From ba2dfe98c9f8e9b67ca0f896344f6be9fefc221a Mon Sep 17 00:00:00 2001
From: Luc Grosheintz <luc.grosheintz@gmail.com>
Date: Mon, 11 Nov 2024 10:04:43 +0100
Subject: [PATCH 1/2] Update `highfive@3.0.0-beta1`.

---
 3rdparty/HighFive | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/3rdparty/HighFive b/3rdparty/HighFive
index 4a326f35..9cbd8349 160000
--- a/3rdparty/HighFive
+++ b/3rdparty/HighFive
@@ -1 +1 @@
-Subproject commit 4a326f350d93d5847368105f840a1bd7e4094969
+Subproject commit 9cbd8349b24c6225f001187cd4d2b2c052b8ffe3

From 667d240bebb2af2f358d1a58f7a8e6787cb931fa Mon Sep 17 00:00:00 2001
From: Luc Grosheintz <luc.grosheintz@gmail.com>
Date: Mon, 11 Nov 2024 10:33:39 +0100
Subject: [PATCH 2/2] Modernize HighFive usage.

---
 src/readers/morphologyHDF5.cpp        | 12 ++----------
 src/readers/vasculatureHDF5.cpp       |  7 ++-----
 tests/test_vasculature_morphology.cpp |  4 +---
 3 files changed, 5 insertions(+), 18 deletions(-)

diff --git a/src/readers/morphologyHDF5.cpp b/src/readers/morphologyHDF5.cpp
index fc6a3725..c285a706 100644
--- a/src/readers/morphologyHDF5.cpp
+++ b/src/readers/morphologyHDF5.cpp
@@ -194,11 +194,7 @@ void MorphologyHDF5::_readPoints(int firstSectionOffset) {
                            "': incorrect number of columns for points");
     }
 
-    std::vector<std::array<floatType, pointColumns>> hdf5Data(numberPoints);
-
-    if (!hdf5Data.empty()) {
-        pointsDataSet.read(hdf5Data.front().data());
-    }
+    auto hdf5Data = pointsDataSet.read<std::vector<std::array<floatType, pointColumns>>>();
 
     const bool hasSoma = firstSectionOffset != 0;
     const bool hasNeurites = static_cast<size_t>(firstSectionOffset) < numberPoints;
@@ -252,11 +248,7 @@ int MorphologyHDF5::_readSections() {
                            " bad number of dimensions in 'structure' dataspace"));
     }
 
-    std::vector<std::array<int, structureV1Columns>> vec(dims[0]);
-    if (dims[0] > 0) {
-        structure.read(vec.front().data());
-    }
-
+    auto vec = structure.read<std::vector<std::array<int, structureV1Columns>>>();
     assert(!vec.empty());
 
     bool hasSoma = true;
diff --git a/src/readers/vasculatureHDF5.cpp b/src/readers/vasculatureHDF5.cpp
index deb6ea34..8b97a74b 100644
--- a/src/readers/vasculatureHDF5.cpp
+++ b/src/readers/vasculatureHDF5.cpp
@@ -81,9 +81,7 @@ void VasculatureHDF5::_readSections() {
     auto& sections = _properties.get_mut<vasculature::property::VascSection>();
     auto selection = _sections->select({0, 0}, {_sectionsDims[0], 1});
 
-    std::vector<unsigned int> vec;
-    vec.resize(_sectionsDims[0]);
-    selection.read(vec);
+    auto vec = selection.squeezeMemSpace({1}).read<std::vector<unsigned int>>();
 
     for (auto p : vec) {
         sections.push_back(p);
@@ -94,8 +92,7 @@ void VasculatureHDF5::_readSectionTypes() {
     auto& types = _properties.get_mut<vasculature::property::SectionType>();
 
     auto selection = _sections->select({0, 1}, {_sectionsDims[0], 1});
-    types.resize(_sectionsDims[0]);
-    selection.read(types);
+    selection.squeezeMemSpace({1}).read(types);
     for (int type : types) {
         if (type > SECTION_CUSTOM || type < 0) {
             const auto err = details::ErrorMessages(_uri);
diff --git a/tests/test_vasculature_morphology.cpp b/tests/test_vasculature_morphology.cpp
index 3a3ac08a..3b854e1e 100644
--- a/tests/test_vasculature_morphology.cpp
+++ b/tests/test_vasculature_morphology.cpp
@@ -59,9 +59,7 @@ TEST_CASE("vasculature_section_connectivity", "[vasculature]") {
 
     REQUIRE(section_connectivity.size() == n_connections);
 
-    std::vector<std::array<unsigned int, 2>> expected_connectivity(n_connections);
-
-    dset.read(expected_connectivity.front().data());
+    auto expected_connectivity = dset.read<std::vector<std::array<unsigned int, 2>>>();
 
     REQUIRE(section_connectivity == expected_connectivity);
 }