From 51d09f7d1efa390484ef721008ba21d9c9485dcd Mon Sep 17 00:00:00 2001
From: Ben Cumming <louncharf@gmail.com>
Date: Mon, 15 Jan 2018 10:49:59 +0100
Subject: [PATCH] Make cell type copyable by default (#430)
* Enable `cell` copy constructor, remove special tag type used to guard `cell` cloning.
* Provide sane defaults for `recipe` methods.
---
example/miniapp/miniapp_recipes.cpp | 4 ---
src/cell.hpp | 27 +++++++++----------
src/common_types.hpp | 1 +
src/common_types_io.cpp | 13 +++++++++
src/fvm_multicell.hpp | 2 +-
src/recipe.hpp | 20 +++++++++-----
.../test_communicator.cpp | 16 -----------
.../test_domain_decomposition.cpp | 3 ---
tests/simple_recipes.hpp | 17 +++---------
tests/unit/test_cell.cpp | 2 +-
tests/unit/test_domain_decomposition.cpp | 16 -----------
tests/validation/validate_ball_and_stick.cpp | 1 -
.../validate_compartment_policy.cpp | 1 -
tests/validation/validate_kinetic.cpp | 1 -
tests/validation/validate_soma.cpp | 1 -
tests/validation/validate_synapses.cpp | 1 -
16 files changed, 45 insertions(+), 81 deletions(-)
diff --git a/example/miniapp/miniapp_recipes.cpp b/example/miniapp/miniapp_recipes.cpp
index 017236d4..69690387 100644
--- a/example/miniapp/miniapp_recipes.cpp
+++ b/example/miniapp/miniapp_recipes.cpp
@@ -176,10 +176,6 @@ public:
}
}
- std::vector<event_generator_ptr> event_generators(cell_gid_type) const override {
- return {};
- }
-
protected:
template <typename RNG>
cell_connection draw_connection_params(RNG& rng) const {
diff --git a/src/cell.hpp b/src/cell.hpp
index 200691b7..a4d81592 100644
--- a/src/cell.hpp
+++ b/src/cell.hpp
@@ -54,10 +54,6 @@ struct cell_global_properties {
std::map<std::string, specialized_mechanism> special_mechs;
};
-// used in constructor below
-struct clone_cell_t {};
-constexpr clone_cell_t clone_cell{};
-
/// high-level abstract representation of a cell and its segments
class cell {
public:
@@ -81,22 +77,25 @@ public:
double threshold;
};
- // constructor
+ /// Default constructor
cell();
- // Sometimes we really do want a copy (pending big morphology refactor).
- cell(clone_cell_t, const cell& other):
+ /// Copy constructor
+ cell(const cell& other):
parents_(other.parents_),
stimuli_(other.stimuli_),
synapses_(other.synapses_),
spike_detectors_(other.spike_detectors_)
- {
- // unique_ptr's cannot be copy constructed, do a manual assignment
- segments_.reserve(other.segments_.size());
- for (const auto& s: other.segments_) {
- segments_.push_back(s->clone());
- }
- }
+ {
+ // unique_ptr's cannot be copy constructed, do a manual assignment
+ segments_.reserve(other.segments_.size());
+ for (const auto& s: other.segments_) {
+ segments_.push_back(s->clone());
+ }
+ }
+
+ /// Move constructor
+ cell(cell&& other) = default;
/// Return the kind of cell, used for grouping into cell_groups
cell_kind get_cell_kind() const {
diff --git a/src/common_types.hpp b/src/common_types.hpp
index 2cc32034..19a5aacf 100644
--- a/src/common_types.hpp
+++ b/src/common_types.hpp
@@ -76,6 +76,7 @@ enum cell_kind {
} // namespace arb
std::ostream& operator<<(std::ostream& O, arb::cell_member_type m);
+std::ostream& operator<<(std::ostream& O, arb::cell_kind k);
namespace std {
template <> struct hash<arb::cell_member_type> {
diff --git a/src/common_types_io.cpp b/src/common_types_io.cpp
index 4850d5d8..9e478115 100644
--- a/src/common_types_io.cpp
+++ b/src/common_types_io.cpp
@@ -6,3 +6,16 @@ std::ostream& operator<<(std::ostream& O, arb::cell_member_type m) {
return O << m.gid << ':' << m.index;
}
+std::ostream& operator<<(std::ostream& o, arb::cell_kind k) {
+ o << "cell_kind::";
+ switch (k) {
+ case arb::cell_kind::regular_spike_source:
+ return o << "regular_spike_source";
+ case arb::cell_kind::cable1d_neuron:
+ return o << "cable1d_neuron";
+ case arb::cell_kind::data_spike_source:
+ return o << "data_spike_source";
+ }
+ return o;
+}
+
diff --git a/src/fvm_multicell.hpp b/src/fvm_multicell.hpp
index 3eb1fb1a..aac92841 100644
--- a/src/fvm_multicell.hpp
+++ b/src/fvm_multicell.hpp
@@ -638,7 +638,7 @@ void fvm_multicell<Backend>::initialize(
std::vector<cell> cells;
cells.reserve(gids.size());
for (auto gid: gids) {
- cells.push_back(any_cast<cell>(rec.get_cell_description(gid)));
+ cells.push_back(std::move(any_cast<cell>(rec.get_cell_description(gid))));
}
auto cell_num_compartments =
diff --git a/src/recipe.hpp b/src/recipe.hpp
index 54ba235d..a8981dbc 100644
--- a/src/recipe.hpp
+++ b/src/recipe.hpp
@@ -60,14 +60,20 @@ public:
virtual util::unique_any get_cell_description(cell_gid_type gid) const = 0;
virtual cell_kind get_cell_kind(cell_gid_type) const = 0;
- virtual cell_size_type num_sources(cell_gid_type) const = 0;
- virtual cell_size_type num_targets(cell_gid_type) const = 0;
- virtual cell_size_type num_probes(cell_gid_type) const = 0;
+ virtual cell_size_type num_sources(cell_gid_type) const { return 0; }
+ virtual cell_size_type num_targets(cell_gid_type) const { return 0; }
+ virtual cell_size_type num_probes(cell_gid_type) const { return 0; }
+
+ virtual std::vector<event_generator_ptr> event_generators(cell_gid_type) const {
+ return {};
+ }
+ virtual std::vector<cell_connection> connections_on(cell_gid_type) const {
+ return {};
+ }
+ virtual probe_info get_probe(cell_member_type) const {
+ throw std::logic_error("no probes");
+ }
- virtual std::vector<event_generator_ptr> event_generators(cell_gid_type) const = 0;
-
- virtual std::vector<cell_connection> connections_on(cell_gid_type) const = 0;
- virtual probe_info get_probe(cell_member_type probe_id) const = 0;
// Global property type will be specific to given cell kind.
virtual util::any get_global_properties(cell_kind) const { return util::any{}; };
diff --git a/tests/global_communication/test_communicator.cpp b/tests/global_communication/test_communicator.cpp
index 21d7be0e..2a5238a4 100644
--- a/tests/global_communication/test_communicator.cpp
+++ b/tests/global_communication/test_communicator.cpp
@@ -213,14 +213,6 @@ namespace {
1.0f)}; // delay
}
- std::vector<event_generator_ptr> event_generators(cell_gid_type) const override {
- return {};
- }
-
- probe_info get_probe(cell_member_type) const override {
- throw std::logic_error("no probes");
- }
-
private:
cell_size_type size_;
cell_size_type ranks_;
@@ -286,14 +278,6 @@ namespace {
return cons;
}
- std::vector<event_generator_ptr> event_generators(cell_gid_type) const override {
- return {};
- }
-
- probe_info get_probe(cell_member_type) const override {
- throw std::logic_error("no probes");
- }
-
private:
cell_size_type size_;
cell_size_type ranks_;
diff --git a/tests/global_communication/test_domain_decomposition.cpp b/tests/global_communication/test_domain_decomposition.cpp
index 119dded9..d6cef200 100644
--- a/tests/global_communication/test_domain_decomposition.cpp
+++ b/tests/global_communication/test_domain_decomposition.cpp
@@ -58,9 +58,6 @@ namespace {
return {};
}
- probe_info get_probe(cell_member_type) const override {
- throw std::logic_error("no probes");
- }
private:
cell_size_type size_;
diff --git a/tests/simple_recipes.hpp b/tests/simple_recipes.hpp
index 509f6dab..8e7218c0 100644
--- a/tests/simple_recipes.hpp
+++ b/tests/simple_recipes.hpp
@@ -20,14 +20,6 @@ public:
return probes_.count(i)? probes_.at(i).size(): 0;
}
- std::vector<event_generator_ptr> event_generators(cell_gid_type) const override {
- return {};
- }
-
- std::vector<cell_connection> connections_on(cell_gid_type) const override {
- return {};
- }
-
virtual probe_info get_probe(cell_member_type probe_id) const override {
return probes_.at(probe_id.gid).at(probe_id.index);
}
@@ -76,9 +68,6 @@ public:
cell_size_type num_cells() const override { return n_; }
cell_kind get_cell_kind(cell_gid_type) const override { return Kind; }
- cell_size_type num_sources(cell_gid_type) const override { return 0; }
- cell_size_type num_targets(cell_gid_type) const override { return 0; }
-
util::unique_any get_cell_description(cell_gid_type) const override {
return util::make_unique_any<Description>(desc_);
}
@@ -98,13 +87,13 @@ public:
template <typename Seq>
explicit cable1d_recipe(const Seq& cells) {
for (const auto& c: cells) {
- cells_.emplace_back(clone_cell, c);
+ cells_.emplace_back(c);
}
}
explicit cable1d_recipe(const cell& c) {
cells_.reserve(1);
- cells_.emplace_back(clone_cell, c);
+ cells_.emplace_back(c);
}
cell_size_type num_cells() const override { return cells_.size(); }
@@ -119,7 +108,7 @@ public:
}
util::unique_any get_cell_description(cell_gid_type i) const override {
- return util::make_unique_any<cell>(clone_cell, cells_[i]);
+ return util::make_unique_any<cell>(cells_[i]);
}
protected:
diff --git a/tests/unit/test_cell.cpp b/tests/unit/test_cell.cpp
index 587f8fa9..58981bfa 100644
--- a/tests/unit/test_cell.cpp
+++ b/tests/unit/test_cell.cpp
@@ -224,7 +224,7 @@ TEST(cell, clone)
// make clone
- cell d(clone_cell, c);
+ cell d(c);
// check equality
diff --git a/tests/unit/test_domain_decomposition.cpp b/tests/unit/test_domain_decomposition.cpp
index c6cf69fa..2bafbf40 100644
--- a/tests/unit/test_domain_decomposition.cpp
+++ b/tests/unit/test_domain_decomposition.cpp
@@ -38,22 +38,6 @@ namespace {
cell_kind::cable1d_neuron;
}
- cell_size_type num_sources(cell_gid_type) const override { return 0; }
- cell_size_type num_targets(cell_gid_type) const override { return 0; }
- cell_size_type num_probes(cell_gid_type) const override { return 0; }
-
- std::vector<cell_connection> connections_on(cell_gid_type) const override {
- return {};
- }
-
- std::vector<event_generator_ptr> event_generators(cell_gid_type) const override {
- return {};
- }
-
- probe_info get_probe(cell_member_type) const override {
- throw std::logic_error("no probes");
- }
-
private:
cell_size_type size_;
};
diff --git a/tests/validation/validate_ball_and_stick.cpp b/tests/validation/validate_ball_and_stick.cpp
index b5fd2290..7f804268 100644
--- a/tests/validation/validate_ball_and_stick.cpp
+++ b/tests/validation/validate_ball_and_stick.cpp
@@ -2,7 +2,6 @@
#include <cell.hpp>
#include <common_types.hpp>
-#include <fvm_multicell.hpp>
#include <load_balance.hpp>
#include <hardware/node_info.hpp>
#include <hardware/gpu.hpp>
diff --git a/tests/validation/validate_compartment_policy.cpp b/tests/validation/validate_compartment_policy.cpp
index 75d5ee0d..c9ee4d36 100644
--- a/tests/validation/validate_compartment_policy.cpp
+++ b/tests/validation/validate_compartment_policy.cpp
@@ -5,7 +5,6 @@
#include <common_types.hpp>
#include <cell.hpp>
-#include <fvm_multicell.hpp>
#include <model.hpp>
#include <recipe.hpp>
#include <simple_sampler.hpp>
diff --git a/tests/validation/validate_kinetic.cpp b/tests/validation/validate_kinetic.cpp
index b0077df1..83cc8d18 100644
--- a/tests/validation/validate_kinetic.cpp
+++ b/tests/validation/validate_kinetic.cpp
@@ -4,7 +4,6 @@
#include <common_types.hpp>
#include <cell.hpp>
-#include <fvm_multicell.hpp>
#include <hardware/node_info.hpp>
#include <hardware/gpu.hpp>
#include <load_balance.hpp>
diff --git a/tests/validation/validate_soma.cpp b/tests/validation/validate_soma.cpp
index 86f8dfd1..8d0e3e8e 100644
--- a/tests/validation/validate_soma.cpp
+++ b/tests/validation/validate_soma.cpp
@@ -2,7 +2,6 @@
#include <common_types.hpp>
#include <cell.hpp>
-#include <fvm_multicell.hpp>
#include <hardware/gpu.hpp>
#include <hardware/node_info.hpp>
#include <load_balance.hpp>
diff --git a/tests/validation/validate_synapses.cpp b/tests/validation/validate_synapses.cpp
index 7b611ca9..31a7bf3f 100644
--- a/tests/validation/validate_synapses.cpp
+++ b/tests/validation/validate_synapses.cpp
@@ -1,6 +1,5 @@
#include <cell.hpp>
#include <cell_group.hpp>
-#include <fvm_multicell.hpp>
#include <hardware/node_info.hpp>
#include <hardware/gpu.hpp>
#include <json/json.hpp>
--
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