Merge pull request #2543 from SCIInstitute/amorris/merge-6.7

Merge ShapeWorks 6.7.0 changes

Author: akenmorris

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

@@ -12,6 +12,7 @@ on:
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
   BUILD_TYPE: Release
+  MACOSX_DEPLOYMENT_TARGET: "12.0"
   SW_CLOUD_LOGIN: ${{ secrets.CLOUD_LOGIN }}
   CACHE_HOST: ${{ secrets.SSH_HOST }}
   GA_MEASUREMENT_ID: ${{ secrets.GA_MEASUREMENT_ID }}
@@ -55,7 +56,7 @@ jobs:
       uses: actions/cache/restore@v3
       with:
         path: /Users/runner/install
-        key: ${{ runner.os }}-arm64-deps-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+        key: ${{ runner.os }}-arm64-deps-osx${{ env.MACOSX_DEPLOYMENT_TARGET }}-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
 
     - name: Build Dependencies
       if: steps.cache-deps-restore.outputs.cache-hit != 'true'
@@ -67,11 +68,11 @@ jobs:
       uses: actions/cache/save@v3
       with:
         path: /Users/runner/install
-        key: ${{ runner.os }}-arm64-deps-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+        key: ${{ runner.os }}-arm64-deps-osx${{ env.MACOSX_DEPLOYMENT_TARGET }}-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.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 -Wno-enum-constexpr-conversion" -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 ..
+      run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_LIBTOOL=/usr/bin/libtool -DCMAKE_CXX_FLAGS="-g -Wno-enum-constexpr-conversion" -DCMAKE_OSX_DEPLOYMENT_TARGET=$MACOSX_DEPLOYMENT_TARGET -DCMAKE_PREFIX_PATH=$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}

.github/workflows/build-mac.yml

@@ -12,6 +12,7 @@ on:
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
   BUILD_TYPE: Release
+  MACOSX_DEPLOYMENT_TARGET: "12.0"
   SW_CLOUD_LOGIN: ${{ secrets.CLOUD_LOGIN }}
   CACHE_HOST: ${{ secrets.SSH_HOST }}
   GA_MEASUREMENT_ID: ${{ secrets.GA_MEASUREMENT_ID }}
@@ -56,7 +57,7 @@ jobs:
       uses: actions/cache/restore@v3
       with:
         path: /Users/runner/install
-        key: ${{ runner.os }}-intel-deps-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+        key: ${{ runner.os }}-intel-deps-osx${{ env.MACOSX_DEPLOYMENT_TARGET }}-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
 
     - name: Build Dependencies
       shell: bash -l {0}
@@ -67,11 +68,11 @@ jobs:
       uses: actions/cache/save@v3
       with:
         path: /Users/runner/install
-        key: ${{ runner.os }}-intel-deps-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+        key: ${{ runner.os }}-intel-deps-osx${{ env.MACOSX_DEPLOYMENT_TARGET }}-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.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=OFF -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET ..
+      run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_LIBTOOL=/usr/bin/libtool -DCMAKE_CXX_FLAGS=-g -DCMAKE_OSX_DEPLOYMENT_TARGET=$MACOSX_DEPLOYMENT_TARGET -DCMAKE_PREFIX_PATH=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DPython3_ROOT_DIR:FILEPATH=${CONDA_PREFIX} -DUSE_OPENMP=OFF -DBuild_Studio=ON -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DBUILD_DOCUMENTATION=OFF -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET ..
 
     - name: make
       shell: bash -l {0}

CMakeLists.txt

@@ -4,9 +4,9 @@ cmake_minimum_required(VERSION 3.20)
 # SHAPEWORKS VERSION
 ###########################################
 SET(SHAPEWORKS_MAJOR_VERSION 6 CACHE INTERNAL "Major version number" FORCE)
-SET(SHAPEWORKS_MINOR_VERSION 7 CACHE INTERNAL "Minor version number" FORCE)
+SET(SHAPEWORKS_MINOR_VERSION 8 CACHE INTERNAL "Minor version number" FORCE)
 SET(SHAPEWORKS_PATCH_VERSION 0 CACHE INTERNAL "Patch version number" FORCE)
-SET(SHAPEWORKS_VERSION_STRING "6.7.0-dev")
+SET(SHAPEWORKS_VERSION_STRING "6.8.0-dev")
 SET(SHAPEWORKS_VERSION "${SHAPEWORKS_MAJOR_VERSION}.${SHAPEWORKS_MINOR_VERSION}.${SHAPEWORKS_PATCH_VERSION}")
 
 # First, check that files were checked out properly using git-lfs

Installation/install_python_module.sh

@@ -4,7 +4,7 @@
 # Ensures conda Python module is able to locate correct shapeworks_py binary module.
 
 
-CONDA_INSTALL_DIR=`pip show shapeworks | grep Location | awk '{print $2}'`/shapeworks
+CONDA_INSTALL_DIR=`python -m pip show shapeworks | grep Location | awk '{print $2}'`/shapeworks
 
 # check if $CONDA_INSTALL_DIR is under $CONDA_PREFIX
 if [[ "$CONDA_INSTALL_DIR" != "$CONDA_PREFIX"* ]]; then

Libs/Application/Job/PythonWorker.h

@@ -18,7 +18,7 @@ class PythonWorker : public QObject {
   Q_OBJECT
 
  public:
-  constexpr static const char* python_api_version = "6.7";
+  constexpr static const char* python_api_version = "6.8";
 
   PythonWorker();
   ~PythonWorker();

Python/shapeworks/shapeworks/utils.py

@@ -172,7 +172,7 @@ def compute_line_indices(n, is_closed=True):
 
 
 def get_api_version():
-    return "6.7"
+    return "6.8"
 
 
 def set_sw_logger(log_object):

devenv.sh

@@ -11,7 +11,7 @@
 # compiled portion of the Python bindings).
 #
 
-SW_MAJOR_VERSION=6.7
+SW_MAJOR_VERSION=6.8
 
 (return 0 2>/dev/null) && sourced=1 || sourced=0
 

docs/dev/release-process.md

@@ -19,7 +19,7 @@ SET(SHAPEWORKS_VERSION "${SHAPEWORKS_MAJOR_VERSION}.${SHAPEWORKS_MINOR_VERSION}.
 
 TODO - This should be automated from a single place
 
-- `Studio/Python/PythonWorker.h`
+- `Libs/Application/Job/PythonWorker.h`
 
 ```
   constexpr static const char* python_api_version = "6.5";
@@ -46,6 +46,12 @@ python -c "import sys; print(sys.prefix)" > "%USERPROFILE%\.shapeworks\python_ho
 echo %PATH% > "%USERPROFILE%\.shapeworks\path_6.5.txt"
 ```
 
+- `devenv.sh`
+
+```
+SW_MAJOR_VERSION=6.5
+```
+
 * Update Release Notes
 
 - Update `docs/about/release_notes.md` with the new release notes

install_shapeworks.bat

@@ -85,9 +85,9 @@ call .\Installation\install_python_module.bat || goto :error
 call .\Installation\conda_env_setup.bat || goto :error
 
 md "%USERPROFILE%\.shapeworks"
-python -c "import sys; print('\n'.join(sys.path))" > "%USERPROFILE%\.shapeworks\python_path_6.7.txt"
-python -c "import sys; print(sys.prefix)" > "%USERPROFILE%\.shapeworks\python_home_6.7.txt"
-echo %PATH% > "%USERPROFILE%\.shapeworks\path_6.7.txt"
+python -c "import sys; print('\n'.join(sys.path))" > "%USERPROFILE%\.shapeworks\python_path_6.8.txt"
+python -c "import sys; print(sys.prefix)" > "%USERPROFILE%\.shapeworks\python_home_6.8.txt"
+echo %PATH% > "%USERPROFILE%\.shapeworks\path_6.8.txt"
 call conda info
 
 REM === Validating installation ===

install_shapeworks.sh

@@ -2,7 +2,7 @@
 # Installs conda environment for building ShapeWorks
 #
 
-SW_MAJOR_VERSION=6.7
+SW_MAJOR_VERSION=6.8
 
 # Set up logging
 INSTALL_LOG="install_shapeworks_$(date +%Y%m%d_%H%M%S).log"
@@ -173,7 +173,7 @@ function install_conda() {
   if [[ $(uname -s) == "Darwin" ]] && [[ $(uname -m) == "x86_64" ]]; then
     # Intel Mac - use older versions with NumPy 1.x
     if ! python -m light_the_torch install torch==2.2.2 torchaudio==2.2.2 torchvision==0.17.2; then return 1; fi
-    pip install "numpy<2"
+    python -m pip install "numpy<2"
   else
     # Apple Silicon, Linux, Windows - use latest with NumPy 2.x support
     if ! python -m light_the_torch install torch==2.8.0 torchaudio==2.8.0 torchvision==0.23.0; then return 1; fi
@@ -183,13 +183,13 @@ function install_conda() {
   # open3d needs to be installed differently on each platform so it's not part of python_requirements.txt
   OPEN3D_INSTALLED=NO
   if [[ "$(uname)" == "Linux" ]]; then
-      if pip install open3d-cpu==0.19.0; then
+      if python -m pip install open3d-cpu==0.19.0; then
         OPEN3D_INSTALLED=YES
       else
         echo "WARNING: open3d-cpu could not be installed. Network analysis features will not be available."
       fi
   elif [[ "$(uname)" == "Darwin" ]]; then
-      if pip install open3d==0.19.0; then
+      if python -m pip install open3d==0.19.0; then
         OPEN3D_INSTALLED=YES
         if [[ "$(uname -m)" == "arm64" ]]; then
           pushd $CONDA_PREFIX/lib/python3.12/site-packages/open3d/cpu
@@ -202,7 +202,7 @@ function install_conda() {
         echo "WARNING: open3d could not be installed. Network analysis features will not be available."
       fi
   else
-      if pip install open3d==0.19.0; then
+      if python -m pip install open3d==0.19.0; then
         OPEN3D_INSTALLED=YES
       else
         echo "WARNING: open3d could not be installed. Network analysis features will not be available."
@@ -211,9 +211,9 @@ function install_conda() {
 
   for package in DataAugmentationUtilsPackage DatasetUtilsPackage MONAILabelPackage DeepSSMUtilsPackage DocumentationUtilsPackage ShapeCohortGenPackage shapeworks ; do
     if [[ -e Python/${package}.tar.gz ]] ; then
-      if ! pip install Python/${package}.tar.gz;        then return 1; fi
+      if ! python -m pip install Python/${package}.tar.gz;        then return 1; fi
     else
-      if ! pip install Python/${package};               then return 1; fi
+      if ! python -m pip install Python/${package};               then return 1; fi
     fi
   done
 
@@ -270,7 +270,7 @@ if install_conda; then
   conda list
 
   echo "Pip installed packages:"
-  pip list
+  python -m pip list
 
   conda clean -t -y