all painted items.
"""
+
@typing.overload
def place(self, locations: str, synapse: synapse, label: str) -> decor:
"""
Place one instance of 'synapse' on each location in 'locations'.The group of synapses has the label 'label', used for forming connections between cells.
"""
+
@typing.overload
def place(self, locations: str, junction: junction, label: str) -> decor:
"""
Place one instance of 'junction' on each location in 'locations'.The group of junctions has the label 'label', used for forming gap-junction connections between cells.
"""
+
@typing.overload
def place(self, locations: str, iclamp: iclamp, label: str) -> decor:
"""
Add a current stimulus at each location in locations.The group of current stimuli has the label 'label'.
"""
+
@typing.overload
def place(self, locations: str, detector: threshold_detector, label: str) -> decor:
"""
Add a voltage spike detector at each location in locations.The group of spike detectors has the label 'label', used for forming connections between cells.
"""
+
def placements(
self,
) -> list[tuple[str, iclamp | threshold_detector | synapse | junction, str]]:
"""
Return a view of all placed items.
"""
+
def set_ion(
self,
ion: str,
@@ -1017,6 +1092,7 @@ class decor:
reversal potential is global for all compartments in the cell, and can't be
overriden locally.
"""
+
def set_property(
self,
Vm: units.quantity | None = None,
@@ -1069,32 +1145,38 @@ class domain_decomposition:
"""
Query the domain id that a cell assigned to (using global identifier gid).
"""
+
@property
def domain_id(self) -> int:
"""
The index of the local domain.
Always 0 for non-distributed models, and corresponds to the MPI rank for distributed runs.
"""
+
@property
def groups(self) -> list[group_description]:
"""
Descriptions of the cell groups on the local domain.
"""
+
@property
def num_domains(self) -> int:
"""
Number of domains that the model is distributed over.
"""
+
@property
def num_global_cells(self) -> int:
"""
Total number of cells in the global model (sum of num_local_cells over all domains).
"""
+
@property
def num_groups(self) -> int:
"""
Total number of cell groups in the local domain.
"""
+
@property
def num_local_cells(self) -> int:
"""
@@ -1111,6 +1193,7 @@ class event_generator:
weight: The weight of events to deliver.
sched: A schedule of the events.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -1118,6 +1201,7 @@ class event_generator:
"""
The target synapse (gid, local_id).
"""
+
@target.setter
def target(self, arg0: cell_local_label) -> None: ...
@property
@@ -1125,6 +1209,7 @@ class event_generator:
"""
The weight of events to deliver.
"""
+
@weight.setter
def weight(self, arg0: float) -> None: ...
@@ -1138,23 +1223,27 @@ class explicit_schedule(schedule_base):
"""
Construct an empty explicit schedule.
"""
+
@typing.overload
def __init__(self, times: list[units.quantity]) -> None:
"""
Construct an explicit schedule with argument:
times: A list of times [ms], [] by default.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
def events(self, arg0: float, arg1: float) -> list[float]:
"""
A view of monotonically increasing time values in the half-open interval [t0, t1) in [ms].
"""
+
@property
def times_ms(self) -> list[float]:
"""
A list of times [ms].
"""
+
@times_ms.setter
def times_ms(self, arg1: list[float]) -> None: ...
@@ -1185,6 +1274,7 @@ class gap_junction_connection:
local: local half of the gap junction connection.
weight: Gap junction connection weight [unit-less].
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -1192,6 +1282,7 @@ class gap_junction_connection:
"""
Local label of the gap junction connection.
"""
+
@local.setter
def local(self, arg0: cell_local_label) -> None: ...
@property
@@ -1199,6 +1290,7 @@ class gap_junction_connection:
"""
Remote gid and label of the gap junction connection.
"""
+
@peer.setter
def peer(self, arg0: cell_global_label) -> None: ...
@property
@@ -1206,6 +1298,7 @@ class gap_junction_connection:
"""
Gap junction connection weight [unit-less].
"""
+
@weight.setter
def weight(self, arg0: float) -> None: ...
@@ -1218,6 +1311,7 @@ class group_description:
"""
Construct a group description with cell kind, list of gids, and backend kind.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -1225,11 +1319,13 @@ class group_description:
"""
The hardware backend on which the cell group will run.
"""
+
@property
def gids(self) -> list[int]:
"""
The list of gids of the cells in the group.
"""
+
@property
def kind(self) -> cell_kind:
"""
@@ -1254,6 +1350,7 @@ class iclamp:
"""
Construct finite duration current clamp, constant amplitude
"""
+
@typing.overload
def __init__(
self,
@@ -1265,6 +1362,7 @@ class iclamp:
"""
Construct constant amplitude current clamp
"""
+
@typing.overload
def __init__(
self,
@@ -1276,6 +1374,7 @@ class iclamp:
"""
Construct current clamp according to (time, amplitude) linear envelope
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -1283,11 +1382,13 @@ class iclamp:
"""
List of (time [ms], amplitude [nA]) points comprising the piecewise linear envelope
"""
+
@property
def frequency(self) -> float:
"""
Oscillation frequency (kHz), zero implies DC stimulus.
"""
+
@property
def phase(self) -> float:
"""
@@ -1308,31 +1409,37 @@ class ion_data:
"""
Valence.
"""
+
@property
def diffusivity(self) -> float | None:
"""
Diffusivity.
"""
+
@property
def external_concentration(self) -> float | None:
"""
External concentration.
"""
+
@property
def internal_concentration(self) -> float | None:
"""
Internal concentration.
"""
+
@property
def reversal_concentration(self) -> float | None:
"""
Reversal potential.
"""
+
@property
def reversal_potential(self) -> float | None:
"""
Reversal potential.
"""
+
@property
def reversal_potential_method(self) -> str:
"""
@@ -1374,44 +1481,52 @@ class isometry:
"""
Construct a rotation isometry of angle theta about the axis in direction (x, y, z).
"""
+
@staticmethod
@typing.overload
def rotate(theta: float, axis: tuple) -> isometry:
"""
Construct a rotation isometry of angle theta about the given axis in the direction described by a tuple.
"""
+
@staticmethod
@typing.overload
def translate(x: float, y: float, z: float) -> isometry:
"""
Construct a translation isometry from displacements x, y, and z.
"""
+
@staticmethod
@typing.overload
def translate(arg0: tuple) -> isometry:
"""
Construct a translation isometry from the first three components of a tuple.
"""
+
@staticmethod
@typing.overload
def translate(arg0: mpoint) -> isometry:
"""
Construct a translation isometry from the x, y, and z components of an mpoint.
"""
+
@typing.overload
def __call__(self, arg0: mpoint) -> mpoint:
"""
Apply isometry to mpoint argument.
"""
+
@typing.overload
def __call__(self, arg0: tuple) -> tuple:
"""
Apply isometry to first three components of tuple argument.
"""
+
def __init__(self) -> None:
"""
Construct a trivial isometry.
"""
+
def __mul__(self, arg0: isometry) -> isometry: ...
class junction:
@@ -1450,6 +1565,7 @@ class label_dict:
"""
Import the entries of a another label dictionary with an optional prefix.
"""
+
def __contains__(self, arg0: str) -> bool: ...
def __getitem__(self, arg0: str) -> str: ...
@typing.overload
@@ -1457,21 +1573,25 @@ class label_dict:
"""
Create an empty label dictionary.
"""
+
@typing.overload
def __init__(self, arg0: dict[str, str]) -> None:
"""
Initialize a label dictionary from a dictionary with string labels as keys, and corresponding definitions as strings.
"""
+
@typing.overload
def __init__(self, arg0: label_dict) -> None:
"""
Initialize a label dictionary from another one
"""
+
@typing.overload
def __init__(self, arg0: typing.Iterator) -> None:
"""
Initialize a label dictionary from an iterable of key, definition pairs
"""
+
def __iter__(self) -> typing.Iterator: ...
def __len__(self) -> int: ...
def __repr__(self) -> str: ...
@@ -1485,18 +1605,21 @@ class label_dict:
- dend: (tag 3)
- apic: (tag 4)
"""
+
def items(self) -> typing.Iterator: ...
def keys(self) -> typing.Iterator: ...
def update(self, other: label_dict) -> None:
"""
The label_dict to be importedImport the entries of a another label dictionary.
"""
+
def values(self) -> typing.Iterator: ...
@property
def locsets(self) -> list[str]:
"""
The locset definitions.
"""
+
@property
def regions(self) -> list[str]:
"""
@@ -1529,6 +1652,7 @@ class lif_cell:
* V_m: Initial value of the Membrane potential [mV].
* t_ref: Refractory period [ms].
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -1536,6 +1660,7 @@ class lif_cell:
"""
Membrane capacitance [pF].
"""
+
@C_m.setter
def C_m(self, arg0: units.quantity) -> None: ...
@property
@@ -1543,6 +1668,7 @@ class lif_cell:
"""
Resting potential [mV].
"""
+
@E_L.setter
def E_L(self, arg0: units.quantity) -> None: ...
@property
@@ -1550,6 +1676,7 @@ class lif_cell:
"""
Reset potential [mV].
"""
+
@E_R.setter
def E_R(self, arg0: units.quantity) -> None: ...
@property
@@ -1557,6 +1684,7 @@ class lif_cell:
"""
Initial value of the Membrane potential [mV].
"""
+
@V_m.setter
def V_m(self, arg0: units.quantity) -> None: ...
@property
@@ -1564,6 +1692,7 @@ class lif_cell:
"""
Firing threshold [mV].
"""
+
@V_th.setter
def V_th(self, arg0: units.quantity) -> None: ...
@property
@@ -1571,6 +1700,7 @@ class lif_cell:
"""
Label of the single build-in source on the cell.
"""
+
@source.setter
def source(self, arg0: str) -> None: ...
@property
@@ -1578,6 +1708,7 @@ class lif_cell:
"""
Refractory period [ms].
"""
+
@t_ref.setter
def t_ref(self, arg0: units.quantity) -> None: ...
@property
@@ -1585,6 +1716,7 @@ class lif_cell:
"""
Label of the single build-in target on the cell.
"""
+
@target.setter
def target(self, arg0: str) -> None: ...
@property
@@ -1592,6 +1724,7 @@ class lif_cell:
"""
Membrane potential decaying constant [ms].
"""
+
@tau_m.setter
def tau_m(self, arg0: units.quantity) -> None: ...
@@ -1613,6 +1746,7 @@ class location:
branch: The id of the branch.
pos: The relative position (from 0., proximal, to 1., distal) on the branch.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -1620,6 +1754,7 @@ class location:
"""
The id of the branch.
"""
+
@property
def pos(self) -> float:
"""
@@ -1632,6 +1767,7 @@ class mechanism:
"""
The name of the mechanism
"""
+
@typing.overload
def __init__(self, name: str, params: dict[str, float]) -> None:
"""
@@ -1644,6 +1780,7 @@ class mechanism:
Example overriding a global parameter:
m = arbor.mechanism('nernst/R=8.3145,F=96485')
"""
+
@typing.overload
def __init__(self, name: str, **kwargs) -> None:
"""
@@ -1656,17 +1793,20 @@ class mechanism:
Example overriding a global parameter:
m = arbor.mechanism('nernst/R=8.3145,F=96485')
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
def set(self, name: str, value: float) -> None:
"""
Set parameter value.
"""
+
@property
def name(self) -> str:
"""
The name of the mechanism.
"""
+
@property
def values(self) -> dict[str, float]:
"""
@@ -1703,31 +1843,37 @@ class mechanism_info:
"""
Global fields have one value common to an instance of a mechanism, are constant in time and set at instantiation.
"""
+
@property
def ions(self) -> dict[str, ion_dependency]:
"""
Ion dependencies.
"""
+
@property
def kind(self) -> str:
"""
String representation of the kind of the mechanism.
"""
+
@property
def linear(self) -> bool:
"""
True if a synapse mechanism has linear current contributions so that multiple instances on the same compartment can be coalesced.
"""
+
@property
def parameters(self) -> dict[str, mechanism_field]:
"""
Parameter fields may vary across the extent of a mechanism, but are constant in time and set at instantiation.
"""
+
@property
def post_events(self) -> bool:
"""
True if a synapse mechanism has a `POST_EVENT` procedure defined.
"""
+
@property
def state(self) -> dict[str, mechanism_field]:
"""
@@ -1762,15 +1908,18 @@ class meter_manager:
"""
Create a new checkpoint. Records the time since the last checkpoint(or the call to start if no previous checkpoints exist),and restarts the timer for the next checkpoint.
"""
+
def start(self, context: context) -> None:
"""
Start the metering. Records a time stamp, that marks the start of the first checkpoint timing region.
"""
+
@property
def checkpoint_names(self) -> list[str]:
"""
A list of all metering checkpoint names.
"""
+
@property
def times(self) -> list[float]:
"""
@@ -1798,23 +1947,28 @@ class morphology:
"""
The child branches of branch i.
"""
+
def branch_parent(self, i: int) -> int:
"""
The parent branch of branch i.
"""
+
def branch_segments(self, i: int) -> list[msegment]:
"""
A list of the segments in branch i, ordered from proximal to distal ends of the branch.
"""
+
def to_segment_tree(self) -> segment_tree:
"""
Convert this morphology to a segment_tree.
"""
+
@property
def empty(self) -> bool:
"""
Whether the morphology is empty.
"""
+
@property
def num_branches(self) -> int:
"""
@@ -1826,10 +1980,12 @@ class morphology_provider:
"""
Construct a morphology provider.
"""
+
def reify_locset(self, arg0: str) -> list[location]:
"""
Turn a locset into a list of locations.
"""
+
def reify_region(self, arg0: str) -> extent:
"""
Turn a region into an extent.
@@ -1843,11 +1999,13 @@ class mpoint:
"""
Create an mpoint object from parameters x, y, z, and radius, specified in µm.
"""
+
@typing.overload
def __init__(self, arg0: tuple) -> None:
"""
Create an mpoint object from a tuple (x, y, z, radius), specified in µm.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -1855,16 +2013,19 @@ class mpoint:
"""
Radius of cable at sample location centred at coordinates [μm].
"""
+
@property
def x(self) -> float:
"""
X coordinate [μm].
"""
+
@property
def y(self) -> float:
"""
Y coordinate [μm].
"""
+
@property
def z(self) -> float:
"""
@@ -1877,11 +2038,13 @@ class msegment:
"""
the location and radius of the distal end.
"""
+
@property
def prox(self) -> mpoint:
"""
the location and radius of the proximal end.
"""
+
@property
def tag(self) -> int:
"""
@@ -1893,22 +2056,26 @@ class neuroml:
"""
Construct NML morphology from filename or stream.
"""
+
def cell_ids(self) -> list[str]:
"""
Query top-level cells.
"""
+
def cell_morphology(
self, cell_id: str, allow_spherical_root: bool = False
) -> neuroml_morph_data | None:
"""
Retrieve nml_morph_data associated with cell_id.
"""
+
def morphology(
self, morph_id: str, allow_spherical_root: bool = False
) -> neuroml_morph_data | None:
"""
Retrieve top-level nml_morph_data associated with morph_id.
"""
+
def morphology_ids(self) -> list[str]:
"""
Query top-level standalone morphologies.
@@ -1919,29 +2086,35 @@ class neuroml_morph_data:
"""
Label dictionary containing one region expression for each segmentGroup id.
"""
+
def named_segments(self) -> label_dict:
"""
Label dictionary containing one region expression for each name applied to one or more segments.
"""
+
def segments(self) -> label_dict:
"""
Label dictionary containing one region expression for each segment id.
"""
+
@property
def cell_id(self) -> str | None:
"""
Cell id, or empty if morphology was taken from a top-level <morphology> element.
"""
+
@property
def group_segments(self) -> dict[str, list[int]]:
"""
Map from segmentGroup ids to their corresponding segment ids.
"""
+
@property
def id(self) -> str:
"""
Morphology id.
"""
+
@property
def morphology(self) -> morphology:
"""
@@ -1968,6 +2141,7 @@ class partition_hint:
Must be positive, else set to default value.
prefer_gpu: Whether GPU is preferred, True by default.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -1975,6 +2149,7 @@ class partition_hint:
"""
The size of cell group assigned to CPU.
"""
+
@cpu_group_size.setter
def cpu_group_size(self, arg0: int) -> None: ...
@property
@@ -1982,6 +2157,7 @@ class partition_hint:
"""
The size of cell group assigned to GPU.
"""
+
@gpu_group_size.setter
def gpu_group_size(self, arg0: int) -> None: ...
@property
@@ -1989,6 +2165,7 @@ class partition_hint:
"""
Whether GPU usage is preferred.
"""
+
@prefer_gpu.setter
def prefer_gpu(self, arg0: bool) -> None: ...
@@ -1997,22 +2174,27 @@ class place_pwlin:
"""
Construct a piecewise-linear placement object from the given morphology and optional isometry.
"""
+
def all_at(self, location: location) -> list[mpoint]:
"""
Return list of all possible interpolated mpoints corresponding to the location argument.
"""
+
def all_segments(self, arg0: list[cable]) -> list[msegment]:
"""
Return maximal list of non-overlapping full or partial msegments whose union is coterminous with the extent of the given list of cables.
"""
+
def at(self, location: location) -> mpoint:
"""
Return an interpolated mpoint corresponding to the location argument.
"""
+
def closest(self, arg0: float, arg1: float, arg2: float) -> tuple:
"""
Find the location on the morphology that is closest to a 3d point. Returns the location and its distance from the point.
"""
+
def segments(self, arg0: list[cable]) -> list[msegment]:
"""
Return minimal list of full or partial msegments whose union is coterminous with the extent of the given list of cables.
@@ -2038,17 +2220,20 @@ class poisson_schedule(schedule_base):
seed: The seed for the random number generator, 0 by default.
tstop: No events delivered after this time [ms], None by default.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
def events(self, arg0: units.quantity, arg1: units.quantity) -> list[float]:
"""
A view of monotonically increasing time values in the half-open interval [t0, t1).
"""
+
@property
def freq(self) -> units.quantity:
"""
The expected frequency [kHz].
"""
+
@freq.setter
def freq(self, arg1: units.quantity) -> None: ...
@property
@@ -2056,6 +2241,7 @@ class poisson_schedule(schedule_base):
"""
The seed for the random number generator.
"""
+
@seed.setter
def seed(self, arg0: int) -> None: ...
@property
@@ -2063,6 +2249,7 @@ class poisson_schedule(schedule_base):
"""
The delivery time of the first event in the sequence [ms].
"""
+
@tstart.setter
def tstart(self, arg1: units.quantity) -> None: ...
@property
@@ -2070,6 +2257,7 @@ class poisson_schedule(schedule_base):
"""
No events delivered after this time [ms].
"""
+
@tstop.setter
def tstop(self, arg1: units.quantity) -> None: ...
@@ -2097,6 +2285,7 @@ class proc_allocation:
bind_procs: Create process binding mask.
bind_threads: Create thread binding mask.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -2104,6 +2293,7 @@ class proc_allocation:
"""
Try to bind MPI procs?
"""
+
@bind_procs.setter
def bind_procs(self, arg1: bool) -> None: ...
@property
@@ -2111,6 +2301,7 @@ class proc_allocation:
"""
Try to bind threads?
"""
+
@bind_threads.setter
def bind_threads(self, arg1: bool) -> None: ...
@property
@@ -2119,6 +2310,7 @@ class proc_allocation:
The identifier of the GPU to use.
Corresponds to the integer parameter used to identify GPUs in CUDA API calls.
"""
+
@gpu_id.setter
def gpu_id(self, arg1: typing.Any) -> None: ...
@property
@@ -2126,11 +2318,13 @@ class proc_allocation:
"""
Whether a GPU is being used (True/False).
"""
+
@property
def threads(self) -> int:
"""
The number of threads available locally for execution.
"""
+
@threads.setter
def threads(self, arg1: int) -> None: ...
@@ -2146,34 +2340,42 @@ class recipe:
"""
High level description of the cell with global identifier gid.
"""
+
def cell_kind(self, gid: int) -> cell_kind:
"""
The kind of cell with global identifier gid.
"""
+
def connections_on(self, gid: int) -> list[connection]:
"""
A list of all the incoming connections to gid, [] by default.
"""
+
def event_generators(self, gid: int) -> list[typing.Any]:
"""
A list of all the event generators that are attached to gid, [] by default.
"""
+
def external_connections_on(self, gid: int) -> list[connection]:
"""
A list of all the incoming connections from _remote_ locations to gid, [] by default.
"""
+
def gap_junctions_on(self, gid: int) -> list[gap_junction_connection]:
"""
A list of the gap junctions connected to gid, [] by default.
"""
+
def global_properties(self, kind: cell_kind) -> typing.Any:
"""
The default properties applied to all cells of type 'kind' in the model.
"""
+
def num_cells(self) -> int:
"""
The number of cells in the model.
"""
+
def probes(self, gid: int) -> list[probe]:
"""
The probes to allow monitoring.
@@ -2197,23 +2399,27 @@ class regular_schedule(schedule_base):
dt: The interval between time points [ms].
tstop: No events delivered after this time [ms], None by default.
"""
+
@typing.overload
def __init__(self, dt: units.quantity) -> None:
"""
Construct a regular schedule, starting from t = 0 and never terminating, with arguments:
dt: The interval between time points [ms].
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
def events(self, arg0: float, arg1: float) -> list[float]:
"""
A view of monotonically increasing time values in the half-open interval [t0, t1).
"""
+
@property
def dt(self) -> units.quantity:
"""
The interval between time points [ms].
"""
+
@dt.setter
def dt(self, arg1: units.quantity) -> None: ...
@property
@@ -2221,6 +2427,7 @@ class regular_schedule(schedule_base):
"""
The delivery time of the first event in the sequence [ms].
"""
+
@tstart.setter
def tstart(self, arg1: units.quantity) -> None: ...
@property
@@ -2228,6 +2435,7 @@ class regular_schedule(schedule_base):
"""
No events delivered after this time [ms].
"""
+
@tstop.setter
def tstop(self, arg1: units.quantity | None) -> None: ...
@@ -2278,11 +2486,13 @@ class segment_tree:
"""
Append a segment to the tree.
"""
+
@typing.overload
def append(self, parent: int, dist: mpoint, tag: int) -> int:
"""
Append a segment to the tree.
"""
+
@typing.overload
def append(
self, parent: int, x: float, y: float, z: float, radius: float, tag: int
@@ -2290,54 +2500,66 @@ class segment_tree:
"""
Append a segment to the tree, using the distal location of the parent segment as the proximal end.
"""
+
def apply_isometry(self, arg0: isometry) -> segment_tree:
"""
Apply an isometry to all segments in the tree.
"""
+
def equivalent(self, arg0: segment_tree) -> bool:
"""
Two trees are equivalent, but not neccessarily identical, ie they have the same segments and structure.
"""
+
def is_fork(self, i: int) -> bool:
"""
True if segment has more than one child.
"""
+
def is_root(self, i: int) -> bool:
"""
True if segment has no parent.
"""
+
def is_terminal(self, i: int) -> bool:
"""
True if segment has no children.
"""
+
def join_at(self, arg0: int, arg1: segment_tree) -> segment_tree:
"""
Join two subtrees at a given id, such that said id becomes the parent of the inserted sub-tree.
"""
+
def reserve(self, arg0: int) -> None: ...
def split_at(self, arg0: int) -> tuple[segment_tree, segment_tree]:
"""
Split into a pair of trees at the given id, such that one tree is the subtree rooted at id and the other is the original tree without said subtree.
"""
+
def tag_roots(self, arg0: int) -> list[int]:
"""
Get roots of tag region of this segment tree.
"""
+
@property
def empty(self) -> bool:
"""
Indicates whether the tree is empty (i.e. whether it has size 0)
"""
+
@property
def parents(self) -> list[int]:
"""
A list with the parent index of each segment.
"""
+
@property
def segments(self) -> list[msegment]:
"""
A list of the segments.
"""
+
@property
def size(self) -> int:
"""
@@ -2404,83 +2626,101 @@ class simulation:
according to the domain decomposition and computational resources described by a
context. Initialize PRNG using seed
"""
+
def clear_samplers(self) -> None:
"""
Clearing spike and sample information. restoring memory
"""
+
@typing.overload
def probe_metadata(self, probeset_id: cell_address) -> list:
"""
Retrieve metadata associated with given probe id.
"""
+
@typing.overload
def probe_metadata(self, addr: tuple[int, str]) -> list:
"""
Retrieve metadata associated with given probe id.
"""
+
@typing.overload
def probe_metadata(self, gid: int, tag: str) -> list:
"""
Retrieve metadata associated with given probe id.
"""
+
def progress_banner(self) -> None:
"""
Show a text progress bar during simulation.
"""
+
def record(self, arg0: spike_recording) -> None:
"""
Disable or enable local or global spike recording.
"""
+
def remove_all_samplers(self, arg0: int) -> None:
"""
Remove all sampling on the simulatr.
"""
+
def remove_sampler(self, handle: int) -> None:
"""
Remove sampling associated with the given handle.
"""
+
def reset(self) -> None:
"""
Reset the state of the simulation to its initial state.
"""
+
def run(self, tfinal: units.quantity, dt: units.quantity = ...) -> float:
"""
Run the simulation from current simulation time to tfinal [ms], with maximum time step size dt [ms].
"""
+
@typing.overload
def sample(self, probeset_id: cell_address, schedule: schedule_base) -> int:
"""
Record data from probes with given probeset_id according to supplied schedule.
Returns handle for retrieving data or removing the sampling.
"""
+
@typing.overload
def sample(self, gid: int, tag: str, schedule: schedule_base) -> int:
"""
Record data from probes with given probeset_id=(gid, tag) according to supplied schedule.
Returns handle for retrieving data or removing the sampling.
"""
+
@typing.overload
def sample(self, probeset_id: tuple[int, str], schedule: schedule_base) -> int:
"""
Record data from probes with given probeset_id=(gid, tag) according to supplied schedule.
Returns handle for retrieving data or removing the sampling.
"""
+
def samples(self, handle: int) -> list:
"""
Retrieve sample data as a list, one element per probe associated with the query.
"""
+
def serialize(self) -> str:
"""
Serialize the simulation object to a JSON string.
"""
+
def set_remote_spike_filter(self, pred: typing.Callable[[spike], bool]) -> None:
"""
Add a callback to filter spikes going out over external connections. `pred` isa callable on the `spike` type. **Caution**: This will be extremely slow; use C++ if you want to make use of this.
"""
+
def spikes(self) -> typing.Any:
"""
Retrieve recorded spikes as numpy array.
"""
+
def update(self, recipe: recipe) -> None:
"""
Rebuild the connection table from recipe::connections_on and the eventgenerators based on recipe::event_generators.
@@ -2498,6 +2738,7 @@ class single_cell_model:
"""
Build single cell model from cable cell components
"""
+
@typing.overload
def __init__(
self, morph: morphology, decor: decor, labels: label_dict = ...
@@ -2505,11 +2746,13 @@ class single_cell_model:
"""
Build single cell model from cable cell components
"""
+
@typing.overload
def __init__(self, cell: cable_cell) -> None:
"""
Initialise a single cell model for a cable cell.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
def event_generator(self, event_generator: event_generator) -> None:
@@ -2517,6 +2760,7 @@ class single_cell_model:
Register an event generator.
event_generator: An Arbor event generator.
"""
+
@typing.overload
def probe(self, what: str, where: str, tag: str, frequency: units.quantity) -> None:
"""
@@ -2526,6 +2770,7 @@ class single_cell_model:
tag: Unique name for this probe.
frequency: The target frequency at which to sample [kHz].
"""
+
@typing.overload
def probe(
self, what: str, where: location, tag: str, frequency: units.quantity
@@ -2537,20 +2782,24 @@ class single_cell_model:
tag: Unique name for this probe.
frequency: The target frequency at which to sample [kHz].
"""
+
def run(self, tfinal: units.quantity, dt: units.quantity = ...) -> None:
"""
Run model from t=0 to t=tfinal ms.
"""
+
@property
def cable_cell(self) -> cable_cell:
"""
The cable cell held by this model.
"""
+
@property
def properties(self) -> cable_global_properties:
"""
Global properties.
"""
+
@properties.setter
def properties(self, arg0: cable_global_properties) -> None: ...
@property
@@ -2558,6 +2807,7 @@ class single_cell_model:
"""
Holds spike times [ms] after a call to run().
"""
+
@property
def traces(self) -> list[trace]:
"""
@@ -2573,6 +2823,7 @@ class spike:
"""
The global identifier of the cell.
"""
+
@source.setter
def source(self, arg0: cell_member) -> None: ...
@property
@@ -2580,6 +2831,7 @@ class spike:
"""
The time of spike.
"""
+
@time.setter
def time(self, arg0: float) -> None: ...
@@ -2626,18 +2878,21 @@ class spike_source_cell:
Construct a spike source cell with a single source labeled 'source_label'.
The cell generates spikes on 'source_label' at regular intervals.
"""
+
@typing.overload
def __init__(self, source_label: str, schedule: explicit_schedule) -> None:
"""
Construct a spike source cell with a single source labeled 'source_label'.
The cell generates spikes on 'source_label' at a sequence of user-defined times.
"""
+
@typing.overload
def __init__(self, source_label: str, schedule: poisson_schedule) -> None:
"""
Construct a spike source cell with a single source labeled 'source_label'.
The cell generates spikes on 'source_label' at times defined by a Poisson sequence.
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@@ -2683,6 +2938,7 @@ class threshold_detector:
"""
Voltage threshold of spike detector [mV]
"""
+
def __repr__(self) -> str: ...
def __str__(self) -> str: ...
@property
@@ -2703,16 +2959,19 @@ class trace:
"""
Location on cell morphology.
"""
+
@property
def time(self) -> list[float]:
"""
Time stamps of samples [ms].
"""
+
@property
def value(self) -> list[float]:
"""
Sample values.
"""
+
@property
def variable(self) -> str:
"""
diff --git a/python/stubs/arbor/_arbor/env.pyi b/python/stubs/arbor/_arbor/env.pyi
index 103e23303334f797a3b6c05e67c61aa2e7938cac..72be0ec6daa5b91edafccfa43ccdd9bb0c80e14a 100644
--- a/python/stubs/arbor/_arbor/env.pyi
+++ b/python/stubs/arbor/_arbor/env.pyi
@@ -1,6 +1,7 @@
"""
Wrappers for arborenv.
"""
+
from __future__ import annotations
import arbor._arbor
import typing
diff --git a/python/stubs/arbor/_arbor/units.pyi b/python/stubs/arbor/_arbor/units.pyi
index f5a79e4944891e1c6c1ee5fa9c591f76b36481c1..aa567155747f5974d9ff785e8f8bc23409ea8c40 100644
--- a/python/stubs/arbor/_arbor/units.pyi
+++ b/python/stubs/arbor/_arbor/units.pyi
@@ -1,6 +1,7 @@
"""
Units and quantities for driving the user interface.
"""
+
from __future__ import annotations
import typing
@@ -78,12 +79,14 @@ class quantity:
"""
Convert quantity to string.
"""
+
def __rmul__(self, arg0: float) -> quantity: ...
def __rtruediv__(self, arg0: float) -> quantity: ...
def __str__(self) -> str:
"""
Convert quantity to string.
"""
+
def __sub__(self, arg0: quantity) -> quantity: ...
@typing.overload
def __truediv__(self, arg0: quantity) -> quantity: ...
@@ -95,11 +98,13 @@ class quantity:
"""
Convert quantity to given unit and return magnitude.
"""
+
@property
def units(self) -> unit:
"""
Return units.
"""
+
@property
def value(self) -> float:
"""
@@ -123,12 +128,14 @@ class unit:
"""
Convert unit to string.
"""
+
def __rmul__(self, arg0: float) -> quantity: ...
def __rtruediv__(self, arg0: float) -> quantity: ...
def __str__(self) -> str:
"""
Convert unit to string.
"""
+
@typing.overload
def __truediv__(self, arg0: unit) -> unit: ...
@typing.overload
diff --git a/scripts/tsplot b/scripts/tsplot
index ee0f839cf4f334db6e3cf832e89ce4b162f4f44e..024bde08bdaf5a5332051e94099a03c3859be735 100755
--- a/scripts/tsplot
+++ b/scripts/tsplot
@@ -11,7 +11,7 @@ import matplotlib as M
import matplotlib.pyplot as P
import numbers
from functools import reduce
-from itertools import chain, islice, cycle
+from itertools import islice, cycle
# Read timeseries data from multiple files, plot each in one panel, with common
# time axis, and optionally sharing a vertical axis as governed by the configuration.
diff --git a/test/unit/test_sde.cpp b/test/unit/test_sde.cpp
index 87f19824f35b9a4fe3a19093d442c46c7aef870a..d0d8b6570888d7fbee6ea6afd3a8167753e01f1f 100644
--- a/test/unit/test_sde.cpp
+++ b/test/unit/test_sde.cpp
@@ -377,8 +377,8 @@ public:
// generic advance method used for all pertinent mechanisms
// first argument indicates the number of random variables
void advance_common(unsigned int n_rv, arb_mechanism_ppack* pp) {
- const auto width = pp->width;
- arb_value_type* ptr = archive_ptr->claim(width * n_rv);
+ auto width = pp->width;
+ arb_value_type* ptr = archive_ptr->claim(width*n_rv);
for (arb_size_type j=0; j<n_rv; ++j) {
for (arb_size_type i=0; i<width; ++i) {
ptr[j*width+i] = pp->random_numbers[j][i];
@@ -413,7 +413,7 @@ TEST(sde, reproducibility) {
// simulation parameters
unsigned ncells = 4;
unsigned ncvs = 2;
- auto const dt = 0.5*arb::units::ms;
+ auto const dt = 0.5*U::ms;
unsigned nsteps = 6;
// Decorations with a bunch of stochastic processes
@@ -494,7 +494,7 @@ TEST(sde, normality) {
unsigned ncells = 4;
unsigned nsynapses = 100;
unsigned ncvs = 100;
- auto dt = 0.5*arb::units::ms;;
+ auto dt = 0.5*U::ms;;
unsigned nsteps = 50;
// make labels (and locations for synapses)
@@ -651,7 +651,7 @@ TEST(sde, solver) {
unsigned ncells = 4;
unsigned nsynapses = 2000;
unsigned ncvs = 1;
- auto dt = 1.0/512*arb::units::ms; // need relatively small time steps due to low accuracy
+ auto dt = 1.0/512*U::ms; // need relatively small time steps due to low accuracy
unsigned nsteps = 100;
unsigned nsims = 4;
@@ -806,7 +806,7 @@ TEST(sde, coupled) {
unsigned ncells = 4;
unsigned nsynapses = 2000;
unsigned ncvs = 1;
- auto dt = 1.0/512*arb::units::ms; // need relatively small time steps due to low accuracy
+ auto dt = 1.0/512*U::ms; // need relatively small time steps due to low accuracy
unsigned nsteps = 100;
unsigned nsims = 4;