From b41ecc25e2da9d0fcfd04b3731b233d97b089a10 Mon Sep 17 00:00:00 2001
From: Brent Huisman <brenthuisman@users.noreply.github.com>
Date: Mon, 4 Oct 2021 10:35:28 +0200
Subject: [PATCH] Name and describe arguments to constructors where ambiguous
in `pyarb`. (#1678)
Fixes #1666
---
python/cells.cpp | 14 ++++++++------
python/mechanism.cpp | 4 +++-
python/mpi.cpp | 5 ++++-
3 files changed, 15 insertions(+), 8 deletions(-)
diff --git a/python/cells.cpp b/python/cells.cpp
index 9d745cde..0d4e6a44 100644
--- a/python/cells.cpp
+++ b/python/cells.cpp
@@ -267,7 +267,8 @@ void register_cells(pybind11::module& m) {
pybind11::class_<arb::cv_policy> cv_policy(m, "cv_policy",
"Describes the rules used to discretize (compartmentalise) a cable cell morphology.");
cv_policy
- .def(pybind11::init([](const std::string& s) { return arborio::parse_cv_policy_expression(s).unwrap(); }))
+ .def(pybind11::init([](const std::string& expression) { return arborio::parse_cv_policy_expression(expression).unwrap(); }),
+ "expression"_a, "A valid CV policy expression")
.def_property_readonly("domain",
[](const arb::cv_policy& p) {return util::pprintf("{}", p.domain());},
"The domain on which the policy is applied.")
@@ -369,9 +370,8 @@ void register_cells(pybind11::module& m) {
"A spike detector, generates a spike when voltage crosses a threshold. Can be used as source endpoint for an arbor.connection.");
detector
.def(pybind11::init(
- [](double thresh) {
- return arb::threshold_detector{thresh};
- }), "threshold"_a)
+ [](double thresh) { return arb::threshold_detector{thresh}; }),
+ "threshold"_a, "Voltage threshold of spike detector [mV]")
.def_readonly("threshold", &arb::threshold_detector::threshold, "Voltage threshold of spike detector [mV]")
.def("__repr__", [](const arb::threshold_detector& d){
return util::pprintf("<arbor.threshold_detector: threshold {} mV>", d.threshold);})
@@ -594,13 +594,15 @@ void register_cells(pybind11::module& m) {
.def(pybind11::init(
[](const arb::morphology& m, const label_dict_proxy& labels, const arb::decor& d) {
return arb::cable_cell(m, labels.dict, d);
- }), "morphology"_a, "labels"_a, "decor"_a)
+ }),
+ "morphology"_a, "labels"_a, "decor"_a,
+ "Construct with a morphology, label dictionary and decor.")
.def(pybind11::init(
[](const arb::segment_tree& t, const label_dict_proxy& labels, const arb::decor& d) {
return arb::cable_cell(arb::morphology(t), labels.dict, d);
}),
"segment_tree"_a, "labels"_a, "decor"_a,
- "Construct with a morphology derived from a segment tree.")
+ "Construct with a morphology derived from a segment tree, label dictionary and decor.")
.def_property_readonly("num_branches",
[](const arb::cable_cell& c) {return c.morphology().num_branches();},
"The number of unbranched cable sections in the morphology.")
diff --git a/python/mechanism.cpp b/python/mechanism.cpp
index 0d74a21f..5519a918 100644
--- a/python/mechanism.cpp
+++ b/python/mechanism.cpp
@@ -204,7 +204,9 @@ void register_mechanisms(pybind11::module& m) {
pybind11::class_<arb::mechanism_desc> mechanism_desc(m, "mechanism");
mechanism_desc
- .def(pybind11::init([](const char* n) {return arb::mechanism_desc{n};}))
+ .def(pybind11::init([](const char* name) {return arb::mechanism_desc{name};}),
+ "name"_a, "The name of the mechanism"
+ )
// allow construction of a description with parameters provided in a dictionary:
// mech = arbor.mechanism('mech_name', {'param1': 1.2, 'param2': 3.14})
.def(pybind11::init(
diff --git a/python/mpi.cpp b/python/mpi.cpp
index 57ea410b..d3de709f 100644
--- a/python/mpi.cpp
+++ b/python/mpi.cpp
@@ -97,11 +97,14 @@ std::ostream& operator<<(std::ostream& o, const mpi_comm_shim& c) {
void register_mpi(pybind11::module& m) {
using namespace std::string_literals;
+ using namespace pybind11::literals;
pybind11::class_<mpi_comm_shim> mpi_comm(m, "mpi_comm");
mpi_comm
.def(pybind11::init<>())
- .def(pybind11::init([](pybind11::object o){return mpi_comm_shim(o);}))
+ .def(pybind11::init(
+ [](pybind11::object o){ return mpi_comm_shim(o); }),
+ "mpi_comm_obj"_a, "MPI communicator object.")
.def("__str__", util::to_string<mpi_comm_shim>)
.def("__repr__", util::to_string<mpi_comm_shim>);
--
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