Merge pull request #161 from MetaCell/feature/PSYNEU-140

#PSYNEU-140 - Fixing installation process on Mac and Linux, #PSYNEU-138 - Add bash scripts to install and run psyneulinkviewer in mac and linux, updates read me with instructions

package/README.md

@@ -1,29 +1,122 @@
-# PsyNeuLinkView Package Building
+# Installing on Linux
 
-To build pip package
+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
 ```
-cd package
-python3 -m build
+cd ~
+```
+
+And run installer 
+```
+sudo bash -i linux_installer.sh
 ```
 
-To upload to distribution server. You will need token shared privately. 
+The application should open up after succesfully installing psyneulinkviewer.
+
+# 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
 ```
-twine upload dist/*
+cd ~
 ```
 
-To pip install local package created in previous steps
+And run installer 
 ```
-python3 -m pip install --no-index --find-links=package_directory_path + "/dist" psyneulinkview
+sudo bash -i mac_installer.sh
 ```
 
-# PsyNeuLinkView Installing from PyPI
+The application should open up after succesfully installing psyneulinkviewer.
+
 
-To install from PyPi
+# Installation process inside script
+
+The scripts above run the following commands in order:
+
+Firs installs the python module 'psyneulinkviewer' from PyPi
 ```
-pip install psyneulinkview --extra-index-url https://pypi.org/project/psyneulinkview
+sudo pip install psyneulinkviewer
 ```
+This commands installs required libraries and packages. Also creates a conda enviroment where the needed packages are installed.
 
-To run psyneulinkviewer
+After successfully installing the python package above, it reset the user's bash profile to apply the settings changes 
+- Linux
+```
+source ~/.profile  
+```
+
+- Mac 
+```
+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:
+
+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
+
+Psyneulinkviewer requires:
+
+- Python 3.11 and pip
+- Pip packages : psyneulink, graphviz, wget, packaging and requests
+- Conda 4.9.1 or above
+- Node 4.19.0 or above
+- Rosetta ( on Mac)
+
+All of these are downloaded and installed as part of psyneulinkviewer installation process.
+
+# Testing Models
+
+If all went well with installation, you should see the application running as in screenshot below :
+![image](https://github.com/user-attachments/assets/ec84044c-287a-4e39-bdf7-aa27cdc486f9)
+
+To test models, download [these models](https://github.com/MetaCell/PsyNeuLinkView/tree/feature/PSYNEU-140/test_models) and import one at a time to test. Each time a Model is open, the previous one will disappear. I recommend you start with the models inside 'working_tests', as those are the ones we know for sure should we working.
+
+To import go to File -> Open Models 
+
+# PsyNeuLinkView Package Building
+
+To build pip package
+```
+cd package
+python3 -m pip install build
+python3 -m build --sdist
+```
+
+To test local build
+```
+pip install dist/psyneulinkviewer-VERSIOn.tar.gz
+```
+
+To upload to distribution server. You will need token shared privately to be able to upload. 
+```
+python3 -m twine upload dist/*
+```
+
+To upload to test Pypi server
+```
+python3 -m twine upload --repository testpypi dist/*
+```

package/linux_installer.sh

@@ -0,0 +1,2 @@
+#!/usr/bin/env bash -l
+pip install -vv psyneulinkviewer && source ~/.profile && conda activate psyneulinkview && psyneulinkviewer

package/mac_installer.sh

@@ -0,0 +1,2 @@
+#!/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/

package/psyneulinkviewer/conda.py

@@ -3,38 +3,91 @@
 import sys
 import subprocess
 import logging
-import configuration
-import wget
 import platform
+import re
 from setuptools import setup, find_packages
 from setuptools.command.install import install
-from packaging.version import Version
+from psyneulinkviewer import configuration
 
 logger = logging.getLogger(__name__)
 logging.basicConfig(level=logging.INFO)
 
-def activate_env():
-    logging.info("Creating conda environment ")
-    subprocess.run(configuration.create_env, shell=True)
+conda_installed = False
 
-    logging.info("Activating conda ")
-    subprocess.run(configuration.activate_env, shell=True)
+def create_env():
+    env_name = None
+    try:
+        envs = subprocess.run(
+            ["conda", "env","list"],
+            capture_output = True,
+            text = True 
+        ).stdout
+        if envs is not None:
+            envs = envs.splitlines()
+            env_name = list(filter(lambda s: configuration.env_name in str(s), envs))[0]
+            env_name = str(env_name).split()[0]
+            logging.info("Environment found %s", env_name)
+        if env_name == configuration.env_name:
+            logging.info("Conda environment found %s", env_name)
+    except Exception as error:
+        logging.info("Conda environment not found")
+
+    if env_name is None:
+        command = get_conda_installed_path() + configuration.create_env
+        logging.info("Creating conda environment %s", command)
+        subprocess.run(command, shell=True)
+
+
+def shell_source(script):
+    """Sometime you want to emulate the action of "source" in bash,
+    settings some environment variables. Here is a way to do it."""
+    import subprocess, os
+    pipe = subprocess.Popen(". %s; env" % script, stdout=subprocess.PIPE, shell=True)
+    output = pipe.communicate()[0]
+    logging.info("Output %s", output)
+    env = dict((line.split("=", 1) for line in output.splitlines()))
+    os.environ.update(env)
 
 def install_conda():
-    if os.name == 'posix':
-        bash_file = wget.download(configuration.linux_conda_bash, out="psyneulinkviewer")
+    import wget
+    if platform.system() == 'Linux':
+        bash_file = wget.download(configuration.linux_conda_bash, out="tmp")
     elif platform.system() == 'Darwin':
-        bash_file = wget.download(configuration.mac_conda_bashf)
+        bash_file = wget.download(configuration.mac_conda_bash)
 
     logging.info("Installing conda %s", bash_file)
     logging.info(bash_file)
     subprocess.run("chmod +x " + bash_file, shell=True)
-    subprocess.run(bash_file + " -b -u -p ~/miniconda3", shell=True)
+    subprocess.run("bash " + bash_file + " -b -u -p " + configuration.conda_installation_path, shell=True)
+    subprocess.run(configuration.conda_binary + " init bash", shell=True)
+    subprocess.run(configuration.conda_binary + " init zsh", shell=True)
 
-    activate_env()
     logging.info("Clean up ")
     subprocess.run("rm -rf " + bash_file, shell=True)
 
+    conda_installed = True
+
+def get_conda_installed_path():
+    installation_path = detect_activated_conda_location()
+    logging.info("installation_path %s ", installation_path)
+    if installation_path is None:
+        if platform.system() == "Darwin":
+            installation_path = configuration.conda_installation_path_mac_default
+        logging.info("installation_path %s ", conda_installed)
+        installation_path = configuration.conda_installation_path
+
+    return installation_path.strip()
+
+def conda_binary_path():
+    installation_path = detect_activated_conda_location()
+    if conda_installed:
+        installation_path = configuration.conda_installation_path
+    else:
+        if installation_path is None:
+            if platform.system() == "Darwin":
+                installation_path = configuration.conda_installation_path_mac_default
+
+    return installation_path
 
 def check_conda_installation():
     conda_version = None
@@ -54,35 +107,59 @@ def check_conda_installation():
 
     if conda_version is None:
         logging.info("Conda is not installed")
-        user_input = input("Do you want to continue with conda installation? (yes/no): ")
-        if user_input.lower() in ["yes", "y"]:
-            logging.info("Continuing with conda installation...")
-            install_conda()
+        install_conda()
+    else:
+        from packaging.version import Version
+        if Version(conda_version) > Version(configuration.conda_required_version):
+            logging.info("Conda version exists and valid, %s", conda_version)
         else:
-            logging.error("Exiting, conda must be installed to continue...")
-            sys.exit()
+            logging.info("Conda version not up to date, updating version")
+            install_conda()
 
-    if Version(conda_version) > Version(configuration.conda_required_version):
-        logging.info("Conda version exists and valid, %s", conda_version)
+    env_name = detect_activated_conda()
+
+    if env_name is not None:
+        logging.info("Conda environment found and activated %s", env_name)
     else:
-        logging.error("Conda version not up to date, update required")
-        install_conda()
-        
+        create_env()
+
+def detect_activated_conda() :
     env_name = None
     try:
-        envs = subprocess.run(
-            ["conda", "env","list"],
+        env_name = subprocess.run(
+            ["conda", "info"],
             capture_output = True,
             text = True 
         ).stdout
-        if envs is not None:
-            envs = envs.splitlines()
-        active_env = list(filter(lambda s: '*' in str(s), envs))[0]
-        env_name = str(active_env).split()[0]
+        if env_name:
+            env_name = re.search('(?<=active environment : )(\w+)', env_name)
+            env_name = env_name.group(1)
+            if env_name == "None":
+                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
     except Exception as error:
-        logging.error("Environment not found active: %s ", error)
+        logging.info("Environment not found active: %s ", error)
+
+    return env_name
 
-    if env_name is not None:
-        logging.info("Conda environment found and activated %s", env_name)
-    else:
-        activate_env()
+def detect_activated_conda_location() :
+    env_location = None
+    try:
+        env_location = subprocess.run(
+            ["conda", "info"],
+            capture_output = True,
+            text = True 
+        ).stdout
+        if env_location:
+            env_location = re.search('(?<=base environment : )(/[a-zA-Z0-9\./]*[\s]?)', env_location)
+            env_location = env_location.group(0)
+    except Exception as error:
+        logging.info("Environment not found active: %s ", error)
+
+    return env_location

package/configuration.py → package/psyneulinkviewer/configuration.py

@@ -4,15 +4,28 @@
 
 releases_url = 'https://api.github.com/repos/MetaCell/PsyNeuLinkView/releases'
 application_url = "psyneulinkviewer-linux-x64/psyneulinkviewer"
+application_url_mac = "psyneulinkviewer-linux-x64/psyneulinkviewer.app"
+
+
+#Symlink
 symlink = "/usr/local/bin/psyneulinkviewer"
 extract_location = "/usr/local/bin"
 
 linux_conda_bash = "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"
 mac_conda_bash = "https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh"
 
-env_name = "psyneulinkviewer"
-create_env = "conda create --name " + env_name + " python=3.11"
-activate_env = "conda activate " + env_name
+env_name = "psyneulinkview"
+
+conda_installation_path = "~/miniconda3"
+conda_installation_path_mac_default = "/opt/miniconda3"
+
+conda_binary = "~/miniconda3/bin/conda"
+conda_binary_mac_default = "/opt/miniconda3/bin/conda"
+
+create_env = "/bin/conda create --name " + env_name + " python=3.11"
+
+binary_commands = " --verbose --no-capture-output --live-stream python -c 'from psyneulinkviewer.start import continue_on_conda; continue_on_conda()'"
+continue_on_conda_new_env = "/bin/conda run -n " + env_name + binary_commands
 
 rosetta_installation = "softwareupdate --install-rosetta --agree-to-license"