diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0d522c7d5c15fb7f4bf3cd4e45924ae57a9bd750..abce9d7acbb240b6c2d6e0e49a0c273d4683c9b3 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -152,7 +152,7 @@ set(CMAKE_CXX_EXTENSIONS OFF)
# in the same CMakeLists.txt in which the target is defined.
# Interface library `arbor-config-defs` collects configure-time defines
-# for arbor, arborenv, arborio and arbornml, of the form ARB_HAVE_XXX. These
+# for arbor, arborenv, arborio, of the form ARB_HAVE_XXX. These
# defines should _not_ be used in any installed public headers.
add_library(arbor-config-defs INTERFACE)
@@ -171,13 +171,6 @@ add_library(arborenv-private-deps INTERFACE)
target_link_libraries(arborenv-private-deps INTERFACE arbor-config-defs)
install(TARGETS arborenv-private-deps EXPORT arbor-targets)
-# Interface library `arbornml-private-deps` collects dependencies, options etc.
-# for the arbornml library.
-
-add_library(arbornml-private-deps INTERFACE)
-target_link_libraries(arbornml-private-deps INTERFACE arbor-config-defs)
-install(TARGETS arbornml-private-deps EXPORT arbor-targets)
-
# Interface library `arborio-private-deps` collects dependencies, options etc.
# for the arborio library.
@@ -192,12 +185,12 @@ install(TARGETS arborio-private-deps EXPORT arbor-targets)
add_library(arbor-public-deps INTERFACE)
install(TARGETS arbor-public-deps EXPORT arbor-targets)
-# Interface library `arbornml-public-deps` collects requirements for the
-# users of the arbornml library (e.g. xml libs) that will become part
-# of arbornml's PUBLIC interface.
+# Interface library `arborio-public-deps` collects requirements for the
+# users of the arborio library (e.g. xml libs) that will become part
+# of arborio's PUBLIC interface.
-add_library(arbornml-public-deps INTERFACE)
-install(TARGETS arbornml-public-deps EXPORT arbornml-targets)
+add_library(arborio-public-deps INTERFACE)
+install(TARGETS arborio-public-deps EXPORT arborio-targets)
# External libraries in `ext` sub-directory: json, tinyopt and randon123.
# Creates interface libraries `ext-json`, `ext-tinyopt` and `ext-random123`
@@ -218,7 +211,7 @@ set(arbor_export_dependencies)
# Keep track of which 'components' of arbor are included (this is
# currently just 'MPI' support and 'neuroml' for NeuroML support in
-# libarbornml.)
+# libarborio.)
set(arbor_supported_components)
@@ -439,11 +432,6 @@ add_subdirectory(arborenv)
# arborio, arborio-public-headers:
add_subdirectory(arborio)
-# arbornml, arbornml-public-headers:
-if(ARB_WITH_NEUROML)
- add_subdirectory(arbornml)
-endif()
-
# unit, unit-mpi, unit-local, unit-modcc
add_subdirectory(test)
@@ -493,7 +481,6 @@ endif()
set(arbor_override_import_lang)
set(arbor_add_import_libs)
set(arborenv_add_import_libs)
-set(arbornml_add_import_libs)
set(arborio_add_import_libs)
if(ARB_WITH_GPU)
diff --git a/arbor/include/CMakeLists.txt b/arbor/include/CMakeLists.txt
index ebc48ee4f0b0b2bf97adb790e30175fb15a675da..b61d4a6d45ed4be0176ce18213511a1b00bef474 100644
--- a/arbor/include/CMakeLists.txt
+++ b/arbor/include/CMakeLists.txt
@@ -38,6 +38,10 @@ if(ARB_WITH_GPU)
# define ARB_GPU_ENABLED in version.hpp
list(APPEND arb_features GPU)
endif()
+if(ARB_WITH_NEUROML)
+ # define ARB_NEUROML_ENABLED in version.hpp
+ list(APPEND arb_features NEUROML)
+endif()
if(ARB_WITH_PROFILING)
# define ARB_PROFILE_ENABLED in version.hpp
list(APPEND arb_features PROFILE)
diff --git a/arborio/CMakeLists.txt b/arborio/CMakeLists.txt
index e07ce90d4ad50dcedece2352043487c5aab618d6..4cc0e2a3ac6512f49928d191048d81d2a5974569 100644
--- a/arborio/CMakeLists.txt
+++ b/arborio/CMakeLists.txt
@@ -1,6 +1,16 @@
set(arborio-sources
swcio.cpp
)
+if(ARB_WITH_NEUROML)
+ list(APPEND arborio-sources
+ arbornml.cpp
+ parse_morphology.cpp
+ with_xml.cpp
+ xmlwrap.cpp
+ )
+endif()
+
+find_package(LibXml2 REQUIRED)
add_library(arborio ${arborio-sources})
@@ -10,7 +20,16 @@ target_include_directories(arborio-public-headers INTERFACE
$<INSTALL_INTERFACE:include>
)
-target_link_libraries(arborio PUBLIC arbor arborio-public-headers)
+if(ARB_WITH_NEUROML)
+ target_link_libraries(arborio PUBLIC arbor arborio-public-headers LibXml2::LibXml2)
+ list(APPEND arbor_export_dependencies "LibXml2")
+ set(arbor_export_dependencies "${arbor_export_dependencies}" PARENT_SCOPE)
+ list(APPEND arbor_supported_components "neuroml")
+ set(arbor_supported_components "${arbor_supported_components}" PARENT_SCOPE)
+else ()
+ target_link_libraries(arborio PUBLIC arbor arborio-public-headers)
+endif()
+
target_link_libraries(arborio PRIVATE arbor-config-defs arborio-private-deps)
install(DIRECTORY include/arborio
diff --git a/arbornml/arbornml.cpp b/arborio/arbornml.cpp
similarity index 60%
rename from arbornml/arbornml.cpp
rename to arborio/arbornml.cpp
index 15c5f5551d4662c438d970d5b708ccdd4e9e9012..0ee14b0814f425eed81c281da00628660ec05fc9 100644
--- a/arbornml/arbornml.cpp
+++ b/arborio/arbornml.cpp
@@ -3,8 +3,7 @@
#include <string>
#include <vector>
-#include <arbornml/arbornml.hpp>
-#include <arbornml/nmlexcept.hpp>
+#include <arborio/arbornml.hpp>
#include "parse_morphology.hpp"
#include "xmlwrap.hpp"
@@ -12,7 +11,57 @@
using std::optional;
using std::nullopt;
-namespace arbnml {
+namespace arborio {
+
+static std::string fmt_error(const char* prefix, const std::string& err, unsigned line) {
+ return prefix + (line==0? err: "line " + std::to_string(line) + ": " + err);
+}
+
+xml_error::xml_error(const std::string& xml_error_msg, unsigned line):
+ neuroml_exception(fmt_error("xml error: ", xml_error_msg, line)),
+ xml_error_msg(xml_error_msg),
+ line(line)
+{}
+
+no_document::no_document():
+ neuroml_exception("no NeuroML document to parse")
+{}
+
+parse_error::parse_error(const std::string& error_msg, unsigned line):
+ neuroml_exception(fmt_error("parse error: ", error_msg, line)),
+ error_msg(error_msg),
+ line(line)
+{}
+
+bad_segment::bad_segment(unsigned long long segment_id, unsigned line):
+ neuroml_exception(
+ fmt_error(
+ "bad morphology segment: ",
+ "segment "+(segment_id+1==0? "unknown": "\""+std::to_string(segment_id)+"\""),
+ line)),
+ segment_id(segment_id),
+ line(line)
+{}
+
+bad_segment_group::bad_segment_group(const std::string& group_id, unsigned line):
+ neuroml_exception(
+ fmt_error(
+ "bad morphology segmentGroup: ",
+ "segmentGroup id "+(group_id.empty()? "unknown": "\""+group_id+"\""),
+ line)),
+ group_id(group_id),
+ line(line)
+{}
+
+cyclic_dependency::cyclic_dependency(const std::string& id, unsigned line):
+ neuroml_exception(
+ fmt_error(
+ "cyclic dependency: ",
+ "element id \""+id+"\"",
+ line)),
+ id(id),
+ line(line)
+{}
struct neuroml_impl {
xml_doc doc;
@@ -93,4 +142,4 @@ optional<morphology_data> neuroml::cell_morphology(const std::string& cell_id) c
return M;
}
-} // namespace arbnml
+} // namespace arborio
diff --git a/arbornml/include/arbornml/arbornml.hpp b/arborio/include/arborio/arbornml.hpp
similarity index 54%
rename from arbornml/include/arbornml/arbornml.hpp
rename to arborio/include/arborio/arbornml.hpp
index b925aaedebdd35176a0d659bf862fdf0c006b7c6..0f3d939e5049450245754201889eeabcd12abfda 100644
--- a/arbornml/include/arbornml/arbornml.hpp
+++ b/arborio/include/arborio/arbornml.hpp
@@ -1,5 +1,7 @@
#pragma once
+#include <cstddef>
+#include <stdexcept>
#include <optional>
#include <memory>
#include <string>
@@ -9,7 +11,58 @@
#include <arbor/morph/label_dict.hpp>
#include <arbor/morph/morphology.hpp>
-namespace arbnml {
+namespace arborio {
+
+// Common base-class for neuroml run-time errors.
+struct neuroml_exception: std::runtime_error {
+ neuroml_exception(const std::string& what_arg):
+ std::runtime_error(what_arg)
+ {}
+};
+
+// Generic XML error (as reported by libxml2).
+struct xml_error: neuroml_exception {
+ xml_error(const std::string& xml_error_msg, unsigned line = 0);
+ std::string xml_error_msg;
+ unsigned line;
+};
+
+// Can't parse NeuroML if we don't have a document.
+struct no_document: neuroml_exception {
+ no_document();
+};
+
+// Generic error parsing NeuroML data.
+struct parse_error: neuroml_exception {
+ parse_error(const std::string& error_msg, unsigned line = 0);
+ std::string error_msg;
+ unsigned line;
+};
+
+// NeuroML morphology error: improper segment data, e.g. bad id specification,
+// segment parent does not exist, fractionAlong is out of bounds, missing
+// required <proximal> data.
+struct bad_segment: neuroml_exception {
+ bad_segment(unsigned long long segment_id, unsigned line = 0);
+ unsigned long long segment_id;
+ unsigned line;
+};
+
+// NeuroML morphology error: improper segmentGroup data, e.g. malformed
+// element data, missing referenced segments or groups, etc.
+struct bad_segment_group: neuroml_exception {
+ bad_segment_group(const std::string& group_id, unsigned line = 0);
+ std::string group_id;
+ unsigned line;
+};
+
+// A segment or segmentGroup ultimately refers to itself via `parent`
+// or `include` elements respectively.
+struct cyclic_dependency: neuroml_exception {
+ cyclic_dependency(const std::string& id, unsigned line = 0);
+ std::string id;
+ unsigned line;
+};
// Collect and parse morphology elements from XML.
// No validation is performed against the NeuroML v2 schema.
@@ -71,4 +124,4 @@ private:
std::unique_ptr<neuroml_impl> impl_;
};
-} // namespace arbnml
+} // namespace arborio
diff --git a/arbornml/include/arbornml/with_xml.hpp b/arborio/include/arborio/with_xml.hpp
similarity index 80%
rename from arbornml/include/arbornml/with_xml.hpp
rename to arborio/include/arborio/with_xml.hpp
index c308451f7ba5618450cdbb79f3d156216a73ce0d..d176daa00413a182869fcec94aa61d12de45e42a 100644
--- a/arbornml/include/arbornml/with_xml.hpp
+++ b/arborio/include/arborio/with_xml.hpp
@@ -2,11 +2,11 @@
// Wrap initialization and cleanup of libxml2 library.
//
-// Use of `with_xml` is only necessary if arbornml is being
+// Use of `with_xml` is only necessary if arborio is being
// used in a multithreaded context and the client code is
// not managing libxml2 initialization and cleanup.
-namespace arbnml {
+namespace arborio {
struct with_xml {
with_xml();
@@ -21,4 +21,4 @@ struct with_xml {
bool run_cleanup_;
};
-} // namespace arbnml
+} // namespace arborio
diff --git a/arbornml/parse_morphology.cpp b/arborio/parse_morphology.cpp
similarity index 99%
rename from arbornml/parse_morphology.cpp
rename to arborio/parse_morphology.cpp
index 3f3cbf556c5903fc0825d4e577f41e18064a7f9b..d7adc67a7a1edc28aa64d0a601322e01ba37ce8b 100644
--- a/arbornml/parse_morphology.cpp
+++ b/arborio/parse_morphology.cpp
@@ -14,8 +14,7 @@
#include <arbor/morph/stitch.hpp>
#include <arbor/util/expected.hpp>
-#include <arbornml/arbornml.hpp>
-#include <arbornml/nmlexcept.hpp>
+#include <arborio/arbornml.hpp>
#include "parse_morphology.hpp"
#include "xmlwrap.hpp"
@@ -25,7 +24,7 @@ using arb::region;
using arb::util::expected;
using arb::util::unexpected;
-namespace arbnml {
+namespace arborio {
// Box is a container of size 0 or 1.
@@ -554,4 +553,4 @@ morphology_data parse_morphology_element(xml_xpathctx ctx, xml_node morph) {
return M;
}
-} // namespace arbnml
+} // namespace arborio
diff --git a/arbornml/parse_morphology.hpp b/arborio/parse_morphology.hpp
similarity index 60%
rename from arbornml/parse_morphology.hpp
rename to arborio/parse_morphology.hpp
index 305dcb6b13f694437a9686253bf09ac3235d69a6..0ced56cd683067a4ebc12fc94c9fafdd82fa6354 100644
--- a/arbornml/parse_morphology.hpp
+++ b/arborio/parse_morphology.hpp
@@ -1,10 +1,10 @@
#pragma once
-#include <arbornml/arbornml.hpp>
+#include <arborio/arbornml.hpp>
#include "xmlwrap.hpp"
-namespace arbnml {
+namespace arborio {
morphology_data parse_morphology_element(xml_xpathctx ctx, xml_node morph);
-} // namespace arbnml
+} // namespace arborio
diff --git a/arbornml/with_xml.cpp b/arborio/with_xml.cpp
similarity index 83%
rename from arbornml/with_xml.cpp
rename to arborio/with_xml.cpp
index c7ae41d0278d61053aabb73f3a741ee8d9c2bb0d..269c174d31b6da67a4f2fd841150ad5065079f8a 100644
--- a/arbornml/with_xml.cpp
+++ b/arborio/with_xml.cpp
@@ -1,8 +1,8 @@
-#include <arbornml/with_xml.hpp>
+#include <arborio/with_xml.hpp>
#include <libxml/parser.h>
-namespace arbnml {
+namespace arborio {
with_xml::with_xml(): run_cleanup_(true) {
// Initialize before any multithreaded access by library or client code.
@@ -19,4 +19,4 @@ with_xml::~with_xml() {
}
}
-} // namespace arbnml
+} // namespace arborio
diff --git a/arbornml/xmlwrap.cpp b/arborio/xmlwrap.cpp
similarity index 95%
rename from arbornml/xmlwrap.cpp
rename to arborio/xmlwrap.cpp
index c46b129284a106d94cea0dba974a9f2d22b60ca1..126f2ca6f1ff740cfbc4215c7e63e2a9f1efcafb 100644
--- a/arbornml/xmlwrap.cpp
+++ b/arborio/xmlwrap.cpp
@@ -12,11 +12,9 @@
#include <libxml/xmlerror.h>
-#include <arbornml/nmlexcept.hpp>
-
#include "xmlwrap.hpp"
-namespace arbnml {
+namespace arborio {
namespace detail {
@@ -95,14 +93,14 @@ void throw_on_xml_generic_error(void *, const char* msg, ...) {
vsnprintf(&err[0], err.size(), msg, vb);
va_end(vb);
- throw ::arbnml::xml_error(err);
+ throw ::arborio::xml_error(err);
}
void throw_on_xml_structured_error(void *ctx, xmlErrorPtr errp) {
if (errp->level!=1) { // ignore warnings!
std::string msg(errp->message);
if (!msg.empty() && msg.back()=='\n') msg.pop_back();
- throw ::arbnml::xml_error(msg, errp->line);
+ throw ::arborio::xml_error(msg, errp->line);
}
}
@@ -125,4 +123,4 @@ xml_error_scope::~xml_error_scope() {
xmlStructuredErrorContext = structured_context_;
}
-} // namespace arbnml
+} // namespace arborio
diff --git a/arbornml/xmlwrap.hpp b/arborio/xmlwrap.hpp
similarity index 98%
rename from arbornml/xmlwrap.hpp
rename to arborio/xmlwrap.hpp
index d914bc69f3009d358bcd948675b7f108a48373e2..0993b9ba0665d5f7002c614ef416a69cea007667 100644
--- a/arbornml/xmlwrap.hpp
+++ b/arborio/xmlwrap.hpp
@@ -14,9 +14,9 @@
#include <libxml/xpath.h>
#include <libxml/xpathInternals.h>
-#include <arbornml/nmlexcept.hpp>
+#include "arborio/arbornml.hpp"
-namespace arbnml {
+namespace arborio {
// `non_negative` represents the corresponding constraint in the schema, which
// can mean any arbitrarily large non-negtative integer value.
@@ -300,7 +300,7 @@ inline std::string xpath_escape(const std::string& x) {
// xml_error_scope object will restore the original error handling
// behaviour on destruction.
//
-// Errors are turned into arbnml::xml_error exceptions and thrown,
+// Errors are turned into arborio::xml_error exceptions and thrown,
// while warnings are ignored (libxml2 warnings are highly innocuous).
struct xml_error_scope {
@@ -314,4 +314,4 @@ struct xml_error_scope {
void* structured_context_;
};
-} // namespace arbnml
+} // namespace arborio
diff --git a/arbornml/CMakeLists.txt b/arbornml/CMakeLists.txt
deleted file mode 100644
index a4d944980f8402f18dc731672caf817a9212eb5e..0000000000000000000000000000000000000000
--- a/arbornml/CMakeLists.txt
+++ /dev/null
@@ -1,32 +0,0 @@
-set(arbornml-sources
- arbornml.cpp
- nmlexcept.cpp
- parse_morphology.cpp
- with_xml.cpp
- xmlwrap.cpp
-)
-
-find_package(LibXml2 REQUIRED)
-
-add_library(arbornml ${arbornml-sources})
-
-add_library(arbornml-public-headers INTERFACE)
-target_include_directories(arbornml-public-headers INTERFACE
- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
- $<INSTALL_INTERFACE:include>
-)
-
-target_link_libraries(arbornml PUBLIC arbor arbornml-public-headers LibXml2::LibXml2)
-target_link_libraries(arbornml PRIVATE arbor-config-defs arbornml-private-deps)
-
-install(DIRECTORY include/arbornml
- DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
- FILES_MATCHING PATTERN "*.hpp")
-
-install(TARGETS arbornml-public-headers EXPORT arbor-targets)
-install(TARGETS arbornml EXPORT arbor-targets ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-
-list(APPEND arbor_export_dependencies "LibXml2")
-set(arbor_export_dependencies "${arbor_export_dependencies}" PARENT_SCOPE)
-list(APPEND arbor_supported_components "neuroml")
-set(arbor_supported_components "${arbor_supported_components}" PARENT_SCOPE)
diff --git a/arbornml/include/arbornml/nmlexcept.hpp b/arbornml/include/arbornml/nmlexcept.hpp
deleted file mode 100644
index bba15a80062678fc53846b9437e2c3e1032e9b10..0000000000000000000000000000000000000000
--- a/arbornml/include/arbornml/nmlexcept.hpp
+++ /dev/null
@@ -1,67 +0,0 @@
-#pragma once
-
-#include <cstddef>
-#include <stdexcept>
-#include <string>
-
-namespace arbnml {
-
-// Common base-class for arbnml run-time errors.
-
-struct neuroml_exception: std::runtime_error {
- neuroml_exception(const std::string& what_arg):
- std::runtime_error(what_arg)
- {}
-};
-
-// Generic XML error (as reported by libxml2).
-
-struct xml_error: neuroml_exception {
- xml_error(const std::string& xml_error_msg, unsigned line = 0);
- std::string xml_error_msg;
- unsigned line;
-};
-
-// Can't parse NeuroML if we don't have a document.
-
-struct no_document: neuroml_exception {
- no_document();
-};
-
-// Generic error parsing NeuroML data.
-
-struct parse_error: neuroml_exception {
- parse_error(const std::string& error_msg, unsigned line = 0);
- std::string error_msg;
- unsigned line;
-};
-
-// NeuroML morphology error: improper segment data, e.g. bad id specification,
-// segment parent does not exist, fractionAlong is out of bounds, missing
-// required <proximal> data.
-
-struct bad_segment: neuroml_exception {
- bad_segment(unsigned long long segment_id, unsigned line = 0);
- unsigned long long segment_id;
- unsigned line;
-};
-
-// NeuroML morphology error: improper segmentGroup data, e.g. malformed
-// element data, missing referenced segments or groups, etc.
-
-struct bad_segment_group: neuroml_exception {
- bad_segment_group(const std::string& group_id, unsigned line = 0);
- std::string group_id;
- unsigned line;
-};
-
-// A segment or segmentGroup ultimately refers to itself via `parent`
-// or `include` elements respectively.
-
-struct cyclic_dependency: neuroml_exception {
- cyclic_dependency(const std::string& id, unsigned line = 0);
- std::string id;
- unsigned line;
-};
-
-} // namespace arbnml
diff --git a/arbornml/nmlexcept.cpp b/arbornml/nmlexcept.cpp
deleted file mode 100644
index 7ad1c8cac289b0d5ea869e8db40173c5b27be392..0000000000000000000000000000000000000000
--- a/arbornml/nmlexcept.cpp
+++ /dev/null
@@ -1,57 +0,0 @@
-#include <string>
-
-#include <arbornml/nmlexcept.hpp>
-
-namespace arbnml {
-
-static std::string fmt_error(const char* prefix, const std::string& err, unsigned line) {
- return prefix + (line==0? err: "line " + std::to_string(line) + ": " + err);
-}
-
-xml_error::xml_error(const std::string& xml_error_msg, unsigned line):
- neuroml_exception(fmt_error("xml error: ", xml_error_msg, line)),
- xml_error_msg(xml_error_msg),
- line(line)
-{}
-
-no_document::no_document():
- neuroml_exception("no NeuroML document to parse")
-{}
-
-parse_error::parse_error(const std::string& error_msg, unsigned line):
- neuroml_exception(fmt_error("parse error: ", error_msg, line)),
- error_msg(error_msg),
- line(line)
-{}
-
-bad_segment::bad_segment(unsigned long long segment_id, unsigned line):
- neuroml_exception(
- fmt_error(
- "bad morphology segment: ",
- "segment "+(segment_id+1==0? "unknown": "\""+std::to_string(segment_id)+"\""),
- line)),
- segment_id(segment_id),
- line(line)
-{}
-
-bad_segment_group::bad_segment_group(const std::string& group_id, unsigned line):
- neuroml_exception(
- fmt_error(
- "bad morphology segmentGroup: ",
- "segmentGroup id "+(group_id.empty()? "unknown": "\""+group_id+"\""),
- line)),
- group_id(group_id),
- line(line)
-{}
-
-cyclic_dependency::cyclic_dependency(const std::string& id, unsigned line):
- neuroml_exception(
- fmt_error(
- "cyclic dependency: ",
- "element id \""+id+"\"",
- line)),
- id(id),
- line(line)
-{}
-
-} // namespace arbnml
diff --git a/cmake/arbor-config.cmake.in b/cmake/arbor-config.cmake.in
index d551de69d3108bfc7ff2f8553f0e6ae3bcc256db..d7b056d91738ae3c8fb1f05565c2da9cf906ed1b 100644
--- a/cmake/arbor-config.cmake.in
+++ b/cmake/arbor-config.cmake.in
@@ -21,7 +21,7 @@ endforeach()
set(_override_lang @arbor_override_import_lang@)
if(_override_lang)
- foreach(target arbor::arbor arbor::arborenv arbor::arbornml)
+ foreach(target arbor::arbor arbor::arborenv arbor::arborio)
if(TARGET ${target})
set_target_properties(${target} PROPERTIES IMPORTED_LINK_INTERFACE_LANGUAGES_@arbor_build_config@ "${_override_lang}")
endif()
@@ -53,5 +53,5 @@ set(ARB_CXXOPT_ARCH @ARB_CXXOPT_ARCH@)
_append_property(arbor::arbor INTERFACE_LINK_LIBRARIES @arbor_add_import_libs@)
_append_property(arbor::arborenv INTERFACE_LINK_LIBRARIES @arborenv_add_import_libs@)
-_append_property(arbor::arbornml INTERFACE_LINK_LIBRARIES @arbornml_add_import_libs@)
+_append_property(arbor::arborio INTERFACE_LINK_LIBRARIES @arborio_add_import_libs@)
diff --git a/doc/cpp/neuroml.rst b/doc/cpp/neuroml.rst
index d495b6616f3af04cbcc9e0cecb9ef885512772ca..290e74b2e698444640b08b742ccc5c72d6221097 100644
--- a/doc/cpp/neuroml.rst
+++ b/doc/cpp/neuroml.rst
@@ -8,32 +8,31 @@ Arbor offers limited support for models described in
This is not built by default, but can be enabled by
providing the `-DARB_NEUROML=ON` argument to CMake at
configuration time (see :ref:`install-neuroml`). This will
-build the ``arbornml`` libray and defines the corresponding
-``arbor::arbornml`` CMake target.
+build the ``arborio`` libray with neuroml support.
-The ``arbornml`` library uses `libxml2 <http://xmlsoft.org/>`_
-for XML parsing. Applications using ``arbornml`` will need to
-link against ``libxml2`` in addition, though this is performed
-implicitly within CMake projects that add ``arbor::arbornml``
+The ``arborio`` library uses `libxml2 <http://xmlsoft.org/>`_
+for XML parsing. Applications using NeuroML through ``arborio``
+will need to link against ``libxml2`` in addition, though this
+is performed implicitly within CMake projects that add ``arbor::arborio``
as a link library.
-All classes and functions provided by the ``arbornml`` library
-are provided in the ``arbnml`` namespace.
+All classes and functions provided by the ``arborio`` library
+are provided in the ``arborio`` namespace.
Libxml2 interface
-----------------
Libxml2 offers threadsafe XML parsing, but not by default. If
-the application uses ``arbornml`` in an unthreaded context, or
-has already explicitly initialized ``libxml2``, nothing more
-needs to be done. Otherwise, the ``libxml2`` function ``xmlInitParser()``
-must be called explicitly.
+the application uses NeuromML support from ``arborio`` in an
+unthreaded context, or has already explicitly initialized ``libxml2``,
+nothing more needs to be done. Otherwise, the ``libxml2`` function
+``xmlInitParser()`` must be called explicitly.
-``arbornml`` provides a helper guard object for this purpose, defined
-in ``arbornml/with_xml.hpp``:
+``arborio`` provides a helper guard object for this purpose, defined
+in ``arborio/with_xml.hpp``:
-.. cpp:namespace:: arbnml
+.. cpp:namespace:: arborio
.. cpp:class:: with_xml
@@ -44,11 +43,11 @@ in ``arbornml/with_xml.hpp``:
NeuroML 2 morphology support
----------------------------
-NeuroML documents are represented by the ``arbnml::neuroml`` class,
+NeuroML documents are represented by the ``arborio::neuroml`` class,
which in turn provides methods for the identification and translation
of morphology data. ``neuroml`` objects are moveable and move-assignable, but not copyable.
-An implementation limitation restrictes valid segment id values to
+An implementation limitation restricts valid segment id values to
those which can be represented by an ``unsigned long long`` value.
.. cpp:class:: neuroml
@@ -111,14 +110,14 @@ segment group.
.. cpp:member:: std::unordered_map<std::string, std::vector<unsigned long long>> group_segments
- A map from taking each segment group id to its corresponding collection of segments.
+ A map from each segment group id to its corresponding collection of segments.
Exceptions
----------
-All NeuroML-specific exceptions are defined in ``arbornml/nmlexcept.hpp``, and are
-derived from ``arbnml::neuroml_exception`` which in turn is derived from ``std::runtime_error``.
+All NeuroML-specific exceptions are defined in ``arborio/arbornml.hpp``, and are
+derived from ``arborio::neuroml_exception`` which in turn is derived from ``std::runtime_error``.
With the exception of the ``no_document`` exception, all contain an unsigned member ``line``
which is intended to identify the problematic construct within the document.
diff --git a/doc/install/build_install.rst b/doc/install/build_install.rst
index c1810c3b699d35e8f2504a729f733ee176def754..7181512c400ba5c03c833a99852637511510947c 100644
--- a/doc/install/build_install.rst
+++ b/doc/install/build_install.rst
@@ -129,9 +129,10 @@ NeuroML
~~~~~~~
Arbor supports reading cell morphologies defined in NeuroML version 2 through
-an additional NeuroML support library ``arbornml``. This library requires
-`libxml2 <http://xmlsoft.org>`_ for the parsing of NeuroML2 XML. See :ref:`install-neuroml` for
-more information.
+an additional support library ``arborio``. This library requires
+`libxml2 <http://xmlsoft.org>`_ for the parsing of NeuroML2 XML, if it is built
+with NeuroML support enabled.
+See :ref:`install-neuroml` for more information.
Documentation
@@ -485,27 +486,27 @@ NeuroML support
---------------
Arbor has limited support for NeuroML version 2 through an additional library
-``arbornml``. This library will be built if the option ``-DARB_WITH_NEUROML=ON``
-is passed to CMake at configuration time. ``arbornml`` depends upon the
-the ``libxml2`` library for XML parsing.
+``arborio``. This library will be built with NeuroML support if the option
+``-DARB_WITH_NEUROML=ON`` is passed to CMake at configuration time.
+``arborio`` depends upon the the ``libxml2`` library for XML parsing.
-With NeuroML support enabled, Arbor will additionally install the static library
-``libarbornml.a``. Applications using this functionality will need to link
+Arbor will additionally install the static library ``libarborio.a``.
+Applications using this functionality will need to link
against this library in addition to the main Arbor library and ``libxml2``.
For example:
.. code-block:: bash
- g++ -std=c++17 -pthread mycode.cpp -larbornml -larbor -lxml2
+ g++ -std=c++17 -pthread mycode.cpp -larborio -larbor -lxml2
For projects using CMake, Arbor NeuroML support can be required with the
-component ``neuroml``. The corresponding CMake library target is ``arbor::arbornml``.
+component ``neuroml``. The corresponding CMake library target is ``arbor::arborio``.
.. code-block:: cmake
find_package(arbor COMPONENTS neuroml)
# ...
- target_link_libraries(myapp arbor::arbornml)
+ target_link_libraries(myapp arbor::arborio)
.. _install:
diff --git a/doc/python/morphology.rst b/doc/python/morphology.rst
index ef9eabb5be25c60ffb973f76d29bb67f128db841..8ffa546686379541589a8527da5df8e598d37965 100644
--- a/doc/python/morphology.rst
+++ b/doc/python/morphology.rst
@@ -482,3 +482,86 @@ Cell morphology
Compose the two isometries to form a new isometry that applies *b* and then applies *a*.
Note that rotations are composed as being with respect to the *intrinsic* coordinate system,
while translations are always taken to be with respect to the *extrinsic* absolute coordinate system.
+
+
+.. py:class:: neuroml_morph_data
+
+ A :class:`neuroml_morphology_data` object contains a representation of a morphology defined in
+ NeuroML.
+
+
+ .. py:attribute:: cell_id
+ :type: optional<str>
+
+ The id attribute of the cell that was used to find the morphology in the NeuroML document, if any.
+
+ .. py:attribute:: id
+ :type: str
+
+ The id attribute of the morphology.
+
+ .. py:attribute:: group_segments
+ :type: dict[str, list[long]]
+
+ A map from each segment group id to its corresponding collection of segments.
+
+ .. py:method:: segments
+
+ Returns a label dictionary with a region entry for each segment, keyed by the segment id (as a string).
+
+ :rtype: label_dict
+
+ .. py:method:: named_segments
+
+ Returns a label dictionary with a region entry for each name attribute given to one or more segments.
+ The region corresponds to the union of all segments sharing the same name attribute.
+
+ :rtype: label_dict
+
+ .. py:method:: groups
+
+ Returns a label dictionary with a region entry for each defined segment group.
+
+ :rtype: label_dict
+
+.. py:class:: neuroml
+
+ A :class:`neuroml` object represent NeuroML documents, and provides methods for the identification and
+ translation of morphology data.
+
+ An implementation limitation restricts valid segment id values to those which can be represented by an
+ unsigned long long value.
+
+ .. py:method:: neuroml(filename)
+
+ Build a NeuroML document representation from the supplied file contents.
+
+ :param str filename: the name of the NeuroML file.
+
+ .. py:method:: cell_ids()
+
+ Return the id of each ``<cell>`` element defined in the NeuroML document.
+
+ :rtype: list[str]
+
+ .. py:method:: morphology_ids()
+
+ Return the id of each top-level ``<morphology>`` element defined in the NeuroML document.
+
+ :rtype: list[str]
+
+ .. py:method:: morphology(morph_id)
+
+ Returns a representation of the top-level morphology with the supplied morph_id if it could be found.
+ Parse errors or an inconsistent representation will raise an exception.
+
+ :param str morph_id: ID of the top-level morphology.
+ :rtype: optional(neuroml_morph_data)
+
+ .. py:method:: cell_morphology(cell_id)
+
+ Returns a representation of the morphology associated with the cell with the supplied cell_id if it
+ could be found. Parse errors or an inconsistent representation will raise an exception.
+
+ :param str morph_id: ID of the cell.
+ :rtype: optional(neuroml_morph_data)
\ No newline at end of file
diff --git a/python/cells.cpp b/python/cells.cpp
index bc9d15468b82964bf630ef9d5a9cefb3773e44be..2f610f569ef3e798a922f387b0cd6d56a888d18d 100644
--- a/python/cells.cpp
+++ b/python/cells.cpp
@@ -28,105 +28,13 @@
#include "arbor/cv_policy.hpp"
#include "conversion.hpp"
#include "error.hpp"
+#include "proxy.hpp"
#include "pybind11/cast.h"
#include "pybind11/pytypes.h"
#include "schedule.hpp"
#include "strprintf.hpp"
namespace pyarb {
-//
-// proxies
-//
-
-struct label_dict_proxy {
- using str_map = std::unordered_map<std::string, std::string>;
- arb::label_dict dict;
- str_map cache;
- std::vector<std::string> locsets;
- std::vector<std::string> regions;
-
- label_dict_proxy() = default;
-
- label_dict_proxy(const str_map& in) {
- for (auto& i: in) {
- set(i.first.c_str(), i.second.c_str());
- }
- }
-
- std::size_t size() const {
- return locsets.size() + regions.size();
- }
-
- void set(const char* name, const char* desc) {
- using namespace std::string_literals;
- // The following code takes an input name and a region or locset
- // description, e.g.:
- // name='reg', desc='(tag 4)'
- // name='loc', desc='(terminal)'
- // name='foo', desc='(join (tag 2) (tag 3))'
- // Then it parses the description, and tests whether the description
- // is a region or locset, and updates the label dictionary appropriately.
- // Errors occur when:
- // * a region is described with a name that matches an existing locset
- // (and vice versa.)
- // * the description is not well formed, e.g. it contains a syntax error.
- // * the description is well-formed, but describes neither a region or locset.
- try{
- // Evaluate the s-expression to build a region/locset.
- auto result = arb::parse_label_expression(desc);
- if (!result) { // an error parsing / evaluating description.
- throw result.error();
- }
- else if (result->type()==typeid(arb::region)) { // describes a region.
- dict.set(name, std::move(std::any_cast<arb::region&>(*result)));
- auto it = std::lower_bound(regions.begin(), regions.end(), name);
- if (it==regions.end() || *it!=name) regions.insert(it, name);
- }
- else if (result->type()==typeid(arb::locset)) { // describes a locset.
- dict.set(name, std::move(std::any_cast<arb::locset&>(*result)));
- auto it = std::lower_bound(locsets.begin(), locsets.end(), name);
- if (it==locsets.end() || *it!=name) locsets.insert(it, name);
- }
- else {
- // Successfully parsed an expression that is neither region nor locset.
- throw util::pprintf("The defninition of '{} = {}' does not define a valid region or locset.", name, desc);
- }
- // The entry was added succesfully: store it in the cache.
- cache[name] = desc;
- }
- catch (std::string msg) {
- const char* base = "\nError adding the label '{}' = '{}'\n{}\n";
-
- throw std::runtime_error(util::pprintf(base, name, desc, msg));
- }
- // Exceptions are thrown in parse or eval if an unexpected error occured.
- catch (std::exception& e) {
- const char* msg =
- "\n----- internal error -------------------------------------------"
- "\nError parsing the label: '{}' = '{}'"
- "\n"
- "\n{}"
- "\n"
- "\nPlease file a bug report with this full error message at:"
- "\n github.com/arbor-sim/arbor/issues"
- "\n----------------------------------------------------------------";
- throw arb::arbor_internal_error(util::pprintf(msg, name, desc, e.what()));
- }
- }
-
- std::string to_string() const {
- std::string s;
- s += "(label_dict";
- for (auto& x: dict.regions()) {
- s += util::pprintf(" (region \"{}\" {})", x.first, x.second);
- }
- for (auto& x: dict.locsets()) {
- s += util::pprintf(" (locset \"{}\" {})", x.first, x.second);
- }
- s += ")";
- return s;
- }
-};
// This isn't pretty. Partly because the information in the global parameters
// is all over the place.
diff --git a/python/morphology.cpp b/python/morphology.cpp
index 06100d9f41884b1187d07dfa162eac2330d381fb..aa0425b4ba18d46170c3c6118cee63867968b481 100644
--- a/python/morphology.cpp
+++ b/python/morphology.cpp
@@ -10,10 +10,16 @@
#include <arbor/morph/place_pwlin.hpp>
#include <arbor/morph/primitives.hpp>
#include <arbor/morph/segment_tree.hpp>
+#include <arbor/version.hpp>
#include <arborio/swcio.hpp>
+#ifdef ARB_NEUROML_ENABLED
+#include <arborio/arbornml.hpp>
+#endif
+
#include "error.hpp"
+#include "proxy.hpp"
#include "strprintf.hpp"
namespace py = pybind11;
@@ -363,6 +369,91 @@ void register_morphology(py::module& m) {
[](const arb::morphology& m) {
return util::pprintf("<arbor.morphology:\n{}>", m);
});
+
+#ifdef ARB_NEUROML_ENABLED
+ // arborio::morphology_data
+ py::class_<arborio::morphology_data> nml_morph_data(m, "neuroml_morph_data");
+ nml_morph_data
+ .def_readonly("cell_id",
+ &arborio::morphology_data::cell_id,
+ "Cell id, or empty if morphology was taken from a top-level <morphology> element.")
+ .def_readonly("id",
+ &arborio::morphology_data::id,
+ "Morphology id.")
+ .def_readonly("morphology",
+ &arborio::morphology_data::morphology,
+ "Morphology constructed from a signle NeuroML <morphology> element.")
+ .def("segments",
+ [](const arborio::morphology_data& md) {return label_dict_proxy(md.segments);},
+ "Label dictionary containing one region expression for each segment id.")
+ .def("named_segments",
+ [](const arborio::morphology_data& md) {return label_dict_proxy(md.named_segments);},
+ "Label dictionary containing one region expression for each name applied to one or more segments.")
+ .def("groups",
+ [](const arborio::morphology_data& md) {return label_dict_proxy(md.groups);},
+ "Label dictionary containing one region expression for each segmentGroup id.")
+ .def_readonly("group_segments",
+ &arborio::morphology_data::group_segments,
+ "Map from segmentGroup ids to their corresponding segment ids.");
+
+ // arborio::neuroml
+ py::class_<arborio::neuroml> neuroml(m, "neuroml");
+ neuroml
+ // constructors
+ .def(py::init(
+ [](std::string fname){
+ std::ifstream fid{fname};
+ if (!fid.good()) {
+ throw pyarb_error(util::pprintf("can't open file '{}'", fname));
+ }
+ try {
+ std::string string_data((std::istreambuf_iterator<char>(fid)),
+ std::istreambuf_iterator<char>());
+ return arborio::neuroml(string_data);
+ }
+ catch (arborio::neuroml_exception& e) {
+ // Try to produce helpful error messages for SWC parsing errors.
+ throw pyarb_error(
+ util::pprintf("NeuroML error processing file {}: ", fname, e.what()));
+ }
+ }))
+ .def("cell_ids",
+ [](const arborio::neuroml& nml) {
+ try {
+ return nml.cell_ids();
+ }
+ catch (arborio::neuroml_exception& e) {
+ throw util::pprintf("NeuroML error: {}", e.what());
+ }
+ },"Query top-level cells.")
+ .def("morphology_ids",
+ [](const arborio::neuroml& nml) {
+ try {
+ return nml.morphology_ids();
+ }
+ catch (arborio::neuroml_exception& e) {
+ throw util::pprintf("NeuroML error: {}", e.what());
+ }
+ },"Query top-level standalone morphologies.")
+ .def("morphology",
+ [](const arborio::neuroml& nml, const std::string& morph_id) {
+ try {
+ return nml.morphology(morph_id);
+ }
+ catch (arborio::neuroml_exception& e) {
+ throw util::pprintf("NeuroML error: {}", e.what());
+ }
+ },"morph_id"_a,"Retrieve top-level nml_morph_data associated with morph_id.")
+ .def("cell_morphology",
+ [](const arborio::neuroml& nml, const std::string& cell_id) {
+ try {
+ return nml.cell_morphology(cell_id);
+ }
+ catch (arborio::neuroml_exception& e) {
+ throw util::pprintf("NeuroML error: {}", e.what());
+ }
+ },"morph_id"_a,"Retrieve nml_morph_data associated with cell_id.");
+#endif
}
} // namespace pyarb
diff --git a/python/proxy.hpp b/python/proxy.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..d47ab761b745d7947bd80ccd65d1f8d00ff5582d
--- /dev/null
+++ b/python/proxy.hpp
@@ -0,0 +1,102 @@
+#pragma once
+
+#include <any>
+
+#include <arbor/morph/label_dict.hpp>
+#include <arbor/morph/label_parse.hpp>
+
+#include "strprintf.hpp"
+
+namespace pyarb {
+struct label_dict_proxy {
+ using str_map = std::unordered_map<std::string, std::string>;
+ arb::label_dict dict;
+ str_map cache;
+ std::vector<std::string> locsets;
+ std::vector<std::string> regions;
+
+ label_dict_proxy() = default;
+
+ label_dict_proxy(const str_map& in) {
+ for (auto& i: in) {
+ set(i.first.c_str(), i.second.c_str());
+ }
+ }
+
+ label_dict_proxy(const arb::label_dict& label_dict): dict(label_dict) {}
+
+ std::size_t size() const {
+ return locsets.size() + regions.size();
+ }
+
+ void set(const char* name, const char* desc) {
+ using namespace std::string_literals;
+ // The following code takes an input name and a region or locset
+ // description, e.g.:
+ // name='reg', desc='(tag 4)'
+ // name='loc', desc='(terminal)'
+ // name='foo', desc='(join (tag 2) (tag 3))'
+ // Then it parses the description, and tests whether the description
+ // is a region or locset, and updates the label dictionary appropriately.
+ // Errors occur when:
+ // * a region is described with a name that matches an existing locset
+ // (and vice versa.)
+ // * the description is not well formed, e.g. it contains a syntax error.
+ // * the description is well-formed, but describes neither a region or locset.
+ try{
+ // Evaluate the s-expression to build a region/locset.
+ auto result = arb::parse_label_expression(desc);
+ if (!result) { // an error parsing / evaluating description.
+ throw result.error();
+ }
+ else if (result->type()==typeid(arb::region)) { // describes a region.
+ dict.set(name, std::move(std::any_cast<arb::region&>(*result)));
+ auto it = std::lower_bound(regions.begin(), regions.end(), name);
+ if (it==regions.end() || *it!=name) regions.insert(it, name);
+ }
+ else if (result->type()==typeid(arb::locset)) { // describes a locset.
+ dict.set(name, std::move(std::any_cast<arb::locset&>(*result)));
+ auto it = std::lower_bound(locsets.begin(), locsets.end(), name);
+ if (it==locsets.end() || *it!=name) locsets.insert(it, name);
+ }
+ else {
+ // Successfully parsed an expression that is neither region nor locset.
+ throw util::pprintf("The defninition of '{} = {}' does not define a valid region or locset.", name, desc);
+ }
+ // The entry was added succesfully: store it in the cache.
+ cache[name] = desc;
+ }
+ catch (std::string msg) {
+ const char* base = "\nError adding the label '{}' = '{}'\n{}\n";
+
+ throw std::runtime_error(util::pprintf(base, name, desc, msg));
+ }
+ // Exceptions are thrown in parse or eval if an unexpected error occured.
+ catch (std::exception& e) {
+ const char* msg =
+ "\n----- internal error -------------------------------------------"
+ "\nError parsing the label: '{}' = '{}'"
+ "\n"
+ "\n{}"
+ "\n"
+ "\nPlease file a bug report with this full error message at:"
+ "\n github.com/arbor-sim/arbor/issues"
+ "\n----------------------------------------------------------------";
+ throw arb::arbor_internal_error(util::pprintf(msg, name, desc, e.what()));
+ }
+ }
+
+ std::string to_string() const {
+ std::string s;
+ s += "(label_dict";
+ for (auto& x: dict.regions()) {
+ s += util::pprintf(" (region \"{}\" {})", x.first, x.second);
+ }
+ for (auto& x: dict.locsets()) {
+ s += util::pprintf(" (locset \"{}\" {})", x.first, x.second);
+ }
+ s += ")";
+ return s;
+ }
+};
+}
diff --git a/setup.py b/setup.py
index 8d62906ade5d3d80080539569da8deca9a239eb3..9bb49a0e13633d695252ee8d5dcea61c75b68a78 100644
--- a/setup.py
+++ b/setup.py
@@ -19,6 +19,7 @@ class CL_opt:
'gpu': 'none',
'vec': False,
'arch': 'native',
+ 'neuroml': False,
'bundled': True}
def settings(self):
@@ -54,6 +55,7 @@ class install_command(install):
'none, cuda, cuda-clang, hip'),
('vec', None, 'enable vectorization'),
('arch=', None, 'cpu architecture, e.g. haswell, skylake, armv8.2-a+sve, znver2 (default native).'),
+ ('neuroml', None, 'enable parsing neuroml morphologies in Arbor (requires libxml)')
('sysdeps', None, 'don\'t use bundled 3rd party C++ dependencies (pybind11 and json). This flag forces use of dependencies installed on the system.')
]
@@ -63,6 +65,7 @@ class install_command(install):
self.gpu = None
self.arch = None
self.vec = None
+ self.neuroml = None
self.sysdeps = None
def finalize_options(self):
@@ -79,6 +82,8 @@ class install_command(install):
opt['vec'] = self.vec is not None
# arch : target CPU micro-architecture (string).
opt['arch'] = "native" if self.arch is None else self.arch
+ # neuroml : compile with neuroml support for morphologies.
+ opt['neuroml'] = self.neuroml is not None
# bundled : use bundled/git-submoduled 3rd party libraries.
# By default use bundled libs.
opt['bundled'] = self.sysdeps is None
@@ -112,6 +117,7 @@ class cmake_build(build_ext):
'-DARB_VECTORIZE={}'.format('on' if opt['vec'] else 'off'),
'-DARB_ARCH={}'.format(opt['arch']),
'-DARB_GPU={}'.format(opt['gpu']),
+ '-DARB_WITH_NEUROML={}'.format( 'on' if opt['neuroml'] else 'off'),
'-DARB_USE_BUNDLED_LIBS={}'.format('on' if opt['bundled'] else 'off'),
'-DCMAKE_BUILD_TYPE=Release' # we compile with debug symbols in release mode.
]
diff --git a/test/unit/CMakeLists.txt b/test/unit/CMakeLists.txt
index b2474313344aa152b684188db00b5829878cf481..81de2e85a8c13e78144ee8f68feac185ce965f62 100644
--- a/test/unit/CMakeLists.txt
+++ b/test/unit/CMakeLists.txt
@@ -237,7 +237,3 @@ target_compile_definitions(unit PRIVATE "-DDATADIR=\"${CMAKE_CURRENT_SOURCE_DIR}
target_compile_definitions(unit PRIVATE "-DLIBDIR=\"${PROJECT_BINARY_DIR}/lib\"")
target_include_directories(unit PRIVATE "${CMAKE_CURRENT_BINARY_DIR}")
target_link_libraries(unit PRIVATE gtest arbor arborenv arborio arbor-private-headers arbor-sup)
-
-if(ARB_WITH_NEUROML)
- target_link_libraries(unit PRIVATE arbornml)
-endif()
diff --git a/test/unit/test_nml_morphology.cpp b/test/unit/test_nml_morphology.cpp
index 3c685a0801d8f19ddeaf73f614e15621efeba081..6860aa80543c9dbf8087f9e3491861969a260489 100644
--- a/test/unit/test_nml_morphology.cpp
+++ b/test/unit/test_nml_morphology.cpp
@@ -6,9 +6,8 @@
#include <arbor/morph/place_pwlin.hpp>
#include <arbor/morph/primitives.hpp>
-#include <arbornml/arbornml.hpp>
-#include <arbornml/nmlexcept.hpp>
-#include <arbornml/with_xml.hpp>
+#include <arborio/arbornml.hpp>
+#include <arborio/with_xml.hpp>
#include "../test/gtest.h"
#include "morph_pred.hpp"
@@ -18,10 +17,10 @@ using testing::region_eq;
TEST(neuroml, with_xml) {
// This (hopefully) will not blow up.
{
- arbnml::with_xml scope;
+ arborio::with_xml scope;
}
{
- arbnml::with_xml scope;
+ arborio::with_xml scope;
}
}
@@ -30,7 +29,7 @@ TEST(neuroml, with_xml) {
TEST(neuroml, morph_badxml) {
std::string illformed = "<wha?";
- EXPECT_THROW(arbnml::neuroml{illformed}, arbnml::xml_error);
+ EXPECT_THROW(arborio::neuroml{illformed}, arborio::xml_error);
}
TEST(neuroml, morph_none) {
@@ -38,13 +37,13 @@ TEST(neuroml, morph_none) {
{
std::string empty1 = R"~(<?xml version="1.0" encoding="UTF-8"?><foo/>)~";
- arbnml::neuroml N1(empty1);
+ arborio::neuroml N1(empty1);
EXPECT_TRUE(N1.cell_ids().empty());
EXPECT_TRUE(N1.morphology_ids().empty());
std::string empty2 = "<foo/>";
- arbnml::neuroml N2(empty2);
+ arborio::neuroml N2(empty2);
EXPECT_TRUE(N2.cell_ids().empty());
EXPECT_TRUE(N2.morphology_ids().empty());
}
@@ -56,7 +55,7 @@ R"~(<?xml version="1.0" encoding="UTF-8"?>
<neuroml xmlns="http://www.neuroml.org/schema/neuroml2">
</neuroml>)~";
- arbnml::neuroml N3(empty3);
+ arborio::neuroml N3(empty3);
EXPECT_TRUE(N3.cell_ids().empty());
EXPECT_TRUE(N3.morphology_ids().empty());
}
@@ -80,7 +79,7 @@ R"~(
using svector = std::vector<std::string>;
- arbnml::neuroml N(doc);
+ arborio::neuroml N(doc);
svector m_ids = N.morphology_ids(); // only top-level!
std::sort(m_ids.begin(), m_ids.end());
@@ -90,7 +89,7 @@ R"~(
std::sort(c_ids.begin(), c_ids.end());
EXPECT_EQ((svector{"c3", "c4"}), c_ids);
- arbnml::morphology_data mdata;
+ arborio::morphology_data mdata;
mdata = N.cell_morphology("c4").value();
EXPECT_EQ("c4", mdata.cell_id);
@@ -174,10 +173,10 @@ R"~(
</neuroml>
)~";
- arbnml::neuroml N(doc);
+ arborio::neuroml N(doc);
{
- arbnml::morphology_data m1 = N.morphology("m1").value();
+ arborio::morphology_data m1 = N.morphology("m1").value();
label_dict labels;
labels.import(m1.segments, "seg:");
mprovider P(m1.morphology, labels);
@@ -190,7 +189,7 @@ R"~(
}
{
- arbnml::morphology_data m2 = N.morphology("m2").value();
+ arborio::morphology_data m2 = N.morphology("m2").value();
label_dict labels;
labels.import(m2.segments, "seg:");
mprovider P(m2.morphology, labels);
@@ -218,7 +217,7 @@ R"~(
}
{
- arbnml::morphology_data m3 = N.morphology("m3").value();
+ arborio::morphology_data m3 = N.morphology("m3").value();
label_dict labels;
labels.import(m3.segments, "seg:");
mprovider P(m3.morphology, labels);
@@ -252,7 +251,7 @@ R"~(
}
{
for (const char* m_name: {"m4", "m5"}) {
- arbnml::morphology_data m4_or_5 = N.morphology(m_name).value();
+ arborio::morphology_data m4_or_5 = N.morphology(m_name).value();
label_dict labels;
labels.import(m4_or_5.segments, "seg:");
mprovider P(m4_or_5.morphology, labels);
@@ -354,14 +353,14 @@ R"~(
</neuroml>
)~";
- arbnml::neuroml N(doc);
+ arborio::neuroml N(doc);
- EXPECT_THROW(N.morphology("no-proximal").value(), arbnml::bad_segment);
- EXPECT_THROW(N.morphology("no-such-parent").value(), arbnml::bad_segment);
- EXPECT_THROW(N.morphology("cyclic-dependency").value(), arbnml::cyclic_dependency);
- EXPECT_THROW(N.morphology("duplicate-id").value(), arbnml::bad_segment);
- EXPECT_THROW(N.morphology("bad-segment-id").value(), arbnml::bad_segment);
- EXPECT_THROW(N.morphology("another-bad-segment-id").value(), arbnml::bad_segment);
+ EXPECT_THROW(N.morphology("no-proximal").value(), arborio::bad_segment);
+ EXPECT_THROW(N.morphology("no-such-parent").value(), arborio::bad_segment);
+ EXPECT_THROW(N.morphology("cyclic-dependency").value(), arborio::cyclic_dependency);
+ EXPECT_THROW(N.morphology("duplicate-id").value(), arborio::bad_segment);
+ EXPECT_THROW(N.morphology("bad-segment-id").value(), arborio::bad_segment);
+ EXPECT_THROW(N.morphology("another-bad-segment-id").value(), arborio::bad_segment);
}
TEST(neuroml, simple_groups) {
@@ -441,11 +440,11 @@ R"~(
</neuroml>
)~";
- arbnml::neuroml N(doc);
+ arborio::neuroml N(doc);
using reg::named;
{
- arbnml::morphology_data m1 = N.morphology("m1").value();
+ arborio::morphology_data m1 = N.morphology("m1").value();
label_dict labels;
labels.import(m1.segments);
labels.import(m1.groups);
@@ -456,7 +455,7 @@ R"~(
EXPECT_TRUE(region_eq(P, named("group-c"), join(named("2"), named("1"))));
}
{
- arbnml::morphology_data m2 = N.morphology("m2").value();
+ arborio::morphology_data m2 = N.morphology("m2").value();
label_dict labels;
labels.import(m2.segments);
labels.import(m2.groups);
@@ -508,11 +507,11 @@ R"~(
</neuroml>
)~";
- arbnml::neuroml N(doc);
+ arborio::neuroml N(doc);
- EXPECT_THROW(N.morphology("no-such-segment").value(), arbnml::bad_segment_group);
- EXPECT_THROW(N.morphology("no-such-group").value(), arbnml::bad_segment_group);
- EXPECT_THROW(N.morphology("cyclic-dependency").value(), arbnml::cyclic_dependency);
+ EXPECT_THROW(N.morphology("no-such-segment").value(), arborio::bad_segment_group);
+ EXPECT_THROW(N.morphology("no-such-group").value(), arborio::bad_segment_group);
+ EXPECT_THROW(N.morphology("cyclic-dependency").value(), arborio::cyclic_dependency);
}
@@ -612,9 +611,9 @@ R"~(
</neuroml>
)~";
- arbnml::neuroml N(doc);
+ arborio::neuroml N(doc);
- arbnml::morphology_data m1 = N.morphology("m1").value();
+ arborio::morphology_data m1 = N.morphology("m1").value();
label_dict labels;
labels.import(m1.segments);
labels.import(m1.groups);