From a6ddd515364cbe9e81a3fb24e96276b9608c29c9 Mon Sep 17 00:00:00 2001
From: akuesters <42005107+akuesters@users.noreply.github.com>
Date: Tue, 4 Jun 2019 16:32:38 +0200
Subject: [PATCH] Py feature recipe wo probes (#768)
Fixes #760
Wraps arbor recipe (without probes, i.e. num_probes, probe_info, get_probe) including
- cell_connection,
- gap_junction_connection,
- recipe with
- num_cells
- cell_description
- cell_kind
- num_sources
- num_targets
- num_gap_junctions_sites
- event_generators
- connections_on
- gap_junctions_on
- global_properties
- enum cell_kind in `identifiers.cpp`
---
python/CMakeLists.txt | 1 +
python/context.cpp | 7 +-
python/event_generator.cpp | 44 ++--
python/event_generator.hpp | 22 ++
python/identifiers.cpp | 11 +
python/mpi.cpp | 2 +-
python/pyarb.cpp | 2 +
python/recipe.cpp | 232 ++++++++++++++++++++++
python/recipe.hpp | 163 +++++++++++++++
python/test/unit/test_contexts.py | 8 +-
python/test/unit/test_event_generators.py | 12 +-
11 files changed, 461 insertions(+), 43 deletions(-)
create mode 100644 python/event_generator.hpp
create mode 100644 python/recipe.cpp
create mode 100644 python/recipe.hpp
diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
index 4b37a939..8065522a 100644
--- a/python/CMakeLists.txt
+++ b/python/CMakeLists.txt
@@ -22,6 +22,7 @@ add_library(pyarb MODULE
identifiers.cpp
mpi.cpp
pyarb.cpp
+ recipe.cpp
strings.cpp
)
diff --git a/python/context.cpp b/python/context.cpp
index 4e7dde4f..04cb3ab0 100644
--- a/python/context.cpp
+++ b/python/context.cpp
@@ -38,11 +38,11 @@ struct proc_allocation_shim {
// getter and setter (in order to assert when being set)
void set_gpu_id(pybind11::object gpu) {
- gpu_id = py2optional<int>(gpu, "gpu id must be None, or a non-negative integer.", is_nonneg_int);
+ gpu_id = py2optional<int>(gpu, "gpu_id must be None, or a non-negative integer", is_nonneg_int);
};
void set_num_threads(int threads) {
- pyarb::assert_throw([](int n) { return n>0; }(threads), "threads must be a positive integer.");
+ pyarb::assert_throw([](int n) { return n>0; }(threads), "threads must be a positive integer");
num_threads = threads;
};
@@ -153,8 +153,7 @@ void register_contexts(pybind11::module& m) {
#else
.def(pybind11::init(
[](int threads, pybind11::object gpu){
- auto gpu_id = py2optional<int>(gpu,
- "gpu id must be None, or a non-negative integer.", is_nonneg_int);
+ auto gpu_id = py2optional<int>(gpu, "gpu_id must be None, or a non-negative integer", is_nonneg_int);
return context_shim(arb::make_context(arb::proc_allocation(threads, gpu_id.value_or(-1))));
}),
"threads"_a=1, "gpu_id"_a=pybind11::none(),
diff --git a/python/event_generator.cpp b/python/event_generator.cpp
index f31bbe15..9344a3fd 100644
--- a/python/event_generator.cpp
+++ b/python/event_generator.cpp
@@ -3,7 +3,6 @@
#include <string>
#include <arbor/common_types.hpp>
-#include <arbor/event_generator.hpp>
#include <arbor/schedule.hpp>
#include <pybind11/pybind11.h>
@@ -12,6 +11,7 @@
#include "conversion.hpp"
#include "error.hpp"
+#include "event_generator.hpp"
namespace pyarb {
@@ -41,13 +41,13 @@ struct regular_schedule_shim {
// getter and setter (in order to assert when being set)
void set_tstart(pybind11::object t) {
- tstart = py2optional<time_type>(t, "tstart must a non-negative number, or None.", is_nonneg);
+ tstart = py2optional<time_type>(t, "tstart must a non-negative number, or None", is_nonneg);
};
void set_tstop(pybind11::object t) {
- tstop = py2optional<time_type>(t, "tstop must a non-negative number, or None.", is_nonneg);
+ tstop = py2optional<time_type>(t, "tstop must a non-negative number, or None", is_nonneg);
};
void set_dt(time_type delta_t) {
- pyarb::assert_throw(is_nonneg(delta_t), "dt must be a non-negative number.");
+ pyarb::assert_throw(is_nonneg(delta_t), "dt must be a non-negative number");
dt = delta_t;
};
@@ -90,7 +90,7 @@ struct explicit_schedule_shim {
// Assert that there are no negative times
if (times.size()) {
pyarb::assert_throw(is_nonneg(times[0]),
- "explicit time schedule can not contain negative values.");
+ "explicit time schedule can not contain negative values");
}
};
@@ -123,12 +123,12 @@ struct poisson_schedule_shim {
}
void set_tstart(time_type t) {
- pyarb::assert_throw(is_nonneg(t), "tstart must be a non-negative number.");
+ pyarb::assert_throw(is_nonneg(t), "tstart must be a non-negative number");
tstart = t;
};
void set_freq(time_type f) {
- pyarb::assert_throw(is_nonneg(f), "frequency must be a non-negative number.");
+ pyarb::assert_throw(is_nonneg(f), "frequency must be a non-negative number");
freq = f;
};
@@ -141,6 +141,15 @@ struct poisson_schedule_shim {
}
};
+template <typename Sched>
+event_generator_shim make_event_generator(
+ arb::cell_member_type target,
+ double weight,
+ const Sched& sched)
+{
+ return event_generator_shim(target, weight, sched.schedule());
+}
+
// Helper template for printing C++ optional types in Python.
// Prints either the value, or None if optional value is not set.
template <typename T>
@@ -184,27 +193,6 @@ std::string schedule_poisson_string(const poisson_schedule_shim& p) {
return s.str();
};
-struct event_generator_shim {
- arb::cell_member_type target;
- double weight;
- arb::schedule time_sched;
-
- event_generator_shim(arb::cell_member_type cell, double event_weight, arb::schedule sched):
- target(cell),
- weight(event_weight),
- time_sched(std::move(sched))
- {}
-};
-
-template <typename Sched>
-event_generator_shim make_event_generator(
- arb::cell_member_type target,
- double weight,
- const Sched& sched)
-{
- return event_generator_shim(target, weight, sched.schedule());
-}
-
void register_event_generators(pybind11::module& m) {
using namespace pybind11::literals;
using time_type = arb::time_type;
diff --git a/python/event_generator.hpp b/python/event_generator.hpp
new file mode 100644
index 00000000..ed41c10e
--- /dev/null
+++ b/python/event_generator.hpp
@@ -0,0 +1,22 @@
+#pragma once
+
+#include <arbor/common_types.hpp>
+#include <arbor/schedule.hpp>
+
+#include <pybind11/pybind11.h>
+
+namespace pyarb {
+
+struct event_generator_shim {
+ arb::cell_member_type target;
+ double weight;
+ arb::schedule time_sched;
+
+ event_generator_shim(arb::cell_member_type cell, double event_weight, arb::schedule sched):
+ target(cell),
+ weight(event_weight),
+ time_sched(std::move(sched))
+ {}
+};
+
+} // namespace pyarb
diff --git a/python/identifiers.cpp b/python/identifiers.cpp
index cb6159a2..3aae5a61 100644
--- a/python/identifiers.cpp
+++ b/python/identifiers.cpp
@@ -38,6 +38,17 @@ void register_identifiers(pybind11::module& m) {
"Cell-local index of the item.")
.def("__str__", &cell_member_string)
.def("__repr__", &cell_member_string);
+
+ pybind11::enum_<arb::cell_kind>(m, "cell_kind",
+ "Enumeration used to identify the cell kind, used by the model to group equal kinds in the same cell group.")
+ .value("benchmark", arb::cell_kind::benchmark,
+ "Proxy cell used for benchmarking.")
+ .value("cable", arb::cell_kind::cable,
+ "A cell with morphology described by branching 1D cable segments.")
+ .value("lif", arb::cell_kind::lif,
+ "Leaky-integrate and fire neuron.")
+ .value("spike_source", arb::cell_kind::spike_source,
+ "Proxy cell that generates spikes from a spike sequence provided by the user.");
}
} // namespace pyarb
diff --git a/python/mpi.cpp b/python/mpi.cpp
index 16a2b362..15f1b5df 100644
--- a/python/mpi.cpp
+++ b/python/mpi.cpp
@@ -32,7 +32,7 @@ MPI_Comm convert_to_mpi_comm(pybind11::object o) {
return *PyMPIComm_Get(o.ptr());
}
#endif
- throw arb::mpi_error(MPI_ERR_OTHER, "Unable to convert to an MPI Communicatior.");
+ throw arb::mpi_error(MPI_ERR_OTHER, "Unable to convert to an MPI Communicatior");
}
mpi_comm_shim::mpi_comm_shim(pybind11::object o) {
diff --git a/python/pyarb.cpp b/python/pyarb.cpp
index e085141e..c964caa4 100644
--- a/python/pyarb.cpp
+++ b/python/pyarb.cpp
@@ -13,6 +13,7 @@ void register_identifiers(pybind11::module& m);
#ifdef ARB_MPI_ENABLED
void register_mpi(pybind11::module& m);
#endif
+void register_recipe(pybind11::module& m);
}
PYBIND11_MODULE(arbor, m) {
@@ -26,4 +27,5 @@ PYBIND11_MODULE(arbor, m) {
#ifdef ARB_MPI_ENABLED
pyarb::register_mpi(m);
#endif
+ pyarb::register_recipe(m);
}
diff --git a/python/recipe.cpp b/python/recipe.cpp
new file mode 100644
index 00000000..93d1e2bf
--- /dev/null
+++ b/python/recipe.cpp
@@ -0,0 +1,232 @@
+#include <sstream>
+#include <string>
+#include <vector>
+
+#include <pybind11/pybind11.h>
+#include <pybind11/pytypes.h>
+#include <pybind11/stl.h>
+
+#include <arbor/benchmark_cell.hpp>
+#include <arbor/cable_cell.hpp>
+#include <arbor/event_generator.hpp>
+#include <arbor/lif_cell.hpp>
+#include <arbor/recipe.hpp>
+#include <arbor/spike_source_cell.hpp>
+
+#include "error.hpp"
+#include "event_generator.hpp"
+#include "recipe.hpp"
+
+namespace pyarb {
+
+// ========================================= Unwrap =========================================
+// The py::recipe::cell_decription returns a pybind11::object, that is
+// unwrapped and copied into a arb::util::unique_any.
+
+arb::util::unique_any py_recipe_shim::get_cell_description(arb::cell_gid_type gid) const {
+ using pybind11::isinstance;
+ using pybind11::cast;
+
+ // Aquire the GIL because it must be held when calling isinstance and cast.
+ auto guard = pybind11::gil_scoped_acquire();
+
+ // Get the python object pyarb::cell_description from the python front end
+ pybind11::object o = impl_->cell_description(gid);
+
+ if (isinstance<arb::cable_cell>(o)) {
+ return arb::util::unique_any(cast<arb::cable_cell>(o));
+ }
+
+ else if (isinstance<arb::lif_cell>(o)) {
+ return arb::util::unique_any(cast<arb::lif_cell>(o));
+ }
+
+ else if (isinstance<arb::spike_source_cell>(o)) {
+ return arb::util::unique_any(cast<arb::spike_source_cell>(o));
+ }
+
+ else if (isinstance<arb::benchmark_cell>(o)) {
+ return arb::util::unique_any(cast<arb::benchmark_cell>(o));
+ }
+
+ throw pyarb_error(
+ "recipe.cell_description returned \""
+ + std::string(pybind11::str(o))
+ + "\" which does not describe a known Arbor cell type");
+}
+
+// The py::recipe::global_properties returns a pybind11::object, that is
+// unwrapped and copied into a arb::util::any.
+arb::util::any py_recipe_shim::get_global_properties(arb::cell_kind kind) const {
+ using pybind11::isinstance;
+ using pybind11::cast;
+
+ // Aquire the GIL because it must be held when calling isinstance and cast.
+ auto guard = pybind11::gil_scoped_acquire();
+
+ // Get the python object pyarb::global_properties from the python front end
+ pybind11::object o = impl_->global_properties(kind);
+
+ if (kind == arb::cell_kind::cable) {
+ return arb::util::any(cast<arb::cable_cell_global_properties>(o));
+ }
+
+ else return arb::util::any{};
+
+ throw pyarb_error(
+ "recipe.global_properties returned \""
+ + std::string(pybind11::str(o))
+ + "\" which does not describe a known Arbor global property description");
+
+}
+
+std::vector<arb::event_generator> py_recipe_shim::event_generators(arb::cell_gid_type gid) const {
+ using namespace std::string_literals;
+ using pybind11::isinstance;
+ using pybind11::cast;
+
+ // Aquire the GIL because it must be held when calling isinstance and cast.
+ auto guard = pybind11::gil_scoped_acquire();
+
+ // Get the python list of pyarb::event_generator_shim from the python front end.
+ auto pygens = impl_->event_generators(gid);
+
+ std::vector<arb::event_generator> gens;
+ gens.reserve(pygens.size());
+
+ for (auto& g: pygens) {
+ // check that a valid Python event_generator was passed.
+ if (!isinstance<pyarb::event_generator_shim>(g)) {
+ std::stringstream s;
+ s << "recipe supplied an invalid event generator for gid "
+ << gid << ": " << pybind11::str(g);
+ throw pyarb_error(s.str());
+ }
+ // get a reference to the python event_generator
+ auto& p = cast<const pyarb::event_generator_shim&>(g);
+
+ // convert the event_generator to an arb::event_generator
+ gens.push_back(arb::schedule_generator({gid, p.target.index}, p.weight, std::move(p.time_sched)));
+ }
+
+ return gens;
+}
+
+// TODO: implement py_recipe_shim::probe_info
+
+std::string connection_string(const arb::cell_connection& c) {
+ std::stringstream s;
+ s << "<connection: (" << c.source.gid << "," << c.source.index << ")"
+ << " -> (" << c.dest.gid << "," << c.dest.index << ")"
+ << " , delay " << c.delay << ", weight " << c.weight << ">";
+ return s.str();
+}
+
+std::string gap_junction_connection_string(const arb::gap_junction_connection& gc) {
+ std::stringstream s;
+ s << "<connection: (" << gc.local.gid << "," << gc.local.index << ")"
+ << " -> (" << gc.peer.gid << "," << gc.peer.index << ")"
+ << " , conductance " << gc.ggap << ">";
+ return s.str();
+}
+
+void register_recipe(pybind11::module& m) {
+ using namespace pybind11::literals;
+
+ // Connections
+ pybind11::class_<arb::cell_connection> cell_connection(m, "cell_connection",
+ "Describes a connection between two cells:\n"
+ "a pre-synaptic source and a post-synaptic destination.");
+ cell_connection
+ .def(pybind11::init<>(
+ [](){return arb::cell_connection({0u,0u}, {0u,0u}, 0.f, 0.f);}),
+ "Construct a connection with default arguments:\n"
+ " source: gid 0, index 0.\n"
+ " destination: gid 0, index 0.\n"
+ " weight: 0.\n"
+ " delay: 0 ms.\n")
+ .def(pybind11::init<arb::cell_member_type, arb::cell_member_type, float, float>(),
+ "source"_a, "destination"_a, "weight"_a = 0.f, "delay"_a = 0.f,
+ "Construct a connection with arguments:\n"
+ " source: The source end point of the connection.\n"
+ " destination: The destination end point of the connection.\n"
+ " weight: The weight delivered to the target synapse (dimensionless with interpretation specific to synapse type of target, default 0.).\n"
+ " delay: The delay of the connection (unit: ms, default 0.).\n")
+ .def_readwrite("source", &arb::cell_connection::source,
+ "The source of the connection.")
+ .def_readwrite("destination", &arb::cell_connection::dest,
+ "The destination of the connection.")
+ .def_readwrite("weight", &arb::cell_connection::weight,
+ "The weight of the connection (unit: Sâ‹…cmâ»Â²).")
+ .def_readwrite("delay", &arb::cell_connection::delay,
+ "The delay time of the connection (unit: ms).")
+ .def("__str__", &connection_string)
+ .def("__repr__", &connection_string);
+
+ // Gap Junction Connections
+ pybind11::class_<arb::gap_junction_connection> gap_junction_connection(m, "gap_junction_connection",
+ "Describes a gap junction between two gap junction sites.");
+ gap_junction_connection
+ .def(pybind11::init<>(
+ [](){return arb::gap_junction_connection({0u,0u}, {0u,0u}, 0.f);}),
+ "Construct a gap junction connection with default arguments:\n"
+ " local: gid 0, index 0.\n"
+ " peer: gid 0, index 0.\n"
+ " ggap: 0 μS.\n")
+ .def(pybind11::init<arb::cell_member_type, arb::cell_member_type, double>(),
+ "local"_a, "peer"_a, "ggap"_a = 0.f,
+ "Construct a gap junction connection with arguments:\n"
+ " local: One half of the gap junction connection.\n"
+ " peer: Other half of the gap junction connection.\n"
+ " ggap: Gap junction conductance (unit: μS, default 0.).\n")
+ .def_readwrite("local", &arb::gap_junction_connection::local,
+ "One half of the gap junction connection.")
+ .def_readwrite("peer", &arb::gap_junction_connection::peer,
+ "Other half of the gap junction connection.")
+ .def_readwrite("ggap", &arb::gap_junction_connection::ggap,
+ "Gap junction conductance (unit: μS).")
+ .def("__str__", &gap_junction_connection_string)
+ .def("__repr__", &gap_junction_connection_string);
+
+ // Recipes
+ pybind11::class_<py_recipe,
+ py_recipe_trampoline,
+ std::shared_ptr<py_recipe>>
+ recipe(m, "recipe", pybind11::dynamic_attr(),
+ "A description of a model, describing the cells and the network via a cell-centric interface.");
+ recipe
+ .def(pybind11::init<>())
+ .def("num_cells", &py_recipe::num_cells, "The number of cells in the model.")
+ .def("cell_description", &py_recipe::cell_description, pybind11::return_value_policy::copy,
+ "gid"_a,
+ "High level description of the cell with global identifier gid.")
+ .def("cell_kind", &py_recipe::cell_kind,
+ "gid"_a,
+ "The kind of cell with global identifier gid.")
+ .def("num_sources", &py_recipe::num_sources,
+ "gid"_a,
+ "The number of spike sources on gid (default 0).")
+ .def("num_targets", &py_recipe::num_targets,
+ "gid"_a,
+ "The number of post-synaptic sites on gid (default 0).")
+ // TODO: py_recipe::num_probes
+ .def("num_gap_junction_sites", &py_recipe::num_gap_junction_sites,
+ "gid"_a,
+ "The number of gap junction sites on gid (default 0).")
+ .def("event_generators", &py_recipe::event_generators,
+ "gid"_a,
+ "A list of all the event generators that are attached to gid (default []).")
+ .def("connections_on", &py_recipe::connections_on,
+ "gid"_a,
+ "A list of all the incoming connections to gid (default []).")
+ .def("gap_junctions_on", &py_recipe::gap_junctions_on,
+ "gid"_a,
+ "A list of the gap junctions connected to gid (default []).")
+ // TODO: py_recipe::get_probe
+ .def("global_properties", &py_recipe::global_properties, pybind11::return_value_policy::copy,
+ "cell_kind"_a,
+ "Global property type specific to a given cell kind.")
+ .def("__str__", [](const py_recipe&){return "<pyarb.recipe>";})
+ .def("__repr__", [](const py_recipe&){return "<pyarb.recipe>";});
+}
+} // namespace pyarb
diff --git a/python/recipe.hpp b/python/recipe.hpp
new file mode 100644
index 00000000..4e83c276
--- /dev/null
+++ b/python/recipe.hpp
@@ -0,0 +1,163 @@
+#pragma once
+
+#include <vector>
+
+#include <pybind11/pybind11.h>
+#include <pybind11/pytypes.h>
+#include <pybind11/stl.h>
+
+#include <arbor/event_generator.hpp>
+#include <arbor/recipe.hpp>
+
+namespace pyarb {
+
+// pyarb::recipe is the recipe interface used by Python.
+// Calls that return generic types return pybind11::object, to avoid
+// having to wrap some C++ types used by the C++ interface (specifically
+// util::unique_any, util::any, std::unique_ptr, etc.)
+// For example, requests for cell description return pybind11::object, instead
+// of util::unique_any used by the C++ recipe interface.
+// The py_recipe_shim unwraps the python objects, and forwards them
+// to the C++ back end.
+
+class py_recipe {
+public:
+ py_recipe() = default;
+ virtual ~py_recipe() {}
+
+ virtual arb::cell_size_type num_cells() const = 0;
+
+ virtual pybind11::object cell_description(arb::cell_gid_type gid) const = 0;
+ virtual arb::cell_kind cell_kind(arb::cell_gid_type gid) const = 0;
+
+ virtual arb::cell_size_type num_sources(arb::cell_gid_type) const { return 0; }
+ virtual arb::cell_size_type num_targets(arb::cell_gid_type) const { return 0; }
+
+ //TODO: virtual arb::cell_size_type num_probes(arb::cell_gid_type) const { return 0; }
+
+ virtual arb::cell_size_type num_gap_junction_sites(arb::cell_gid_type gid) const {
+ return gap_junctions_on(gid).size();
+ }
+
+ virtual std::vector<pybind11::object> event_generators(arb::cell_gid_type gid) const {
+ auto guard = pybind11::gil_scoped_acquire();
+ return {};
+ }
+
+ virtual std::vector<arb::cell_connection> connections_on(arb::cell_gid_type gid) const { return {}; }
+ virtual std::vector<arb::gap_junction_connection> gap_junctions_on(arb::cell_gid_type) const { return {}; }
+
+ //TODO: virtual pybind11::object get_probe (arb::cell_member_type id) const {...}
+
+ virtual pybind11::object global_properties(arb::cell_kind kind) const = 0;
+};
+
+class py_recipe_trampoline: public py_recipe {
+public:
+ arb::cell_size_type num_cells() const override {
+ PYBIND11_OVERLOAD_PURE(arb::cell_size_type, py_recipe, num_cells);
+ }
+
+ pybind11::object cell_description(arb::cell_gid_type gid) const override {
+ PYBIND11_OVERLOAD_PURE(pybind11::object, py_recipe, cell_description, gid);
+ }
+
+ arb::cell_kind cell_kind(arb::cell_gid_type gid) const override {
+ PYBIND11_OVERLOAD_PURE(arb::cell_kind, py_recipe, cell_kind, gid);
+ }
+
+ arb::cell_size_type num_sources(arb::cell_gid_type gid) const override {
+ PYBIND11_OVERLOAD(arb::cell_size_type, py_recipe, num_sources, gid);
+ }
+
+ arb::cell_size_type num_targets(arb::cell_gid_type gid) const override {
+ PYBIND11_OVERLOAD(arb::cell_size_type, py_recipe, num_targets, gid);
+ }
+
+ //TODO: arb::cell_size_type num_probes(arb::cell_gid_type)
+
+ arb::cell_size_type num_gap_junction_sites(arb::cell_gid_type gid) const override {
+ PYBIND11_OVERLOAD(arb::cell_size_type, py_recipe, num_gap_junction_sites, gid);
+ }
+
+ std::vector<pybind11::object> event_generators(arb::cell_gid_type gid) const override {
+ PYBIND11_OVERLOAD(std::vector<pybind11::object>, py_recipe, event_generators, gid);
+ }
+
+ std::vector<arb::cell_connection> connections_on(arb::cell_gid_type gid) const override {
+ PYBIND11_OVERLOAD(std::vector<arb::cell_connection>, py_recipe, connections_on, gid);
+ }
+
+ std::vector<arb::gap_junction_connection> gap_junctions_on(arb::cell_gid_type gid) const override {
+ PYBIND11_OVERLOAD(std::vector<arb::gap_junction_connection>, py_recipe, gap_junctions_on, gid);
+ }
+
+ //TODO: pybind11::object get_probe(arb::cell_member_type id)
+
+ pybind11::object global_properties(arb::cell_kind kind) const override {
+ PYBIND11_OVERLOAD_PURE(pybind11::object, py_recipe, global_properties, kind);
+ }
+};
+
+// A recipe shim that holds a pyarb::recipe implementation.
+// Unwraps/translates python-side output from pyarb::recipe and forwards
+// to arb::recipe.
+// For example, unwrap cell descriptions stored in PyObject, and rewrap
+// in util::unique_any.
+
+class py_recipe_shim: public arb::recipe {
+ // pointer to the python recipe implementation
+ std::shared_ptr<py_recipe> impl_;
+
+public:
+ using recipe::recipe;
+
+ py_recipe_shim(std::shared_ptr<py_recipe> r): impl_(std::move(r)) {}
+
+ arb::cell_size_type num_cells() const override {
+ return impl_->num_cells();
+ }
+
+ // The pyarb::recipe::cell_decription returns a pybind11::object, that is
+ // unwrapped and copied into a util::unique_any.
+ arb::util::unique_any get_cell_description(arb::cell_gid_type gid) const override;
+
+ arb::cell_kind get_cell_kind(arb::cell_gid_type gid) const override {
+ return impl_->cell_kind(gid);
+ }
+
+ arb::cell_size_type num_sources(arb::cell_gid_type gid) const override {
+ return impl_->num_sources(gid);
+ }
+
+ arb::cell_size_type num_targets(arb::cell_gid_type gid) const override {
+ return impl_->num_targets(gid);
+ }
+
+/* //TODO: arb::cell_size_type num_probes(arb::cell_gid_type gid) const override {
+ return impl_->num_probes(gid);
+ }
+*/
+ arb::cell_size_type num_gap_junction_sites(arb::cell_gid_type gid) const override {
+ return impl_->num_gap_junction_sites(gid);
+ }
+
+ std::vector<arb::event_generator> event_generators(arb::cell_gid_type gid) const override;
+
+ std::vector<arb::cell_connection> connections_on(arb::cell_gid_type gid) const override {
+ return impl_->connections_on(gid);
+ }
+
+ std::vector<arb::gap_junction_connection> gap_junctions_on(arb::cell_gid_type gid) const override {
+ return impl_->gap_junctions_on(gid);
+ }
+
+ //TODO: arb::probe_info get_probe(arb::cell_member_type id) const override
+
+ // The pyarb::recipe::global_properties returns a pybind11::object, that is
+ // unwrapped and copied into a util::any.
+ arb::util::any get_global_properties(arb::cell_kind kind) const override;
+
+};
+
+} // namespace pyarb
diff --git a/python/test/unit/test_contexts.py b/python/test/unit/test_contexts.py
index e007207f..a445bb15 100644
--- a/python/test/unit/test_contexts.py
+++ b/python/test/unit/test_contexts.py
@@ -42,18 +42,18 @@ class Contexts(unittest.TestCase):
def test_exceptions_allocation(self):
with self.assertRaisesRegex(RuntimeError,
- "gpu id must be None, or a non-negative integer."):
+ "gpu_id must be None, or a non-negative integer"):
arb.proc_allocation(gpu_id = 1.)
with self.assertRaisesRegex(RuntimeError,
- "gpu id must be None, or a non-negative integer."):
+ "gpu_id must be None, or a non-negative integer"):
arb.proc_allocation(gpu_id = -1)
with self.assertRaisesRegex(RuntimeError,
- "gpu id must be None, or a non-negative integer."):
+ "gpu_id must be None, or a non-negative integer"):
arb.proc_allocation(gpu_id = 'gpu_id')
with self.assertRaises(TypeError):
arb.proc_allocation(threads = 1.)
with self.assertRaisesRegex(RuntimeError,
- "threads must be a positive integer."):
+ "threads must be a positive integer"):
arb.proc_allocation(threads = 0)
with self.assertRaises(TypeError):
arb.proc_allocation(threads = None)
diff --git a/python/test/unit/test_event_generators.py b/python/test/unit/test_event_generators.py
index 5febad17..b64119c8 100644
--- a/python/test/unit/test_event_generators.py
+++ b/python/test/unit/test_event_generators.py
@@ -51,17 +51,17 @@ class RegularSchedule(unittest.TestCase):
def test_exceptions_regular_schedule(self):
with self.assertRaisesRegex(RuntimeError,
- "tstart must a non-negative number, or None."):
+ "tstart must a non-negative number, or None"):
arb.regular_schedule(tstart = -1.)
with self.assertRaisesRegex(RuntimeError,
- "dt must be a non-negative number."):
+ "dt must be a non-negative number"):
arb.regular_schedule(dt = -0.1)
with self.assertRaises(TypeError):
arb.regular_schedule(dt = None)
with self.assertRaises(TypeError):
arb.regular_schedule(dt = 'dt')
with self.assertRaisesRegex(RuntimeError,
- "tstop must a non-negative number, or None."):
+ "tstop must a non-negative number, or None"):
arb.regular_schedule(tstop = 'tstop')
class ExplicitSchedule(unittest.TestCase):
@@ -86,7 +86,7 @@ class ExplicitSchedule(unittest.TestCase):
def test_exceptions_explicit_schedule(self):
with self.assertRaisesRegex(RuntimeError,
- "explicit time schedule can not contain negative values."):
+ "explicit time schedule can not contain negative values"):
arb.explicit_schedule([-1])
with self.assertRaises(TypeError):
arb.explicit_schedule(['times'])
@@ -128,14 +128,14 @@ class PoissonSchedule(unittest.TestCase):
def test_exceptions_poisson_schedule(self):
with self.assertRaisesRegex(RuntimeError,
- "tstart must be a non-negative number."):
+ "tstart must be a non-negative number"):
arb.poisson_schedule(tstart = -10.)
with self.assertRaises(TypeError):
arb.poisson_schedule(tstart = None)
with self.assertRaises(TypeError):
arb.poisson_schedule(tstart = 'tstart')
with self.assertRaisesRegex(RuntimeError,
- "frequency must be a non-negative number."):
+ "frequency must be a non-negative number"):
arb.poisson_schedule(freq = -100.)
with self.assertRaises(TypeError):
arb.poisson_schedule(freq = 'freq')
--
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