Merge branch 'dev' into cmake_app_bundles

.clang-tidy

@@ -0,0 +1,16 @@
+Checks: >
+  -*,
+  bugprone-*,
+  clang-analyzer-*,
+  concurrency-*,
+  cppcoreguidelines-*,
+  misc-*,
+  performance-*,
+  portability-*,
+  readability-*,
+  -bugprone-easily-swappable-parameters,
+  -cppcoreguidelines-avoid-magic-numbers,
+  -readability-braces-around-statements,
+  -readability-identifier-length,
+  -readability-magic-numbers,
+HeaderFilterRegex: '*.(h|hpp)'

.github/workflows/checks.yml

@@ -47,15 +47,17 @@ jobs:
         -D MRTRIX_BUILD_TESTS=ON
         -D MRTRIX_STL_DEBUGGING=ON
         -D MRTRIX_WARNINGS_AS_ERRORS=ON
+        -D CMAKE_C_COMPILER=clang
+        -D CMAKE_CXX_COMPILER=clang++
 
     - name: build
       run: cmake --build build
 
     - name: unit tests
-      run: cd build && ctest -R unit
+      run: cd build && ctest -R unit --output-on-failure
 
     - name: binary tests
-      run: cd build && ctest -R bin
+      run: cd build && ctest -R bin --output-on-failure
 
   linux-gcc-build:
 
@@ -101,10 +103,10 @@ jobs:
       run: cmake --build build
 
     - name: unit tests
-      run: cd build && ctest -R unit
+      run: cd build && ctest -R unit --output-on-failure
 
     - name: binary tests
-      run: cd build && ctest -R bin
+      run: cd build && ctest -R bin --output-on-failure
 
   macos-build:
 
@@ -152,10 +154,10 @@ jobs:
       run: cmake --build build
 
     - name: unit tests
-      run: cd build && ctest -R unit
+      run: cd build && ctest -R unit --output-on-failure
 
     - name: binary tests
-      run: cd build && ctest -R bin
+      run: cd build && ctest -R bin --output-on-failure
 
     - name: check command documentation
       run: ./docs/generate_user_docs.sh --build-dir ./build && git diff --exit-code docs/
@@ -222,10 +224,10 @@ jobs:
         run: cmake --build build
 
       - name: unit tests
-        run: cd build && ctest -R unit
+        run: cd build && ctest -R unit --output-on-failure
 
       - name: binary tests
-        run: cd build && ctest -R bin
+        run: cd build && ctest -R bin --output-on-failure
 
   secondary-checks:
     runs-on: ubuntu-latest

.github/workflows/clang-tidy.yml

@@ -0,0 +1,19 @@
+name: clang-tidy-review
+
+on: [pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+
+    - uses: ZedThree/[email protected]
+      id: review
+      with:
+        apt_packages: g++,libqt5opengl5-dev,libqt5svg5-dev,libglvnd-dev,libeigen3-dev,zlib1g-dev,libfftw3-dev,ninja-build
+        cmake_command: cmake . -DCMAKE_EXPORT_COMPILE_COMMANDS=on
+        config_file: .clang-tidy
+
+    - uses: ZedThree/clang-tidy-review/[email protected]
+      id: upload-review

CMakeLists.txt

@@ -1,6 +1,7 @@
 cmake_minimum_required(VERSION 3.16 FATAL_ERROR)
 
-project(mrtrix3 VERSION 3.0.4)
+project(mrtrix3 LANGUAGES CXX VERSION 3.0.4)
+
 include(GNUInstallDirs)
 
 string(TIMESTAMP CURRENT_YEAR "%Y")
@@ -29,8 +30,6 @@ else()
     set(QT_MAJOR_VERSION 5)
 endif()
 
-option(BUILD_GUI "Build the MRtrix3 GUI" ON)
-
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
@@ -139,4 +138,5 @@ add_custom_target(Github SOURCES
     .github/workflows/package-macos-anaconda.yml
     .github/workflows/package-macos-native.yml
     .github/workflows/package-windows-msys2.yml
+    .github/workflows/clang-tidy.yml
 )

check_syntax

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (c) 2008-2023 the MRtrix3 contributors.
+# Copyright (c) 2008-2024 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -64,20 +64,6 @@ for f in $(find cmd core src -type f -name '*.h' -o -name '*.cpp' | $grep -v '_m
 # remove quoted strings:
   cat .check_syntax2.tmp | perl -pe 's/(")(\\"|.)*?"//g' > .check_syntax.tmp
 
-# detect any instances of std::vector:
-  res="$res"$(
-    cat .check_syntax.tmp | \
-# match for the parts we're interested in and output just the bits that match:
-    $grep -Po '(?<!::)std::vector\b'
-  )
-
-
-# detect any instances of std::make_shared:
-  res="$res"$(
-    cat .check_syntax.tmp | \
-# match for the parts we're interested in and output just the bits that match:
-    $grep -Po '(?<!::)std::make_shared\b'
-  )
 
 # detect any instances of "using namespace std;":
   res="$res"$(
@@ -126,8 +112,6 @@ else
   echo "" >> $LOG
   echo "Please check the following syntax requirements:
   - Add MEMALIGN() or NOMEMALIGN macro to any class declarations identified above;
-  - Replace all occurrences of std::vector<> with MR::vector<> (or just vector<>);
-  - Avoid use of std::make_shared();
   - Replace all instances of std::abs() with MR::abs() (or just abs());
   - Replace all instances of %zu in print() calls with PRI_SIZET." >> $LOG
   exit 1

clang-format-all

@@ -1,6 +1,6 @@
 #!/usr/env/python3
 
-# Copyright (c) 2008-2023 the MRtrix3 contributors.
+# Copyright (c) 2008-2024 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/5tt2gmwmi.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/5tt2vis.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/5ttcheck.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/5ttedit.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/afdconnectivity.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -215,7 +215,7 @@ value_type AFDConnectivity::get(const std::string &path) {
     if (all_fixels) {
 
       // All fixels contribute to the result
-      for (vector<AFDConnFixel>::const_iterator i = fixels.begin(); i != fixels.end(); ++i) {
+      for (std::vector<AFDConnFixel>::const_iterator i = fixels.begin(); i != fixels.end(); ++i) {
         if (i->is_selected())
           sum_volumes += i->get_FOD();
       }

cmd/amp2response.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -101,8 +101,8 @@ Eigen::Matrix<default_type, 3, 3> gen_rotation_matrix(const Eigen::Vector3d &dir
   return R;
 }
 
-vector<size_t> all_volumes(const size_t num) {
-  vector<size_t> result(num);
+std::vector<size_t> all_volumes(const size_t num) {
+  std::vector<size_t> result(num);
   for (size_t i = 0; i != num; ++i)
     result[i] = i;
   return result;
@@ -112,7 +112,7 @@ class Accumulator {
 public:
   class Shared {
   public:
-    Shared(int lmax, const vector<size_t> &volumes, const Eigen::MatrixXd &dirs)
+    Shared(int lmax, const std::vector<size_t> &volumes, const Eigen::MatrixXd &dirs)
         : lmax(lmax),
           dirs(dirs),
           volumes(volumes),
@@ -122,7 +122,7 @@ class Accumulator {
 
     const int lmax;
     const Eigen::MatrixXd &dirs;
-    const vector<size_t> &volumes;
+    const std::vector<size_t> &volumes;
     Eigen::MatrixXd M;
     Eigen::VectorXd b;
     size_t count;
@@ -196,8 +196,8 @@ void run() {
   auto header = Header::open(argument[0]);
 
   // May be dealing with multiple shells
-  vector<Eigen::MatrixXd> dirs_azel;
-  vector<vector<size_t>> volumes;
+  std::vector<Eigen::MatrixXd> dirs_azel;
+  std::vector<std::vector<size_t>> volumes;
   std::unique_ptr<DWI::Shells> shells;
 
   auto opt = get_options("directions");
@@ -207,7 +207,7 @@ void run() {
   } else {
     auto hit = header.keyval().find("directions");
     if (hit != header.keyval().end()) {
-      vector<default_type> dir_vector;
+      std::vector<default_type> dir_vector;
       for (auto line : split_lines(hit->second)) {
         auto v = parse_floats(line);
         dir_vector.insert(dir_vector.end(), v.begin(), v.end());
@@ -230,7 +230,7 @@ void run() {
     }
   }
 
-  vector<uint32_t> lmax;
+  std::vector<uint32_t> lmax;
   uint32_t max_lmax = 0;
   opt = get_options("lmax");
   if (get_options("isotropic").size()) {

cmd/amp2sh.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -81,14 +81,14 @@ class Amp2SHCommon {
 public:
   template <class MatrixType>
   Amp2SHCommon(const MatrixType &sh2amp,
-               const vector<size_t> &bzeros,
-               const vector<size_t> &dwis,
+               const std::vector<size_t> &bzeros,
+               const std::vector<size_t> &dwis,
                bool normalise_to_bzero)
       : sh2amp(sh2amp), amp2sh(Math::pinv(sh2amp)), bzeros(bzeros), dwis(dwis), normalise(normalise_to_bzero) {}
 
   Eigen::MatrixXd sh2amp, amp2sh;
-  const vector<size_t> &bzeros;
-  const vector<size_t> &dwis;
+  const std::vector<size_t> &bzeros;
+  const std::vector<size_t> &dwis;
   bool normalise;
 };
 
@@ -175,7 +175,7 @@ void run() {
   auto amp = Image<value_type>::open(argument[0]).with_direct_io(3);
   Header header(amp);
 
-  vector<size_t> bzeros, dwis;
+  std::vector<size_t> bzeros, dwis;
   Eigen::MatrixXd dirs;
   auto opt = get_options("directions");
   if (opt.size()) {
@@ -185,7 +185,7 @@ void run() {
   } else {
     auto hit = header.keyval().find("directions");
     if (hit != header.keyval().end()) {
-      vector<default_type> dir_vector;
+      std::vector<default_type> dir_vector;
       for (auto line : split_lines(hit->second)) {
         auto v = parse_floats(line);
         dir_vector.insert(dir_vector.end(), v.begin(), v.end());

cmd/connectome2tck.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -158,9 +158,9 @@ void run() {
   Tractography::Properties properties;
   Tractography::Reader<float> reader(argument[0], properties);
 
-  vector<vector<node_t>> assignments_lists;
+  std::vector<std::vector<node_t>> assignments_lists;
   assignments_lists.reserve(to<size_t>(properties["count"]));
-  vector<NodePair> assignments_pairs;
+  std::vector<NodePair> assignments_pairs;
   bool nonpair_found = false;
   node_t max_node_index = 0;
   {
@@ -172,7 +172,7 @@ void run() {
       if (line.empty())
         continue;
       std::stringstream line_stream(line);
-      vector<node_t> nodes;
+      std::vector<node_t> nodes;
       while (1) {
         node_t n;
         line_stream >> n;
@@ -216,7 +216,7 @@ void run() {
   const bool keep_self = get_options("keep_self").size();
 
   // Get the list of nodes of interest
-  vector<node_t> nodes;
+  std::vector<node_t> nodes;
   opt = get_options("nodes");
   bool manual_node_list = false;
   if (opt.size()) {
@@ -256,8 +256,8 @@ void run() {
     // Load the node image, get the centres of mass
     // Generate exemplars - these can _only_ be done per edge, and requires a mutex per edge to multi-thread
     auto image = Image<node_t>::open(opt[0][0]);
-    vector<Eigen::Vector3f> COMs(max_node_index + 1, Eigen::Vector3f(0.0f, 0.0f, 0.0f));
-    vector<size_t> volumes(max_node_index + 1, 0);
+    std::vector<Eigen::Vector3f> COMs(max_node_index + 1, Eigen::Vector3f(0.0f, 0.0f, 0.0f));
+    std::vector<size_t> volumes(max_node_index + 1, 0);
     for (auto i = Loop()(image); i; ++i) {
       const node_t index = image.value();
       if (index) {
@@ -344,7 +344,7 @@ void run() {
       } else {
         // For each node in the list, write one file for an exemplar to every other node
         ProgressBar progress("writing exemplars to files", nodes.size() * COMs.size());
-        for (vector<node_t>::const_iterator n = nodes.begin(); n != nodes.end(); ++n) {
+        for (std::vector<node_t>::const_iterator n = nodes.begin(); n != nodes.end(); ++n) {
           for (size_t i = first_node; i != COMs.size(); ++i) {
             generator.write(*n,
                             i,
@@ -356,7 +356,7 @@ void run() {
       }
     } else if (file_format == 1) { // One file per node
       ProgressBar progress("writing exemplars to files", nodes.size());
-      for (vector<node_t>::const_iterator n = nodes.begin(); n != nodes.end(); ++n) {
+      for (std::vector<node_t>::const_iterator n = nodes.begin(); n != nodes.end(); ++n) {
         generator.write(
             *n, prefix + str(*n) + ".tck", weights_prefix.size() ? (weights_prefix + str(*n) + ".csv") : "");
         ++progress;
@@ -399,7 +399,7 @@ void run() {
       INFO("A total of " + str(writer.file_count()) + " output track files will be generated (one for each edge)");
       break;
     case 1: // One file per node
-      for (vector<node_t>::const_iterator i = nodes.begin(); i != nodes.end(); ++i)
+      for (std::vector<node_t>::const_iterator i = nodes.begin(); i != nodes.end(); ++i)
         writer.add(*i, prefix + str(*i) + ".tck", weights_prefix.size() ? (weights_prefix + str(*i) + ".csv") : "");
       INFO("A total of " + str(writer.file_count()) + " output track files will be generated (one for each node)");
       break;

cmd/connectomeedit.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this