Merge pull request #2243 from SCIInstitute/fix_mac_action

Fix mac GitHub Action and add Mac Arm64

.github/workflows/build-mac-arm64.yml

@@ -0,0 +1,126 @@
+name: Mac Arm64 Build
+
+on:
+  push:
+    branches:
+      - master
+      - release_v*
+    tags:
+    - '*'
+  pull_request:
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Release
+  SW_CLOUD_LOGIN: ${{ secrets.CLOUD_LOGIN }}
+  CACHE_HOST: ${{ secrets.SSH_HOST }}
+  GA_MEASUREMENT_ID: ${{ secrets.GA_MEASUREMENT_ID }}
+  GA_API_SECRET: ${{ secrets.GA_API_SECRET }}
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+
+    runs-on: macos-latest
+
+    steps:
+
+    - name: Install SSH Key
+      uses: shimataro/ssh-key-action@v2
+      with:
+        key: ${{ secrets.SSH_PRIVATE_KEY }}
+        known_hosts: ${{ secrets.KNOWN_HOSTS }}
+
+    - name: Setup Miniconda
+      uses: conda-incubator/setup-miniconda@v3.0.4
+
+    - name: OS Setup
+      run: |
+        sudo chown -R $UID $CONDA
+        conda init zsh
+        source ~/.zshrc
+        brew install ccache pigz gnu-tar coreutils
+
+    - name: Checkout code
+      uses: actions/checkout@v3
+      with:
+        lfs: true
+
+    - name: Get tags
+      run: git fetch --unshallow origin +refs/tags/*:refs/tags/*
+
+    - name: Restore Caches
+      shell: bash -l {0}
+      run: .github/workflows/restore_caches.sh
+
+    - name: Conda Installs
+      shell: bash -l {0}
+      run: .github/workflows/gha_conda.sh
+
+    - name: Build Dependencies
+      shell: bash -l {0}
+      run: .github/workflows/gha_deps.sh
+
+    - name: cmake
+      shell: bash -l {0}
+      run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_LIBTOOL=/usr/bin/libtool -DCMAKE_CXX_FLAGS=-g -DCMAKE_PREFIX_PATH=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DPython3_ROOT_DIR:FILEPATH=${CONDA_PREFIX} -DUSE_OPENMP=OFF -DBuild_Studio=ON -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DBUILD_DOCUMENTATION=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET ..
+
+    - name: make
+      shell: bash -l {0}
+      run: conda activate shapeworks && cd build && make -j4
+
+    - name: make install
+      shell: bash -l {0}
+      run: conda activate shapeworks && cd build && make install
+
+    - name: Build Binary Package
+      shell: bash -l {0}
+      env:
+        PR_NUMBER: ${{ github.event.number }}
+      run: conda activate shapeworks && source ./devenv.sh ./build/bin && ./Support/package.sh tag ${GITHUB_WORKSPACE}/shapeworks-install $HOME/install
+
+    - name: Download test data
+      shell: bash -l {0}
+      run: .github/workflows/download_test_data.sh
+
+    - name: make test
+      shell: bash -l {0}
+      run: conda activate shapeworks && source ./devenv.sh ./build/bin && cd build && ctest -VV
+
+    - uses: actions/upload-artifact@v2
+      with:
+        name: artifact-${{github.sha}}-mac-arm64
+        path: ${{runner.workspace}}/ShapeWorks/artifacts
+
+    - name: Deploy
+      id: deploy
+      if: github.ref == 'refs/heads/master'
+      uses: marvinpinto/action-automatic-releases@latest
+      with:
+        repo_token: "${{ secrets.GITHUB_TOKEN }}"
+        automatic_release_tag: "dev-mac-arm64"
+        prerelease: true
+        title: "Development Build for Mac Arm64"
+        files: |
+             ${{runner.workspace}}/ShapeWorks/artifacts/*.zip
+             ${{runner.workspace}}/ShapeWorks/artifacts/*.pkg
+
+    - name: Deploy Docs
+      if: github.ref == 'refs/heads/master'
+      shell: bash -l {0}
+      run: conda activate shapeworks && source ./devenv.sh ./build/bin && ./Support/deploy_docs.sh ${GITHUB_WORKSPACE}/build
+      env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Store ccache
+      shell: bash -l {0}
+      run: .github/workflows/store_ccache.sh
+
+    - name: Copy artifact
+      shell: bash -l {0}
+      run: cd ${{runner.workspace}}/ShapeWorks && ${GITHUB_WORKSPACE}/.github/workflows/copy_artifact.sh artifact-${{github.sha}}-mac-arm64 artifacts
+

.github/workflows/build-mac.yml

@@ -24,7 +24,7 @@ concurrency:
 jobs:
   build:
 
-    runs-on: macos-latest
+    runs-on: macos-12
 
     steps:
 
@@ -36,6 +36,9 @@ jobs:
 
     - name: OS Setup
       run: |
+        ls /usr/local
+        uname -m
+        echo $CONDA
         sudo chown -R $UID $CONDA
         conda init zsh
         source ~/.zshrc

.github/workflows/common.sh

@@ -11,8 +11,14 @@ SCRIPT_PATH=`dirname $SCRIPT`
 
 if [[ "$OSTYPE" == "darwin"* ]]; then
     source ~/.zshrc
-    PLATFORM="mac"
-    CONDA_PATH="/usr/local/miniconda/envs/shapeworks"
+    # check arch
+    if [[ "$(uname -m)" == "arm64" ]]; then
+        PLATFORM="mac-arm64"
+	CONDA_PATH="/Users/runner/miniconda3/envs/shapeworks"
+    else
+        PLATFORM="mac-intel"
+	CONDA_PATH="/usr/local/miniconda/envs/shapeworks"
+    fi
     DEP_PATH="$HOME/install"
     CCACHE_DIR="/Users/runner/Library/Caches/ccache"
     USE_CCACHE="ON"

.github/workflows/gha_deps.sh

@@ -18,17 +18,24 @@ else
     export BUILD_DIR=$HOME/build
     export FILE="/tmp/${DEP_FILE}"
     if [[ "$PLATFORM" == "windows" ]]; then
-	export INSTALL_DIR="C:\deps"
-	export BUILD_DIR="/c/bdeps"
-	export FILE="${DEP_FILE}"
+      export INSTALL_DIR="C:\deps"
+      export BUILD_DIR="/c/bdeps"
+      export FILE="${DEP_FILE}"
     fi
 
     NPROCS=4
-    export SDKROOT=$HOME/MacOSX10.15.sdk # only needed for MacOS obviously
+
+    # if intel mac and not arm64, using uname -m to detect arm64
+    if [[ "$PLATFORM" == "mac-intel" ]]; then
+        export SDKROOT=$HOME/MacOSX10.15.sdk # only needed for MacOS obviously
+        export MACOSX_DEPLOYMENT_TARGET=10.15
+    fi
+
     if [[ "$PLATFORM" == "linux" ]]; then
-	# GHA runner is running out of resources with 4 now on linux
+        # GHA runner is running out of resources with 4 now on linux
 	NPROCS=2
     fi
+
     ./build_dependencies.sh --build-type=$BUILD_TYPE --num-procs=$NPROCS --clean-after
     rm -rf $BUILD_DIR
 

Applications/shapeworks/ImageCommands.cpp

@@ -1127,7 +1127,7 @@ void CompareImage::buildParser()
   parser.add_option("--name").action("store").type("string").set_default("").help("Compare this image with another.");
   parser.add_option("--verifyall").action("store").type("bool").set_default(true).help("Also verify origin, spacing, and direction matches [default: true].");
   parser.add_option("--tolerance").action("store").type("double").set_default(0.0).help("Allowed percentage of pixel differences [default: %default].");
-  parser.add_option("--precision").action("store").type("double").set_default(1e-12).help("Allowed difference between two pixels for them to still be considered equal [default: 1e-12].");
+  parser.add_option("--precision").action("store").type("double").set_default(1e-5).help("Allowed difference between two pixels for them to still be considered equal [default: 1e-5].");
 
   Command::buildParser();
 }

Libs/Analyze/Analyze.cpp

@@ -12,15 +12,21 @@ using json = nlohmann::ordered_json;
 
 namespace shapeworks {
 
+//---------------------------------------------------------------------------
+static double round(double value, int digits = 6) {
+  double multiplier = pow(10.0, digits);
+  return std::round(value * multiplier) / multiplier;
+}
+
 //---------------------------------------------------------------------------
 static json get_eigen_vectors(ParticleShapeStatistics* stats) {
-    auto values = stats->get_eigen_vectors();
+  auto values = stats->get_eigen_vectors();
 
   std::vector<double> vals;
   for (size_t i = values.cols() - 1, ii = 0; i > 0; i--, ii++) {
     auto col = values.col(i);
     for (int j = 0; j < col.size(); j++) {
-      vals.push_back(col[j]);
+      vals.push_back(round(col[j]));
     }
   }
 
@@ -217,7 +223,7 @@ void Analyze::run_offline_analysis(std::string outfile, float range, float steps
     json jmode;
     jmode["mode"] = mode + 1;
     double eigen_value = eigen_vals[mode];
-    jmode["eigen_value"] = eigen_value;
+    jmode["eigen_value"] = round(eigen_value);
     SW_LOG("eigen value [{}]: {}", mode, eigen_value);
 
     double cumulation = 0;
@@ -227,11 +233,11 @@ void Analyze::run_offline_analysis(std::string outfile, float range, float steps
 
     double explained_variance = eigen_vals[mode] / sum * 100;
     double cumulative_explained_variance = cumulation / sum * 100;
-    jmode["explained_variance"] = explained_variance;
-    jmode["cumulative_explained_variance"] = cumulative_explained_variance;
+    jmode["explained_variance"] = round(explained_variance);
+    jmode["cumulative_explained_variance"] = round(cumulative_explained_variance);
     SW_LOG("explained_variance [{}]: {:.2f}", mode, explained_variance);
     SW_LOG("cumulative_explained_variance [{}]: {:.2f}", mode, cumulative_explained_variance);
-    
+
     double lambda = sqrt(stats_.get_eigen_values()[m]);
 
     std::vector<json> jmodes;
@@ -244,8 +250,8 @@ void Analyze::run_offline_analysis(std::string outfile, float range, float steps
         auto mode_meshes = shape->get_reconstructed_meshes(true);
 
         json item;
-        item["pca_value"] = pca_value_param;
-        item["lambda"] = lambda * pca_value_param;
+        item["pca_value"] = round(pca_value_param);
+        item["lambda"] = round(lambda * pca_value_param);
 
         std::vector<std::string> items;
         std::vector<std::string> worlds;
@@ -278,7 +284,12 @@ void Analyze::run_offline_analysis(std::string outfile, float range, float steps
   }
 
   j["eigen_vectors"] = get_eigen_vectors(&stats_);
-  j["eigen_values"] = stats_.get_eigen_values();
+  auto eigen_values = stats_.get_eigen_values();
+  // round them
+  for (auto& value : eigen_values) {
+    value = round(value);
+  }
+  j["eigen_values"] = eigen_values;
   j["modes"] = modes;
   j["charts"] = create_charts(&stats_);
 
@@ -342,11 +353,11 @@ Particles Analyze::get_shape_points(int mode, double value) {
   if (mode + 2 > stats_.get_eigen_values().size()) {
     mode = stats_.get_eigen_values().size() - 2;
   }
-  
+
   unsigned int m = stats_.get_eigen_vectors().cols() - (mode + 1);
-  
+
   Eigen::VectorXd e = stats_.get_eigen_vectors().col(m);
-  
+
   double lambda = sqrt(stats_.get_eigen_values()[m]);
 
   std::vector<double> vals;
@@ -489,7 +500,7 @@ bool Analyze::compute_stats() {
       return false;
     }
   }
-  
+
   stats_.import_points(points, group_ids);
   stats_.compute_modes();
 
@@ -617,7 +628,7 @@ Particles Analyze::get_group_shape_particles(double ratio) {
   if (!compute_stats()) {
     return Particles();
   }
-  
+
   auto particles = stats_.get_group1_mean() + (stats_.get_group_difference() * ratio);
 
   return convert_from_combined(particles);

Libs/Image/Image.h

@@ -271,7 +271,7 @@ class Image {
   ImageIterator iterator();
 
   /// compares this with another image using the region of interest filter
-  bool compare(const Image& other, bool verifyall = true, double tolerance = 0.0, double precision = 1e-12) const;
+  bool compare(const Image& other, bool verifyall = true, double tolerance = 0.0, double precision = 1e-6) const;
 
   /// compares this with another image using the region of interest filter
   bool operator==(const Image& other) const { return compare(other); }

Libs/Mesh/Mesh.cpp

@@ -814,7 +814,9 @@ Field Mesh::geodesicDistance(const std::vector<Point3> curve) const {
   for (int i = 0; i < curve.size(); i++) {
     Field distance = geodesicDistance(curve[i]);
     for (int j = 0; j < numPoints(); j++) {
-      if (distance->GetTuple1(j) < minDistance->GetTuple1(j)) minDistance->SetValue(j, distance->GetTuple1(j));
+      if (distance->GetTuple1(j) < minDistance->GetTuple1(j)) {
+        minDistance->SetValue(j, distance->GetTuple1(j));
+      }
     }
   }
 
@@ -1429,35 +1431,44 @@ bool Mesh::compareAllFaces(const Mesh& other_mesh) const {
 
   // helper function to print out the cell indices
   auto printCells = [](vtkCell* cell1, vtkCell* cell2) {
-    printf("[ ");
+    std::cout << "[ ";
     for (int i = 0; i < cell1->GetNumberOfPoints(); i++) {
-      printf("%lld ", cell1->GetPointId(i));
+      std::cout << cell1->GetPointId(i) << " ";
     }
-    printf("], [ ");
+    std::cout << "], [ ";
     for (int i = 0; i < cell2->GetNumberOfPoints(); i++) {
-      printf("%lld ", cell2->GetPointId(i));
+      std::cout << cell2->GetPointId(i) << " ";
     }
-    printf("]");
+    std::cout << "]";
   };
 
   for (int i = 0; i < this->poly_data_->GetNumberOfCells(); i++) {
     vtkCell* cell1 = this->poly_data_->GetCell(i);
     vtkCell* cell2 = other_mesh.poly_data_->GetCell(i);
 
     if (cell1->GetNumberOfPoints() != cell2->GetNumberOfPoints()) {
-      printf("%ith face not equal (", i);
+      std::cout << i << "th face not equal (";
       printCells(cell1, cell2);
-      printf(")\n");
+      std::cout << ")\n";
       return false;
     }
 
+    std::vector<vtkIdType> cell1Points(cell1->GetNumberOfPoints());
+    std::vector<vtkIdType> cell2Points(cell2->GetNumberOfPoints());
+
     for (int pi = 0; pi < cell1->GetNumberOfPoints(); pi++) {
-      if (cell1->GetPointId(pi) != cell2->GetPointId(pi)) {
-        printf("%ith face not equal (", i);
-        printCells(cell1, cell2);
-        printf(")\n");
-        return false;
-      }
+      cell1Points[pi] = cell1->GetPointId(pi);
+      cell2Points[pi] = cell2->GetPointId(pi);
+    }
+
+    std::sort(cell1Points.begin(), cell1Points.end());
+    std::sort(cell2Points.begin(), cell2Points.end());
+
+    if (cell1Points != cell2Points) {
+      std::cout << i << "th face not equal (";
+      printCells(cell1, cell2);
+      std::cout << ")\n";
+      return false;
     }
   }
 
@@ -1521,7 +1532,7 @@ bool Mesh::compareField(const Mesh& other_mesh, const std::string& name1, const
           return false;
         }
       } else {
-        if (!epsEqual(v1, v2, 1e-5)) {
+        if (!epsEqual(v1, v2, 1e-3)) {
           printf("%ith values not equal (%0.8f != %0.8f)\n", i, v1, v2);
           return false;
         }