From 4d6fd6ac819ba543a8564c0a860ff4e456861b46 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nadir=20Rom=C3=A1n=20Guerrero?=
 <NadirRoGue@users.noreply.github.com>
Date: Tue, 13 Jun 2023 14:26:27 +0200
Subject: [PATCH] BRAYNS 550 - Update libsonata and morphio dependencies
 (#1184)

---
 .gitlab-ci.viz.yml                            |  1 +
 .../api/circuit/MorphologyCircuitBuilder.cpp  | 14 --------
 plugins/deps/CMakeLists.txt                   | 35 +++++++++++++++----
 3 files changed, 29 insertions(+), 21 deletions(-)

diff --git a/.gitlab-ci.viz.yml b/.gitlab-ci.viz.yml
index 149f567be..5fcaacdb9 100644
--- a/.gitlab-ci.viz.yml
+++ b/.gitlab-ci.viz.yml
@@ -4,6 +4,7 @@ stages:
 
 include:
   - project: viz/ci/gitlabpipelines
+    ref: update_cpp_ubuntu_version
     file: index.yml
 
 ubuntu-clangformat-check:
diff --git a/plugins/CircuitExplorer/api/circuit/MorphologyCircuitBuilder.cpp b/plugins/CircuitExplorer/api/circuit/MorphologyCircuitBuilder.cpp
index d111b6df2..17f7b934d 100644
--- a/plugins/CircuitExplorer/api/circuit/MorphologyCircuitBuilder.cpp
+++ b/plugins/CircuitExplorer/api/circuit/MorphologyCircuitBuilder.cpp
@@ -72,17 +72,6 @@ class MorphologyMapBuilder
     }
 };
 
-class MorphIOSingletonFixer
-{
-public:
-    static void fix(const MorphologyMap &map)
-    {
-        auto it = map.pathToCellIndices.begin();
-        auto path = it->first;
-        NeuronMorphologyReader::read(path, true, true, true);
-    }
-};
-
 class ParallelMorphologyLoader
 {
 public:
@@ -103,9 +92,6 @@ class ParallelMorphologyLoader
         auto dendrites = morphologyParameters.load_dendrites;
         auto pipeline = NeuronMorphologyPipeline::fromParameters(morphologyParameters);
 
-        // TODO: Remove once a new version of MorphIO is released (current version is 3.3.4)
-        MorphIOSingletonFixer::fix(morphologyMap);
-
         auto loadFn = [&](const std::string &path, const std::vector<size_t> &indices)
         {
             auto morphology = NeuronMorphologyReader::read(path, soma, axon, dendrites);
diff --git a/plugins/deps/CMakeLists.txt b/plugins/deps/CMakeLists.txt
index a1a5c256b..17ff3452d 100644
--- a/plugins/deps/CMakeLists.txt
+++ b/plugins/deps/CMakeLists.txt
@@ -8,6 +8,8 @@ include(FetchContent)
 set(CMAKE_EXPORT_NO_PACKAGE_REGISTRY ON)
 set(CMAKE_INSTALL_LIBDIR lib)
 
+find_package(Git REQUIRED)
+
 # =============================================================================
 # libsonata
 # =============================================================================
@@ -17,18 +19,34 @@ if(BRAYNS_CIRCUITEXPLORER_ENABLED OR BRAYNS_DTI_ENABLED AND NOT sonata_FOUND AND
         FetchContent_Declare(
             libsonata
             GIT_REPOSITORY https://github.com/BlueBrain/libsonata.git
-            GIT_TAG v0.1.20
-            GIT_SHALLOW OFF # Required for its own CMakeLists.txt not to fail
+            GIT_TAG v0.1.21
+            GIT_SHALLOW ON
             GIT_SUBMODULES_RECURSE ON
             SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/libsonata
         )
         FetchContent_Populate(libsonata)
     endif()
 
+    # MorphIO requires latest version of HighFive. (2.7.1)
+    # libsonata version of HighFive is 2.4.0
+    # We have to use libsonata version of HighFive because libsonata CMakeLists.txt both adds
+    # the dependency and compiles the library.
+    # MorphIO separates this in two CMakeLists, so we can build the library and use libsonata HighFive.
+    # TL;DR WE CANNOT MAKE LIBSONATA USE A DIFFERENT HIGHTFIVE THAN ITS OWN. WE NEED TO UPDATE IT TO BE
+    # VALID FOR MORPHIO AS WELL.
+    message(STATUS "> Updating libsonata's HighFive to v2.7.1")
+    execute_process(
+        COMMAND ${GIT_EXECUTABLE} checkout v2.7.1
+        WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR}/libsonata/extlib/HighFive
+        RESULT_VARIABLE GIT_SUBMOD_RESULT
+        OUTPUT_QUIET)
+    if(NOT GIT_SUBMOD_RESULT EQUAL "0")
+        message(FATAL_ERROR "Could not update libsonata's HighFive dependency")
+    endif()
+
     set(EXTLIB_FROM_SUBMODULES ON CACHE BOOL "" FORCE)
     set(SONATA_TESTS OFF CACHE BOOL "" FORCE)
-
-    # Force C++14 for GCC < 12.2.0
+    SET(SONATA_CXX_WARNINGS OFF CACHE BOOL "" FORCE)
     set(CMAKE_CXX_STANDARD 14 CACHE STRING "" FORCE)
 
     add_subdirectory(libsonata)
@@ -44,7 +62,7 @@ if(BRAYNS_CIRCUITEXPLORER_ENABLED OR BRAYNS_DTI_ENABLED AND NOT MorphIO_FOUND AN
         FetchContent_Declare(
             MorphIO
             GIT_REPOSITORY https://github.com/BlueBrain/MorphIO.git
-            GIT_TAG v3.3.3
+            GIT_TAG v3.3.5
             GIT_SHALLOW ON
             GIT_SUBMODULES_RECURSE ON
             SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/MorphIO
@@ -63,11 +81,14 @@ if(BRAYNS_CIRCUITEXPLORER_ENABLED OR BRAYNS_DTI_ENABLED AND NOT MorphIO_FOUND AN
     add_library(lexertl INTERFACE)
     target_include_directories(lexertl SYSTEM INTERFACE MorphIO/3rdparty/lexertl14/include)
 
+    add_library(ghc_filesystem INTERFACE)
+    target_include_directories(ghc_filesystem SYSTEM INTERFACE MorphIO/3rdparty/ghc_filesystem/include)
+
     # Retrieve version
-    set(MORPHIO_VERSION_STRING "3.3.2")
+    set(MORPHIO_VERSION_STRING "3.3.5")
     set(MorphIO_VERSION_MAJOR 3)
     set(MorphIO_VERSION_MINOR 3)
-    set(MorphIO_VERSION_PATCH 2)
+    set(MorphIO_VERSION_PATCH 5)
 
     # Morphio
     add_subdirectory(MorphIO/src)