Fix osx distribution

build_tools/BUILD_INSTRUCTIONS.md

@@ -19,6 +19,10 @@ for the ChiSurf.app. Unnecessary folders and file listed in `remove_list.txt`
 are stripped from the ChiSurf.app folder. Finally, the ChiSurf.app is bundeled 
 in a .dmg image that is placed in the ``dist`` folder. 
 
+```
+./osx/build-osx-app.sh -f=../env_osx.yml -i=../chisurf/gui/resources/icons/cs_logo.png -n=ChiSurf -m=chisurf -p=.. -o=../dist
+```
+
 ## Windows
 
 The Windows installation of ChiSurf is effectively a conda environment with

build_tools/osx/build-osx-app.sh

@@ -11,12 +11,12 @@ get_abs_filename() {
   echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")"
 }
 
+
 export ICON_FILE=icon.png
-export CONDA_ENVIRONMENT_YAML=environment.yml
+export CONDA_ENVIRONMENT_YAML=env_osx.yml
+
 # The directory of the build-osx-app.sh script
-export SCRIPT_DIR="."
-SCRIPT_DIR=$("pwd")
-echo $SCRIPT_DIR
+export SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
 
 function print_usage() {
     echo "build-osx-app.sh [-i] [--template] $APP_NAME.app
@@ -85,26 +85,47 @@ case $i in
     shift
 done
 
+
 # The target directory of the .app
 mkdir "$OUTPUT_PATH"
+OUTPUT_PATH=$(cd "$OUTPUT_PATH" && pwd)
+PYTHON_MODULE_PATH=$(cd "$PYTHON_MODULE_PATH" && pwd)
+
 export APP_FOLDER=${1:-$OUTPUT_PATH/$APP_NAME.app}
-APP_FOLDER="$(cd "$(dirname "$APP_FOLDER")" && pwd)/$(basename "$APP_FOLDER")"
-echo "App folder: $APP_FOLDER"
-mkdir "$APP_FOLDER"
+mkdir -p "$APP_FOLDER"
+APP_FOLDER=$(cd "$APP_FOLDER" && pwd)
 
-source $CONDA_PREFIX/etc/profile.d/conda.sh
 mamba env create -f $CONDA_ENVIRONMENT_YAML --prefix "$APP_FOLDER/Contents" --force
 conda activate "$APP_FOLDER/Contents"
 mamba install -y nomkl jinja2
-mkdir "$APP_FOLDER/Contents/MacOS"
-mkdir "$APP_FOLDER/Contents/Resources"
+mkdir -p "$APP_FOLDER/Contents/MacOS"
+mkdir -p "$APP_FOLDER/Contents/Resources"
 
 cd $PYTHON_MODULE_PATH
-cp -R $PYTHON_MODULE "$APP_FOLDER/Contents"
+export SITE_PACKAGE_PATH=`$APP_FOLDER/Contents/bin/python -c 'import site; print(site.getsitepackages()[0])'`
+cp -R $PYTHON_MODULE $SITE_PACKAGE_PATH
+
+function print_values() {
+    echo "Input values:"
+    echo "-----------------------"
+    echo "Conda Environment YAML: $CONDA_ENVIRONMENT_YAML"
+    echo "Icon File:              $ICON_FILE"
+    echo "Python Module:          $PYTHON_MODULE"
+    echo "App Name:               $APP_NAME"
+    echo "Output Path:            $OUTPUT_PATH"
+    echo "Python Module Path:     $PYTHON_MODULE_PATH"
+    echo "Site package Path:      $SITE_PACKAGE_PATH"
+    echo "App folder:             $APP_FOLDER"
+    echo "-----------------------"
+}
+print_values
+
 
-# generate icns file
+# generate icons file
 cd $SCRIPT_DIR
 python generate-iconset.py $SCRIPT_DIR/resources/AppIcon.png
+python generate-iconset.py resources/VolumeIcon.png
+
 # also update the icon with fileicon
 $SCRIPT_DIR/fileicon set "$APP_FOLDER" "$SCRIPT_DIR/resources/AppIcon.icns"
 
@@ -117,26 +138,21 @@ $SCRIPT_DIR/create_app_plist.py \
   -i $SCRIPT_DIR/resources/AppIcon.icns \
   -p $SCRIPT_DIR/plist_template \
   -t $SCRIPT_DIR/launch_template
-cd $SCRIPT_DIR
+cd $APP_FOLDER/Contents
+./bin/python -m compileall .
 
-echo Remove files and folders from content folder: "$CONTENT_FOLDER"
-while read p; do
-  echo "removing: $APP_FOLDER/Contents/$p"
-  rm -rf $CONTENT_FOLDER$p
-done <"$SCRIPT_DIR/remove_list.txt"
-
-test -f ../dist/$APP_NAME-Installer.dmg && rm ../dist/$APP_NAME-Installer.dmg
-python generate-iconset.py resources/VolumeIcon.png
+cd $SCRIPT_DIR
 ./create-dmg/create-dmg \
   --volname "$APP_NAME Installer" \
+  --volicon "./resources/VolumeIcon.icns" \
   --window-pos 200 120 \
   --window-size 800 400 \
   --icon-size 100 \
   --icon "$APP_NAME.app" 200 190 \
   --hide-extension "$APP_NAME.app" \
   --app-drop-link 600 185 \
-  --volicon resources/VolumeIcon.icns \
+  --skip-jenkins \
+  --sandbox-safe \
+  --no-internet-enable \
   "$OUTPUT_PATH/$APP_NAME-Installer.dmg" \
-  "$OUTPUT_PATH"
-./fileicon set "$OUTPUT_PATH/$APP_NAME-Installer.dmg" ./resources/VolumeIcon.icns
-rm -rf $OUTPUT_PATH/$APP_NAME.app
+  "$APP_FOLDER/.."

env_osx.yml

@@ -0,0 +1,41 @@
+name: chisurf
+
+channels:
+  - conda-forge
+  - tpeulen
+  - defaults
+
+dependencies:
+  - python =3.10
+  - numpy <=1.23
+  - pyyaml
+  - pyqtgraph
+  - matplotlib
+  - deprecation
+  - scikit-fluorescence
+  - typing_extensions 4.2.*
+  - typing-extensions 4.2
+  - typing_utils 0.1.*
+  - scipy 1.11.*
+  - numba 0.57.*
+  - tttrlib
+  - imp
+  - mdtraj
+  - pdb2pqr 3.6.1
+  - propka
+  - ipython 7.*.*
+  - chinet >=0.0.8
+  - labellib
+  - pyopencl 2023.*
+  - pytools 2023.*
+  - emcee 3.1.*
+  - pyopengl 3.1.*
+  - pymol-open-source 2.5.*
+  - tttrconvert
+  - qscintilla2
+  - k2dist
+  - python-docx 1.0.*
+  - qtconsole 5.*
+  - ndxplorer
+  - clsmview
+  - pyqtwebengine