From 13131745410a16982d21a641cc9e13dff18ed96b Mon Sep 17 00:00:00 2001
From: thorstenhater <24411438+thorstenhater@users.noreply.github.com>
Date: Mon, 2 Nov 2020 13:03:01 +0100
Subject: [PATCH] Interface/merge cat names (#1208)
* Add interface for querying names.
* Add derived mechanisms to list, clean-up.
* Add unit tests.
* Add python bindings and docs.
---
arbor/include/arbor/mechcat.hpp | 3 +++
arbor/mechcat.cpp | 13 ++++++++++
doc/python/mechanisms.rst | 6 +++++
python/mechanism.cpp | 4 +++-
test/unit/test_mechcat.cpp | 42 +++++++++++++++++++++++++++++++++
5 files changed, 67 insertions(+), 1 deletion(-)
diff --git a/arbor/include/arbor/mechcat.hpp b/arbor/include/arbor/mechcat.hpp
index 0fc0a23f..436edbc2 100644
--- a/arbor/include/arbor/mechcat.hpp
+++ b/arbor/include/arbor/mechcat.hpp
@@ -110,6 +110,9 @@ public:
~mechanism_catalogue();
+ // Grab a collection of all mechanism names in the catalogue.
+ std::vector<std::string> mechanism_names() const;
+
private:
std::unique_ptr<catalogue_state> state_;
diff --git a/arbor/mechcat.cpp b/arbor/mechcat.cpp
index 3fac9e80..001ab95e 100644
--- a/arbor/mechcat.cpp
+++ b/arbor/mechcat.cpp
@@ -8,6 +8,7 @@
#include <arbor/mechcat.hpp>
#include <arbor/util/expected.hpp>
+#include "util/rangeutil.hpp"
#include "util/maputil.hpp"
/* Notes on implementation:
@@ -479,6 +480,14 @@ struct catalogue_state {
return over;
}
+ // Collect all mechanism names present in this catalogue
+ std::vector<std::string> mechanism_names() const {
+ std::vector<std::string> result;
+ util::assign(result, util::keys(info_map_));
+ util::append(result, util::keys(derived_map_));
+ return result;
+ }
+
// Schemata for (un-derived) mechanisms.
string_map<mechanism_info_ptr> info_map_;
@@ -495,6 +504,10 @@ mechanism_catalogue::mechanism_catalogue():
state_(new catalogue_state)
{}
+std::vector<std::string> mechanism_catalogue::mechanism_names() const {
+ return state_->mechanism_names();
+}
+
mechanism_catalogue::mechanism_catalogue(mechanism_catalogue&& other) = default;
mechanism_catalogue& mechanism_catalogue::operator=(mechanism_catalogue&& other) = default;
diff --git a/doc/python/mechanisms.rst b/doc/python/mechanisms.rst
index e31f137a..b55aa460 100644
--- a/doc/python/mechanisms.rst
+++ b/doc/python/mechanisms.rst
@@ -280,6 +280,12 @@ Mechanism catalogues
:return: mechanism metadata
:rtype: :class:`mechanism_info`
+ .. py:method:: names()
+
+ Return a list names of all the mechanisms in the catalogue.
+
+ :return: list
+
.. py:method:: derive(name, parent, globals={}, ions={})
Derive a new mechanism with *name* from the mechanism *parent*.
diff --git a/python/mechanism.cpp b/python/mechanism.cpp
index 9c65cc2d..e0fc9846 100644
--- a/python/mechanism.cpp
+++ b/python/mechanism.cpp
@@ -107,7 +107,9 @@ void register_mechanisms(pybind11::module& m) {
cat
.def(pybind11::init<const arb::mechanism_catalogue&>())
.def("has", &arb::mechanism_catalogue::has,
- "name"_a, "Is 'name' in the catalogue?")
+ "name"_a, "Is 'name' in the catalogue?")
+ .def("keys", &arb::mechanism_catalogue::mechanism_names,
+ "Return a list of all mechanisms in this catalogues.")
.def("is_derived", &arb::mechanism_catalogue::is_derived,
"name"_a, "Is 'name' a derived mechanism or can it be implicitly derived?")
.def("__getitem__",
diff --git a/test/unit/test_mechcat.cpp b/test/unit/test_mechcat.cpp
index 31526aa2..ffd6b265 100644
--- a/test/unit/test_mechcat.cpp
+++ b/test/unit/test_mechcat.cpp
@@ -244,6 +244,48 @@ TEST(mechcat, fingerprint) {
arb::fingerprint_mismatch);
}
+TEST(mechcat, names) {
+ // All names are caught; covers `add' and `derive'
+ {
+ auto cat = build_fake_catalogue();
+ auto names = cat.mechanism_names();
+ auto expect = std::vector<std::string>{"bleeble", "burble", "fleeb", "fleeb1", "fleeb2", "fleeb3", "special_fleeb"};
+ std::sort(names.begin(), names.end());
+ EXPECT_EQ(names, expect);
+ }
+
+ // Deriving names does not add to catalogue
+ {
+ auto cat = build_fake_catalogue();
+ auto info = cat["burble/quux=3,xyzzy=4"];
+ auto names = cat.mechanism_names();
+ auto expect = std::vector<std::string>{"bleeble", "burble", "fleeb", "fleeb1", "fleeb2", "fleeb3", "special_fleeb"};
+ std::sort(names.begin(), names.end());
+ EXPECT_EQ(names, expect);
+ }
+
+ // Deleting a mechanism removes it and all derived from it.
+ {
+ auto cat = build_fake_catalogue();
+ cat.remove("fleeb");
+ auto names = cat.mechanism_names();
+ auto expect = std::vector<std::string>{"bleeble", "burble"};
+ std::sort(names.begin(), names.end());
+ EXPECT_EQ(names, expect);
+ }
+
+ // Empty means empty.
+ {
+ auto cat = build_fake_catalogue();
+ cat.remove("fleeb");
+ cat.remove("burble");
+ auto names = cat.mechanism_names();
+ auto expect = std::vector<std::string>{};
+ std::sort(names.begin(), names.end());
+ EXPECT_EQ(names, expect);
+ }
+}
+
TEST(mechcat, derived_info) {
auto cat = build_fake_catalogue();
--
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