diff --git a/.github/workflows/test-everything.yml b/.github/workflows/test-everything.yml
index 143d04c1f812e3099d342fea4aae333704a3cca7..43f84aae12de5f495999a5f6e9711c327fd2388d 100644
--- a/.github/workflows/test-everything.yml
+++ b/.github/workflows/test-everything.yml
@@ -97,11 +97,11 @@ jobs:
if: ${{ startsWith(matrix.config.os, 'ubuntu') }}
run: |
sudo apt-get update
- sudo apt-get install -y libxml2-dev libopenmpi-dev ninja-build ccache ${{ matrix.config.cc }}
+ sudo apt-get install -y libopenmpi-dev ninja-build ccache ${{ matrix.config.cc }}
- name: "MacOS: get build dependencies"
if: ${{ startsWith(matrix.config.os, 'macos') }}
run: |
- brew install libxml2 openmpi ninja ccache
+ brew install openmpi ninja ccache
- name: Set up cmake
uses: jwlawson/actions-setup-cmake@v1.13
with:
@@ -151,7 +151,7 @@ jobs:
export PATH="/usr/lib/ccache:/usr/local/opt/ccache/libexec:$PATH"
mkdir build
cd build
- cmake .. -GNinja -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC -DARB_WITH_PYTHON=ON -DARB_VECTORIZE=${{ matrix.config.simd }} -DPython3_EXECUTABLE=`which python` -DARB_WITH_MPI=${{ matrix.config.mpi }} -DARB_USE_BUNDLED_LIBS=ON -DARB_WITH_NEUROML=ON -DARB_WITH_ASSERTIONS=ON
+ cmake .. -GNinja -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC -DARB_WITH_PYTHON=ON -DARB_VECTORIZE=${{ matrix.config.simd }} -DPython3_EXECUTABLE=`which python` -DARB_WITH_MPI=${{ matrix.config.mpi }} -DARB_USE_BUNDLED_LIBS=ON -DARB_WITH_ASSERTIONS=ON
ninja -j4 tests examples pyarb html
cd -
- if: ${{ matrix.variant == 'shared' }}
@@ -160,7 +160,7 @@ jobs:
export PATH="/usr/lib/ccache:/usr/local/opt/ccache/libexec:$PATH"
mkdir build
cd build
- cmake .. -GNinja -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC -DARB_WITH_PYTHON=ON -DARB_VECTORIZE=${{ matrix.config.simd }} -DPython3_EXECUTABLE=`which python` -DARB_WITH_MPI=${{ matrix.config.mpi }} -DARB_USE_BUNDLED_LIBS=ON -DARB_WITH_NEUROML=ON -DARB_WITH_ASSERTIONS=ON -DBUILD_SHARED_LIBS=ON
+ cmake .. -GNinja -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC -DARB_WITH_PYTHON=ON -DARB_VECTORIZE=${{ matrix.config.simd }} -DPython3_EXECUTABLE=`which python` -DARB_WITH_MPI=${{ matrix.config.mpi }} -DARB_USE_BUNDLED_LIBS=ON -DARB_WITH_ASSERTIONS=ON -DBUILD_SHARED_LIBS=ON
ninja -j4 tests examples pyarb html
cd -
- name: Install arbor
diff --git a/.gitmodules b/.gitmodules
index ca46a262d5db14196120ca1bdb374881f5d0c320..cd515e55423d824434cdb01dc86558a8a87ecd7d 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -22,4 +22,7 @@
path = ext/googletest
url = https://github.com/google/googletest.git
branch = main
-
+[submodule "ext/pugixml"]
+ path = ext/pugixml
+ url = https://github.com/zeux/pugixml.git
+ branch = master
diff --git a/ATTRIBUTIONS.md b/ATTRIBUTIONS.md
index 1f7b99e1df39d5ac5dd87b762f91bd561ebfab10..6229eeba5f7f680af11d4409929f4ae926f51c90 100644
--- a/ATTRIBUTIONS.md
+++ b/ATTRIBUTIONS.md
@@ -58,6 +58,13 @@ BSD License.
http://llvm.org/
+# PugiXML
+
+A simple and fast C++ XML processing library.
+MIT License.
+
+https://github.com/zeux/pugixml
+
## Transcendentals intrinsics
The numerical algorithms for the transcendentals intrinsics are based on the
diff --git a/CMakeLists.txt b/CMakeLists.txt
index bb84ea9d2ec7de54adba103572ba210ee321ffbc..8fa2643dd685e12f4b7140727fdf60cd370db7b8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -82,12 +82,6 @@ option(ARB_WITH_PROFILING "use built-in profiling" OFF)
option(ARB_WITH_ASSERTIONS "enable arb_assert() assertions in code" OFF)
-#----------------------------------------------------------
-# NeuroML support library:
-#----------------------------------------------------------
-
-option(ARB_WITH_NEUROML "build NeuroML support library" OFF)
-
#----------------------------------------------------------
# Python front end for Arbor:
#----------------------------------------------------------
@@ -227,6 +221,7 @@ install(FILES mechanisms/BuildModules.cmake DESTINATION ${ARB_INSTALL_DATADIR})
# Creates interface libraries `ext-json`, `ext-tinyopt` and `ext-random123`
cmake_dependent_option(ARB_USE_BUNDLED_FMT "Use bundled FMT lib." ON "ARB_USE_BUNDLED_LIBS" OFF)
+cmake_dependent_option(ARB_USE_BUNDLED_PUGIXML "Use bundled XML lib." ON "ARB_USE_BUNDLED_LIBS" OFF)
cmake_dependent_option(ARB_USE_BUNDLED_JSON "Use bundled Niels Lohmann's json library." ON "ARB_USE_BUNDLED_LIBS" OFF)
if(NOT ARB_USE_BUNDLED_JSON)
diff --git a/arbor/include/CMakeLists.txt b/arbor/include/CMakeLists.txt
index 461b7d5428a26628f6bfc71881f05a750bdc6ed9..bf912d3c1c4f203c7b3ec3f301e0a4be4a8c7059 100644
--- a/arbor/include/CMakeLists.txt
+++ b/arbor/include/CMakeLists.txt
@@ -38,10 +38,8 @@ 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()
+# This is provided for legacy reasons, now always on.
+list(APPEND arb_features NEUROML)
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 6db6b46fc27f2a8930dd95387a67b2854c9b5482..1e40f43922f68684569c9f8d5851493e74b30218 100644
--- a/arborio/CMakeLists.txt
+++ b/arborio/CMakeLists.txt
@@ -5,19 +5,19 @@ set(arborio-sources
cableio.cpp
cv_policy_parse.cpp
label_parse.cpp
-)
-if(ARB_WITH_NEUROML)
- list(APPEND arborio-sources
- neuroml.cpp
- nml_parse_morphology.cpp
- xml.cpp
- xmlwrap.cpp)
- find_package(LibXml2 REQUIRED)
-endif()
-
+ neuroml.cpp
+ nml_parse_morphology.cpp)
add_library(arborio ${arborio-sources})
+if (ARB_USE_BUNDLED_PUGIXML)
+ target_include_directories(arborio PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/../ext/pugixml/src>)
+ target_compile_definitions(arborio PRIVATE PUGIXML_HEADER_ONLY)
+else()
+ find_package(pugixml REQUIRED)
+ target_link_libraries(arborio PUBLIC pugixml::pugixml)
+endif()
+
add_library(arborio-public-headers INTERFACE)
add_library(arborio-private-headers INTERFACE)
@@ -29,15 +29,9 @@ target_include_directories(arborio-public-headers INTERFACE
target_include_directories(arborio-private-headers INTERFACE
"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>")
-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 PUBLIC arbor arborio-public-headers)
+list(APPEND arbor_supported_components "neuroml")
+set(arbor_supported_components "${arbor_supported_components}" PARENT_SCOPE)
target_link_libraries(arborio PRIVATE arbor-config-defs arborio-private-deps)
diff --git a/arborio/include/arborio/neuroml.hpp b/arborio/include/arborio/neuroml.hpp
index 3646548e6f773b106a3414994434041f406b4b90..7d889581b4c948fd25fe141699a84e9790f97301 100644
--- a/arborio/include/arborio/neuroml.hpp
+++ b/arborio/include/arborio/neuroml.hpp
@@ -14,6 +14,15 @@
namespace arborio {
+// `non_negative` represents the corresponding constraint in the schema, which
+// can mean any arbitrarily large non-negative integer value.
+//
+// A faithful representation would use an arbitrary-size 'big' integer or a
+// string, but for ease of implementation (and a bit more speed) we restrict it
+// to whatever we can fit in an unsigned long long.
+
+using non_negative = unsigned long long;
+
// Common base-class for neuroml run-time errors.
struct ARB_SYMBOL_VISIBLE neuroml_exception: std::runtime_error {
neuroml_exception(const std::string& what_arg):
@@ -28,34 +37,30 @@ struct ARB_SYMBOL_VISIBLE nml_no_document: neuroml_exception {
// Generic error parsing NeuroML data.
struct ARB_SYMBOL_VISIBLE nml_parse_error: neuroml_exception {
- nml_parse_error(const std::string& error_msg, unsigned line = 0);
+ nml_parse_error(const std::string& error_msg);
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 ARB_SYMBOL_VISIBLE nml_bad_segment: neuroml_exception {
- nml_bad_segment(unsigned long long segment_id, unsigned line = 0);
+ nml_bad_segment(unsigned long long segment_id);
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 ARB_SYMBOL_VISIBLE nml_bad_segment_group: neuroml_exception {
- nml_bad_segment_group(const std::string& group_id, unsigned line = 0);
+ nml_bad_segment_group(const std::string& group_id);
std::string group_id;
- unsigned line;
};
// A segment or segmentGroup ultimately refers to itself via `parent`
// or `include` elements respectively.
struct ARB_SYMBOL_VISIBLE nml_cyclic_dependency: neuroml_exception {
- nml_cyclic_dependency(const std::string& id, unsigned line = 0);
+ nml_cyclic_dependency(const std::string& id);
std::string id;
- unsigned line;
};
// Collect and parse morphology elements from XML.
diff --git a/arborio/include/arborio/xml.hpp b/arborio/include/arborio/xml.hpp
deleted file mode 100644
index bedc54fdf2ee5ca8f084f38fcf578a4eaeed1566..0000000000000000000000000000000000000000
--- a/arborio/include/arborio/xml.hpp
+++ /dev/null
@@ -1,38 +0,0 @@
-#pragma once
-
-#include <stdexcept>
-#include <string>
-
-#include <arborio/export.hpp>
-
-// XML related interfaces deriving from the underlying XML implementation library.
-
-namespace arborio {
-
-// Generic XML error (as reported by libxml2).
-struct ARB_SYMBOL_VISIBLE xml_error: std::runtime_error {
- xml_error(const std::string& xml_error_msg, unsigned line = 0);
- std::string xml_error_msg;
- unsigned line;
-};
-
-// Wrap initialization and cleanup of libxml2 library.
-//
-// 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.
-
-struct ARB_ARBORIO_API with_xml {
- with_xml();
- ~with_xml();
-
- with_xml(with_xml&&);
- with_xml(const with_xml&) = delete;
-
- with_xml& operator=(const with_xml&) = delete;
- with_xml& operator=(with_xml&&) = delete;
-
- bool run_cleanup_;
-};
-
-} // namespace arborio
diff --git a/arborio/neuroml.cpp b/arborio/neuroml.cpp
index 31dcc80777c40ffaa1ae42dffe5aeb96493f32ea..554b7a6db494c5f489554f28f6a8a13175bd49a0 100644
--- a/arborio/neuroml.cpp
+++ b/arborio/neuroml.cpp
@@ -6,75 +6,47 @@
#include <arborio/neuroml.hpp>
#include "nml_parse_morphology.hpp"
-#include "xmlwrap.hpp"
+#include "xml.hpp"
using std::optional;
using std::nullopt;
-using namespace arborio::xmlwrap;
-
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);
-}
-
nml_no_document::nml_no_document():
neuroml_exception("no NeuroML document to parse")
{}
-nml_parse_error::nml_parse_error(const std::string& error_msg, unsigned line):
- neuroml_exception(fmt_error("parse error: ", error_msg, line)),
- error_msg(error_msg),
- line(line)
+nml_parse_error::nml_parse_error(const std::string& error_msg):
+ neuroml_exception("parse error: " + error_msg),
+ error_msg(error_msg)
{}
-nml_bad_segment::nml_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)
+nml_bad_segment::nml_bad_segment(unsigned long long segment_id):
+ neuroml_exception("bad morphology segment: id="+(segment_id+1==0? "unknown": "\""+std::to_string(segment_id)+"\"")),
+ segment_id(segment_id)
{}
-nml_bad_segment_group::nml_bad_segment_group(const std::string& group_id, unsigned line):
+nml_bad_segment_group::nml_bad_segment_group(const std::string& group_id):
neuroml_exception(
- fmt_error(
- "bad morphology segmentGroup: ",
- "segmentGroup id "+(group_id.empty()? "unknown": "\""+group_id+"\""),
- line)),
- group_id(group_id),
- line(line)
+ "bad morphology segmentGroup: id=" + (group_id.empty()? "unknown": "\""+group_id+"\"")),
+ group_id(group_id)
{}
-nml_cyclic_dependency::nml_cyclic_dependency(const std::string& id, unsigned line):
- neuroml_exception(
- fmt_error(
- "cyclic dependency: ",
- "element id \""+id+"\"",
- line)),
- id(id),
- line(line)
+nml_cyclic_dependency::nml_cyclic_dependency(const std::string& id):
+ neuroml_exception("cyclic dependency: id \""+id+"\""),
+ id(id)
{}
struct ARB_ARBORIO_API neuroml_impl {
xml_doc doc;
+ std::string raw;
neuroml_impl() {}
- explicit neuroml_impl(std::string text) {
- xml_error_scope err;
- doc = xml_doc(text);
- }
-
- xml_xpathctx make_context() const {
- if (!doc) throw nml_no_document{};
-
- auto ctx = xpath_context(doc);
- ctx.register_ns("nml", "http://www.neuroml.org/schema/neuroml2");
- return ctx;
+ explicit neuroml_impl(std::string text): raw{text} {
+ auto res = doc.load_buffer_inplace(raw.data(), raw.size()+1);
+ if (res.status) throw nml_parse_error{res.description()};
}
};
@@ -87,53 +59,39 @@ neuroml& neuroml::operator=(neuroml&&) = default;
neuroml::~neuroml() = default;
std::vector<std::string> neuroml::cell_ids() const {
- xml_error_scope err;
+ auto matches = impl_->doc.select_nodes("//neuroml/cell/@id");
std::vector<std::string> result;
-
- auto ctx = impl_->make_context();
- auto matches = ctx.query("//nml:neuroml/nml:cell/@id");
-
result.reserve(matches.size());
- for (auto node: matches) {
- result.push_back(std::string(node.content()));
+ for (const auto& it: matches) {
+ result.push_back(it.attribute().as_string());
}
-
return result;
}
std::vector<std::string> neuroml::morphology_ids() const {
- xml_error_scope err;
+ auto matches = impl_->doc.select_nodes("//neuroml/morphology/@id");
std::vector<std::string> result;
-
- auto ctx = impl_->make_context();
- auto matches = ctx.query("//nml:neuroml/nml:morphology/@id");
-
result.reserve(matches.size());
- for (auto node: matches) {
- result.push_back(std::string(node.content()));
+ for (const auto& it: matches) {
+ result.push_back(it.attribute().as_string());
}
-
return result;
}
optional<nml_morphology_data> neuroml::morphology(const std::string& morph_id, enum neuroml_options::values options) const {
- xml_error_scope err;
- auto ctx = impl_->make_context();
- auto matches = ctx.query("//nml:neuroml/nml:morphology[@id="+xpath_escape(morph_id)+"]");
-
- return matches.empty()? nullopt: optional(nml_parse_morphology_element(ctx, matches[0], options));
+ auto id = xpath_escape(morph_id);
+ auto query = "//neuroml/morphology[@id=" + id + "]";
+ auto match = impl_->doc.select_node(query.data()).node();
+ if (match.empty()) return {};
+ return nml_parse_morphology_element(match, options);
}
optional<nml_morphology_data> neuroml::cell_morphology(const std::string& cell_id, enum neuroml_options::values options) const {
- xml_error_scope err;
- auto ctx = impl_->make_context();
- auto matches = ctx.query(
- "( //nml:neuroml/nml:morphology[@id=string((//nml:neuroml/nml:cell[@id="+xpath_escape(cell_id)+"]/@morphology)[1])] | "
- " //nml:neuroml/nml:cell[@id="+xpath_escape(cell_id)+"]/nml:morphology )[1]");
-
- if (matches.empty()) return nullopt;
-
- nml_morphology_data M = nml_parse_morphology_element(ctx, matches[0], options);
+ auto id = "//neuroml/cell[@id=" + xpath_escape(cell_id) + "]";
+ auto query = "(//neuroml/morphology[@id=string((" + id + "/@morphology)[1])] | " + id + "/morphology)[1]";
+ auto match = impl_->doc.select_node(query.data()).node();
+ if (match.empty()) return nullopt;
+ nml_morphology_data M = nml_parse_morphology_element(match, options);
M.cell_id = cell_id;
return M;
}
diff --git a/arborio/nml_parse_morphology.cpp b/arborio/nml_parse_morphology.cpp
index 24203ea18451fdcdb7ef3004d00bce8139429503..84201e49d5d29af033343489ccb72a51bf38663e 100644
--- a/arborio/nml_parse_morphology.cpp
+++ b/arborio/nml_parse_morphology.cpp
@@ -17,7 +17,7 @@
#include <arborio/neuroml.hpp>
#include "nml_parse_morphology.hpp"
-#include "xmlwrap.hpp"
+#include "xml.hpp"
using std::optional;
using arb::region;
@@ -25,7 +25,6 @@ using arb::util::expected;
using arb::util::unexpected;
using namespace std::literals;
-using namespace arborio::xmlwrap;
namespace arborio {
@@ -132,22 +131,6 @@ expected<std::vector<std::size_t>, cycle_detected> topological_sort(std::size_t
return depth;
}
-template <typename T>
-struct propx {
- explicit propx(xml_node n, const char* attr, optional<T> dflt = std::nullopt) {
- if (auto x = n.prop<T>(attr, dflt)) {
- result_ = std::move(x.value());
- }
- else {
- throw nml_parse_error(x.error().error, x.error().line);
- }
- }
-
- operator T() && { return std::move(result_); }
- operator T() const& { return result_; }
- T result_;
-};
-
} // namespace
@@ -162,10 +145,6 @@ struct neuroml_segment {
optional<non_negative> parent_id;
double along = 1;
bool spherical = false;
-
- // Data for error reporting:
- unsigned line = 0;
-
// Topological depth:
std::size_t tdepth = 0;
};
@@ -174,9 +153,6 @@ struct neuroml_segment_group_subtree {
// Interval determined by segment ids.
// Represents both `<path>` and `<subTree>` elements.
optional<non_negative> from, to;
-
- // Data for error reporting:
- unsigned line = 0;
};
struct neuroml_segment_group_info {
@@ -184,9 +160,6 @@ struct neuroml_segment_group_info {
std::vector<non_negative> segments;
std::vector<std::string> includes;
std::vector<neuroml_segment_group_subtree> subtrees;
-
- // Data for error reporting:
- unsigned line = 0;
};
// Processing of parsed segment/segmentGroup data:
@@ -227,14 +200,14 @@ struct neuroml_segment_tree {
// Build index, throw on duplicate id.
for (std::size_t i = 0; i<n_seg; ++i) {
if (!index_.insert({segments_[i].id, i}).second) {
- throw nml_bad_segment(segments_[i].id, segments_[i].line);
+ throw nml_bad_segment(segments_[i].id);
}
}
// Check parent relationship is sound.
for (const auto& s: segments_) {
if (s.parent_id && !index_.count(*s.parent_id)) {
- throw nml_bad_segment(s.id, s.line); // No such parent id.
+ throw nml_bad_segment(s.id); // No such parent id.
}
}
@@ -251,12 +224,12 @@ struct neuroml_segment_tree {
}
else {
const auto& seg = segments_[depths.error().index];
- throw nml_cyclic_dependency(nl_to_string(seg.id), seg.line);
+ throw nml_cyclic_dependency(std::to_string(seg.id));
}
std::sort(segments_.begin(), segments_.end(), [](auto& a, auto& b) { return a.tdepth<b.tdepth; });
// Check for multiple roots:
- if (n_seg>1 && segments_[1].tdepth==0) throw nml_bad_segment(segments_[1].id, segments_[1].line);
+ if (n_seg>1 && segments_[1].tdepth==0) throw nml_bad_segment(segments_[1].id);
// Update index:
for (std::size_t i = 0; i<n_seg; ++i) {
@@ -285,11 +258,8 @@ static std::unordered_map<std::string, std::vector<non_negative>> evaluate_segme
// Expand subTree/path specifications:
for (auto& g: groups) {
- unsigned line = g.line;
try {
for (auto& subtree: g.subtrees) {
- line = subtree.line;
-
if (!subtree.from && !subtree.to) {
// Matches all segments:
for (auto& seg: segtree) {
@@ -326,7 +296,7 @@ static std::unordered_map<std::string, std::vector<non_negative>> evaluate_segme
}
}
catch (...) {
- throw nml_bad_segment_group(g.id, line);
+ throw nml_bad_segment_group(g.id);
}
}
@@ -334,7 +304,7 @@ static std::unordered_map<std::string, std::vector<non_negative>> evaluate_segme
std::unordered_map<std::string, std::size_t> index;
for (std::size_t i = 0; i<n_group; ++i) {
if (!index.insert({groups[i].id, i}).second) {
- throw nml_bad_segment_group(groups[i].id, groups[i].line);
+ throw nml_bad_segment_group(groups[i].id);
}
}
@@ -344,7 +314,7 @@ static std::unordered_map<std::string, std::vector<non_negative>> evaluate_segme
const auto& includes = groups[i].includes;
index_to_included_indices[i].reserve(includes.size());
for (auto& id: includes) {
- if (!index.count(id)) throw nml_bad_segment_group(groups[i].id, groups[i].line);
+ if (!index.count(id)) throw nml_bad_segment_group(groups[i].id);
index_to_included_indices[i].push_back(index.at(id));
}
}
@@ -358,7 +328,7 @@ static std::unordered_map<std::string, std::vector<non_negative>> evaluate_segme
}
else {
const auto& group = groups[depths.error().index];
- throw nml_cyclic_dependency(group.id, group.line);
+ throw nml_cyclic_dependency(group.id);
}
// Accumulate included group segments, following topological order.
@@ -396,7 +366,7 @@ static arb::stitched_morphology construct_morphology(const neuroml_segment_tree&
// Construct result from topologically sorted segments.
for (const auto& s: segtree) {
- arb::mstitch stitch(nl_to_string(s.id), s.distal);
+ arb::mstitch stitch(std::to_string(s.id), s.distal);
double along = s.along;
if (s.spherical) {
@@ -418,7 +388,7 @@ static arb::stitched_morphology construct_morphology(const neuroml_segment_tree&
}
if (s.parent_id) {
- builder.add(stitch, nl_to_string(s.parent_id.value()), along);
+ builder.add(stitch, std::to_string(s.parent_id.value()), along);
}
else {
builder.add(stitch);
@@ -428,57 +398,49 @@ static arb::stitched_morphology construct_morphology(const neuroml_segment_tree&
return arb::stitched_morphology(std::move(builder));
}
-nml_morphology_data nml_parse_morphology_element(xml_xpathctx ctx, xml_node morph, enum neuroml_options::values options) {
+nml_morphology_data nml_parse_morphology_element(const xml_node& morph,
+ enum neuroml_options::values options) {
using namespace neuroml_options;
nml_morphology_data M;
- M.id = propx<std::string>(morph, "id", ""s);
+ M.id = get_attr<std::string>(morph, "id");
std::vector<neuroml_segment> segments;
- // TODO: precompile xpath queries for nml:distal, nml:proximal, nml:parent.
- const char* q_parent = "./nml:parent";
- const char* q_proximal = "./nml:proximal";
- const char* q_distal = "./nml:distal";
+ const char* q_parent = "./parent";
+ const char* q_proximal = "./proximal";
+ const char* q_distal = "./distal";
- for (auto n: ctx.query(morph, "./nml:segment")) {
+ for (auto xn: morph.select_nodes("./segment")) {
+ auto n = xn.node();
neuroml_segment seg;
- int line = n.line(); // for error context!
-
try {
- seg.id = -1;
- seg.id = propx<non_negative>(n, "id");
- std::string name = propx<std::string>(n, "name", ""s);
-
- auto result = ctx.query(n, q_parent);
- if (!result.empty()) {
- line = result[0].line();
- seg.parent_id = propx<non_negative>(result[0], "segment");
- seg.along = propx<double>(result[0], "fractionAlong", 1.0);
+ seg.id = get_attr<unsigned>(n, "id");
+ auto name = get_attr<std::string>(n, "name", "");
+ auto parent = n.select_node(q_parent).node();
+ if (!parent.empty()) {
+ seg.parent_id = get_attr<unsigned>(parent, "segment");
+ seg.along = get_attr<double>(parent, "fractionAlong", 1.0);
}
- result = ctx.query(n, q_proximal);
- if (!result.empty()) {
- line = result[0].line();
- double x = propx<double>(result[0], "x");
- double y = propx<double>(result[0], "y");
- double z = propx<double>(result[0], "z");
- double diameter = propx<double>(result[0], "diameter");
- if (diameter<0) throw nml_bad_segment(seg.id, n.line());
-
+ auto prox = n.select_node(q_proximal).node();
+ if (!prox.empty()) {
+ double x = get_attr<double>(prox, "x");
+ double y = get_attr<double>(prox, "y");
+ double z = get_attr<double>(prox, "z");
+ double diameter = get_attr<double>(prox, "diameter");
+ if (diameter<0) throw nml_bad_segment(seg.id);
seg.proximal = arb::mpoint{x, y, z, diameter/2};
}
- if (!seg.parent_id && !seg.proximal) throw nml_bad_segment(seg.id, n.line());
-
- result = ctx.query(n, q_distal);
- if (!result.empty()) {
- line = result[0].line();
- double x = propx<double>(result[0], "x");
- double y = propx<double>(result[0], "y");
- double z = propx<double>(result[0], "z");
- double diameter = propx<double>(result[0], "diameter");
- if (diameter<0) throw nml_bad_segment(seg.id, n.line());
+ if (!seg.parent_id && !seg.proximal) throw nml_bad_segment(seg.id);
+ auto dist = n.select_node(q_distal).node();
+ if (!dist.empty()) {
+ double x = get_attr<double>(dist, "x");
+ double y = get_attr<double>(dist, "y");
+ double z = get_attr<double>(dist, "z");
+ double diameter = get_attr<double>(dist, "diameter");
+ if (diameter<0) throw nml_bad_segment(seg.id);
seg.distal = arb::mpoint{x, y, z, diameter/2};
// Set spherical flag if we have no parent, options has allow_spherical_root flag,
@@ -486,14 +448,12 @@ nml_morphology_data nml_parse_morphology_element(xml_xpathctx ctx, xml_node morp
seg.spherical = (options & allow_spherical_root) && !seg.parent_id && seg.proximal && seg.proximal.value()==seg.distal;
}
else {
- throw nml_bad_segment(seg.id, n.line());
+ throw nml_bad_segment(seg.id);
}
}
catch (nml_parse_error& e) {
- throw nml_bad_segment(seg.id, line);
+ throw nml_bad_segment(seg.id);
}
-
- seg.line = n.line();
segments.push_back(std::move(seg));
}
@@ -502,65 +462,53 @@ nml_morphology_data nml_parse_morphology_element(xml_xpathctx ctx, xml_node morp
// Compute tree now to save further parsing if something goes wrong.
neuroml_segment_tree segtree(std::move(segments));
- // TODO: precompile xpath queries for following:
- const char* q_member = "./nml:member";
- const char* q_include = "./nml:include";
- const char* q_path = "./nml:path";
- const char* q_from = "./nml:from";
- const char* q_to = "./nml:to";
- const char* q_subtree = "./nml:subTree";
+ const char* q_member = "./member";
+ const char* q_include = "./include";
+ const char* q_path = "./path";
+ const char* q_from = "./from";
+ const char* q_to = "./to";
+ const char* q_subtree = "./subTree";
std::vector<neuroml_segment_group_info> groups;
- for (auto n: ctx.query(morph, "./nml:segmentGroup")) {
+ for (auto xn: morph.select_nodes("./segmentGroup")) {
+ auto n = xn.node();
neuroml_segment_group_info group;
- int line = n.line(); // for error context!
-
try {
- group.id = propx<std::string>(n, "id");
- for (auto elem: ctx.query(n, q_member)) {
- line = elem.line();
- auto seg_id = propx<non_negative>(elem, "segment");
- if (!segtree.contains(seg_id)) throw nml_bad_segment_group(group.id, line);
- group.segments.push_back(propx<non_negative>(elem, "segment"));
+ group.id = get_attr<std::string>(n, "id");
+ for (auto xelem: n.select_nodes(q_member)) {
+ auto elem = xelem.node();
+ auto seg_id = get_attr<unsigned>(elem, "segment");;
+ if (!segtree.contains(seg_id)) throw nml_bad_segment_group(group.id);
+ group.segments.push_back(get_attr<unsigned>(elem, "segment"));
}
- for (auto elem: ctx.query(n, q_include)) {
- line = elem.line();
- group.includes.push_back(propx<std::string>(elem, "segmentGroup"));
+ for (auto xelem: n.select_nodes(q_include)) {
+ auto elem = xelem.node();
+ group.includes.push_back(get_attr<std::string>(elem, "segmentGroup"));
}
// Treat `<path>` and `<subTree>` identically:
- auto parse_subtree_elem = [&](auto& elem) {
- line = elem.line();
- auto froms = ctx.query(elem, q_from);
- auto tos = ctx.query(elem, q_to);
+ auto parse_subtree_elem = [&](const auto& elem) {
+ auto froms = elem.select_node(q_from).node();
+ auto tos = elem.select_node(q_to).node();
neuroml_segment_group_subtree sub;
- sub.line = line;
- if (!froms.empty()) {
- line = froms[0].line();
- sub.from = propx<non_negative>(froms[0], "segment");
- }
- if (!tos.empty()) {
- line = tos[0].line();
- sub.to = propx<non_negative>(tos[0], "segment");
- }
-
+ if (!froms.empty()) sub.from = get_attr<unsigned>(froms, "segment");
+ if (!tos.empty()) sub.to = get_attr<unsigned>(tos, "segment");
return sub;
};
- for (auto elem: ctx.query(n, q_path)) {
- group.subtrees.push_back(parse_subtree_elem(elem));
+ for (auto elem: n.select_nodes(q_path)) {
+ group.subtrees.push_back(parse_subtree_elem(elem.node()));
}
- for (auto elem: ctx.query(n, q_subtree)) {
- group.subtrees.push_back(parse_subtree_elem(elem));
+ for (auto elem: n.select_nodes(q_subtree)) {
+ group.subtrees.push_back(parse_subtree_elem(elem.node()));
}
}
catch (nml_parse_error& e) {
- throw nml_bad_segment_group(group.id, line);
+ throw nml_bad_segment_group(group.id);
}
- group.line = n.line();
groups.push_back(std::move(group));
}
@@ -586,7 +534,7 @@ nml_morphology_data nml_parse_morphology_element(xml_xpathctx ctx, xml_node morp
arb::region r;
auto ids = name_to_ids.equal_range(name);
for (auto i = ids.first; i!=ids.second; ++i) {
- r = join(std::move(r), M.segments.regions().at(nl_to_string(i->second)));
+ r = join(std::move(r), M.segments.regions().at(std::to_string(i->second)));
}
M.named_segments.set(name, std::move(r));
}
@@ -594,7 +542,7 @@ nml_morphology_data nml_parse_morphology_element(xml_xpathctx ctx, xml_node morp
for (const auto& [group_id, segment_ids]: M.group_segments) {
arb::region r;
for (auto id: segment_ids) {
- r = join(std::move(r), M.segments.regions().at(nl_to_string(id)));
+ r = join(std::move(r), M.segments.regions().at(std::to_string(id)));
}
M.groups.set(group_id, std::move(r));
}
diff --git a/arborio/nml_parse_morphology.hpp b/arborio/nml_parse_morphology.hpp
index 80e88a0594a52331caf6b316c7d577e9162729a4..eb185604cd767b638133d62cc4dcce3dd691bf84 100644
--- a/arborio/nml_parse_morphology.hpp
+++ b/arborio/nml_parse_morphology.hpp
@@ -1,10 +1,11 @@
#pragma once
#include <arborio/neuroml.hpp>
-#include "xmlwrap.hpp"
+
+#include <pugixml.hpp>
namespace arborio {
-nml_morphology_data nml_parse_morphology_element(xmlwrap::xml_xpathctx ctx, xmlwrap::xml_node morph, enum neuroml_options::values);
+nml_morphology_data nml_parse_morphology_element(const pugi::xml_node& morph, enum neuroml_options::values);
} // namespace arborio
diff --git a/arborio/xml.cpp b/arborio/xml.cpp
deleted file mode 100644
index 6e8a19e4a37722290405dc1e39e2dd6b2e928f87..0000000000000000000000000000000000000000
--- a/arborio/xml.cpp
+++ /dev/null
@@ -1,33 +0,0 @@
-#include <stdexcept>
-#include <string>
-
-#include <libxml/parser.h>
-
-#include <arborio/xml.hpp>
-
-// Implementations for exposed libxml2 interfaces.
-
-namespace arborio {
-
-xml_error::xml_error(const std::string& xml_error_msg, unsigned line):
- std::runtime_error(std::string("xml error: ") + (line? "line " + std::to_string(line): "") + xml_error_msg),
- xml_error_msg(xml_error_msg),
- line(line)
-{}
-
-with_xml::with_xml(): run_cleanup_(true) {
- // Initialize before any multithreaded access by library or client code.
- xmlInitParser();
-}
-
-with_xml::with_xml(with_xml&& other): run_cleanup_(other.run_cleanup_) {
- other.run_cleanup_ = false;
-}
-
-with_xml::~with_xml() {
- if (run_cleanup_) {
- xmlCleanupParser();
- }
-}
-
-} // namespace arborio
diff --git a/arborio/xml.hpp b/arborio/xml.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..2d0d3f3282eedbcdd9dd3d7741ca3f4394c8c806
--- /dev/null
+++ b/arborio/xml.hpp
@@ -0,0 +1,75 @@
+#pragma once
+
+#include <arborio/neuroml.hpp>
+
+#include <iostream>
+#include <string>
+#include <optional>
+
+#include <pugixml.hpp>
+
+namespace arborio {
+
+using xml_node = pugi::xml_node;
+using xml_doc = pugi::xml_document;
+
+template<typename T>
+T get_attr(const xml_node& n,
+ const std::string& a,
+ std::optional<T> d={}) {
+ auto attr = n.attribute(a.data());
+ if (attr.empty()) {
+ if (!d) throw nml_parse_error("Required attribute " + a + " is empty/absent.");
+ return *d;
+ }
+ std::string val = attr.value();
+ if constexpr (std::is_same_v<T, double>) {
+ return std::stod(val);
+ }
+ if constexpr (std::is_same_v<T, std::string>) {
+ return val;
+ }
+ if constexpr (std::is_unsigned_v<T>) {
+ std::size_t n = 0;
+ long long int i = std::stoull(val, &n);
+ // Either we didn't consume all chars -- eg 1.6 -- or we consumed all, but the result is negative.
+ // This _should_ be considered a bug in std::toull...
+ if (n != val.size() || i < 0) throw nml_parse_error("Couldn't parse unsigned integer: " + val);
+ return i;
+ }
+ throw std::runtime_error{"Not implemented"};
+}
+
+inline
+std::string xpath_escape(const std::string& x) {
+ auto npos = std::string::npos;
+ if (x.find_first_of("'")==npos) {
+ return "'"+x+"'";
+ }
+ else if (x.find_first_of("\"")==npos) {
+ return "\""+x+"\"";
+ }
+ else {
+ std::string r = "concat(";
+ std::string::size_type i = 0;
+ for (;;) {
+ auto j = x.find_first_of("'", i);
+ r += "'";
+ r.append(x, i, j==npos? j: j-i);
+ r += "'";
+ if (j==npos) break;
+ r += ",\"";
+ i = j+1;
+ j = x.find_first_not_of("'",i);
+ r.append(x, i, j==npos? j: j-i);
+ r += "\"";
+ if (j==npos) break;
+ r += ",";
+ i = j+1;
+ }
+ r += ")";
+ return r;
+ }
+}
+
+}
diff --git a/arborio/xmlwrap.cpp b/arborio/xmlwrap.cpp
deleted file mode 100644
index 6f791b2b922d4d34d1f498b014c9733c3093dd49..0000000000000000000000000000000000000000
--- a/arborio/xmlwrap.cpp
+++ /dev/null
@@ -1,128 +0,0 @@
-#include <cerrno>
-#include <charconv>
-#include <cstdarg>
-#include <cstddef>
-#include <cstdlib>
-#include <cstring>
-#include <limits>
-#include <locale>
-#include <sstream>
-#include <string>
-#include <vector>
-
-#include <libxml/xmlerror.h>
-
-#include "xmlwrap.hpp"
-
-namespace arborio {
-namespace xmlwrap {
-
-namespace detail {
-
-// Note: widely missing library support for floating point std::from_chars.
-
-template <typename V>
-bool from_cstr_(V& out, const char* s) {
- auto [p, ec] = std::from_chars(s, s+std::strlen(s), out);
- return ec==std::errc{} && !*p;
-}
-
-template <typename V>
-std::string nl_to_string_(const V& v, unsigned digits_estimate) {
- std::vector<char> digits(digits_estimate);
- for (;;) {
- if (auto [p, ec] = std::to_chars(digits.data(), digits.data()+digits.size(), v); ec == std::errc{}) {
- return std::string(digits.data(), p);
- }
-
- digits_estimate *= 2;
- digits.resize(digits_estimate);
- }
-}
-
-} // namespace detail
-
-
-bool nl_from_cstr(std::string& out, const char* content) {
- out = content;
- return true;
-}
-
-bool nl_from_cstr(long long& out, const char* content) {
- return detail::from_cstr_(out, content);
-}
-
-bool nl_from_cstr(non_negative& out, const char* content) {
- return detail::from_cstr_(out, content);
-}
-
-bool nl_from_cstr(double& out, const char* content) {
- // Note: library support is widely missing for floating point std::from_chars,
- // so can't just do:
- // return detail::from_cstr_(out, content);
- //
- // std::strtod() will use the current C locale, so that's out: anticipating the
- // decimal point character is a race condition.
-
- std::istringstream is{std::string(content)};
- is.imbue(std::locale::classic());
-
- double x;
- is >> x;
- if (!is || !is.eof()) return false;
- out = x;
- return true;
-}
-
-std::string nl_to_string(non_negative n) {
- return detail::nl_to_string_(n, std::numeric_limits<non_negative>::digits10);
-}
-
-std::string nl_to_string(long long n) {
- return detail::nl_to_string_(n, 1+std::numeric_limits<long long>::digits10);
-}
-
-void throw_on_xml_generic_error(void *, const char* msg, ...) {
- va_list va, vb;
- va_start(va, msg);
- va_copy(vb, va);
-
- int r = vsnprintf(nullptr, 0, msg, va);
- va_end(va);
-
- std::string err(r+1, '\0');
- vsnprintf(&err[0], err.size(), msg, vb);
- va_end(vb);
-
- 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 ::arborio::xml_error(msg, errp->line);
- }
-}
-
-xml_error_scope::xml_error_scope() {
- generic_handler_ = xmlGenericError;
- generic_context_ = xmlGenericErrorContext;
-
- structured_handler_ = xmlStructuredError;
- structured_context_ = xmlStructuredErrorContext;
-
- xmlSetGenericErrorFunc(nullptr, &throw_on_xml_generic_error);
- xmlSetStructuredErrorFunc((void*)this, &throw_on_xml_structured_error);
-}
-
-xml_error_scope::~xml_error_scope() {
- xmlGenericError = generic_handler_;
- xmlGenericErrorContext = generic_context_;
-
- xmlStructuredError = structured_handler_;
- xmlStructuredErrorContext = structured_context_;
-}
-
-} // namespace xmlwrap
-} // namespace arborio
diff --git a/arborio/xmlwrap.hpp b/arborio/xmlwrap.hpp
deleted file mode 100644
index a95942a9171af76700ace4b66d033a7ee377026c..0000000000000000000000000000000000000000
--- a/arborio/xmlwrap.hpp
+++ /dev/null
@@ -1,329 +0,0 @@
-#pragma once
-
-// RAII and iterator wrappers for some libxml2 objects.
-
-#include <any>
-#include <cstddef>
-#include <cstdlib>
-#include <memory>
-#include <optional>
-#include <string>
-#include <utility>
-
-#include <libxml/parser.h>
-#include <libxml/xpath.h>
-#include <libxml/xpathInternals.h>
-
-#include <arbor/util/expected.hpp>
-#include <arborio/xml.hpp>
-
-namespace arborio {
-namespace xmlwrap {
-
-struct bad_property {
- std::string error;
- unsigned line = 0;
-};
-
-// `non_negative` represents the corresponding constraint in the schema, which
-// can mean any arbitrarily large non-negtative integer value.
-//
-// A faithful representation would use an arbitrary-size 'big' integer or
-// a string, but for ease of implementation (and a bit more speed) we restrict
-// it to whatever we can fit in an unsigned long long.
-
-using non_negative = unsigned long long;
-
-// String wrappers around `to_chars` for attribute types we care about.
-// (`nl` is meant to stand for "no locale".)
-
-std::string nl_to_string(non_negative);
-std::string nl_to_string(long long);
-
-// Parse attribute content as the representation of a specific type.
-// Return true if successful.
-
-bool nl_from_cstr(std::string& out, const char* content);
-bool nl_from_cstr(non_negative& out, const char* content);
-bool nl_from_cstr(long long& out, const char* content);
-bool nl_from_cstr(double& out, const char* content);
-
-// Wrap xmlChar* NUL-terminated string that requires deallocation.
-
-struct xml_string {
- explicit xml_string(const xmlChar* p): p_(p, xml_string::deleter) {}
-
- operator const char*() const {
- return reinterpret_cast<const char*>(p_.get());
- }
-
-private:
- std::shared_ptr<const xmlChar> p_;
- static void deleter(const xmlChar* x) { xmlFree((void*)x); }
-};
-
-// Wrappers below are generally constructed with two arguments,
-// a pointer corresponding to the libxml2 object, and a dependency
-// object (typically shared_ptr<X> for some X) that guards the
-// lifetime of another object upon which this depends.
-
-template <typename XmlType>
-void trivial_dealloc(XmlType*) {}
-
-template <typename XmlType, void (*xml_dealloc)(XmlType *) = &trivial_dealloc<XmlType>>
-struct xml_base {
- xml_base(XmlType* p, std::any depends = {}):
- p_(p, xml_dealloc),
- depends_(std::move(depends))
- {}
-
-protected:
- // Access to raw wrapped pointer type.
- XmlType* get() const { return p_.get(); }
-
- // Copy of shared_ptr<> governing lifetime of referenced object.
- auto self() const { return p_; }
-
- // Copy of dependency object.
- std::any depends() const { return depends_; }
-
-private:
- std::shared_ptr<XmlType> p_;
- std::any depends_;
-};
-
-// xmlNode RAII wrapper (non-owning).
-
-struct xml_node: protected xml_base<xmlNode> {
- using base = xml_base<xmlNode>;
- explicit xml_node(xmlNode* p, std::any depends):
- base(p, std::move(depends))
- {}
-
- bool is_element() const { return get()->type==XML_ELEMENT_NODE; }
- bool is_attr() const { return get()->type==XML_ATTRIBUTE_NODE; }
- xml_string content() const { return xml_string(xmlNodeGetContent(get())); }
- unsigned line() const { return get()->line; }
-
- bool has_prop(const char* name) const { return xmlHasProp(get(), (const xmlChar*)name); }
-
- template <typename T>
- arb::util::expected<T, bad_property> prop(const char* name, std::optional<T> default_value = std::nullopt) const {
- using arb::util::unexpected;
-
- xmlChar* c = xmlGetProp(get(), (const xmlChar*)(name));
- if (!c) {
- if (default_value) return default_value.value();
- else return unexpected(bad_property{"missing required attribute", get()->line});
- }
-
- T v;
- if (nl_from_cstr(v, reinterpret_cast<const char*>(c))) return v;
- else return unexpected(bad_property{"attribute type error", get()->line});
- }
-
- using base::get; // (unsafe access)
-};
-
-// xmlNodeSet RAII wrapper; resource lifetime is governed by an xmlXPathObject.
-
-struct xml_nodeset: protected xml_base<xmlNodeSet> {
- using base = xml_base<xmlNodeSet>;
-
- xml_nodeset(): xml_nodeset(nullptr, std::any{}) {}
-
- xml_nodeset(xmlNodeSet* p, std::any depends):
- base(p, std::move(depends))
- {}
-
- struct iterator {
- using value_type = xml_node;
- using difference_type = std::ptrdiff_t;
- using reference = value_type; // yeah, not a real random access iterator
- using pointer = value_type*;
- using iterator_category = std::random_access_iterator_tag;
-
- explicit iterator(xmlNodePtr* p, const xml_nodeset* ns_ptr): p_(p), ns_ptr_(ns_ptr) {}
-
- bool operator==(iterator i) const { return p_==i.p_; }
- bool operator!=(iterator i) const { return p_!=i.p_; }
- bool operator<(iterator i) const { return p_<i.p_; }
- bool operator<=(iterator i) const { return p_<=i.p_; }
- bool operator>(iterator i) const { return p_>i.p_; }
- bool operator>=(iterator i) const { return p_>=i.p_; }
-
- reference operator*() const { return ns_ptr_->mk_xml_node(*p_); }
-
- struct ptr_proxy {
- xml_node inner_;
- const xml_node* operator->() const { return &inner_; }
- };
- ptr_proxy operator->() const { return ptr_proxy{ns_ptr_->mk_xml_node(*p_)}; }
-
- iterator& operator++() { return ++p_, *this; }
- iterator operator++(int) {
- iterator x(*this);
- return ++p_, x;
- }
-
- iterator& operator--() { return --p_, *this; }
- iterator operator--(int) {
- iterator x(*this);
- return --p_, x;
- }
-
- iterator& operator+=(ptrdiff_t n) { return p_ += n, *this; }
- iterator& operator-=(ptrdiff_t n) { return p_ -= n, *this; }
- reference operator[](ptrdiff_t n) { return *(*this+n); }
-
- iterator operator+(ptrdiff_t n) {
- iterator i(*this);
- return i += n;
- }
- friend iterator operator+(ptrdiff_t n, iterator i) { return i+n; }
-
- iterator operator-(ptrdiff_t n) {
- iterator i(*this);
- return i -= n;
- }
- friend iterator operator-(ptrdiff_t n, iterator i) { return i-n; }
-
- ptrdiff_t operator=(iterator i) { return p_-i.p_; }
-
- private:
- xmlNode** p_;
- const xml_nodeset* ns_ptr_;
- };
-
- iterator begin() const { return iterator{get()? get()->nodeTab: nullptr, this}; }
- iterator end() const { return iterator{get()? get()->nodeTab+get()->nodeNr: nullptr, this}; }
-
- iterator::reference operator[](int i) const { return begin()[i]; }
- std::size_t size() const { return get()? get()->nodeNr: 0u; }
- bool empty() const { return size()==0u; }
-
-private:
- // Construct xml_node wrapper with the same lifetime dependency as this node set.
- xml_node mk_xml_node(xmlNode* p) const {
- return xml_node{p, depends()};
- }
-};
-
-// xmlPathObj RAII wrapper; lifetime of xmlPathObj governs lifetime of node set.
-
-struct xml_xpathobj: protected xml_base<xmlXPathObject, xmlXPathFreeObject> {
- using base = xml_base<xmlXPathObject, xmlXPathFreeObject>;
-
- explicit xml_xpathobj(xmlXPathObject* p, std::any depends):
- base(p, std::move(depends))
- {}
-
- xml_nodeset nodes() {
- return get()->type==XPATH_NODESET? xml_nodeset{get()->nodesetval, self()}: xml_nodeset{};
- }
-};
-
-// xmlXPathContext RAII wrapper.
-
-struct xml_xpathctx: protected xml_base<xmlXPathContext, xmlXPathFreeContext> {
- using base = xml_base<xmlXPathContext, xmlXPathFreeContext>;
-
- explicit xml_xpathctx(xmlXPathContext* p, std::any depends):
- base(p, std::move(depends))
- {}
-
- void register_ns(const char* ns, const char* uri) {
- xmlXPathRegisterNs(get(), (const xmlChar*)ns, (const xmlChar*)uri);
- }
-
- xml_nodeset query(const char* q) {
- return xml_xpathobj{xmlXPathEvalExpression((xmlChar*)q, get()), self()}.nodes();
- }
- xml_nodeset query(const std::string& q) { return query(q.c_str()); }
-
- xml_nodeset query(xml_node context, const char* q) {
- return xml_xpathobj{xmlXPathNodeEval(context.get(), (xmlChar*)q, get()), self()}.nodes();
- }
- xml_nodeset query(xml_node context, const std::string& q) { return query(std::move(context), q.c_str()); }
-};
-
-// xmlDoc RAII wrapper.
-
-struct xml_doc: protected xml_base<xmlDoc, xmlFreeDoc> {
- using base = xml_base<xmlDoc, xmlFreeDoc>;
-
- xml_doc(): xml_doc(nullptr) {}
-
- explicit xml_doc(std::string the_doc):
- // 'Pretty sure' we don't need to keep the string after the tree is built. Pretty sure.
- xml_doc(xmlReadMemory(the_doc.c_str(), the_doc.length(), "", nullptr, xml_options))
- {}
-
- // TODO: (... add other ctors ...)
-
- friend xml_xpathctx xpath_context(const xml_doc& doc) {
- return xml_xpathctx{xmlXPathNewContext(doc.get()), doc.self()};
- }
-
- explicit operator bool() const { return get(); }
-
-private:
- explicit xml_doc(xmlDoc* p): base(p) {}
- static constexpr int xml_options = XML_PARSE_NOENT | XML_PARSE_NONET;
-};
-
-// Escape a string for use as string expression within an XPath expression.
-
-inline std::string xpath_escape(const std::string& x) {
- auto npos = std::string::npos;
- if (x.find_first_of("'")==npos) {
- return "'"+x+"'";
- }
- else if (x.find_first_of("\"")==npos) {
- return "\""+x+"\"";
- }
- else {
- std::string r = "concat(";
- std::string::size_type i = 0;
- for (;;) {
- auto j = x.find_first_of("'", i);
- r += "'";
- r.append(x, i, j==npos? j: j-i);
- r += "'";
- if (j==npos) break;
- r += ",\"";
- i = j+1;
- j = x.find_first_not_of("'",i);
- r.append(x, i, j==npos? j: j-i);
- r += "\"";
- if (j==npos) break;
- r += ",";
- i = j+1;
- }
- r += ")";
- return r;
- }
-}
-
-// Error management:
-//
-// Use xml_error_scope to catch libxml2 warnings and errors. The
-// xml_error_scope object will restore the original error handling
-// behaviour on destruction.
-//
-// Errors are turned into arborio::xml_error exceptions and thrown,
-// while warnings are ignored (libxml2 warnings are highly innocuous).
-
-struct xml_error_scope {
- xml_error_scope();
- ~xml_error_scope();
-
- xmlGenericErrorFunc generic_handler_;
- void* generic_context_;
-
- xmlStructuredErrorFunc structured_handler_;
- void* structured_context_;
-};
-
-} // namespace xmlwrap
-} // namespace arborio
diff --git a/doc/contrib/dependency-management.rst b/doc/contrib/dependency-management.rst
index e36ad2e2b19ebef829193f0f31a4316c97d1068c..ad783e269266770cfee855800a93129e14cc79ac 100644
--- a/doc/contrib/dependency-management.rst
+++ b/doc/contrib/dependency-management.rst
@@ -7,7 +7,7 @@ Arbor relies on a (small) number of dependencies. We can distinguish three kinds
0. Source management dependencies: Git.
1. Build dependencies. E.g. CMake, compilers like GCC or CUDA.
-2. Linking dependencies. E.g. MPI, libxml2.
+2. Linking dependencies. E.g. MPI.
3. Source dependencies. These are present as `git submodules <https://git-scm.com/docs/git-submodule>`_ or as copy in ``ext/``. Their use is optional: users who need integration with their package manager (e.g. apt, spack, yum) can link to those versions instead.
Note that the actual dependencies of your build configuration may vary.
diff --git a/doc/cpp/morphology.rst b/doc/cpp/morphology.rst
index 68e7e9f1f34d0e337d19cd9aa1ab7f5ef914e995..1de631528ce54e847e352191eebd316557a7533f 100644
--- a/doc/cpp/morphology.rst
+++ b/doc/cpp/morphology.rst
@@ -579,39 +579,8 @@ NeuroML
-------
Arbor offers limited support for models described in `NeuroML version 2
-<https://neuroml.org/neuromlv2>`_. This is not built by default, but can be
-enabled by providing the `-DARB_WITH_NEUROML=ON` argument to CMake at configuration
-time (see :ref:`install-neuroml`). This will build the ``arborio`` libray with
-neuroml support.
-
-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 ``arborio`` library are provided in
-the ``arborio`` namespace.
-
-Libxml2 interface
-^^^^^^^^^^^^^^^^^
-
-Libxml2 offers threadsafe XML parsing, but not by default. If 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.
-
-``arborio`` provides a helper guard object for this purpose, defined
-in ``arborio/xml.hpp``:
-
-.. cpp:namespace:: arborio
-
-.. cpp:class:: with_xml
-
- An RAII guard object that calls ``xmlInitParser()`` upon construction, and
- ``xmlCleanupParser()`` upon destruction. The constructor takes no parameters.
-
-Unhandleable exceptions from ``libxml2`` are forwarded via an exception
-``xml_error``, derived from ``std::runtime_error``.
+<https://neuroml.org/neuromlv2>`_. All classes and functions provided by the
+``arborio`` library are provided in the ``arborio`` namespace.
NeuroML2 morphology support
^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -624,7 +593,7 @@ An implementation limitation restricts valid segment id values to
those which can be represented by an ``unsigned long long`` value.
``arborio::neuroml`` methods can throw an ``arborio::xml_error`` in the instance that
-the underlying libxml2 library reports a problem that cannot be handled by the ``arborio``
+the underlying XML library reports a problem that cannot be handled by the ``arborio``
library. Otherwise, exceptions derived from ``aborio::neuroml_exception`` can be thrown
when encountering problems interpreting the NeuroML document (see :ref:`cppneuromlexceptions` below).
diff --git a/doc/dependencies.csv b/doc/dependencies.csv
index 09b3f141c6a89ddaff1f8f4aaf24b723ab7f0faf..72a5c296d62fe67f724deb277f6a8f505d945197 100644
--- a/doc/dependencies.csv
+++ b/doc/dependencies.csv
@@ -8,13 +8,13 @@ Build option/target,Tool name,Minimum version,Notes,Update criteria
--,Apple Clang,11,Apple LLVM version 11.0.0 (clang-1100.0.33.8),
ARB_GPU,Hip Clang,ROCm 3.9,HIP support is currently experimental.,
ARB_GPU,CUDA,11.0,,"* It is available on all of the target HPC systems (Piz Daint, Juwels Booster)"
-ARB_WITH_NEUROML,libxml2,,,
ARB_WITH_MPI,MPI,,Many MPI implementations are supported.,
"ARB_WITH_MPI, ARB_WITH_PYTHON ",mpi4py,3.1.0,Minimum version depends on compatiblity with your Python and MPI versions. 3.1.0 is the first release to support Python > 3.8.,
html, .. literalinclude:: ../requirements.txt,,See ``doc/requirements.txt``,
unit,googletest,,submodule ``ext/gtest.*``,
bench,Google-benchmark,,submodule ``ext/google-benchmark``,
--,json,,submodule ``ext/json``,
+--,pugi,,submodule ``ext/pugixml``,
--,random123,,submodule ``ext/random123``,
--,fmt,,submodule ``ext/fmt``,
--,tinyopt,,source copy ``ext/tinyopt``,
diff --git a/doc/fileformat/neuroml.rst b/doc/fileformat/neuroml.rst
index ba91b3f9c7ac8524477d07a4a15a4e155252379e..f919e27e9f5331f80197392a02d9415f74698ff3 100644
--- a/doc/fileformat/neuroml.rst
+++ b/doc/fileformat/neuroml.rst
@@ -8,12 +8,10 @@ NeuroML2
"NeuroML2", "``nml``", "✓", "✗"
-Arbor offers limited support for models described in `NeuroML version 2 <https://neuroml.org/neuromlv2>`_.
-This is not built by default (see :ref:`NeuroML support <install-neuroml>` for instructions on how
-to build Arbor with NeuroML).
-
-Once support is enabled, Arbor is able to parse and check the validity of morphologies described in NeuroML files,
-and present the encoded data to the user. This is more than a simple `segment tree`.
+Arbor offers limited support for models described in `NeuroML version 2
+<https://neuroml.org/neuromlv2>`_. Arbor is able to parse and check the validity
+of morphologies described in NeuroML files, and present the encoded data to the
+user. This is more than a simple `segment tree`.
NeuroML can encode in the same file multiple top-level morphologies, as well as cells:
diff --git a/doc/install/build_install.rst b/doc/install/build_install.rst
index a3c964ed57ba319aa9a5727b95efd57f4bfd7e27..c83e57a4c90f1dfb7dda96ecfa201ba58c05011b 100644
--- a/doc/install/build_install.rst
+++ b/doc/install/build_install.rst
@@ -148,11 +148,9 @@ Python package is recommended. See :ref:`install-python` for more information.
NeuroML
~~~~~~~
-Arbor supports reading cell morphologies defined in NeuroML version 2 through
-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.
+Arbor supports reading cell morphologies defined in NeuroML version 2 through an
+additional support library ``arborio``. See :ref:`install-neuroml` for more
+information.
Boost
~~~~~
@@ -534,14 +532,9 @@ NeuroML support
---------------
Arbor has limited support for NeuroML version 2 through an additional library
-``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.
-
-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:
+``arborio``. 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. For example:
.. code-block:: bash
diff --git a/doc/install/python.rst b/doc/install/python.rst
index 10f1d279a4e175335910d94689060cc0598e6b93..2f18d59d2486686c4415e81443da9aa7a58484ec 100644
--- a/doc/install/python.rst
+++ b/doc/install/python.rst
@@ -42,9 +42,9 @@ You are now ready to use Arbor! You can continue reading these documentation pag
for any other platforms than listed above, ``pip`` will attempt a build from source and thus require these
packages as well.
- * Ubuntu/Debian: ``git cmake gcc python3-dev python3-pip libxml2-dev``
- * Fedora/CentOS/OpenSuse: ``git cmake gcc-c++ python3-devel python3-pip libxml2-devel``
- * MacOS: get ``brew`` `here <https://brew.sh>`_ and run ``brew install cmake clang python3 libxml2``
+ * Ubuntu/Debian: ``git cmake gcc python3-dev python3-pip``
+ * Fedora/CentOS/OpenSuse: ``git cmake gcc-c++ python3-devel python3-pip``
+ * MacOS: get ``brew`` `here <https://brew.sh>`_ and run ``brew install cmake clang python3``
* Windows: the simplest way is to use `WSL <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_ and then follow the instructions for Ubuntu.
.. _in_python_custom:
@@ -89,8 +89,6 @@ where you place the arguments separated by space inside the quotes.
The following flags can be used to configure the installation:
-* ``ARB_WITH_NEUROML=<ON|OFF>``: Enable support for NeuroML2 morphologies,
- requires ``libxml2`` library. Default ``OFF``
* ``ARB_WITH_MPI=<ON|OFF>``: Enable MPI support, requires MPI library. Default
``OFF``. If you intend to use ``mpi4py``, you need to install the package before
building Arbor, as binding it requires access to its headers.
diff --git a/doc/python/hardware.rst b/doc/python/hardware.rst
index af51f6b2b1d5f6ef2af7a9372f905840dcece4e4..ecfa7ca8cf9fef289ba1771fea0a7f28f31b0a10 100644
--- a/doc/python/hardware.rst
+++ b/doc/python/hardware.rst
@@ -27,7 +27,6 @@ Helper functions for checking cmake or environment variables, as well as configu
* ``ARB_GPU_ENABLED``
* ``ARB_VECTORIZE``
* ``ARB_WITH_PROFILING``
- * ``ARB_WITH_NEUROML``
* ``ARB_USE_BUNDLED_LIBS``
* ``ARB_VERSION``
* ``ARB_ARCH``
@@ -39,7 +38,7 @@ Helper functions for checking cmake or environment variables, as well as configu
import arbor
arbor.config()
- {'mpi': True, 'mpi4py': True, 'gpu': False, 'vectorize': True, 'profiling': True, 'neuroml': True, 'bundled': True, 'version': '0.5.3-dev', 'arch': 'native'}
+ {'mpi': True, 'mpi4py': True, 'gpu': False, 'vectorize': True, 'profiling': True, 'bundled': True, 'version': '0.5.3-dev', 'arch': 'native'}
.. function:: mpi_init()
diff --git a/ext/pugixml b/ext/pugixml
new file mode 160000
index 0000000000000000000000000000000000000000..08b3433180727ea2f78fe02e860a08471db1e03c
--- /dev/null
+++ b/ext/pugixml
@@ -0,0 +1 @@
+Subproject commit 08b3433180727ea2f78fe02e860a08471db1e03c
diff --git a/pyproject.toml b/pyproject.toml
index 3c897394adc3dbc33c6b2d2263844a6b67c77536..ec34cf9a3399404c62397914ee35c5eb75e23b88 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -71,9 +71,7 @@ MACOSX_DEPLOYMENT_TARGET = "10.15"
[tool.cibuildwheel.linux]
archs = ["x86_64"]
manylinux-x86_64-image = "manylinux2014"
-before-all = "yum -y install libxml2-devel"
repair-wheel-command = "auditwheel repair -w {dest_dir} {wheel} && python3 /project/scripts/patchwheel.py {dest_dir}"
[[tool.cibuildwheel.overrides]]
select = "*-musllinux*"
-before-all = "apk add libxml2-dev"
diff --git a/python/config.cpp b/python/config.cpp
index 62d604eeb873627e4908745a4efa40435562e399..c692ee2e5914955df8b51b6b1486114dcae9cf62 100644
--- a/python/config.cpp
+++ b/python/config.cpp
@@ -46,11 +46,7 @@ pybind11::dict config() {
#else
dict[pybind11::str("profiling")] = pybind11::bool_(false);
#endif
-#ifdef ARB_NEUROML_ENABLED
dict[pybind11::str("neuroml")] = pybind11::bool_(true);
-#else
- dict[pybind11::str("neuroml")] = pybind11::bool_(false);
-#endif
#ifdef ARB_BUNDLED_ENABLED
dict[pybind11::str("bundled")] = pybind11::bool_(true);
#else
diff --git a/python/morphology.cpp b/python/morphology.cpp
index b0ba4367455d733bb50810ef410f2ca214d55ec6..a344b066b19f7795e81ff4ce80bcd265806026af 100644
--- a/python/morphology.cpp
+++ b/python/morphology.cpp
@@ -16,10 +16,7 @@
#include <arborio/label_parse.hpp>
#include <arborio/swcio.hpp>
#include <arborio/neurolucida.hpp>
-
-#ifdef ARB_NEUROML_ENABLED
#include <arborio/neuroml.hpp>
-#endif
#include "util.hpp"
#include "error.hpp"
@@ -388,8 +385,6 @@ void register_morphology(py::module& m) {
pybind11::arg_v("raw", false, "Return a segment tree instead of a fully formed morphology"),
"Load a morphology or segment_tree and meta data from a Neurolucida ASCII .asc file.");
-
-#ifdef ARB_NEUROML_ENABLED
// arborio::morphology_data
py::class_<arborio::nml_morphology_data> nml_morph_data(m, "neuroml_morph_data");
nml_morph_data
@@ -473,7 +468,6 @@ void register_morphology(py::module& m) {
}
}, "cell_id"_a, "allow_spherical_root"_a=false,
"Retrieve nml_morph_data associated with cell_id.");
-#endif // def ARB_NEUROML_ENABLED
}
} // namespace pyarb
diff --git a/scripts/build-wheels.sh b/scripts/build-wheels.sh
index 4b6412da948b8ce2191980cc375f977870b35194..2032822dd83c2ca79b055a31f8032de75f7e7991 100755
--- a/scripts/build-wheels.sh
+++ b/scripts/build-wheels.sh
@@ -13,8 +13,6 @@
set -e -u -x
-yum -y install libxml2-devel
-
rm -rf /src_dir/arbor/_skbuild
rm -rf /opt/python/cp36-cp36m # Python build toolchain does not work on Py3.6
diff --git a/scripts/patchwheel.py b/scripts/patchwheel.py
index c1c6ed46a65186509c54bfe864da6e24ff910a1f..21d3314bcdd972363d823d86e98571d9aafe8964 100644
--- a/scripts/patchwheel.py
+++ b/scripts/patchwheel.py
@@ -40,11 +40,9 @@ for inwheel in parsed_args.path.glob("*.whl"):
subprocess.check_call(f"unzip {inwheel} -d {zipdir}", shell=True)
arborn = list(zipdir.glob("**/_arbor.cpython*.so"))[0]
- libxml2n = list(zipdir.glob("**/libxml2*.so*"))[0]
subprocess.check_call(
f"patchelf --set-rpath '$ORIGIN/../arbor.libs' {arborn}", shell=True
)
- subprocess.check_call(f"patchelf --set-rpath '$ORIGIN' {libxml2n}", shell=True)
# TODO? correct checksum/bytecounts in *.dist-info/RECORD.
# So far, Python does not report mismatches
diff --git a/setup.py b/setup.py
index 30f9ed589d923cfb63b839faa9aff9ffd2484cc5..7e93e6bf98afea2813dffd888cb655a6ec4549e1 100644
--- a/setup.py
+++ b/setup.py
@@ -8,7 +8,6 @@ with_mpi = False
with_gpu = "none"
with_vec = False
arch = "none"
-with_nml = True
use_libs = True
build_type = "Release" # this is ok even for debugging, as we always produce info
@@ -20,7 +19,6 @@ setup(
f"-DARB_VECTORIZE={with_vec}",
f"-DARB_ARCH={arch}",
f"-DARB_GPU={with_gpu}",
- f"-DARB_WITH_NEUROML={with_nml}",
f"-DARB_USE_BUNDLED_LIBS={use_libs}",
f"-DCMAKE_BUILD_TYPE={build_type}",
],
diff --git a/spack/package.py b/spack/package.py
index 7d8c3a10c16a09439d60e6a104a59b32b0f4cc43..2cf738397b1e4979b241d94d69fe81675b6db282 100644
--- a/spack/package.py
+++ b/spack/package.py
@@ -44,7 +44,6 @@ class Arbor(CMakePackage, CudaPackage):
)
variant("doc", default=False, description="Build documentation.")
variant("mpi", default=False, description="Enable MPI support")
- variant("neuroml", default=True, description="Build NeuroML support library.")
variant("python", default=True, description="Enable Python frontend support")
variant(
"vectorize",
@@ -70,9 +69,9 @@ class Arbor(CMakePackage, CudaPackage):
# misc dependencies
depends_on("fmt@7.1:", when="@0.5.3:") # required by the modcc compiler
depends_on("fmt@9.1:", when="@0.7.1:")
+ depends_on("pugixml@1.11:", when="@0.7.1:")
depends_on("nlohmann-json")
depends_on("random123")
- depends_on("libxml2", when="+neuroml")
with when("+cuda"):
depends_on("cuda@10:")
depends_on("cuda@11:", when="@0.7.1:")
@@ -103,7 +102,6 @@ class Arbor(CMakePackage, CudaPackage):
args = [
self.define_from_variant("ARB_WITH_ASSERTIONS", "assertions"),
self.define_from_variant("ARB_WITH_MPI", "mpi"),
- self.define_from_variant("ARB_WITH_NEUROML", "neuroml"),
self.define_from_variant("ARB_WITH_PYTHON", "python"),
self.define_from_variant("ARB_VECTORIZE", "vectorize"),
]
diff --git a/test/unit/CMakeLists.txt b/test/unit/CMakeLists.txt
index 360028f217068ba31da21a905fbc11dfaa8caecb..560045491612534ae3949e5e1d19682bd243a490 100644
--- a/test/unit/CMakeLists.txt
+++ b/test/unit/CMakeLists.txt
@@ -153,6 +153,9 @@ set(unit_sources
mech_private_field_access.cpp
stats.cpp
unit_test_catalogue.cpp
+
+ # neuroml
+ test_nml_morphology.cpp
)
if(ARB_WITH_GPU)
@@ -170,10 +173,6 @@ if(ARB_WITH_GPU)
)
endif()
-if(ARB_WITH_NEUROML)
- list(APPEND unit_sources test_nml_morphology.cpp)
-endif()
-
if(ARB_WITH_CUDA_CLANG OR ARB_WITH_HIP_CLANG)
set_source_files_properties(${unit_sources} PROPERTIES LANGUAGE CXX)
endif()
diff --git a/test/unit/test_nml_morphology.cpp b/test/unit/test_nml_morphology.cpp
index 07b1d2678dbcb4cfef4d60d5a4b46eba2c4a2c1d..8c6ecfc039959a3846a4cd50c671107099fc8780 100644
--- a/test/unit/test_nml_morphology.cpp
+++ b/test/unit/test_nml_morphology.cpp
@@ -7,29 +7,18 @@
#include <arbor/morph/primitives.hpp>
#include <arborio/neuroml.hpp>
-#include <arborio/xml.hpp>
#include <gtest/gtest.h>
#include "morph_pred.hpp"
using testing::region_eq;
-TEST(neuroml, with_xml) {
- // This (hopefully) will not blow up.
- {
- arborio::with_xml scope;
- }
- {
- arborio::with_xml scope;
- }
-}
-
// Tests for basic morphology scanning and collection from XML.
TEST(neuroml, morph_badxml) {
std::string illformed = "<wha?";
- EXPECT_THROW(arborio::neuroml{illformed}, arborio::xml_error);
+ EXPECT_THROW(arborio::neuroml{illformed}, std::runtime_error);
}
TEST(neuroml, morph_none) {
@@ -176,7 +165,7 @@ R"~(
arborio::neuroml N(doc);
{
- arborio::nml_morphology_data m1 = N.morphology("m1").value();
+ auto m1 = N.morphology("m1").value();
label_dict labels;
labels.import(m1.segments, "seg:");
mprovider P(m1.morphology, labels);
@@ -275,6 +264,7 @@ R"~(
EXPECT_EQ(p3, seg1_segments[0].dist);
}
}
+
}
TEST(neuroml, spherical_segments) {
diff --git a/test/unit/test_strprintf.cpp b/test/unit/test_strprintf.cpp
index 2449e8d69740859747982afbb5b54083648286d8..6da58abaaf36430ca2283d51d33ca8e9922c2457 100644
--- a/test/unit/test_strprintf.cpp
+++ b/test/unit/test_strprintf.cpp
@@ -14,12 +14,12 @@ TEST(strprintf, simple) {
char buf[200];
const char* fmt1 = " %% %04d % 3.2f %#016x %c";
- sprintf(buf, fmt1, 3, 7.1e-3, 0x1234ul, 'x');
+ snprintf(buf, 200, fmt1, 3, 7.1e-3, 0x1234ul, 'x');
auto result = strprintf(fmt1, 3, 7.1e-3, 0x1234ul, 'x');
EXPECT_EQ(std::string(buf), result);
const char* fmt2 = "%5s %3s";
- sprintf(buf, fmt2, "bear", "pear");
+ snprintf(buf, 200, fmt2, "bear", "pear");
result = strprintf(fmt2, "bear", "pear");
EXPECT_EQ(std::string(buf), result);
}
@@ -51,12 +51,12 @@ TEST(strprintf, wrappers) {
char buf[200];
auto uptr = std::unique_ptr<int>{new int(17)};
- sprintf(buf, "uptr %p", uptr.get());
+ snprintf(buf, 200, "uptr %p", uptr.get());
EXPECT_EQ(std::string(buf), strprintf("uptr %p", uptr));
auto sptr = std::shared_ptr<double>{new double(19.)};
- sprintf(buf, "sptr %p", sptr.get());
+ snprintf(buf, 200, "sptr %p", sptr.get());
EXPECT_EQ(std::string(buf), strprintf("sptr %p", sptr));