Merge pull request #153 from MetaCell/feature/PSYNEU-134

#PSYNEU-134 - Proof of concept creation python package for psyneulinkview

package/LICENSE

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+Copyright (c) 2018 The Python Packaging Authority
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# PsyNeuLinkView Package Building
+
+To build pip package
+```
+cd package
+python3 -m build
+```
+
+To upload to distribution server. You will need token shared privately. 
+```
+twine upload dist/*
+```
+
+To pip install local package created in previous steps
+```
+python3 -m pip install --no-index --find-links=package_directory_path + "/dist" psyneulinkview
+```
+
+# PsyNeuLinkView Installing from PyPI
+
+To install from PyPi
+```
+pip install psyneulinkview --extra-index-url https://pypi.org/project/psyneulinkview
+```
+
+To run psyneulinkviewer
+```
+psyneulinkviewer
+```

package/configuration.py

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+graphviz = "graphviz"
+psyneulink = "psyneulink"
+conda_required_version = "4.9.1"
+
+releases_url = 'https://api.github.com/repos/MetaCell/PsyNeuLinkView/releases'
+application_url = "psyneulinkviewer-linux-x64/psyneulinkviewer"
+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
+
+rosetta_installation = "softwareupdate --install-rosetta --agree-to-license"
+
+conda_forge = "conda config --add channels conda-forge"
+node_installation = "conda install nodejs"
+node_required_version = "4.19.0"

package/psyneulinkviewer/conda.py

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+import platform
+import os
+import sys
+import subprocess
+import logging
+import configuration
+import wget
+import platform
+from setuptools import setup, find_packages
+from setuptools.command.install import install
+from packaging.version import Version
+
+logger = logging.getLogger(__name__)
+logging.basicConfig(level=logging.INFO)
+
+def activate_env():
+    logging.info("Creating conda environment ")
+    subprocess.run(configuration.create_env, shell=True)
+
+    logging.info("Activating conda ")
+    subprocess.run(configuration.activate_env, shell=True)
+
+def install_conda():
+    if os.name == 'posix':
+        bash_file = wget.download(configuration.linux_conda_bash, out="psyneulinkviewer")
+    elif platform.system() == 'Darwin':
+        bash_file = wget.download(configuration.mac_conda_bashf)
+
+    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)
+
+    activate_env()
+    logging.info("Clean up ")
+    subprocess.run("rm -rf " + bash_file, shell=True)
+
+
+def check_conda_installation():
+    conda_version = None
+    try:
+        conda_version = subprocess.run(
+            ["conda", "--version"],
+            capture_output = True,
+            text = True 
+        ).stdout
+        if conda_version:
+            conda_version = conda_version.split(" ")[1]
+            logging.info("Conda version detected : %s", conda_version)
+    except Exception as error:
+        if not isinstance(error, FileNotFoundError):
+            logging.error("Error with conda installation, exiting setup: %s ", error)
+            sys.exit()
+
+    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()
+        else:
+            logging.error("Exiting, conda must be installed to continue...")
+            sys.exit()
+
+    if Version(conda_version) > Version(configuration.conda_required_version):
+        logging.info("Conda version exists and valid, %s", conda_version)
+    else:
+        logging.error("Conda version not up to date, update required")
+        install_conda()
+
+    env_name = None
+    try:
+        envs = subprocess.run(
+            ["conda", "env","list"],
+            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]
+    except Exception as error:
+        logging.error("Environment not found active: %s ", error)
+
+    if env_name is not None:
+        logging.info("Conda environment found and activated %s", env_name)
+    else:
+        activate_env()

package/psyneulinkviewer/node.py

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+import sys
+import subprocess
+import logging
+import configuration
+from setuptools.command.install import install
+from packaging.version import Version
+
+logger = logging.getLogger(__name__)
+logging.basicConfig(level=logging.INFO)
+
+def install_node():
+    logging.info("Installing node")
+    subprocess.run(configuration.conda_forge, shell=True)
+    subprocess.run(configuration.node_installation, shell=True)
+
+def check_node_installation():
+    node_version = None
+    try:
+        node_version = subprocess.run(
+            ["node", "--version"],
+            capture_output = True,
+            text = True 
+        ).stdout
+    except Exception as error:
+        if not isinstance(error, FileNotFoundError):
+            logging.error("Error with node installation, exiting setup: %s ", error)
+            sys.exit()
+
+    if node_version is None:
+        logging.info("Node is not installed")
+        user_input = input("Do you want to continue with node installation? (yes/no): ")
+        if user_input.lower() in ["yes", "y"]:
+            logging.info("Continuing with node installation...")
+            install_node()
+        else:
+            logging.error("Exiting, node must be installed to continue...")
+            sys.exit()
+
+    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()

package/psyneulinkviewer/rosetta.py

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+import platform
+import subprocess
+import logging
+import configuration
+import platform
+import sys
+from setuptools.command.install import install
+from packaging.version import Version
+
+logger = logging.getLogger(__name__)
+logging.basicConfig(level=logging.INFO)
+
+def install_rosetta():
+    if platform.system() == 'Darwin':
+        logging.info("Installing rosetta")
+        subprocess.run(configuration.rosetta_installation, shell=True)
+
+def check_rosetta_installation():
+    rosetta_version = None
+    try:
+        if platform.system() == 'Darwin':
+            rosetta_version = subprocess.run(
+                ["rosseta", "--version"],
+                capture_output = True,
+                text = True 
+            ).stdout
+            if rosetta_version:
+                rosetta_version = rosetta_version.split(" ")[1]
+                logging.info("Rosseta version detected : %s", rosetta_version)
+    except Exception as error:
+        if not isinstance(error, FileNotFoundError):
+            logging.error("Error with rosetta installation, exiting setup: %s ", error)
+            sys.exit()
+
+    if rosetta_version is None:
+        logging.info("Rosetta ist not installed")
+        user_input = input("Do you want to continue with rosetta installation? (yes/no): ")
+        if user_input.lower() in ["yes", "y"]:
+            logging.info("Continuing with rosetta installation...")
+            install_rosetta()
+        else:
+            logging.error("Exiting, rosetta must be installed to continue...")
+            sys.exit()
+

package/psyneulinkviewer/start.py

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+import re
+import json
+import platform
+import os
+import sys
+import subprocess
+import logging
+import importlib.util
+import tarfile
+import atexit
+from setuptools import setup, find_packages
+from setuptools.command.install import install
+from packaging.version import Version
+from psyneulinkviewer.conda import check_conda_installation
+from psyneulinkviewer.rosetta import check_rosetta_installation
+from psyneulinkviewer.node import check_node_installation
+import configuration
+
+logger = logging.getLogger(__name__)
+logging.basicConfig(level=logging.INFO)
+
+def check_os():
+    if os.name == 'nt':
+        sys.exit('Windows is not supported')
+    else:
+        logging.info("OS version supported")
+
+def check_python():
+    if not sys.version_info.major == 3 and not sys.version_info.minor == 6  :
+        logging.error('Python version not supported, 3.11 is required. %f' , sys.version_info)
+        sys.exit('Python version not supported, 3.11 is required.')
+    else:
+        logging.info("Python version is supported")
+
+def check_graphviz():
+    if importlib.util.find_spec(configuration.graphviz) is None:
+        logging.error(configuration.graphviz +" is not installed, installing")
+        result = subprocess.run(
+            ["pip", "install", "graphviz"],
+            capture_output = True,
+            text = True 
+        )
+    else:
+        logging.info(configuration.graphviz +" is installed")
+
+def check_psyneulink():
+    if importlib.util.find_spec(configuration.psyneulink) is None:
+        logging.error(configuration.psyneulink +" is not installed, installing")
+        result = subprocess.run(
+            ["pip", "install", "psyneulink"],
+            capture_output = True,
+            text = True 
+        )
+    else:
+        logging.info(configuration.psyneulink +" is installed")
+
+
+def get_filename_from_cd(cd):
+    """
+    Get filename from content-disposition
+    """
+    if not cd:
+        return None
+    fname = re.findall('filename=(.+)', cd)
+    if len(fname) == 0:
+        return None
+    return fname[0]
+
+def get_latest_release(installation_path):
+    import requests
+
+    headers = {'Accept': 'application/vnd.github+json','Authorization': 'Bearer JWT', 'X-GitHub-Api-Version' : '2022-11-28'}
+    r = requests.get(configuration.releases_url, allow_redirects=True)
+    releases = json.loads(r.text)
+    assets = releases[0]["assets"]
+
+    target_release = None
+    for asset in assets :
+        if platform.system().lower() in asset['name'] :
+            target_release = asset["browser_download_url"]
+
+    logging.info("System detected %s :", platform.system())
+    logging.info("Target release url found %s :", target_release)
+    logging.info("Downloading release to %s...", installation_path)
+    release_download = requests.get(target_release, allow_redirects=True)
+
+    filename = get_filename_from_cd(release_download.headers.get('content-disposition'))
+    tar_location = os.path.join(installation_path, filename)
+    logging.info("Writing release to %s...", tar_location)
+    open(tar_location, 'wb').write(release_download.content)
+
+    logging.info("Opening compressed file %s", filename)
+    tar = tarfile.open(tar_location)
+    extract_location = configuration.extract_location
+    tar.extractall(path=extract_location)
+    tar.close()
+    logging.info("Release file uncompressed at : %s", extract_location)
+
+    application = os.path.join(extract_location, configuration.application_url)
+    symlink = configuration.symlink
+    logging.info("Creating symlink at : %s", symlink)
+    logging.info("Application at : %s", application)
+    try:
+       if os.path.islink(symlink):
+           os.remove(symlink)
+       os.symlink(application, symlink)
+    except OSError as e:
+       logging.error("Error applying symlin %f ", e)
+
+    logging.info("Symlink created")
+
+    logging.info("*** To launch the application run : **** ")
+    logging.info(" %s " ,symlink)
+
+def prerequisites():
+    check_os()
+    check_python()
+    check_conda_installation()
+    #Install package requirements here
+    check_rosetta_installation()
+    check_node_installation()
+    check_graphviz()
+    check_psyneulink()
+    get_latest_release(os.path.dirname(os.path.realpath(__file__)))
+
+def main():
+    prerequisites()
+
+if __name__ == "__main__":
+    main()

package/requirements.txt

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+wget==3.2
+packaging