From a7f313506236508f3bace3d07c63e02f49f6fefc Mon Sep 17 00:00:00 2001
From: akuesters <42005107+akuesters@users.noreply.github.com>
Date: Thu, 9 May 2019 13:27:06 +0200
Subject: [PATCH] Python feature addition for identifiers and
event_generators/schedules (#723)
Wrapped the following C++ features in Python:
- Identifiers (`cell_member`) + according tests
- `event_generator` and schedules (`regular_schedule`, `explicit_schedule`, `poisson_schedule`) + according tests
---
.travis.yml | 1 +
python/CMakeLists.txt | 3 +-
python/config.cpp | 6 +-
python/context.cpp | 5 +-
python/conversion.hpp | 51 ++++
python/error.hpp | 32 +++
python/event_generator.cpp | 304 ++++++++++++++++++++++
python/exception.cpp | 11 -
python/exception.hpp | 17 --
python/identifiers.cpp | 43 +++
python/mpi.cpp | 4 +-
python/pyarb.cpp | 4 +
python/strings.cpp | 10 +-
python/strings.hpp | 7 +-
python/test/unit/runner.py | 8 +-
python/test/unit/test_contexts.py | 2 +-
python/test/unit/test_event_generators.py | 165 ++++++++++++
python/test/unit/test_identifiers.py | 51 ++++
18 files changed, 680 insertions(+), 44 deletions(-)
create mode 100644 python/conversion.hpp
create mode 100644 python/error.hpp
create mode 100644 python/event_generator.cpp
delete mode 100644 python/exception.cpp
delete mode 100644 python/exception.hpp
create mode 100644 python/identifiers.cpp
create mode 100644 python/test/unit/test_event_generators.py
create mode 100644 python/test/unit/test_identifiers.py
diff --git a/.travis.yml b/.travis.yml
index 252dcbf5..9f9d3eff 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -156,6 +156,7 @@ install:
python$PY get-pip.py
pip --version
fi
+ - if [[ ( "$WITH_PYTHON" == "true" ) && ( "$TRAVIS_OS_NAME" == "osx" ) ]]; then pip$PY install numpy; fi
- |
if [[ "$WITH_DISTRIBUTED" == "mpi" ]]; then
if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
index 7e5b02f3..4b37a939 100644
--- a/python/CMakeLists.txt
+++ b/python/CMakeLists.txt
@@ -18,7 +18,8 @@ add_subdirectory(pybind11)
add_library(pyarb MODULE
config.cpp
context.cpp
- exception.cpp
+ event_generator.cpp
+ identifiers.cpp
mpi.cpp
pyarb.cpp
strings.cpp
diff --git a/python/config.cpp b/python/config.cpp
index 5b1aa2eb..29636c8d 100644
--- a/python/config.cpp
+++ b/python/config.cpp
@@ -1,8 +1,8 @@
-#include <arbor/version.hpp>
-
-#include <sstream>
#include <iomanip>
#include <ios>
+#include <sstream>
+
+#include <arbor/version.hpp>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
diff --git a/python/context.cpp b/python/context.cpp
index b3ddb8c8..61492e59 100644
--- a/python/context.cpp
+++ b/python/context.cpp
@@ -1,16 +1,15 @@
#include <iostream>
-
#include <sstream>
#include <string>
#include <arbor/context.hpp>
#include <arbor/version.hpp>
+#include <pybind11/pybind11.h>
+
#include "context.hpp"
#include "strings.hpp"
-#include <pybind11/pybind11.h>
-
#ifdef ARB_MPI_ENABLED
#include "mpi.hpp"
#endif
diff --git a/python/conversion.hpp b/python/conversion.hpp
new file mode 100644
index 00000000..811eb74e
--- /dev/null
+++ b/python/conversion.hpp
@@ -0,0 +1,51 @@
+#pragma once
+
+#include <pybind11/pybind11.h>
+#include <pybind11/pytypes.h>
+
+#include "error.hpp"
+
+namespace pyarb {
+
+// A helper function for converting from a Python object to a C++ optional wrapper.
+// Throws an runtime_error exception with msg if either the Python object
+// can't be converted to type T, or if the predicate is false for the value.
+template <typename T, typename F>
+arb::util::optional<T> py2optional(pybind11::object o, const char* msg, F&& pred) {
+ bool ok = true;
+ T value;
+
+ if (!o.is_none()) {
+ try {
+ value = o.cast<T>();
+ ok = pred(value);
+ }
+ catch (...) {
+ ok = false;
+ }
+ }
+
+ if (!ok) {
+ throw pyarb_error(msg);
+ }
+
+ return o.is_none()? arb::util::nullopt: arb::util::optional<T>(std::move(value));
+}
+
+template <typename T>
+arb::util::optional<T> py2optional(pybind11::object o, const char* msg) {
+ T value;
+
+ if (!o.is_none()) {
+ try {
+ value = o.cast<T>();
+ }
+ catch (...) {
+ throw pyarb_error(msg);
+ }
+ }
+
+ return o.is_none()? arb::util::nullopt: arb::util::optional<T>(std::move(value));
+}
+
+}
diff --git a/python/error.hpp b/python/error.hpp
new file mode 100644
index 00000000..fbcd5ba7
--- /dev/null
+++ b/python/error.hpp
@@ -0,0 +1,32 @@
+#pragma once
+
+#include <stdexcept>
+#include <string>
+
+#include <arbor/util/optional.hpp>
+
+#include <pybind11/pybind11.h>
+#include <pybind11/pytypes.h>
+#include <pybind11/stl.h>
+
+// from https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html?highlight=boost%3A%3Aoptional#c-17-library-containers
+namespace pybind11 { namespace detail {
+ template <typename T>
+ struct type_caster<arb::util::optional<T>> : optional_caster<arb::util::optional<T>> {};
+}}
+
+namespace pyarb {
+
+// Python wrapper errors
+
+struct pyarb_error: std::runtime_error {
+ pyarb_error(const std::string& what_msg):
+ std::runtime_error(what_msg) {}
+};
+
+static
+void assert_throw(bool pred, const char* msg) {
+ if (!pred) throw pyarb_error(msg);
+}
+
+} // namespace pyarb
diff --git a/python/event_generator.cpp b/python/event_generator.cpp
new file mode 100644
index 00000000..f31bbe15
--- /dev/null
+++ b/python/event_generator.cpp
@@ -0,0 +1,304 @@
+#include <stdexcept>
+#include <sstream>
+#include <string>
+
+#include <arbor/common_types.hpp>
+#include <arbor/event_generator.hpp>
+#include <arbor/schedule.hpp>
+
+#include <pybind11/pybind11.h>
+#include <pybind11/pytypes.h>
+#include <pybind11/stl.h>
+
+#include "conversion.hpp"
+#include "error.hpp"
+
+namespace pyarb {
+
+namespace {
+auto is_nonneg = [](auto&& t){ return t>=0.; };
+}
+
+// A Python shim that holds the information that describes an
+// arb::regular_schedule. This is wrapped in pybind11, and users constructing
+// a regular_schedule in python are manipulating this type. This is converted to
+// an arb::regular_schedule when a C++ recipe is created from a Python recipe.
+struct regular_schedule_shim {
+ using time_type = arb::time_type;
+ using opt_time_type = arb::util::optional<time_type>;
+
+ opt_time_type tstart = {};
+ opt_time_type tstop = {};
+ time_type dt = 0;
+
+ regular_schedule_shim() = default;
+
+ regular_schedule_shim(pybind11::object t0, time_type deltat, pybind11::object t1) {
+ set_tstart(t0);
+ set_tstop(t1);
+ set_dt(deltat);
+ }
+
+ // 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);
+ };
+ void set_tstop(pybind11::object t) {
+ 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.");
+ dt = delta_t;
+ };
+
+ opt_time_type get_tstart() const { return tstart; }
+ opt_time_type get_dt() const { return dt; }
+ opt_time_type get_tstop() const { return tstop; }
+
+ arb::schedule schedule() const {
+ return arb::regular_schedule(
+ tstart.value_or(arb::terminal_time),
+ dt,
+ tstop.value_or(arb::terminal_time));
+ }
+
+};
+
+// A Python shim for arb::explicit_schedule.
+// This is wrapped in pybind11, and users constructing an explicit_schedule in
+// Python are manipulating this type. This is converted to an
+// arb::explicit_schedule when a C++ recipe is created from a Python recipe.
+
+struct explicit_schedule_shim {
+ using time_type = arb::time_type;
+
+ std::vector<time_type> times;
+
+ explicit_schedule_shim() = default;
+
+ explicit_schedule_shim(std::vector<time_type> t) {
+ set_times(t);
+ }
+
+ // getter and setter (in order to assert when being set)
+ void set_times(std::vector<time_type> t) {
+ times = std::move(t);
+ // Sort the times in ascending order if necessary
+ if (!std::is_sorted(times.begin(), times.end())) {
+ std::sort(times.begin(), times.end());
+ }
+ // 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.");
+ }
+ };
+
+ std::vector<time_type> get_times() const { return times; }
+
+ arb::schedule schedule() const {
+ return arb::explicit_schedule(times);
+ }
+};
+
+// A Python shim for arb::poisson_schedule.
+// This is wrapped in pybind11, and users constructing a poisson_schedule in
+// Python are manipulating this type. This is converted to an
+// arb::poisson_schedule when a C++ recipe is created from a Python recipe.
+
+struct poisson_schedule_shim {
+ using rng_type = std::mt19937_64;
+ using time_type = arb::time_type;
+
+ time_type tstart = arb::terminal_time;
+ time_type freq = 10.;
+ rng_type::result_type seed = 0;
+
+ poisson_schedule_shim() = default;
+
+ poisson_schedule_shim(time_type ts, time_type f, rng_type::result_type s) {
+ set_tstart(ts);
+ set_freq(f);
+ seed = s;
+ }
+
+ void set_tstart(time_type t) {
+ 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.");
+ freq = f;
+ };
+
+ const time_type get_tstart() const { return tstart; }
+ const time_type get_freq() const { return freq; }
+
+ arb::schedule schedule() const {
+ // convert frequency to kHz.
+ return arb::poisson_schedule(tstart, freq/1000., rng_type(seed));
+ }
+};
+
+// Helper template for printing C++ optional types in Python.
+// Prints either the value, or None if optional value is not set.
+template <typename T>
+std::string to_string(const arb::util::optional<T>& o, std::string unit) {
+ if (!o) return "None";
+
+ std::stringstream s;
+ s << *o << " " << unit;
+ return s.str();
+}
+
+std::string schedule_regular_string(const regular_schedule_shim& r) {
+ std::stringstream s;
+ s << "<regular_schedule: "
+ << "tstart " << to_string(r.tstart, "ms") << ", "
+ << "dt " << r.dt << " ms, "
+ << "tstop " << to_string(r.tstop, "ms") << ">";
+ return s.str();
+};
+
+std::string schedule_explicit_string(const explicit_schedule_shim& e) {
+ std::stringstream s;
+ s << "<explicit_schedule: times [";
+ bool first = true;
+ for (auto t: e.times) {
+ if (!first) {
+ s << " ";
+ }
+ s << t;
+ first = false;
+ }
+ s << "] ms>";
+ return s.str();
+};
+
+std::string schedule_poisson_string(const poisson_schedule_shim& p) {
+ std::stringstream s;
+ s << "<poisson_schedule: tstart " << p.tstart << " ms"
+ << ", freq " << p.freq << " Hz"
+ << ", seed " << p.seed << ">";
+ 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;
+
+ // Regular schedule
+ pybind11::class_<regular_schedule_shim> regular_schedule(m, "regular_schedule",
+ "Describes a regular schedule with multiples of dt within the interval [tstart, tstop).");
+
+ regular_schedule
+ .def(pybind11::init<pybind11::object, time_type, pybind11::object>(),
+ "tstart"_a = pybind11::none(), "dt"_a = 0., "tstop"_a = pybind11::none(),
+ "Construct a regular schedule with arguments:\n"
+ " tstart: The delivery time of the first event in the sequence (in ms, default None).\n"
+ " dt: The interval between time points (in ms, default 0).\n"
+ " tstop: No events delivered after this time (in ms, default None).")
+ .def_property("tstart", ®ular_schedule_shim::get_tstart, ®ular_schedule_shim::set_tstart,
+ "The delivery time of the first event in the sequence (in ms).")
+ .def_property("tstop", ®ular_schedule_shim::get_tstop, ®ular_schedule_shim::set_tstop,
+ "No events delivered after this time (in ms).")
+ .def_property("dt", ®ular_schedule_shim::get_dt, ®ular_schedule_shim::set_dt,
+ "The interval between time points (in ms).")
+ .def("__str__", &schedule_regular_string)
+ .def("__repr__",&schedule_regular_string);
+
+ // Explicit schedule
+ pybind11::class_<explicit_schedule_shim> explicit_schedule(m, "explicit_schedule",
+ "Describes an explicit schedule at a predetermined (sorted) sequence of times.");
+
+ explicit_schedule
+ .def(pybind11::init<>(),
+ "Construct an empty explicit schedule.\n")
+ .def(pybind11::init<std::vector<time_type>>(),
+ "times"_a,
+ "Construct an explicit schedule with argument:\n"
+ " times: A list of times (in ms, default []).")
+ .def_property("times", &explicit_schedule_shim::get_times, &explicit_schedule_shim::set_times,
+ "A list of times (in ms).")
+ .def("__str__", &schedule_explicit_string)
+ .def("__repr__",&schedule_explicit_string);
+
+ // Poisson schedule
+ pybind11::class_<poisson_schedule_shim> poisson_schedule(m, "poisson_schedule",
+ "Describes a schedule according to a Poisson process.");
+
+ poisson_schedule
+ .def(pybind11::init<time_type, time_type, std::mt19937_64::result_type>(),
+ "tstart"_a = 0., "freq"_a = 10., "seed"_a = 0,
+ "Construct a Poisson schedule with arguments:\n"
+ " tstart: The delivery time of the first event in the sequence (in ms, default 0 ms).\n"
+ " freq: The expected frequency (in Hz, default 10 Hz).\n"
+ " seed: The seed for the random number generator (default 0).")
+ .def_property("tstart", &poisson_schedule_shim::get_tstart, &poisson_schedule_shim::set_tstart,
+ "The delivery time of the first event in the sequence (in ms).")
+ .def_property("freq", &poisson_schedule_shim::get_freq, &poisson_schedule_shim::set_freq,
+ "The expected frequency (in Hz).")
+ .def_readwrite("seed", &poisson_schedule_shim::seed,
+ "The seed for the random number generator.")
+ .def("__str__", &schedule_poisson_string)
+ .def("__repr__",&schedule_poisson_string);
+
+// Event generator
+ pybind11::class_<event_generator_shim> event_generator(m, "event_generator");
+
+ event_generator
+ .def(pybind11::init<>(
+ [](arb::cell_member_type target, double weight, const regular_schedule_shim& sched){
+ return make_event_generator(target, weight, sched);}),
+ "target"_a, "weight"_a, "sched"_a,
+ "Construct an event generator with arguments:\n"
+ " target: The target synapse (gid, local_id).\n"
+ " weight: The weight of events to deliver.\n"
+ " sched: A regular schedule of the events.")
+ .def(pybind11::init<>(
+ [](arb::cell_member_type target, double weight, const explicit_schedule_shim& sched){
+ return make_event_generator(target, weight, sched);}),
+ "target"_a, "weight"_a, "sched"_a,
+ "Construct an event generator with arguments:\n"
+ " target: The target synapse (gid, local_id).\n"
+ " weight: The weight of events to deliver.\n"
+ " sched: An explicit schedule of the events.")
+ .def(pybind11::init<>(
+ [](arb::cell_member_type target, double weight, const poisson_schedule_shim& sched){
+ return make_event_generator(target, weight, sched);}),
+ "target"_a, "weight"_a, "sched"_a,
+ "Construct an event generator with arguments:\n"
+ " target: The target synapse (gid, local_id).\n"
+ " weight: The weight of events to deliver.\n"
+ " sched: A poisson schedule of the events.")
+ .def_readwrite("target", &event_generator_shim::target,
+ "The target synapse (gid, local_id).")
+ .def_readwrite("weight", &event_generator_shim::weight,
+ "The weight of events to deliver.")
+ .def("__str__", [](const event_generator_shim&){return "<arbor.event_generator>";})
+ .def("__repr__", [](const event_generator_shim&){return "<arbor.event_generator>";});
+}
+
+} // namespace pyarb
diff --git a/python/exception.cpp b/python/exception.cpp
deleted file mode 100644
index 3be0e787..00000000
--- a/python/exception.cpp
+++ /dev/null
@@ -1,11 +0,0 @@
-#include <string>
-
-#include "exception.hpp"
-
-namespace pyarb {
-
-python_error::python_error(const std::string& message):
- arbor_exception("arbor python wrapper error: " + message + "\n")
-{}
-
-} // namespace pyarb
diff --git a/python/exception.hpp b/python/exception.hpp
deleted file mode 100644
index 5f352154..00000000
--- a/python/exception.hpp
+++ /dev/null
@@ -1,17 +0,0 @@
-#pragma once
-
-#include <string>
-
-#include <arbor/arbexcept.hpp>
-
-namespace pyarb {
-
-using arb::arbor_exception;
-
-// Python wrapper errors
-
-struct python_error: arbor_exception {
- explicit python_error(const std::string& message);
-};
-
-} // namespace pyarb
diff --git a/python/identifiers.cpp b/python/identifiers.cpp
new file mode 100644
index 00000000..cb6159a2
--- /dev/null
+++ b/python/identifiers.cpp
@@ -0,0 +1,43 @@
+#include <string>
+
+#include <arbor/common_types.hpp>
+
+#include <pybind11/pybind11.h>
+
+#include "strings.hpp"
+
+namespace pyarb {
+
+void register_identifiers(pybind11::module& m) {
+ using namespace pybind11::literals;
+
+ pybind11::class_<arb::cell_member_type> cell_member(m, "cell_member",
+ "For global identification of a cell-local item.\n\n"
+ "Items of cell_member must:\n"
+ "(1) be associated with a unique cell, identified by the member gid;\n"
+ "(2) identify an item within a cell-local collection by the member index.\n");
+
+ cell_member
+ .def(pybind11::init<>(),
+ "Construct a cell member with default values gid = 0 and index = 0.")
+ .def(pybind11::init(
+ [](arb::cell_gid_type gid, arb::cell_lid_type idx) {
+ arb::cell_member_type m;
+ m.gid = gid;
+ m.index = idx;
+ return m;
+ }),
+ "gid"_a,
+ "index"_a,
+ "Construct a cell member with arguments:/n"
+ " gid: The global identifier of the cell.\n"
+ " index: The cell-local index of the item.\n")
+ .def_readwrite("gid", &arb::cell_member_type::gid,
+ "The global identifier of the cell.")
+ .def_readwrite("index", &arb::cell_member_type::index,
+ "Cell-local index of the item.")
+ .def("__str__", &cell_member_string)
+ .def("__repr__", &cell_member_string);
+}
+
+} // namespace pyarb
diff --git a/python/mpi.cpp b/python/mpi.cpp
index b6c14c35..0fd0dbad 100644
--- a/python/mpi.cpp
+++ b/python/mpi.cpp
@@ -6,10 +6,10 @@
#include <pybind11/pybind11.h>
#ifdef ARB_MPI_ENABLED
-#include <arbor/communication/mpi_error.hpp>
-
#include <mpi.h>
+#include <arbor/communication/mpi_error.hpp>
+
#include "mpi.hpp"
#ifdef ARB_WITH_MPI4PY
diff --git a/python/pyarb.cpp b/python/pyarb.cpp
index 1b9d11b5..e085141e 100644
--- a/python/pyarb.cpp
+++ b/python/pyarb.cpp
@@ -8,6 +8,8 @@ namespace pyarb {
void register_config(pybind11::module& m);
void register_contexts(pybind11::module& m);
+void register_event_generators(pybind11::module& m);
+void register_identifiers(pybind11::module& m);
#ifdef ARB_MPI_ENABLED
void register_mpi(pybind11::module& m);
#endif
@@ -19,6 +21,8 @@ PYBIND11_MODULE(arbor, m) {
pyarb::register_config(m);
pyarb::register_contexts(m);
+ pyarb::register_event_generators(m);
+ pyarb::register_identifiers(m);
#ifdef ARB_MPI_ENABLED
pyarb::register_mpi(m);
#endif
diff --git a/python/strings.cpp b/python/strings.cpp
index cf0e2c10..17887666 100644
--- a/python/strings.cpp
+++ b/python/strings.cpp
@@ -1,12 +1,20 @@
-#include <string>
#include <sstream>
+#include <string>
+#include <arbor/common_types.hpp>
#include <arbor/context.hpp>
#include "strings.hpp"
namespace pyarb {
+std::string cell_member_string(const arb::cell_member_type& m) {
+ std::stringstream s;
+ s << "<cell_member: gid " << m.gid
+ << ", index " << m.index << ">";
+ return s.str();
+}
+
std::string context_string(const arb::context& c) {
std::stringstream s;
const bool gpu = arb::has_gpu(c);
diff --git a/python/strings.hpp b/python/strings.hpp
index c0e9bc04..dba70801 100644
--- a/python/strings.hpp
+++ b/python/strings.hpp
@@ -1,15 +1,14 @@
#pragma once
-/*
- * Utilities for generating string representations of types.
- */
-
#include <string>
+#include <arbor/common_types.hpp>
#include <arbor/context.hpp>
+// Utilities for generating string representations of types.
namespace pyarb {
+std::string cell_member_string(const arb::cell_member_type&);
std::string context_string(const arb::context&);
std::string proc_allocation_string(const arb::proc_allocation&);
diff --git a/python/test/unit/runner.py b/python/test/unit/runner.py
index 56cd8a67..1ea70555 100644
--- a/python/test/unit/runner.py
+++ b/python/test/unit/runner.py
@@ -11,14 +11,20 @@ sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../.
try:
import options
import test_contexts
+ import test_identifiers
+ import test_event_generators
# add more if needed
except ModuleNotFoundError:
from test import options
from test.unit import test_contexts
+ from test.unit import test_identifiers
+ from test.unit import test_event_generators
# add more if needed
test_modules = [\
- test_contexts\
+ test_contexts,\
+ test_identifiers,\
+ test_event_generators\
] # add more if needed
def suite():
diff --git a/python/test/unit/test_contexts.py b/python/test/unit/test_contexts.py
index 5e2389e5..6ec70a62 100644
--- a/python/test/unit/test_contexts.py
+++ b/python/test/unit/test_contexts.py
@@ -20,7 +20,7 @@ all tests for non-distributed arb.context
"""
class Contexts(unittest.TestCase):
- def test_default(self):
+ def test_default_context(self):
ctx = arb.context()
def test_resources(self):
diff --git a/python/test/unit/test_event_generators.py b/python/test/unit/test_event_generators.py
new file mode 100644
index 00000000..9c7ef472
--- /dev/null
+++ b/python/test/unit/test_event_generators.py
@@ -0,0 +1,165 @@
+# -*- coding: utf-8 -*-
+#
+# test_event_generators.py
+
+import unittest
+import numpy as np
+
+import arbor as arb
+
+# to be able to run .py file from child directory
+import sys, os
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../')))
+
+try:
+ import options
+except ModuleNotFoundError:
+ from test import options
+
+"""
+all tests for event generators (regular, explicit, poisson)
+"""
+
+class RegularSchedule(unittest.TestCase):
+ def test_none_contor_regular_schedule(self):
+ rs = arb.regular_schedule(tstart=None, tstop=None)
+
+ def test_tstart_dt_tstop_contor_regular_schedule(self):
+ rs = arb.regular_schedule(10., 1., 20.)
+ self.assertEqual(rs.tstart, 10.)
+ self.assertEqual(rs.dt, 1.)
+ self.assertEqual(rs.tstop, 20.)
+
+ def test_set_tstart_dt_tstop_regular_schedule(self):
+ rs = arb.regular_schedule()
+ rs.tstart = 17.
+ rs.dt = 0.5
+ rs.tstop = 42.
+ self.assertEqual(rs.tstart, 17.)
+ self.assertAlmostEqual(rs.dt, 0.5)
+ self.assertEqual(rs.tstop, 42.)
+
+ def test_event_generator_regular_schedule(self):
+ cm = arb.cell_member()
+ cm.gid = 42
+ cm.index = 3
+ rs = arb.regular_schedule(2.0, 1., 100.)
+ rg = arb.event_generator(cm, 3.14, rs)
+ self.assertEqual(rg.target.gid, 42)
+ self.assertEqual(rg.target.index, 3)
+ self.assertAlmostEqual(rg.weight, 3.14)
+
+ def test_exceptions_regular_schedule(self):
+ with self.assertRaisesRegex(RuntimeError,
+ "tstart must a non-negative number, or None."):
+ arb.regular_schedule(tstart=-1.)
+ with self.assertRaisesRegex(RuntimeError,
+ "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."):
+ arb.regular_schedule(tstop='tstop')
+
+class ExplicitSchedule(unittest.TestCase):
+ def test_times_contor_explicit_schedule(self):
+ es = arb.explicit_schedule([1, 2, 3, 4.5])
+ self.assertEqual(es.times, [1, 2, 3, 4.5])
+
+ def test_set_times_explicit_schedule(self):
+ es = arb.explicit_schedule()
+ es.times = [42, 43, 44, 55.5, 100]
+ self.assertEqual(es.times, [42, 43, 44, 55.5, 100])
+
+ def test_event_generator_explicit_schedule(self):
+ cm = arb.cell_member()
+ cm.gid = 0
+ cm.index = 42
+ es = arb.explicit_schedule([0,1,2,3,4.4])
+ eg = arb.event_generator(cm, -0.01, es)
+ self.assertEqual(eg.target.gid, 0)
+ self.assertEqual(eg.target.index, 42)
+ self.assertAlmostEqual(eg.weight, -0.01)
+
+ def test_exceptions_explicit_schedule(self):
+ with self.assertRaisesRegex(RuntimeError,
+ "explicit time schedule can not contain negative values."):
+ arb.explicit_schedule([-1])
+ with self.assertRaises(TypeError):
+ arb.explicit_schedule(['times'])
+ with self.assertRaises(TypeError):
+ arb.explicit_schedule([None])
+ with self.assertRaises(TypeError):
+ arb.explicit_schedule([[1,2,3]])
+
+class PoissonSchedule(unittest.TestCase):
+ def test_freq_seed_contor_poisson_schedule(self):
+ ps = arb.poisson_schedule(freq = 5., seed = 42)
+ self.assertEqual(ps.freq, 5.)
+ self.assertEqual(ps.seed, 42)
+
+ def test_tstart_freq_seed_contor_poisson_schedule(self):
+ ps = arb.poisson_schedule(10., 100., 1000)
+ self.assertEqual(ps.tstart, 10.)
+ self.assertEqual(ps.freq, 100.)
+ self.assertEqual(ps.seed, 1000)
+
+ def test_set_tstart_freq_seed_poisson_schedule(self):
+ ps = arb.poisson_schedule()
+ ps.tstart = 4.5
+ ps.freq = 5.5
+ ps.seed = 83
+ self.assertAlmostEqual(ps.tstart, 4.5)
+ self.assertAlmostEqual(ps.freq, 5.5)
+ self.assertEqual(ps.seed, 83)
+
+ def test_event_generator_poisson_schedule(self):
+ cm = arb.cell_member()
+ cm.gid = 4
+ cm.index = 2
+ ps = arb.poisson_schedule(0., 10., 0)
+ pg = arb.event_generator(cm, 42., ps)
+ self.assertEqual(pg.target.gid, 4)
+ self.assertEqual(pg.target.index, 2)
+ self.assertEqual(pg.weight, 42.)
+
+ def test_exceptions_poisson_schedule(self):
+ with self.assertRaisesRegex(RuntimeError,
+ "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."):
+ arb.poisson_schedule(freq=-100.)
+ with self.assertRaises(TypeError):
+ arb.poisson_schedule(freq="freq")
+ with self.assertRaises(TypeError):
+ arb.poisson_schedule(seed=-1)
+ with self.assertRaises(TypeError):
+ arb.poisson_schedule(seed=10.)
+ with self.assertRaises(TypeError):
+ arb.poisson_schedule(seed="seed")
+ with self.assertRaises(TypeError):
+ arb.poisson_schedule(seed=None)
+
+def suite():
+ # specify class and test functions in tuple (here: all tests starting with 'test' from classes RegularSchedule, ExplicitSchedule and PoissonSchedule
+ suite = unittest.TestSuite()
+ suite.addTests(unittest.makeSuite(RegularSchedule, ('test')))
+ suite.addTests(unittest.makeSuite(ExplicitSchedule, ('test')))
+ suite.addTests(unittest.makeSuite(PoissonSchedule, ('test')))
+ return suite
+
+def run():
+ v = options.parse_arguments().verbosity
+ runner = unittest.TextTestRunner(verbosity = v)
+ runner.run(suite())
+
+if __name__ == "__main__":
+ run()
diff --git a/python/test/unit/test_identifiers.py b/python/test/unit/test_identifiers.py
new file mode 100644
index 00000000..4bd41794
--- /dev/null
+++ b/python/test/unit/test_identifiers.py
@@ -0,0 +1,51 @@
+# -*- coding: utf-8 -*-
+#
+# test_identifiers.py
+
+import unittest
+
+import arbor as arb
+
+# to be able to run .py file from child directory
+import sys, os
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../')))
+
+try:
+ import options
+except ModuleNotFoundError:
+ from test import options
+
+"""
+all tests for identifiers, indexes, kinds
+"""
+
+class CellMembers(unittest.TestCase):
+ def test_default_cell_member(self):
+ cm = arb.cell_member()
+ self.assertEqual(cm.gid, 0)
+ self.assertEqual(cm.index, 0)
+
+ def test_gid_index_contor_cell_member(self):
+ cm = arb.cell_member(17,42)
+ self.assertEqual(cm.gid, 17)
+ self.assertEqual(cm.index, 42)
+
+ def test_set_git_index_cell_member(self):
+ cm = arb.cell_member()
+ cm.gid = 13
+ cm.index = 23
+ self.assertEqual(cm.gid,13)
+ self.assertEqual(cm.index, 23)
+
+def suite():
+ # specify class and test functions in tuple (here: all tests starting with 'test' from class Contexts
+ suite = unittest.makeSuite(CellMembers, ('test'))
+ return suite
+
+def run():
+ v = options.parse_arguments().verbosity
+ runner = unittest.TextTestRunner(verbosity = v)
+ runner.run(suite())
+
+if __name__ == "__main__":
+ run()
--
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