Merge branch 'master' into master

Author: akenmorris

.github/workflows/Dockerfile

@@ -1,17 +1,20 @@
 # Based on old ubuntu to create more compatible binaries
 
 # To build (e.g. for ShapeWorks 6.5):
-#    docker build --progress=plain -t akenmorris/ubuntu-build-box-sw65 .
+#    docker build --progress=plain -t akenmorris/ubuntu-build-box-focal-sw65 .
 # To publish:
-#    docker push akenmorris/ubuntu-build-box-sw65
+#    docker push akenmorris/ubuntu-build-box-focal-sw65
 
-FROM ubuntu:bionic-20230308 AS env
+FROM ubuntu:focal-20240123 AS env
 MAINTAINER [email protected]
 
 # Set environment variables
 ENV PATH=/opt/conda/bin:/opt/rh/devtoolset-9/root/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
 ENV LDFLAGS=-L/opt/conda/lib
 
+ARG DEBIAN_FRONTEND=noninteractive
+ENV TZ=Etc/UTC
+
 # Update
 RUN apt-get update -y && apt-get upgrade -y && apt-get dist-upgrade -y && apt-get install build-essential software-properties-common -y && add-apt-repository ppa:ubuntu-toolchain-r/test -y && apt-get update -y
 

.github/workflows/build-linux-debug.yml

@@ -24,12 +24,12 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
-    container: akenmorris/ubuntu-build-box-sw65
+    container: akenmorris/ubuntu-build-box-focal-sw65
 
     steps:
 
     - name: Install SSH Key
-      uses: shimataro/ssh-key-action@v2
+      uses: shimataro/ssh-key-action@v2.7.0
       with:
         key: ${{ secrets.SSH_PRIVATE_KEY }}
         known_hosts: ${{ secrets.KNOWN_HOSTS }}
@@ -41,7 +41,10 @@ jobs:
       run: df -h
 
     - name: Free some space 
-      run: cd /__t ; rm -rf CodeQL go
+      run: cd /__t ; rm -rf CodeQL go PyPy Python Ruby
+
+    - name: Check usage 
+      run: cd /__t ; du -sh *
 
     - name: Check space2
       run: df -h
@@ -61,35 +64,35 @@ jobs:
       shell: bash -l {0}
       run: .github/workflows/restore_caches.sh
 
-    - name: Check space2
+    - name: Check space3
       run: df -h
 
     - name: Conda Installs
       shell: bash -l {0}
       run: .github/workflows/gha_conda.sh
 
-    - name: Check space3
+    - name: Check space4
       run: df -h
 
     - name: Build Dependencies
       shell: bash -l {0}
       run: .github/workflows/gha_deps.sh
 
-    - name: Check space4
+    - name: Check space5
       run: df -h
 
     - name: cmake
       shell: bash -l {0}
       run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.2 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.1 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON ..
 
-    - name: Check space5
+    - name: Check space6
       run: df -h
 
     - name: make
       shell: bash -l {0}
       run: conda activate shapeworks && cd build && make -j2
 
-    - name: Check space6
+    - name: Check space7
       run: df -h
 
     - name: make install

.github/workflows/build-linux.yml

@@ -25,12 +25,12 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
-    container: akenmorris/ubuntu-build-box-sw65
+    container: akenmorris/ubuntu-build-box-focal-sw65
 
     steps:
 
     - name: Install SSH Key
-      uses: shimataro/ssh-key-action@v2
+      uses: shimataro/ssh-key-action@v2.7.0
       with:
         key: ${{ secrets.SSH_PRIVATE_KEY }}
         known_hosts: ${{ secrets.KNOWN_HOSTS }}

.github/workflows/copy_artifact.sh

@@ -14,18 +14,18 @@ if [[ "$PLATFORM" == "windows" ]]; then
     # install rsync on for windows/msys2 (the one from chocolatey doesn't work)
     # (adapted from https://github.com/GuillaumeFalourd/setup-rsync)
     echo "Installing rsync for Windows/msys2"
-    curl.exe --output rsync-3.2.3-2-x86_64.pkg.tar.zst --url https://repo.msys2.org/msys/x86_64/rsync-3.2.3-1-x86_64.pkg.tar.zst
-    zstd -d rsync-3.2.3-2-x86_64.pkg.tar.zst
-    tar -xvf rsync-3.2.3-2-x86_64.pkg.tar
-    mv usr/bin/rsync.exe "C:\Program Files\Git\usr\bin\\"
-    curl.exe --output libzstd-1.5.2-1-x86_64.pkg.tar.zst https://repo.msys2.org/msys/x86_64/libzstd-1.5.2-1-x86_64.pkg.tar.zst
-    zstd -d libzstd-1.5.2-1-x86_64.pkg.tar.zst
-    tar -xvf libzstd-1.5.2-1-x86_64.pkg.tar
-    mv usr/bin/msys-zstd-1.dll "C:\Program Files\Git\usr\bin\\"
-    curl.exe --output libxxhash-0.8.0-1-x86_64.pkg.tar.zst https://repo.msys2.org/msys/x86_64/libxxhash-0.8.0-1-x86_64.pkg.tar.zst
-    zstd -d libxxhash-0.8.0-1-x86_64.pkg.tar.zst
-    tar -xvf libxxhash-0.8.0-1-x86_64.pkg.tar
-    mv usr/bin/msys-xxhash-0.8.0.dll "C:\Program Files\Git\usr\bin\\"
+
+    # These were the original URLs, but they keep changing and it's time consuming to keep up
+    # So I have just combined them in this windows_rsync.tar.gz that I'm hosting myself
+    
+    # https://repo.msys2.org/msys/x86_64/rsync-3.2.3-1-x86_64.pkg.tar.zst
+    # https://repo.msys2.org/msys/x86_64/libzstd-1.5.2-1-x86_64.pkg.tar.zst
+    # https://repo.msys2.org/msys/x86_64/libxxhash-0.8.1-1-x86_64.pkg.tar.zst
+    curl.exe --output windows_rsync.tar.gz http://www.sci.utah.edu/~amorris/windows_rsync.tar.gz
+
+    tar -xzvf windows_rsync.tar.gz
+    
+    mv usr/bin/* "C:\Program Files\Git\usr\bin\\"
     echo "rsync installed on windows runner"
 fi
 

Applications/shapeworks/MeshCommands.cpp

@@ -1432,6 +1432,7 @@ bool WarpMesh::execute(const optparse::Values &options, SharedCommandData &share
   try {
     MeshWarper warper;
     Mesh inputMesh(inputMeshFilename);
+    inputMesh.clean();
     targetPointsFilenames.push_back(inputPointsFilename);
     ParticleSystemEvaluation particlesystem(targetPointsFilenames);
     Eigen::MatrixXd landmarks;

CMakeLists.txt

@@ -6,7 +6,7 @@ cmake_minimum_required(VERSION 3.20)
 SET(SHAPEWORKS_MAJOR_VERSION 6 CACHE INTERNAL "Major version number" FORCE)
 SET(SHAPEWORKS_MINOR_VERSION 5 CACHE INTERNAL "Minor version number" FORCE)
 SET(SHAPEWORKS_PATCH_VERSION 0 CACHE INTERNAL "Patch version number" FORCE)
-SET(SHAPEWORKS_VERSION_STRING "6.5.0-dev")
+SET(SHAPEWORKS_VERSION_STRING "6.5.0")
 SET(SHAPEWORKS_VERSION "${SHAPEWORKS_MAJOR_VERSION}.${SHAPEWORKS_MINOR_VERSION}.${SHAPEWORKS_PATCH_VERSION}")
 
 # First, check that files were checked out properly using git-lfs

Libs/Analyze/Shape.cpp

@@ -148,12 +148,15 @@ bool Shape::import_global_point_files(std::vector<std::string> filenames) {
   global_point_filenames_.clear();
   for (int i = 0; i < filenames.size(); i++) {
     Eigen::VectorXd points;
-    if (filenames[i] != "") {
-      if (!Shape::import_point_file(filenames[i], points)) {
+    auto filename = filenames[i];
+    // replace \ with /
+    filename = StringUtils::replace_string(filename, "\\", "/");
+    if (filename != "") {
+      if (!Shape::import_point_file(filename, points)) {
         throw std::invalid_argument("Unable to import point file: " + filenames[i]);
       }
     }
-    global_point_filenames_.push_back(filenames[i]);
+    global_point_filenames_.push_back(filename);
     particles_.set_world_particles(i, points);
   }
   subject_->set_world_particle_filenames(global_point_filenames_);
@@ -165,12 +168,15 @@ bool Shape::import_local_point_files(std::vector<std::string> filenames) {
   local_point_filenames_.clear();
   for (int i = 0; i < filenames.size(); i++) {
     Eigen::VectorXd points;
-    if (filenames[i] != "") {
-      if (!Shape::import_point_file(filenames[i], points)) {
+    auto filename = filenames[i];
+    // replace \ with /
+    filename = StringUtils::replace_string(filename, "\\", "/");
+    if (filename != "") {
+      if (!Shape::import_point_file(filename, points)) {
         throw std::invalid_argument("Unable to import point file: " + filenames[i]);
       }
     }
-    local_point_filenames_.push_back(filenames[i]);
+    local_point_filenames_.push_back(filename);
     particles_.set_local_particles(i, points);
   }
   subject_->set_local_particle_filenames(local_point_filenames_);

Libs/Common/Logging.h

@@ -4,6 +4,7 @@
 
 #include <QString>
 #include <functional>
+#include <iostream>
 
 template <>
 struct fmt::formatter<QString> {
@@ -15,6 +16,18 @@ struct fmt::formatter<QString> {
   }
 };
 
+template <typename... Args>
+std::string safe_format(const std::string& fmt_str, const Args&... args) {
+  std::string result;
+  try {
+    result = fmt::format(fmt_str, args...);
+  } catch (const std::exception& e) {
+    // Handle formatting errors here, example:
+    std::cerr << "Error formatting string: " << fmt_str << " : " << e.what() << std::endl;
+  }
+  return result;
+}
+
 namespace shapeworks {
 
 /**
@@ -105,7 +118,7 @@ class Logging {
   void show_progress(double value, const std::string& message);
 
   //! Log a debug message, use SW_DEBUG macro
-  void log_debug(const std::string& message, const int line, const char* file, const char *function) const;
+  void log_debug(const std::string& message, const int line, const char* file, const char* function) const;
 
   //! Log a warning message, use SW_WARN macro
   void log_warning(const std::string& message, const int line, const char* file) const;
@@ -156,44 +169,44 @@ class Logging {
 
 //! Log message macro
 #define SW_LOG(message, ...) \
-  shapeworks::Logging::Instance().log_message(fmt::format(message, ##__VA_ARGS__), __LINE__, __FILE__)
+  shapeworks::Logging::Instance().log_message(safe_format(message, ##__VA_ARGS__), __LINE__, __FILE__);
 
 //! Log warning macro
 #define SW_WARN(message, ...) \
-  shapeworks::Logging::Instance().log_warning(fmt::format(message, ##__VA_ARGS__), __LINE__, __FILE__)
+  shapeworks::Logging::Instance().log_warning(safe_format(message, ##__VA_ARGS__), __LINE__, __FILE__)
 
 //! Log error macro
 #define SW_ERROR(message, ...) \
-  shapeworks::Logging::Instance().log_error(fmt::format(message, ##__VA_ARGS__), __LINE__, __FILE__)
+  shapeworks::Logging::Instance().log_error(safe_format(message, ##__VA_ARGS__), __LINE__, __FILE__)
 
 //! Log debug macro
 #define SW_DEBUG(message, ...) \
-  shapeworks::Logging::Instance().log_debug(fmt::format(message, ##__VA_ARGS__), __LINE__, __FILE__, __FUNCTION__)
+  shapeworks::Logging::Instance().log_debug(safe_format(message, ##__VA_ARGS__), __LINE__, __FILE__, __FUNCTION__)
 
 //! Variable trace macro (e.g. output variable name = <variable value>)
 #define SW_TRACE(x) SW_DEBUG(#x " = {}", x);
 
 //! Log show message macro
 #define SW_MESSAGE(message, ...) \
-  shapeworks::Logging::Instance().show_message(fmt::format(message, ##__VA_ARGS__), __LINE__, __FILE__)
+  shapeworks::Logging::Instance().show_message(safe_format(message, ##__VA_ARGS__), __LINE__, __FILE__)
 
 //! Don't write to log, but set status (e.g. in the Studio statusbar)
 #define SW_STATUS(message, ...) \
-  shapeworks::Logging::Instance().show_status(fmt::format(message, ##__VA_ARGS__), __LINE__, __FILE__)
+  shapeworks::Logging::Instance().show_status(safe_format(message, ##__VA_ARGS__), __LINE__, __FILE__)
 
 #define SW_PROGRESS(value, message, ...) \
-  shapeworks::Logging::Instance().show_progress(value, fmt::format(message, ##__VA_ARGS__));
+  shapeworks::Logging::Instance().show_progress(value, safe_format(message, ##__VA_ARGS__));
 
 //! Close session macro
 #define SW_CLOSE_LOG() shapeworks::Logging::Instance().close_log();
 
 //! Log once macro, will only log the message once
-#define SW_LOG_ONCE(message, ...) \
-{ \
-    static bool logged = false; \
-    if (!logged) { \
+#define SW_LOG_ONCE(message, ...)     \
+  {                                   \
+    static bool logged = false;       \
+    if (!logged) {                    \
       SW_LOG(message, ##__VA_ARGS__); \
-      logged = true; \
-    } \
-}
+      logged = true;                  \
+    }                                 \
+  }
 }  // namespace shapeworks

Libs/Groom/Groom.cpp

@@ -727,13 +727,11 @@ std::string Groom::get_output_filename(std::string input, DomainType domain_type
   // check for and handle name clashes, e.g. a/foo.vtk, b/foo.vtk (see #1387)
   auto base_name = name;
   int count = 2;
-  while (used_names_.find(name) != used_names_.end()) {
-    name = base_name + std::to_string(count++);
+  while (used_names_.find(name + suffix) != used_names_.end()) {
+    name = base_name + "_" + std::to_string(count++);
   }
-  used_names_.insert(name);
-
   auto output = name + suffix;
-
+  used_names_.insert(output);
   return output;
 }
 

Libs/Mesh/Mesh.cpp

@@ -488,7 +488,7 @@ Mesh& Mesh::fixElement() {
   FEMesh* meshFE = import.Load(this->poly_data_);
 
   if (meshFE == nullptr) {
-    throw std::invalid_argument("Unable to read file");
+    throw std::runtime_error("Unable to read mesh file");
   }
 
   FEFixMesh fix;