Try to fix install_shapeworks.sh for mac pkg version (read only /Appl…

…ications/ShapeWorks)

Installation/install_python_module.bat

@@ -1,9 +1,6 @@
 REM Installs the shapeworks python module.
 REM  NOTE: assumes all library dependencies are in this directory\bin
 
-REM install pip module
-call pip install Python\shapeworks.tar.gz
-
 set CONDA_INSTALL_DIR=%CONDA_PREFIX%\lib\site-packages\shapeworks
 
 :: format windows path to use forward slashes

Installation/install_python_module.sh

@@ -3,8 +3,6 @@
 # Installs shapeworks Python module
 # Ensures conda Python module is able to locate correct shapeworks_py binary module.
 
-# install pip module
-if ! pip install Python/shapeworks; then exit -1; fi
 
 CONDA_INSTALL_DIR=`pip show shapeworks | grep Location | awk '{print $2}'`/shapeworks
 

Python/shapeworks/shapeworks/setup_path.py

@@ -1,3 +1,3 @@
 def setup_binary_path():
     import sys
-    sys.path.append("placeholder_string")
+    sys.path.append("/Users/amorris/sci/shapeworks/code/bin")

Support/package.sh

@@ -46,6 +46,14 @@ rm -rf "package/$VERSION"
 
 mkdir -p "package/$VERSION"
 
+# Build python package tarballs
+# Pip can't install these otherwise from a read-only area like /Applications
+for package in DataAugmentationUtilsPackage DatasetUtilsPackage DeepSSMUtilsPackage DocumentationUtilsPackage ShapeCohortGenPackage shapeworks ; do
+    cd Python
+    tar czvf ${package}.tar.gz $package
+    cd ..
+done
+
 BASE_LIB=${INSTALL_DEP_DIR}/lib
 cp -a $INSTALL_DIR/* "package/${VERSION}"
 cp -a Examples "package/${VERSION}"

Support/package_windows.sh

@@ -48,7 +48,8 @@ cp -r $BUILD/bin/Release bin
 rm bin/*Tests.pdb bin/Recon*.pdb bin/Mesh*.pdb
 rm -rf Post
 
-# Build python packages
+# Build python package tarballs
+# Pip can't install these otherwise from a read-only area like C:\Program Files\ShapeWorks
 for package in DataAugmentationUtilsPackage DatasetUtilsPackage DeepSSMUtilsPackage DocumentationUtilsPackage ShapeCohortGenPackage shapeworks ; do
     cd Python
     tar czvf ${package}.tar.gz $package

install_shapeworks.bat

@@ -48,6 +48,8 @@ call pip install Python/DocumentationUtilsPackage.tar.gz
 call pip install Python/DataAugmentationUtilsPackage.tar.gz
 call pip install Python/DeepSSMUtilsPackage.tar.gz
 call pip install Python/ShapeCohortGenPackage.tar.gz
+call pip install Python/shapeworks.tar.gz
+
 
 REM install the shapeworks python module and conda [de]activate scripts
 call .\Installation\install_python_module.bat

install_shapeworks.sh

@@ -188,13 +188,14 @@ function install_conda() {
   if ! pip install seaborn==0.11.2;                     then return 1; fi
   if ! pip install swcc==1.0.5;                         then return 1; fi
   if ! pip install scikit-learn==1.1.1;                 then return 1; fi
-  if ! pip install Python/DatasetUtilsPackage;          then return 1; fi # install the local GirderConnector code as a package
-  if ! pip install Python/DocumentationUtilsPackage;    then return 1; fi # install shapeworks auto-documentation as a package
-  if ! pip install Python/DataAugmentationUtilsPackage; then return 1; fi # install data augmentation code as a package
-  if ! pip install Python/DeepSSMUtilsPackage;          then return 1; fi # install DeepSSM code as a package
-  if ! pip install Python/ShapeCohortGenPackage;        then return 1; fi # install shape cohort generation code as a package
-
 
+  for package in DataAugmentationUtilsPackage DatasetUtilsPackage DeepSSMUtilsPackage DocumentationUtilsPackage ShapeCohortGenPackage shapeworks ; do
+    if [[ -e Python/${package}.tar.gz ]] ; then
+      if ! pip install Python/${package}.tar.gz;        then return 1; fi
+    else
+      if ! pip install Python/${package};               then return 1; fi
+    fi
+  done
 
   ./Installation/install_python_module.sh   # install python module
   ./Installation/conda_env_setup.sh         # install conda [de]activate scripts