Merge pull request #162 from MetaCell/feature/PSYNEU-140

PSYNEU-140 - Install MAC symlink on user directory to avoid Permissions Denied errors. Adds Desktop Icon as part of script installation #145

.gitignore

@@ -48,4 +48,6 @@ yalc.lock
 #prettier config
 .prettierrc.json
 
-.idea
+.idea
+
+package/.eggs

package/README.md

@@ -3,35 +3,72 @@
 Download bash script to install [here](https://raw.githubusercontent.com/MetaCell/PsyNeuLinkView/feature/PSYNEU-140/package/linux_installer.sh).
 It's recommended to download it in your home directory. 
 
-On terminal, go to your root directory
+On terminal, go to your home directory
 ```
 cd ~
 ```
 
+Change file permissions to allow user to run it
+```
+chmod + x linux_installer.sh
+```
+
 And run installer 
 ```
-bash -i linux_installer.sh
+./linux_installer.sh
+```
+
+After installation is done:
+
+If conda environment is already active, run 
+```
+psyneulinkviewer
+```
+
+If conda environment is not active, then run :
+```
+source ~/.profile
+conda activate psyneulinkview
+psyneulinkviewer
 ```
 
-The application should open up after succesfully installing psyneulinkviewer.
+The application should open up succesfully after this. An icon will be visible on the Desktop as well.
 
 # Installing on MAC
 
 Download bash script to install [here](https://raw.githubusercontent.com/MetaCell/PsyNeuLinkView/feature/PSYNEU-140/package/mac_installer.sh).
 It's recommended to download it in your home directory. 
 
-On terminal, go to your root directory
+On terminal, go to your home directory
 ```
 cd ~
 ```
 
+Give user permissions to file
+```
+chmod +x mac_installer.sh
+```
+
 And run installer 
 ```
-bash -i mac_installer.sh
+./mac_installer.sh
+```
+
+After installation is done:
+
+If conda environment is already active, run 
+```
+open ~/psyneulinkviewer-darwin-x64/psyneulinkviewer.app/
 ```
 
-The application should open up after succesfully installing psyneulinkviewer.
+If conda environment is not active, then run :
+```
+source ~/.bash_profile
+conda activate psyneulinkview
+open ~/psyneulinkviewer-darwin-x64/psyneulinkviewer.app/
+```
 
+The application should open up succesfully after this. A desktop icon should be visible as well.
 
 # Installation process inside script
 
@@ -54,27 +91,8 @@ source ~/.profile
 source ~/.bash_profile  
 ```
 
-Then, the conda environment created is activated with command below:
-```
-conda activate psyneulinkview
-```
-
-Finally, the last step of the script opens the psyneulinkviewer application:
+Then, a desktop file is created on the Desktop which allows users to open the application this way
 
-On linux:
-```
-psyneulinkviewer
-```
-
-On Mac:
-```
-open /usr/local/bin/psyneulinkviewer-darwin-x64/psyneulinkviewer.app
-```
-
-The psyneulinkviewer application is installed on user directory:
-```
-/usr/local/bin/
-```
 
 # Psyneulinkviewer Requirements
 

package/linux_installer.sh

@@ -1,2 +1,46 @@
-#!/usr/bin/env bash -l
-pip install -vv psyneulinkviewer && source ~/.profile && conda activate psyneulinkview && psyneulinkviewer
+#!/bin/bash
+pip install -vv psyneulinkviewer --break-system-packages --use-pep517 && . ~/.profile && sudo chown root:root /usr/local/bin/psyneulinkviewer-linux-x64/chrome-sandbox && sudo chmod 4755 /usr/local/bin/psyneulinkviewer-linux-x64/chrome-sandbox
+
+# Variables
+APP_NAME="PsyneulinkViewer"                                  # Name of the application
+SYMLINK_PATH="psyneulinkviewer"           # Symlink to the application you want to launch
+CONDA_ENV=$PSYNEULINK_ENV                                  # Conda environment to activate if none is active
+ICON_PATH="/usr/local/bin/psyneulinkviewer-linux-x64/resources/app/build/logo.png"                 # Path to the custom icon
+DESKTOP_FILE="$HOME/Desktop/$APP_NAME.desktop"     # Path where the desktop shortcut will be created
+
+# Function to check if a conda environment is already active
+is_conda_active() {
+    if [[ -n "$CONDA_DEFAULT_ENV" ]]; then
+        echo "Conda environment '$CONDA_DEFAULT_ENV' is already active."
+        return 0
+    else
+        echo "No active conda environment found. Activating '$CONDA_ENV'..."
+        return 1
+    fi
+}
+
+# Creating the .desktop file for the application
+echo "[Desktop Entry]" > "$DESKTOP_FILE"
+echo "Version=1.0" >> "$DESKTOP_FILE"
+echo "Name=$APP_NAME" >> "$DESKTOP_FILE"
+
+# Create the Exec command: Check if conda environment is active, if not activate the specified one
+echo "Exec=bash -c '. ~/miniconda3/etc/profile.d/conda.sh && \
+conda activate $CONDA_ENV && \
+$SYMLINK_PATH'" >> "$DESKTOP_FILE"
+
+# Set the custom icon
+echo "Icon=$ICON_PATH" >> "$DESKTOP_FILE"
+echo "Type=Application" >> "$DESKTOP_FILE"
+echo "Terminal=false" >> "$DESKTOP_FILE"
+echo "Categories=Application;" >> "$DESKTOP_FILE"
+
+APP_DESKTOP="$HOME/.local/share/applications/$APP_NAME.desktop"
+
+cp "$DESKTOP_FILE" "$APP_DESKTOP"
+# Make the .desktop file executable
+chmod +x "$DESKTOP_FILE"
+rm "$DESKTOP_FILE"
+chmod +x "$APP_DESKTOP"
+
+echo "Application shortcut created at $APP_DESKTOP"

package/mac_installer.sh

@@ -1,2 +1,74 @@
-#!/usr/bin/env bash -l
-pip install -vv psyneulinkviewer --break-system-packages && source ~/.bash_profile && conda activate psyneulinkview && open /usr/local/bin/psyneulinkviewer-darwin-x64/psyneulinkviewer.app/
+#!/bin/bash
+pip install -vv psyneulinkviewer --break-system-packages --use-pep517 && source ~/.bashrc_profile
+
+# Variables - adjust these for your setup
+APP_PATH="$HOME/psyneulinkviewer-darwin-x64/psyneulinkviewer.app/"  # Replace with the full path to the application
+CONDA_ENV=$PSYNEULINK_ENV              # Replace with your Conda environment name
+ICON_PATH="$HOME/psyneulinkviewer-darwin-x64/psyneulinkviewer.app/Contents/Resources/electron.icns"        # Replace with the full path to your custom icon (should be in .icns format)
+SHORTCUT_NAME="PsyneulinkViewer"         # Name for the desktop shortcut
+
+# Define paths
+DESKTOP_PATH="$HOME/Desktop"
+APP_SHORTCUT_PATH="$DESKTOP_PATH/$SHORTCUT_NAME.app"
+COMMAND_FILE_PATH="$APP_SHORTCUT_PATH/Contents/MacOS/$SHORTCUT_NAME"
+ICON_FILE_PATH="$APP_SHORTCUT_PATH/Contents/Resources/$SHORTCUT_NAME.icns"
+
+# Create .app structure
+mkdir -p "$APP_SHORTCUT_PATH/Contents/MacOS"
+mkdir -p "$APP_SHORTCUT_PATH/Contents/Resources"
+
+# Function to check if a conda environment is active
+is_conda_active() {
+    # Check if the CONDA_DEFAULT_ENV variable is set, meaning a conda environment is active
+    if [ -z "$CONDA_DEFAULT_ENV" ]; then
+        return 1 # No active conda environment
+    else
+        return 0 # A conda environment is already active
+    fi
+}
+
+# Write the .command file that launches the app with conda environment
+cat <<EOL > "$COMMAND_FILE_PATH"
+#!/bin/bash
+source ~/.bashrc_profile
+source ~/miniconda3/etc/profile.d/conda.sh
+conda activate $CONDA_ENV
+open "$APP_PATH"
+EOL
+
+# Make the script executable
+chmod +x "$COMMAND_FILE_PATH"
+
+# Copy the custom icon
+cp "$ICON_PATH" "$ICON_FILE_PATH"
+
+# Create Info.plist for the app
+cat <<EOL > "$APP_SHORTCUT_PATH/Contents/Info.plist"
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+    <key>CFBundleExecutable</key>
+    <string>$SHORTCUT_NAME</string>
+    <key>CFBundleIconFile</key>
+    <string>$SHORTCUT_NAME</string>
+    <key>CFBundleIdentifier</key>
+    <string>com.example.$SHORTCUT_NAME</string>
+    <key>CFBundleName</key>
+    <string>$SHORTCUT_NAME</string>
+    <key>CFBundleVersion</key>
+    <string>1.0</string>
+    <key>CFBundlePackageType</key>
+    <string>APPL</string>
+</dict>
+</plist>
+EOL
+
+# Set the correct file permissions for the .app
+chmod -R 755 "$APP_SHORTCUT_PATH"
+
+# Touch the app to refresh Finder so it displays the correct icon
+touch "$APP_SHORTCUT_PATH"
+
+echo "Shortcut created at $DESKTOP_PATH/$SHORTCUT_NAME.app"
+

package/psyneulinkviewer.egg-info/PKG-INFO

@@ -0,0 +1,11 @@
+Metadata-Version: 2.1
+Name: psyneulinkviewer
+Version: 0.4.8
+Home-page: https://github.com/metacell/psyneulinkviewer
+Author: metacell
+Author-email: dev@metacell.us
+Requires-Python: >=3.7
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: wget
+Requires-Dist: packaging<=24.0

package/psyneulinkviewer.egg-info/SOURCES.txt

@@ -0,0 +1,14 @@
+LICENSE
+README.md
+setup.py
+psyneulinkviewer/__init__.py
+psyneulinkviewer/conda.py
+psyneulinkviewer/configuration.py
+psyneulinkviewer/node.py
+psyneulinkviewer/rosetta.py
+psyneulinkviewer/start.py
+psyneulinkviewer.egg-info/PKG-INFO
+psyneulinkviewer.egg-info/SOURCES.txt
+psyneulinkviewer.egg-info/dependency_links.txt
+psyneulinkviewer.egg-info/requires.txt
+psyneulinkviewer.egg-info/top_level.txt

package/psyneulinkviewer.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

package/psyneulinkviewer.egg-info/requires.txt

@@ -0,0 +1,3 @@
+requests
+wget
+packaging<=24.0

package/psyneulinkviewer.egg-info/top_level.txt

@@ -0,0 +1 @@
+psyneulinkviewer

package/psyneulinkviewer/conda.py

@@ -31,6 +31,7 @@ def create_env():
             logging.info("Conda environment found %s", env_name)
     except Exception as error:
         logging.info("Conda environment not found")
+        env_name = None
 
     if env_name is None:
         command = get_conda_installed_path() + configuration.create_env
@@ -51,7 +52,7 @@ def shell_source(script):
 def install_conda():
     import wget
     if platform.system() == 'Linux':
-        bash_file = wget.download(configuration.linux_conda_bash, out="tmp")
+        bash_file = wget.download(configuration.linux_conda_bash)
     elif platform.system() == 'Darwin':
         bash_file = wget.download(configuration.mac_conda_bash)
 
@@ -138,11 +139,7 @@ def detect_activated_conda() :
                 logging.info("Conda environment not detected active : %s", env_name)
                 env_name = None
             else:
-                if env_name == configuration.env_name:
-                    logging.info("Conda environment detected active : %s", env_name)
-                else:
-                    logging.info("Active environment not matching : %s", configuration.env_name)
-                    env_name = None
+                logging.info("Conda environment detected active : %s", env_name)
     except Exception as error:
         logging.info("Environment not found active: %s ", error)
 
@@ -159,6 +156,7 @@ def detect_activated_conda_location() :
         if env_location:
             env_location = re.search('(?<=base environment : )(/[a-zA-Z0-9\./]*[\s]?)', env_location)
             env_location = env_location.group(0)
+            env_location = env_location.strip()
     except Exception as error:
         logging.info("Environment not found active: %s ", error)
 

package/psyneulinkviewer/configuration.py

@@ -4,8 +4,9 @@
 
 releases_url = 'https://api.github.com/repos/MetaCell/PsyNeuLinkView/releases'
 application_url = "psyneulinkviewer-linux-x64/psyneulinkviewer"
-application_url_mac = "psyneulinkviewer-linux-x64/psyneulinkviewer.app"
-
+application_url_mac = "psyneulinkviewer-darwin-x64/psyneulinkviewer.app"
+installation_folder_name = "/psyneulinkviewer-linux-x64"
+installation_folder_name_mac = "/psyneulinkviewer-darwin-x64"
 
 #Symlink
 symlink = "/usr/local/bin/psyneulinkviewer"

package/psyneulinkviewer/node.py

@@ -51,8 +51,12 @@ def check_node_installation():
             logging.error("Exiting, node must be installed to continue...")
             sys.exit()
     from packaging.version import Version
-    if Version(node_version) > Version(configuration.node_required_version):
-        logging.info("Node version exists and valid, %s", node_version)
-    else:
+    if node_version is None:
         logging.error("Node version not up to date, update required")
-        install_node()
+        install_node()
+    else:
+        if Version(node_version) > Version(configuration.node_required_version):
+            logging.info("Node version exists and valid, %s", node_version)
+        else:
+            logging.error("Node version not up to date, update required")
+            install_node()