From ca1356b4f58f32475f374804203ef05afc48bf78 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Thu, 27 Jun 2024 21:52:03 -0700
Subject: [PATCH 01/33] #PSYNEU-134 - POC packacking application as a python
 package installable with 'pip install'.

---
 package/LICENSE         | 19 +++++++++
 package/README.md       |  3 ++
 package/pyproject.toml  | 18 +++++++++
 package/src/__init__.py |  0
 package/src/setup.py    | 89 +++++++++++++++++++++++++++++++++++++++++
 5 files changed, 129 insertions(+)
 create mode 100644 package/LICENSE
 create mode 100644 package/README.md
 create mode 100644 package/pyproject.toml
 create mode 100644 package/src/__init__.py
 create mode 100644 package/src/setup.py

diff --git a/package/LICENSE b/package/LICENSE
new file mode 100644
index 00000000..335ea9d0
--- /dev/null
+++ b/package/LICENSE
@@ -0,0 +1,19 @@
+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.
\ No newline at end of file
diff --git a/package/README.md b/package/README.md
new file mode 100644
index 00000000..bd4c0a5a
--- /dev/null
+++ b/package/README.md
@@ -0,0 +1,3 @@
+# PsyNeuLinkView Package
+
+PsyNeuLinkView package release 0.0.5
\ No newline at end of file
diff --git a/package/pyproject.toml b/package/pyproject.toml
new file mode 100644
index 00000000..2cca7790
--- /dev/null
+++ b/package/pyproject.toml
@@ -0,0 +1,18 @@
+[project]
+name = "PsyNeuLinkView"
+version = "0.0.5"
+authors = [
+  { name="Metacell", email="metacell@metacell.com" },
+]
+description = "Metacell Package"
+readme = "README.md"
+requires-python = "==3.11"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+
+[project.urls]
+Homepage = "https://github.com/Metacell/PsyNeuLinkView"
+Issues = "https://github.com/Metacell/PsyNeuLinkView/issues"
\ No newline at end of file
diff --git a/package/src/__init__.py b/package/src/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/package/src/setup.py b/package/src/setup.py
new file mode 100644
index 00000000..ececef4a
--- /dev/null
+++ b/package/src/setup.py
@@ -0,0 +1,89 @@
+import requests
+import re
+import json
+import platform
+import os
+import logging
+import tarfile
+from setuptools import setup, find_packages
+from setuptools.command.install import install
+
+logger = logging.getLogger(__name__)
+logging.basicConfig(level=logging.INFO)
+
+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):
+    url = 'https://api.github.com/repos/MetaCell/PsyNeuLinkView/releases'
+    headers = {'Accept': 'application/vnd.github+json','Authorization': 'Bearer JWT', 'X-GitHub-Api-Version' : '2022-11-28'}
+    r = requests.get(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'))
+    location = os.path.join(installation_path, filename)
+    logging.info("Writing release to %s...", location)
+    open(location, 'wb').write(release_download.content)
+
+    logging.info("Opening compressed file %s", filename)
+    tar = tarfile.open(location)
+    tar.extractall(path=installation_path)
+    tar.close()
+    logging.info("Release file uncompressed at : %s", location)
+
+    application = os.path.join(installation_path, "psyneulinkviewer-linux-x64/psyneulinkviewer")
+    logging.info("***")
+    logging.info("***")
+    logging.info("***")
+    logging.info("***")
+    logging.info("*** To launch the application run : **** ")
+    logging.info(" %s " , application)
+
+class InstallCommand(install):
+    user_options = install.user_options + [
+        ('path=', None, 'an option that takes a value')
+    ]
+
+    def initialize_options(self):
+        install.initialize_options(self)
+        self.path = None
+
+    def finalize_options(self):
+        # Validate options
+        if self.path is None:
+            self.path = os.path.dirname(os.path.realpath(__file__))
+        super().finalize_options()
+
+
+    def run(self):
+        global path
+        path = self.path # will be 1 or None
+        install.run(self)
+        get_latest_release(self.path)
+
+setup(
+    name="PsyNeuLinkView",
+    version="0.0.5",
+    cmdclass={
+        'install': InstallCommand
+    }
+)
\ No newline at end of file

From dc11b75f7c0c4885b315168ab3a2b7841d4694a0 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Thu, 27 Jun 2024 22:07:08 -0700
Subject: [PATCH 02/33] #PSYNEU-134 -Better logging and symlink creation

---
 package/src/setup.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/package/src/setup.py b/package/src/setup.py
index ececef4a..6ec9cb5a 100644
--- a/package/src/setup.py
+++ b/package/src/setup.py
@@ -51,6 +51,10 @@ def get_latest_release(installation_path):
     logging.info("Release file uncompressed at : %s", location)
 
     application = os.path.join(installation_path, "psyneulinkviewer-linux-x64/psyneulinkviewer")
+    symlink = "/usr/local/bin/psyneulinkviewer"
+    logging.info("Creating symlink at : %s", symlink)
+    os.symlink(application, symlink)
+    logging.info("Symlink created")
     logging.info("***")
     logging.info("***")
     logging.info("***")

From f0e970c12b5a584800efc2ac91554baf41696b9d Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Sun, 30 Jun 2024 09:25:15 -0700
Subject: [PATCH 03/33] #134 - Fix symlink path

---
 package/pyproject.toml     | 18 ------------------
 package/{src => }/setup.py | 30 +++++++++++++++++++-----------
 2 files changed, 19 insertions(+), 29 deletions(-)
 delete mode 100644 package/pyproject.toml
 rename package/{src => }/setup.py (74%)

diff --git a/package/pyproject.toml b/package/pyproject.toml
deleted file mode 100644
index 2cca7790..00000000
--- a/package/pyproject.toml
+++ /dev/null
@@ -1,18 +0,0 @@
-[project]
-name = "PsyNeuLinkView"
-version = "0.0.5"
-authors = [
-  { name="Metacell", email="metacell@metacell.com" },
-]
-description = "Metacell Package"
-readme = "README.md"
-requires-python = "==3.11"
-classifiers = [
-    "Programming Language :: Python :: 3",
-    "License :: OSI Approved :: MIT License",
-    "Operating System :: OS Independent",
-]
-
-[project.urls]
-Homepage = "https://github.com/Metacell/PsyNeuLinkView"
-Issues = "https://github.com/Metacell/PsyNeuLinkView/issues"
\ No newline at end of file
diff --git a/package/src/setup.py b/package/setup.py
similarity index 74%
rename from package/src/setup.py
rename to package/setup.py
index 6ec9cb5a..8e110b97 100644
--- a/package/src/setup.py
+++ b/package/setup.py
@@ -1,4 +1,4 @@
-import requests
+from pip._vendor import requests
 import re
 import json
 import platform
@@ -40,27 +40,35 @@ def get_latest_release(installation_path):
     release_download = requests.get(target_release, allow_redirects=True)
 
     filename = get_filename_from_cd(release_download.headers.get('content-disposition'))
-    location = os.path.join(installation_path, filename)
-    logging.info("Writing release to %s...", location)
-    open(location, 'wb').write(release_download.content)
+    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(location)
-    tar.extractall(path=installation_path)
+    tar = tarfile.open(tar_location)
+    extract_location = "/usr/local/bin"
+    tar.extractall(path=extract_location)
     tar.close()
-    logging.info("Release file uncompressed at : %s", location)
+    logging.info("Release file uncompressed at : %s", extract_location)
 
-    application = os.path.join(installation_path, "psyneulinkviewer-linux-x64/psyneulinkviewer")
+    application = os.path.join(extract_location, "psyneulinkviewer-linux-x64/psyneulinkviewer")
     symlink = "/usr/local/bin/psyneulinkviewer"
     logging.info("Creating symlink at : %s", symlink)
-    os.symlink(application, 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("***")
     logging.info("***")
     logging.info("***")
     logging.info("***")
     logging.info("*** To launch the application run : **** ")
-    logging.info(" %s " , application)
+    logging.info(" %s " ,symlink)
 
 class InstallCommand(install):
     user_options = install.user_options + [
@@ -85,7 +93,7 @@ def run(self):
         get_latest_release(self.path)
 
 setup(
-    name="PsyNeuLinkView",
+    name="psyneulinkview",
     version="0.0.5",
     cmdclass={
         'install': InstallCommand

From e0622fef220e2693b8c1bb46a4b1d8e39dc67d20 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Sun, 30 Jun 2024 09:29:00 -0700
Subject: [PATCH 04/33] #134- Add read me instructions

---
 package/README.md | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/package/README.md b/package/README.md
index bd4c0a5a..ca51137e 100644
--- a/package/README.md
+++ b/package/README.md
@@ -1,3 +1,23 @@
 # PsyNeuLinkView Package
 
-PsyNeuLinkView package release 0.0.5
\ No newline at end of file
+To build pip package
+```
+cd package
+python3 -m build
+```
+
+To pip install package created in previous step
+```
+python3 -m pip install --no-index --find-links={package_directory_path + "/dist"} psyneulinkview
+```
+
+To run psyneulinkviewer
+```
+/usr/local/bin/psyneulinkviewer
+```
+
+or 
+
+```
+psyneulinkviewer
+```
\ No newline at end of file

From 1baba8e096abf31457776b64ea40067595523589 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Wed, 3 Jul 2024 16:17:40 -0700
Subject: [PATCH 05/33] #134 - Add checks for OS, python version, conda
 version, graphviz and psyneulink

---
 package/README.md |  2 +-
 package/setup.py  | 81 +++++++++++++++++++++++++++++++++++++++++++----
 2 files changed, 75 insertions(+), 8 deletions(-)

diff --git a/package/README.md b/package/README.md
index ca51137e..bfd7db8b 100644
--- a/package/README.md
+++ b/package/README.md
@@ -8,7 +8,7 @@ python3 -m build
 
 To pip install package created in previous step
 ```
-python3 -m pip install --no-index --find-links={package_directory_path + "/dist"} psyneulinkview
+python3 -m pip install --no-index --find-links=package_directory_path + "/dist" psyneulinkview
 ```
 
 To run psyneulinkviewer
diff --git a/package/setup.py b/package/setup.py
index 8e110b97..b495a3fe 100644
--- a/package/setup.py
+++ b/package/setup.py
@@ -1,9 +1,11 @@
-from pip._vendor import requests
 import re
 import json
 import platform
 import os
+import sys
+import subprocess
 import logging
+import importlib.util
 import tarfile
 from setuptools import setup, find_packages
 from setuptools.command.install import install
@@ -11,6 +13,62 @@
 logger = logging.getLogger(__name__)
 logging.basicConfig(level=logging.INFO)
 
+graphviz = "graphviz"
+psyneulink = "psyneulink"
+
+def check_os(self):
+    if os.name == 'nt':
+        sys.exit('Windows is not supported')
+    else:
+        logging.info("OS version supported")
+
+def check_python(self):
+    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_conda(self):
+    result = subprocess.run(
+        ["conda", "--version"],
+        capture_output = True,
+        text = True 
+    )
+    logging.info("conda version %s", result.stdout)
+
+def check_rosetta(self):
+    if sys.platform == "darwin":
+        result = subprocess.run(
+            ["rosseta", "--version"],
+            capture_output = True,
+            text = True 
+        )
+        logging.info("rosseta version %s", result.stdout)
+
+def check_graphviz(self):
+    if importlib.util.find_spec(graphviz) is None:
+        logging.error(graphviz +" is not installed, installing")
+        result = subprocess.run(
+            ["pip", "install", "graphviz"],
+            capture_output = True,
+            text = True 
+        )
+    else:
+        logging.info(graphviz +" is installed")
+
+def check_psyneulink(self):
+    if importlib.util.find_spec(psyneulink) is None:
+        logging.error(psyneulink +" is not installed, installing")
+        result = subprocess.run(
+            ["pip", "install", "psyneulink"],
+            capture_output = True,
+            text = True 
+        )
+    else:
+        logging.info(psyneulink +" is installed")
+
+
 def get_filename_from_cd(cd):
     """
     Get filename from content-disposition
@@ -23,6 +81,8 @@ def get_filename_from_cd(cd):
     return fname[0]
 
 def get_latest_release(installation_path):
+    import requests
+
     url = 'https://api.github.com/repos/MetaCell/PsyNeuLinkView/releases'
     headers = {'Accept': 'application/vnd.github+json','Authorization': 'Bearer JWT', 'X-GitHub-Api-Version' : '2022-11-28'}
     r = requests.get(url, allow_redirects=True)
@@ -63,13 +123,19 @@ def get_latest_release(installation_path):
        logging.error("Error applying symlin %f ", e)
 
     logging.info("Symlink created")
-    logging.info("***")
-    logging.info("***")
-    logging.info("***")
-    logging.info("***")
+
     logging.info("*** To launch the application run : **** ")
     logging.info(" %s " ,symlink)
 
+def prerequisites(self):
+    check_os(self)
+    check_python(self)
+    check_conda(self)
+    check_rosetta(self)
+    check_graphviz(self)
+    check_psyneulink(self)
+    get_latest_release(self.path)
+
 class InstallCommand(install):
     user_options = install.user_options + [
         ('path=', None, 'an option that takes a value')
@@ -90,12 +156,13 @@ def run(self):
         global path
         path = self.path # will be 1 or None
         install.run(self)
-        get_latest_release(self.path)
+        prerequisites(self)
 
 setup(
     name="psyneulinkview",
     version="0.0.5",
     cmdclass={
         'install': InstallCommand
-    }
+    },
+    setup_requires=['requests']
 )
\ No newline at end of file

From 73f87b70eb62d6871f8356cb04839f8ea5105dba Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Thu, 4 Jul 2024 08:10:19 -0700
Subject: [PATCH 06/33] #134 - Add entry point to launch psyneulink. Adds dist
 packages

---
 .../psyneulinkview-0.0.5-py3-none-any.whl     | Bin 0 -> 3963 bytes
 package/dist/psyneulinkview-0.0.5.tar.gz      | Bin 0 -> 3530 bytes
 package/{src => psyneulinkviewer}/__init__.py |   0
 package/psyneulinkviewer/start.py             | 155 ++++++++++++++++++
 package/setup.py                              |  40 ++---
 5 files changed, 176 insertions(+), 19 deletions(-)
 create mode 100644 package/dist/psyneulinkview-0.0.5-py3-none-any.whl
 create mode 100644 package/dist/psyneulinkview-0.0.5.tar.gz
 rename package/{src => psyneulinkviewer}/__init__.py (100%)
 create mode 100644 package/psyneulinkviewer/start.py

diff --git a/package/dist/psyneulinkview-0.0.5-py3-none-any.whl b/package/dist/psyneulinkview-0.0.5-py3-none-any.whl
new file mode 100644
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diff --git a/package/src/__init__.py b/package/psyneulinkviewer/__init__.py
similarity index 100%
rename from package/src/__init__.py
rename to package/psyneulinkviewer/__init__.py
diff --git a/package/psyneulinkviewer/start.py b/package/psyneulinkviewer/start.py
new file mode 100644
index 00000000..a673c3f7
--- /dev/null
+++ b/package/psyneulinkviewer/start.py
@@ -0,0 +1,155 @@
+import re
+import json
+import platform
+import os
+import sys
+import subprocess
+import logging
+import importlib.util
+import tarfile
+from setuptools import setup, find_packages
+from setuptools.command.install import install
+
+logger = logging.getLogger(__name__)
+logging.basicConfig(level=logging.INFO)
+
+graphviz = "graphviz"
+psyneulink = "psyneulink"
+symlink = "/usr/local/bin/psyneulinkviewer"
+
+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_conda():
+    result = subprocess.run(
+        ["conda", "--version"],
+        capture_output = True,
+        text = True 
+    )
+    logging.info("conda version %s", result.stdout)
+
+def check_rosetta():
+    if sys.platform == "darwin":
+        result = subprocess.run(
+            ["rosseta", "--version"],
+            capture_output = True,
+            text = True 
+        )
+        logging.info("rosseta version %s", result.stdout)
+
+def check_graphviz():
+    if importlib.util.find_spec(graphviz) is None:
+        logging.error(graphviz +" is not installed, installing")
+        result = subprocess.run(
+            ["pip", "install", "graphviz"],
+            capture_output = True,
+            text = True 
+        )
+    else:
+        logging.info(graphviz +" is installed")
+
+def check_psyneulink():
+    if importlib.util.find_spec(psyneulink) is None:
+        logging.error(psyneulink +" is not installed, installing")
+        result = subprocess.run(
+            ["pip", "install", "psyneulink"],
+            capture_output = True,
+            text = True 
+        )
+    else:
+        logging.info(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
+
+    url = 'https://api.github.com/repos/MetaCell/PsyNeuLinkView/releases'
+    headers = {'Accept': 'application/vnd.github+json','Authorization': 'Bearer JWT', 'X-GitHub-Api-Version' : '2022-11-28'}
+    r = requests.get(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 = "/usr/local/bin"
+    tar.extractall(path=extract_location)
+    tar.close()
+    logging.info("Release file uncompressed at : %s", extract_location)
+
+    application = os.path.join(extract_location, "psyneulinkviewer-linux-x64/psyneulinkviewer")
+    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)
+       result = subprocess.run(
+            [symlink],
+            capture_output = True,
+            text = True 
+        )
+    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()
+    check_rosetta()
+    check_graphviz()
+    check_psyneulink()
+    if os.path.islink(symlink):
+        result = subprocess.run(
+            [symlink],
+            capture_output = True,
+            text = True 
+        )
+    else:
+        get_latest_release(os.path.dirname(os.path.realpath(__file__)))
+
+def main():
+    prerequisites()
+
+if __name__ == "__main__":
+    main()
\ No newline at end of file
diff --git a/package/setup.py b/package/setup.py
index b495a3fe..f11266a3 100644
--- a/package/setup.py
+++ b/package/setup.py
@@ -7,6 +7,7 @@
 import logging
 import importlib.util
 import tarfile
+import atexit
 from setuptools import setup, find_packages
 from setuptools.command.install import install
 
@@ -16,20 +17,20 @@
 graphviz = "graphviz"
 psyneulink = "psyneulink"
 
-def check_os(self):
+def check_os():
     if os.name == 'nt':
         sys.exit('Windows is not supported')
     else:
         logging.info("OS version supported")
 
-def check_python(self):
+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_conda(self):
+def check_conda():
     result = subprocess.run(
         ["conda", "--version"],
         capture_output = True,
@@ -37,7 +38,7 @@ def check_conda(self):
     )
     logging.info("conda version %s", result.stdout)
 
-def check_rosetta(self):
+def check_rosetta():
     if sys.platform == "darwin":
         result = subprocess.run(
             ["rosseta", "--version"],
@@ -46,7 +47,7 @@ def check_rosetta(self):
         )
         logging.info("rosseta version %s", result.stdout)
 
-def check_graphviz(self):
+def check_graphviz():
     if importlib.util.find_spec(graphviz) is None:
         logging.error(graphviz +" is not installed, installing")
         result = subprocess.run(
@@ -57,7 +58,7 @@ def check_graphviz(self):
     else:
         logging.info(graphviz +" is installed")
 
-def check_psyneulink(self):
+def check_psyneulink():
     if importlib.util.find_spec(psyneulink) is None:
         logging.error(psyneulink +" is not installed, installing")
         result = subprocess.run(
@@ -127,14 +128,14 @@ def get_latest_release(installation_path):
     logging.info("*** To launch the application run : **** ")
     logging.info(" %s " ,symlink)
 
-def prerequisites(self):
-    check_os(self)
-    check_python(self)
-    check_conda(self)
-    check_rosetta(self)
-    check_graphviz(self)
-    check_psyneulink(self)
-    get_latest_release(self.path)
+def prerequisites():
+    check_os()
+    check_python()
+    check_conda()
+    check_rosetta()
+    check_graphviz()
+    check_psyneulink()
+    get_latest_release(os.path.dirname(os.path.realpath(__file__)))
 
 class InstallCommand(install):
     user_options = install.user_options + [
@@ -156,13 +157,14 @@ def run(self):
         global path
         path = self.path # will be 1 or None
         install.run(self)
-        prerequisites(self)
 
 setup(
     name="psyneulinkview",
     version="0.0.5",
-    cmdclass={
-        'install': InstallCommand
-    },
-    setup_requires=['requests']
+    setup_requires=['requests'],
+    entry_points={
+            'console_scripts': [
+                'psyneulinkviewer = psyneulinkviewer.start:main',
+            ]
+    }
 )
\ No newline at end of file

From 7f0dd97ef4aadfad24fec09df8891bbc7121b4fb Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 5 Jul 2024 07:38:31 -0700
Subject: [PATCH 07/33] #134 - Add entry point to allow installing and running
 psyneulinkviewer after installation

---
 package/psyneulinkviewer/start.py | 8 ++------
 package/setup.py                  | 2 +-
 2 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/package/psyneulinkviewer/start.py b/package/psyneulinkviewer/start.py
index a673c3f7..3818f1d7 100644
--- a/package/psyneulinkviewer/start.py
+++ b/package/psyneulinkviewer/start.py
@@ -120,9 +120,7 @@ def get_latest_release(installation_path):
            os.remove(symlink)
        os.symlink(application, symlink)
        result = subprocess.run(
-            [symlink],
-            capture_output = True,
-            text = True 
+            [symlink]
         )
     except OSError as e:
        logging.error("Error applying symlin %f ", e)
@@ -141,9 +139,7 @@ def prerequisites():
     check_psyneulink()
     if os.path.islink(symlink):
         result = subprocess.run(
-            [symlink],
-            capture_output = True,
-            text = True 
+            [symlink]
         )
     else:
         get_latest_release(os.path.dirname(os.path.realpath(__file__)))
diff --git a/package/setup.py b/package/setup.py
index f11266a3..4755485b 100644
--- a/package/setup.py
+++ b/package/setup.py
@@ -160,7 +160,7 @@ def run(self):
 
 setup(
     name="psyneulinkview",
-    version="0.0.5",
+    version="0.0.1",
     setup_requires=['requests'],
     entry_points={
             'console_scripts': [

From 4e1479140018e9b8e91f9c4e337759d3ea5c72f5 Mon Sep 17 00:00:00 2001
From: Jesus M <jesus@metacell.us>
Date: Fri, 5 Jul 2024 15:16:31 -0700
Subject: [PATCH 08/33] Update README.md

---
 package/README.md | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/package/README.md b/package/README.md
index bfd7db8b..b7528eb7 100644
--- a/package/README.md
+++ b/package/README.md
@@ -1,4 +1,4 @@
-# PsyNeuLinkView Package
+# PsyNeuLinkView Package Building
 
 To build pip package
 ```
@@ -6,18 +6,24 @@ cd package
 python3 -m build
 ```
 
-To pip install package created in previous step
+To upload to distribution server
 ```
-python3 -m pip install --no-index --find-links=package_directory_path + "/dist" psyneulinkview
+twine upload dist/*
 ```
 
-To run psyneulinkviewer
+To pip install local package created in previous steps
 ```
-/usr/local/bin/psyneulinkviewer
+python3 -m pip install --no-index --find-links=package_directory_path + "/dist" psyneulinkview
 ```
 
-or 
+# PsyNeuLinkView Installing from PyPI
+
+To install from PyPi
+```
+pip install psyneulinkview --extra-index-url https://pypi.org/project/psyneulinkview
+```
 
+To run psyneulinkviewer
 ```
 psyneulinkviewer
-```
\ No newline at end of file
+```

From b481c429403abba3e38789e2ad7d5de9b083fd5c Mon Sep 17 00:00:00 2001
From: Jesus M <jesus@metacell.us>
Date: Fri, 12 Jul 2024 00:52:08 -0700
Subject: [PATCH 09/33] Update README.md

---
 package/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/README.md b/package/README.md
index b7528eb7..b3918df8 100644
--- a/package/README.md
+++ b/package/README.md
@@ -6,7 +6,7 @@ cd package
 python3 -m build
 ```
 
-To upload to distribution server
+To upload to distribution server. You will need token shared privately. 
 ```
 twine upload dist/*
 ```

From 274bd7d620f21a8758af7290b490a941f45c5a2e Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 26 Jul 2024 11:12:51 +0200
Subject: [PATCH 10/33] #PSYNEU-136 - Conda installation as part of pip install
 process

---
 .../build/lib/psyneulinkviewer/__init__.py    |   0
 package/build/lib/psyneulinkviewer/conda.py   |  71 ++++++++
 package/build/lib/psyneulinkviewer/start.py   | 151 ++++++++++++++++++
 package/configuration.py                      |  15 ++
 package/psyneulinkviewer/conda.py             |  72 +++++++++
 package/requirements.txt                      |   2 +
 package/setup.py                              |  43 +++--
 7 files changed, 331 insertions(+), 23 deletions(-)
 create mode 100644 package/build/lib/psyneulinkviewer/__init__.py
 create mode 100644 package/build/lib/psyneulinkviewer/conda.py
 create mode 100644 package/build/lib/psyneulinkviewer/start.py
 create mode 100644 package/configuration.py
 create mode 100644 package/psyneulinkviewer/conda.py
 create mode 100644 package/requirements.txt

diff --git a/package/build/lib/psyneulinkviewer/__init__.py b/package/build/lib/psyneulinkviewer/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/package/build/lib/psyneulinkviewer/conda.py b/package/build/lib/psyneulinkviewer/conda.py
new file mode 100644
index 00000000..8ba6afe3
--- /dev/null
+++ b/package/build/lib/psyneulinkviewer/conda.py
@@ -0,0 +1,71 @@
+import re
+import json
+import platform
+import os
+import sys
+import subprocess
+import logging
+import importlib.util
+import tarfile
+import atexit
+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 ")
+    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 = subprocess.run(
+        ["conda", "--version"],
+        capture_output = True,
+        text = True 
+    ).stdout
+    if conda_version:
+        conda_version = conda_version.split(" ")[1]
+    logging.info("conda version %s", conda_version)
+
+    if conda_version is not None:
+        logging.info("Conda not installed")
+        install_conda()
+    
+    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");
+    
+    envs = subprocess.run(
+        ["conda", "env","list"],
+        capture_output = True,
+        text = True 
+    ).stdout.splitlines()
+    active_env = list(filter(lambda s: '*' in str(s), envs))[0]
+    env_name = str(active_env).split()[0]
+    if env_name is not None:
+        logging.info("Conda environment foudn and activated%s", env_name)
\ No newline at end of file
diff --git a/package/build/lib/psyneulinkviewer/start.py b/package/build/lib/psyneulinkviewer/start.py
new file mode 100644
index 00000000..3818f1d7
--- /dev/null
+++ b/package/build/lib/psyneulinkviewer/start.py
@@ -0,0 +1,151 @@
+import re
+import json
+import platform
+import os
+import sys
+import subprocess
+import logging
+import importlib.util
+import tarfile
+from setuptools import setup, find_packages
+from setuptools.command.install import install
+
+logger = logging.getLogger(__name__)
+logging.basicConfig(level=logging.INFO)
+
+graphviz = "graphviz"
+psyneulink = "psyneulink"
+symlink = "/usr/local/bin/psyneulinkviewer"
+
+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_conda():
+    result = subprocess.run(
+        ["conda", "--version"],
+        capture_output = True,
+        text = True 
+    )
+    logging.info("conda version %s", result.stdout)
+
+def check_rosetta():
+    if sys.platform == "darwin":
+        result = subprocess.run(
+            ["rosseta", "--version"],
+            capture_output = True,
+            text = True 
+        )
+        logging.info("rosseta version %s", result.stdout)
+
+def check_graphviz():
+    if importlib.util.find_spec(graphviz) is None:
+        logging.error(graphviz +" is not installed, installing")
+        result = subprocess.run(
+            ["pip", "install", "graphviz"],
+            capture_output = True,
+            text = True 
+        )
+    else:
+        logging.info(graphviz +" is installed")
+
+def check_psyneulink():
+    if importlib.util.find_spec(psyneulink) is None:
+        logging.error(psyneulink +" is not installed, installing")
+        result = subprocess.run(
+            ["pip", "install", "psyneulink"],
+            capture_output = True,
+            text = True 
+        )
+    else:
+        logging.info(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
+
+    url = 'https://api.github.com/repos/MetaCell/PsyNeuLinkView/releases'
+    headers = {'Accept': 'application/vnd.github+json','Authorization': 'Bearer JWT', 'X-GitHub-Api-Version' : '2022-11-28'}
+    r = requests.get(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 = "/usr/local/bin"
+    tar.extractall(path=extract_location)
+    tar.close()
+    logging.info("Release file uncompressed at : %s", extract_location)
+
+    application = os.path.join(extract_location, "psyneulinkviewer-linux-x64/psyneulinkviewer")
+    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)
+       result = subprocess.run(
+            [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()
+    check_rosetta()
+    check_graphviz()
+    check_psyneulink()
+    if os.path.islink(symlink):
+        result = subprocess.run(
+            [symlink]
+        )
+    else:
+        get_latest_release(os.path.dirname(os.path.realpath(__file__)))
+
+def main():
+    prerequisites()
+
+if __name__ == "__main__":
+    main()
\ No newline at end of file
diff --git a/package/configuration.py b/package/configuration.py
new file mode 100644
index 00000000..24a48df7
--- /dev/null
+++ b/package/configuration.py
@@ -0,0 +1,15 @@
+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
+activate_env = "conda activate " + env_name
diff --git a/package/psyneulinkviewer/conda.py b/package/psyneulinkviewer/conda.py
new file mode 100644
index 00000000..db0e7390
--- /dev/null
+++ b/package/psyneulinkviewer/conda.py
@@ -0,0 +1,72 @@
+import re
+import json
+import platform
+import os
+import sys
+import subprocess
+import logging
+import importlib.util
+import tarfile
+import atexit
+import configuration
+import wget
+import platform
+import requests
+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 ")
+    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 = requests.get(configuration.linux_conda_bash)
+    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 = subprocess.run(
+        ["conda", "--version"],
+        capture_output = True,
+        text = True 
+    ).stdout
+    if conda_version:
+        conda_version = conda_version.split(" ")[1]
+    logging.info("conda version %s", conda_version)
+
+    if conda_version is not None:
+        logging.info("Conda not installed")
+        install_conda()
+    
+    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");
+    
+    envs = subprocess.run(
+        ["conda", "env","list"],
+        capture_output = True,
+        text = True 
+    ).stdout.splitlines()
+    active_env = list(filter(lambda s: '*' in str(s), envs))[0]
+    env_name = str(active_env).split()[0]
+    if env_name is not None:
+        logging.info("Conda environment foudn and activated%s", env_name)
\ No newline at end of file
diff --git a/package/requirements.txt b/package/requirements.txt
new file mode 100644
index 00000000..a379fde6
--- /dev/null
+++ b/package/requirements.txt
@@ -0,0 +1,2 @@
+wget==3.2
+packaging
\ No newline at end of file
diff --git a/package/setup.py b/package/setup.py
index 4755485b..0fe38785 100644
--- a/package/setup.py
+++ b/package/setup.py
@@ -10,13 +10,13 @@
 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
+import configuration
 
 logger = logging.getLogger(__name__)
 logging.basicConfig(level=logging.INFO)
 
-graphviz = "graphviz"
-psyneulink = "psyneulink"
-
 def check_os():
     if os.name == 'nt':
         sys.exit('Windows is not supported')
@@ -30,14 +30,6 @@ def check_python():
     else:
         logging.info("Python version is supported")
 
-def check_conda():
-    result = subprocess.run(
-        ["conda", "--version"],
-        capture_output = True,
-        text = True 
-    )
-    logging.info("conda version %s", result.stdout)
-
 def check_rosetta():
     if sys.platform == "darwin":
         result = subprocess.run(
@@ -48,26 +40,26 @@ def check_rosetta():
         logging.info("rosseta version %s", result.stdout)
 
 def check_graphviz():
-    if importlib.util.find_spec(graphviz) is None:
-        logging.error(graphviz +" is not installed, installing")
+    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(graphviz +" is installed")
+        logging.info(configuration.graphviz +" is installed")
 
 def check_psyneulink():
-    if importlib.util.find_spec(psyneulink) is None:
-        logging.error(psyneulink +" is not installed, installing")
+    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(psyneulink +" is installed")
+        logging.info(configuration.psyneulink +" is installed")
 
 
 def get_filename_from_cd(cd):
@@ -84,9 +76,8 @@ def get_filename_from_cd(cd):
 def get_latest_release(installation_path):
     import requests
 
-    url = 'https://api.github.com/repos/MetaCell/PsyNeuLinkView/releases'
     headers = {'Accept': 'application/vnd.github+json','Authorization': 'Bearer JWT', 'X-GitHub-Api-Version' : '2022-11-28'}
-    r = requests.get(url, allow_redirects=True)
+    r = requests.get(configuration.releases_url, allow_redirects=True)
     releases = json.loads(r.text)
     assets = releases[0]["assets"]
 
@@ -107,13 +98,13 @@ def get_latest_release(installation_path):
 
     logging.info("Opening compressed file %s", filename)
     tar = tarfile.open(tar_location)
-    extract_location = "/usr/local/bin"
+    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, "psyneulinkviewer-linux-x64/psyneulinkviewer")
-    symlink = "/usr/local/bin/psyneulinkviewer"
+    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:
@@ -131,7 +122,8 @@ def get_latest_release(installation_path):
 def prerequisites():
     check_os()
     check_python()
-    check_conda()
+    check_conda_installation()
+    #Install package requirements here
     check_rosetta()
     check_graphviz()
     check_psyneulink()
@@ -155,6 +147,8 @@ def finalize_options(self):
 
     def run(self):
         global path
+        prerequisites()
+        print("pre")
         path = self.path # will be 1 or None
         install.run(self)
 
@@ -166,5 +160,8 @@ def run(self):
             'console_scripts': [
                 'psyneulinkviewer = psyneulinkviewer.start:main',
             ]
+    },
+    cmdclass={
+        'install': InstallCommand
     }
 )
\ No newline at end of file

From 0cc490b9b90d8b775b9f5d304043e3ba3b78ab69 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 26 Jul 2024 11:16:56 +0200
Subject: [PATCH 11/33] #PSYNEU-136 - Clean up logs

---
 package/psyneulinkviewer/conda.py | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/package/psyneulinkviewer/conda.py b/package/psyneulinkviewer/conda.py
index db0e7390..10fe748b 100644
--- a/package/psyneulinkviewer/conda.py
+++ b/package/psyneulinkviewer/conda.py
@@ -1,13 +1,7 @@
-import re
-import json
 import platform
 import os
-import sys
 import subprocess
 import logging
-import importlib.util
-import tarfile
-import atexit
 import configuration
 import wget
 import platform
@@ -50,16 +44,17 @@ def check_conda_installation():
     ).stdout
     if conda_version:
         conda_version = conda_version.split(" ")[1]
-    logging.info("conda version %s", conda_version)
+    logging.info("Conda version detected : %s", conda_version)
 
     if conda_version is not None:
-        logging.info("Conda not installed")
+        logging.info("Conda ist not installed, downloading conda installation.")
         install_conda()
     
     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");
+        logging.error("Conda version not up to date, update required")
+        install_conda()
     
     envs = subprocess.run(
         ["conda", "env","list"],
@@ -69,4 +64,4 @@ def check_conda_installation():
     active_env = list(filter(lambda s: '*' in str(s), envs))[0]
     env_name = str(active_env).split()[0]
     if env_name is not None:
-        logging.info("Conda environment foudn and activated%s", env_name)
\ No newline at end of file
+        logging.info("Conda environment found and activated %s", env_name)
\ No newline at end of file

From 2fa6aa9ecf4c6f4786931cd893d9a7acc931fe27 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 26 Jul 2024 11:35:12 +0200
Subject: [PATCH 12/33] #PSYNEU-136 - Clean up conda installation process

---
 package/psyneulinkviewer/conda.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/package/psyneulinkviewer/conda.py b/package/psyneulinkviewer/conda.py
index 10fe748b..ae75f62c 100644
--- a/package/psyneulinkviewer/conda.py
+++ b/package/psyneulinkviewer/conda.py
@@ -1,11 +1,11 @@
 import platform
 import os
+import sys
 import subprocess
 import logging
 import configuration
 import wget
 import platform
-import requests
 from setuptools import setup, find_packages
 from setuptools.command.install import install
 from packaging.version import Version
@@ -22,7 +22,7 @@ def activate_env():
 
 def install_conda():
     if os.name == 'posix':
-        bash_file = requests.get(configuration.linux_conda_bash)
+        bash_file = wget.download(configuration.linux_conda_bash, out="psyneulinkviewer")
     elif platform.system() == 'Darwin':
         bash_file = wget.download(configuration.mac_conda_bashf)
 
@@ -47,8 +47,14 @@ def check_conda_installation():
     logging.info("Conda version detected : %s", conda_version)
 
     if conda_version is not None:
-        logging.info("Conda ist not installed, downloading conda installation.")
-        install_conda()
+        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)

From 6dee38c4caa31b86e17f65081af163505b2bf634 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 26 Jul 2024 11:38:01 +0200
Subject: [PATCH 13/33] #PSYNEU-137 - Install rosetta as part of  pip
 installation process

---
 package/configuration.py            |  2 ++
 package/psyneulinkviewer/rosetta.py | 37 +++++++++++++++++++++++++++++
 package/setup.py                    |  9 -------
 3 files changed, 39 insertions(+), 9 deletions(-)
 create mode 100644 package/psyneulinkviewer/rosetta.py

diff --git a/package/configuration.py b/package/configuration.py
index 24a48df7..42ca0154 100644
--- a/package/configuration.py
+++ b/package/configuration.py
@@ -13,3 +13,5 @@
 env_name = "psyneulinkviewer"
 create_env = "conda create --name " + env_name
 activate_env = "conda activate " + env_name
+
+rosetta_installation = "softwareupdate --install-rosetta --agree-to-license"
\ No newline at end of file
diff --git a/package/psyneulinkviewer/rosetta.py b/package/psyneulinkviewer/rosetta.py
new file mode 100644
index 00000000..10c630db
--- /dev/null
+++ b/package/psyneulinkviewer/rosetta.py
@@ -0,0 +1,37 @@
+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_conda_installation():
+    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)
+
+        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()
diff --git a/package/setup.py b/package/setup.py
index 0fe38785..15e1d302 100644
--- a/package/setup.py
+++ b/package/setup.py
@@ -30,15 +30,6 @@ def check_python():
     else:
         logging.info("Python version is supported")
 
-def check_rosetta():
-    if sys.platform == "darwin":
-        result = subprocess.run(
-            ["rosseta", "--version"],
-            capture_output = True,
-            text = True 
-        )
-        logging.info("rosseta version %s", result.stdout)
-
 def check_graphviz():
     if importlib.util.find_spec(configuration.graphviz) is None:
         logging.error(configuration.graphviz +" is not installed, installing")

From b3f5c44168d56ef0364e2fdf9281149b7b81ec92 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 26 Jul 2024 16:24:56 +0200
Subject: [PATCH 14/33] #PSYNEU-137 - Cleanup check

---
 package/psyneulinkviewer/conda.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/psyneulinkviewer/conda.py b/package/psyneulinkviewer/conda.py
index ae75f62c..540ad748 100644
--- a/package/psyneulinkviewer/conda.py
+++ b/package/psyneulinkviewer/conda.py
@@ -46,7 +46,7 @@ def check_conda_installation():
         conda_version = conda_version.split(" ")[1]
     logging.info("Conda version detected : %s", conda_version)
 
-    if conda_version is not None:
+    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"]:

From 9fb06a8756f3fd56ac39a3d7fff0cb2857bfface Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 26 Jul 2024 16:43:44 +0200
Subject: [PATCH 15/33] #PSYNEU-137 - Fix import

---
 package/setup.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/package/setup.py b/package/setup.py
index 15e1d302..ec48215d 100644
--- a/package/setup.py
+++ b/package/setup.py
@@ -12,6 +12,7 @@
 from setuptools.command.install import install
 from packaging.version import Version
 from psyneulinkviewer.conda import check_conda_installation
+from psyneulinkviewer.conda import check_rosetta
 import configuration
 
 logger = logging.getLogger(__name__)

From 5d6d8ec7e2b2345e40691ea1f6e1a9da6554ede1 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 26 Jul 2024 16:50:55 +0200
Subject: [PATCH 16/33] #PSYNEU-137 - Fix rosetta installation

---
 package/psyneulinkviewer/rosetta.py | 2 +-
 package/setup.py                    | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/package/psyneulinkviewer/rosetta.py b/package/psyneulinkviewer/rosetta.py
index 10c630db..d710c082 100644
--- a/package/psyneulinkviewer/rosetta.py
+++ b/package/psyneulinkviewer/rosetta.py
@@ -15,7 +15,7 @@ def install_rosetta():
         logging.info("Installing rosetta")
         subprocess.run(configuration.rosetta_installation, shell=True)
 
-def check_conda_installation():
+def check_rosetta_installation():
     if platform.system() == 'Darwin':
         rosetta_version = subprocess.run(
             ["rosseta", "--version"],
diff --git a/package/setup.py b/package/setup.py
index ec48215d..03ed4cb1 100644
--- a/package/setup.py
+++ b/package/setup.py
@@ -12,7 +12,7 @@
 from setuptools.command.install import install
 from packaging.version import Version
 from psyneulinkviewer.conda import check_conda_installation
-from psyneulinkviewer.conda import check_rosetta
+from psyneulinkviewer.rosetta import check_rosetta_installation
 import configuration
 
 logger = logging.getLogger(__name__)
@@ -116,7 +116,7 @@ def prerequisites():
     check_python()
     check_conda_installation()
     #Install package requirements here
-    check_rosetta()
+    check_rosetta_installation()
     check_graphviz()
     check_psyneulink()
     get_latest_release(os.path.dirname(os.path.realpath(__file__)))

From 300f15a768b80e28fe3ee21d5149cc823b54e91d Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 26 Jul 2024 16:53:55 +0200
Subject: [PATCH 17/33] #PSYNEU-135 - Check node version and install if not
 present

---
 package/configuration.py         |  6 ++++-
 package/psyneulinkviewer/node.py | 38 ++++++++++++++++++++++++++++++++
 package/setup.py                 |  4 +++-
 3 files changed, 46 insertions(+), 2 deletions(-)
 create mode 100644 package/psyneulinkviewer/node.py

diff --git a/package/configuration.py b/package/configuration.py
index 42ca0154..538bb202 100644
--- a/package/configuration.py
+++ b/package/configuration.py
@@ -14,4 +14,8 @@
 create_env = "conda create --name " + env_name
 activate_env = "conda activate " + env_name
 
-rosetta_installation = "softwareupdate --install-rosetta --agree-to-license"
\ No newline at end of file
+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"
diff --git a/package/psyneulinkviewer/node.py b/package/psyneulinkviewer/node.py
new file mode 100644
index 00000000..93621df7
--- /dev/null
+++ b/package/psyneulinkviewer/node.py
@@ -0,0 +1,38 @@
+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 = subprocess.run(
+        ["node", "--version"],
+        capture_output = True,
+        text = True 
+    ).stdout
+    logging.info("Node version detected : %s", node_version)
+
+    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()
\ No newline at end of file
diff --git a/package/setup.py b/package/setup.py
index 03ed4cb1..74e1865d 100644
--- a/package/setup.py
+++ b/package/setup.py
@@ -13,6 +13,7 @@
 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__)
@@ -114,9 +115,10 @@ def get_latest_release(installation_path):
 def prerequisites():
     check_os()
     check_python()
-    check_conda_installation()
+    #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__)))

From f7477fbab1c9b1eae2f08281c62c23f6942d6742 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 26 Jul 2024 16:54:54 +0200
Subject: [PATCH 18/33] #PSYNEU-136 - Create conda with python version 3.11

---
 package/configuration.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/configuration.py b/package/configuration.py
index 24a48df7..85303b80 100644
--- a/package/configuration.py
+++ b/package/configuration.py
@@ -11,5 +11,5 @@
 mac_conda_bash = "https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh"
 
 env_name = "psyneulinkviewer"
-create_env = "conda create --name " + env_name
+create_env = "conda create --name " + env_name + " python=3.11"
 activate_env = "conda activate " + env_name

From 54ff1563cb8407cdd462b1c4b155d560646d1adb Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 26 Jul 2024 17:02:28 +0200
Subject: [PATCH 19/33] #PSYNEU-135 - Uncoment line for conda installation

---
 package/setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/setup.py b/package/setup.py
index 74e1865d..0cff02d7 100644
--- a/package/setup.py
+++ b/package/setup.py
@@ -115,7 +115,7 @@ def get_latest_release(installation_path):
 def prerequisites():
     check_os()
     check_python()
-    #check_conda_installation()
+    check_conda_installation()
     #Install package requirements here
     check_rosetta_installation()
     check_node_installation()

From 1c2314c5d380cdb77c376fe1b88671867178bf2b Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 26 Jul 2024 18:23:35 +0200
Subject: [PATCH 20/33] #PSYNEU-134 - Use cmdClass to install prerequesites
 during installation process instead of after

---
 package/setup.py | 141 ++---------------------------------------------
 1 file changed, 5 insertions(+), 136 deletions(-)

diff --git a/package/setup.py b/package/setup.py
index 4755485b..ad636475 100644
--- a/package/setup.py
+++ b/package/setup.py
@@ -1,142 +1,12 @@
-import re
-import json
-import platform
-import os
-import sys
-import subprocess
 import logging
-import importlib.util
-import tarfile
-import atexit
+import os
 from setuptools import setup, find_packages
 from setuptools.command.install import install
+from psyneulinkviewer.start import prerequisites
 
 logger = logging.getLogger(__name__)
 logging.basicConfig(level=logging.INFO)
 
-graphviz = "graphviz"
-psyneulink = "psyneulink"
-
-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_conda():
-    result = subprocess.run(
-        ["conda", "--version"],
-        capture_output = True,
-        text = True 
-    )
-    logging.info("conda version %s", result.stdout)
-
-def check_rosetta():
-    if sys.platform == "darwin":
-        result = subprocess.run(
-            ["rosseta", "--version"],
-            capture_output = True,
-            text = True 
-        )
-        logging.info("rosseta version %s", result.stdout)
-
-def check_graphviz():
-    if importlib.util.find_spec(graphviz) is None:
-        logging.error(graphviz +" is not installed, installing")
-        result = subprocess.run(
-            ["pip", "install", "graphviz"],
-            capture_output = True,
-            text = True 
-        )
-    else:
-        logging.info(graphviz +" is installed")
-
-def check_psyneulink():
-    if importlib.util.find_spec(psyneulink) is None:
-        logging.error(psyneulink +" is not installed, installing")
-        result = subprocess.run(
-            ["pip", "install", "psyneulink"],
-            capture_output = True,
-            text = True 
-        )
-    else:
-        logging.info(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
-
-    url = 'https://api.github.com/repos/MetaCell/PsyNeuLinkView/releases'
-    headers = {'Accept': 'application/vnd.github+json','Authorization': 'Bearer JWT', 'X-GitHub-Api-Version' : '2022-11-28'}
-    r = requests.get(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 = "/usr/local/bin"
-    tar.extractall(path=extract_location)
-    tar.close()
-    logging.info("Release file uncompressed at : %s", extract_location)
-
-    application = os.path.join(extract_location, "psyneulinkviewer-linux-x64/psyneulinkviewer")
-    symlink = "/usr/local/bin/psyneulinkviewer"
-    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()
-    check_rosetta()
-    check_graphviz()
-    check_psyneulink()
-    get_latest_release(os.path.dirname(os.path.realpath(__file__)))
-
 class InstallCommand(install):
     user_options = install.user_options + [
         ('path=', None, 'an option that takes a value')
@@ -157,14 +27,13 @@ def run(self):
         global path
         path = self.path # will be 1 or None
         install.run(self)
+        prerequisites()
 
 setup(
     name="psyneulinkview",
     version="0.0.1",
     setup_requires=['requests'],
-    entry_points={
-            'console_scripts': [
-                'psyneulinkviewer = psyneulinkviewer.start:main',
-            ]
+    cmdclass={
+        'install': InstallCommand,
     }
 )
\ No newline at end of file

From be43f51a8e6aaee454b92d739abc9a78a18a6881 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 26 Jul 2024 18:30:42 +0200
Subject: [PATCH 21/33] #PSYNEU-136 - Update prerequesites in start.py file

---
 package/psyneulinkviewer/start.py | 49 +++++++++++--------------------
 1 file changed, 17 insertions(+), 32 deletions(-)

diff --git a/package/psyneulinkviewer/start.py b/package/psyneulinkviewer/start.py
index 3818f1d7..ee8fab25 100644
--- a/package/psyneulinkviewer/start.py
+++ b/package/psyneulinkviewer/start.py
@@ -7,16 +7,16 @@
 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
+import configuration
 
 logger = logging.getLogger(__name__)
 logging.basicConfig(level=logging.INFO)
 
-graphviz = "graphviz"
-psyneulink = "psyneulink"
-symlink = "/usr/local/bin/psyneulinkviewer"
-
 def check_os():
     if os.name == 'nt':
         sys.exit('Windows is not supported')
@@ -30,14 +30,6 @@ def check_python():
     else:
         logging.info("Python version is supported")
 
-def check_conda():
-    result = subprocess.run(
-        ["conda", "--version"],
-        capture_output = True,
-        text = True 
-    )
-    logging.info("conda version %s", result.stdout)
-
 def check_rosetta():
     if sys.platform == "darwin":
         result = subprocess.run(
@@ -48,26 +40,26 @@ def check_rosetta():
         logging.info("rosseta version %s", result.stdout)
 
 def check_graphviz():
-    if importlib.util.find_spec(graphviz) is None:
-        logging.error(graphviz +" is not installed, installing")
+    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(graphviz +" is installed")
+        logging.info(configuration.graphviz +" is installed")
 
 def check_psyneulink():
-    if importlib.util.find_spec(psyneulink) is None:
-        logging.error(psyneulink +" is not installed, installing")
+    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(psyneulink +" is installed")
+        logging.info(configuration.psyneulink +" is installed")
 
 
 def get_filename_from_cd(cd):
@@ -84,9 +76,8 @@ def get_filename_from_cd(cd):
 def get_latest_release(installation_path):
     import requests
 
-    url = 'https://api.github.com/repos/MetaCell/PsyNeuLinkView/releases'
     headers = {'Accept': 'application/vnd.github+json','Authorization': 'Bearer JWT', 'X-GitHub-Api-Version' : '2022-11-28'}
-    r = requests.get(url, allow_redirects=True)
+    r = requests.get(configuration.releases_url, allow_redirects=True)
     releases = json.loads(r.text)
     assets = releases[0]["assets"]
 
@@ -107,21 +98,19 @@ def get_latest_release(installation_path):
 
     logging.info("Opening compressed file %s", filename)
     tar = tarfile.open(tar_location)
-    extract_location = "/usr/local/bin"
+    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, "psyneulinkviewer-linux-x64/psyneulinkviewer")
+    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)
-       result = subprocess.run(
-            [symlink]
-        )
     except OSError as e:
        logging.error("Error applying symlin %f ", e)
 
@@ -133,16 +122,12 @@ def get_latest_release(installation_path):
 def prerequisites():
     check_os()
     check_python()
-    check_conda()
+    check_conda_installation()
+    #Install package requirements here
     check_rosetta()
     check_graphviz()
     check_psyneulink()
-    if os.path.islink(symlink):
-        result = subprocess.run(
-            [symlink]
-        )
-    else:
-        get_latest_release(os.path.dirname(os.path.realpath(__file__)))
+    get_latest_release(os.path.dirname(os.path.realpath(__file__)))
 
 def main():
     prerequisites()

From fc52ef64370646c7110fd5e51b35edafb1788ee8 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 26 Jul 2024 18:34:32 +0200
Subject: [PATCH 22/33] #PSYNEU-136 - Remove build folder

---
 .../build/lib/psyneulinkviewer/__init__.py    |   0
 package/build/lib/psyneulinkviewer/conda.py   |  71 --------
 package/build/lib/psyneulinkviewer/start.py   | 151 ------------------
 3 files changed, 222 deletions(-)
 delete mode 100644 package/build/lib/psyneulinkviewer/__init__.py
 delete mode 100644 package/build/lib/psyneulinkviewer/conda.py
 delete mode 100644 package/build/lib/psyneulinkviewer/start.py

diff --git a/package/build/lib/psyneulinkviewer/__init__.py b/package/build/lib/psyneulinkviewer/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/package/build/lib/psyneulinkviewer/conda.py b/package/build/lib/psyneulinkviewer/conda.py
deleted file mode 100644
index 8ba6afe3..00000000
--- a/package/build/lib/psyneulinkviewer/conda.py
+++ /dev/null
@@ -1,71 +0,0 @@
-import re
-import json
-import platform
-import os
-import sys
-import subprocess
-import logging
-import importlib.util
-import tarfile
-import atexit
-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 ")
-    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 = subprocess.run(
-        ["conda", "--version"],
-        capture_output = True,
-        text = True 
-    ).stdout
-    if conda_version:
-        conda_version = conda_version.split(" ")[1]
-    logging.info("conda version %s", conda_version)
-
-    if conda_version is not None:
-        logging.info("Conda not installed")
-        install_conda()
-    
-    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");
-    
-    envs = subprocess.run(
-        ["conda", "env","list"],
-        capture_output = True,
-        text = True 
-    ).stdout.splitlines()
-    active_env = list(filter(lambda s: '*' in str(s), envs))[0]
-    env_name = str(active_env).split()[0]
-    if env_name is not None:
-        logging.info("Conda environment foudn and activated%s", env_name)
\ No newline at end of file
diff --git a/package/build/lib/psyneulinkviewer/start.py b/package/build/lib/psyneulinkviewer/start.py
deleted file mode 100644
index 3818f1d7..00000000
--- a/package/build/lib/psyneulinkviewer/start.py
+++ /dev/null
@@ -1,151 +0,0 @@
-import re
-import json
-import platform
-import os
-import sys
-import subprocess
-import logging
-import importlib.util
-import tarfile
-from setuptools import setup, find_packages
-from setuptools.command.install import install
-
-logger = logging.getLogger(__name__)
-logging.basicConfig(level=logging.INFO)
-
-graphviz = "graphviz"
-psyneulink = "psyneulink"
-symlink = "/usr/local/bin/psyneulinkviewer"
-
-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_conda():
-    result = subprocess.run(
-        ["conda", "--version"],
-        capture_output = True,
-        text = True 
-    )
-    logging.info("conda version %s", result.stdout)
-
-def check_rosetta():
-    if sys.platform == "darwin":
-        result = subprocess.run(
-            ["rosseta", "--version"],
-            capture_output = True,
-            text = True 
-        )
-        logging.info("rosseta version %s", result.stdout)
-
-def check_graphviz():
-    if importlib.util.find_spec(graphviz) is None:
-        logging.error(graphviz +" is not installed, installing")
-        result = subprocess.run(
-            ["pip", "install", "graphviz"],
-            capture_output = True,
-            text = True 
-        )
-    else:
-        logging.info(graphviz +" is installed")
-
-def check_psyneulink():
-    if importlib.util.find_spec(psyneulink) is None:
-        logging.error(psyneulink +" is not installed, installing")
-        result = subprocess.run(
-            ["pip", "install", "psyneulink"],
-            capture_output = True,
-            text = True 
-        )
-    else:
-        logging.info(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
-
-    url = 'https://api.github.com/repos/MetaCell/PsyNeuLinkView/releases'
-    headers = {'Accept': 'application/vnd.github+json','Authorization': 'Bearer JWT', 'X-GitHub-Api-Version' : '2022-11-28'}
-    r = requests.get(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 = "/usr/local/bin"
-    tar.extractall(path=extract_location)
-    tar.close()
-    logging.info("Release file uncompressed at : %s", extract_location)
-
-    application = os.path.join(extract_location, "psyneulinkviewer-linux-x64/psyneulinkviewer")
-    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)
-       result = subprocess.run(
-            [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()
-    check_rosetta()
-    check_graphviz()
-    check_psyneulink()
-    if os.path.islink(symlink):
-        result = subprocess.run(
-            [symlink]
-        )
-    else:
-        get_latest_release(os.path.dirname(os.path.realpath(__file__)))
-
-def main():
-    prerequisites()
-
-if __name__ == "__main__":
-    main()
\ No newline at end of file

From bb3b96cde83cbd9796e48dcd81e4fc17f6b81f35 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Fri, 26 Jul 2024 18:52:30 +0200
Subject: [PATCH 23/33] #PSYNEU-135 - Cleanup

---
 package/psyneulinkviewer/rosetta.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/package/psyneulinkviewer/rosetta.py b/package/psyneulinkviewer/rosetta.py
index d710c082..fb79baf0 100644
--- a/package/psyneulinkviewer/rosetta.py
+++ b/package/psyneulinkviewer/rosetta.py
@@ -22,8 +22,6 @@ def check_rosetta_installation():
             capture_output = True,
             text = True 
         ).stdout
-        if rosetta_version:
-            rosetta_version = rosetta_version.split(" ")[1]
         logging.info("Rosseta version detected : %s", rosetta_version)
 
         if rosetta_version is None:

From 00b24131b4d67aa67b958ff9e486dad36909f8d7 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Mon, 29 Jul 2024 14:29:52 +0200
Subject: [PATCH 24/33] #PSYNEU-136 - Wrap installation on try/catch, and fix
 typo

---
 package/psyneulinkviewer/conda.py | 67 +++++++++++++++++--------------
 package/setup.py                  |  4 +-
 2 files changed, 39 insertions(+), 32 deletions(-)

diff --git a/package/psyneulinkviewer/conda.py b/package/psyneulinkviewer/conda.py
index ae75f62c..17a9313a 100644
--- a/package/psyneulinkviewer/conda.py
+++ b/package/psyneulinkviewer/conda.py
@@ -37,37 +37,42 @@ def install_conda():
 
 
 def check_conda_installation():
-    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)
+    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)
 
-    if conda_version is not 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...")
+        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()
+        
+        envs = subprocess.run(
+            ["conda", "env","list"],
+            capture_output = True,
+            text = True 
+        ).stdout.splitlines()
+        active_env = list(filter(lambda s: '*' in str(s), envs))[0]
+        env_name = str(active_env).split()[0]
+        if env_name is not None:
+            logging.info("Conda environment found and activated %s", env_name)
         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()
-    
-    envs = subprocess.run(
-        ["conda", "env","list"],
-        capture_output = True,
-        text = True 
-    ).stdout.splitlines()
-    active_env = list(filter(lambda s: '*' in str(s), envs))[0]
-    env_name = str(active_env).split()[0]
-    if env_name is not None:
-        logging.info("Conda environment found and activated %s", env_name)
\ No newline at end of file
+            activate_env()
+    except Exception as error:
+        logging.error("Error %s ", error)
\ No newline at end of file
diff --git a/package/setup.py b/package/setup.py
index 9dabc6c1..8339933a 100644
--- a/package/setup.py
+++ b/package/setup.py
@@ -34,7 +34,9 @@ def run(self):
 setup(
     name="psyneulinkview",
     version="0.0.1",
-    setup_requires=['requests'],
+    install_requires=['requests',
+                      'wget'
+                      'packaging'],
     cmdclass={
         'install': InstallCommand,
     }

From f3add7894e1849668374b289d07927e39dd8a3a0 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Mon, 29 Jul 2024 14:39:28 +0200
Subject: [PATCH 25/33] #PSYNEU-136 - Better logging

---
 package/psyneulinkviewer/conda.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/psyneulinkviewer/conda.py b/package/psyneulinkviewer/conda.py
index 17a9313a..7c075552 100644
--- a/package/psyneulinkviewer/conda.py
+++ b/package/psyneulinkviewer/conda.py
@@ -75,4 +75,4 @@ def check_conda_installation():
         else:
             activate_env()
     except Exception as error:
-        logging.error("Error %s ", error)
\ No newline at end of file
+        logging.error("Error with conda installation: %s ", error)
\ No newline at end of file

From 0c254d0b5df1c5f822ca6e90065ef3dc74fdb218 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Mon, 29 Jul 2024 14:56:52 +0200
Subject: [PATCH 26/33] #PSYNEU-137 -Wrap rosetta installation into try/catch

---
 package/psyneulinkviewer/rosetta.py | 39 ++++++++++++++++-------------
 1 file changed, 21 insertions(+), 18 deletions(-)

diff --git a/package/psyneulinkviewer/rosetta.py b/package/psyneulinkviewer/rosetta.py
index d710c082..1ffccc2d 100644
--- a/package/psyneulinkviewer/rosetta.py
+++ b/package/psyneulinkviewer/rosetta.py
@@ -16,22 +16,25 @@ def install_rosetta():
         subprocess.run(configuration.rosetta_installation, shell=True)
 
 def check_rosetta_installation():
-    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)
+    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)
 
-        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()
+            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()
+    except Exception as error:
+        logging.error("Error with rosetta installation: %s ", error)

From f0ffa0eca74346bdf52bb5bc2d8219b9767cc471 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Mon, 29 Jul 2024 15:11:38 +0200
Subject: [PATCH 27/33] #PSYNEU-135 - Wrap check node installation with
 try/catch

---
 package/psyneulinkviewer/node.py | 43 +++++++++++++++++---------------
 1 file changed, 23 insertions(+), 20 deletions(-)

diff --git a/package/psyneulinkviewer/node.py b/package/psyneulinkviewer/node.py
index 93621df7..fa2b8f6c 100644
--- a/package/psyneulinkviewer/node.py
+++ b/package/psyneulinkviewer/node.py
@@ -14,25 +14,28 @@ def install_node():
     subprocess.run(configuration.node_installation, shell=True)
 
 def check_node_installation():
-    node_version = subprocess.run(
-        ["node", "--version"],
-        capture_output = True,
-        text = True 
-    ).stdout
-    logging.info("Node version detected : %s", node_version)
+    try:
+        node_version = subprocess.run(
+            ["node", "--version"],
+            capture_output = True,
+            text = True 
+        ).stdout
+        logging.info("Node version detected : %s", node_version)
 
-    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()
+        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("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()
\ No newline at end of file
+            logging.error("Node version not up to date, update required")
+            install_node()
+    except Exception as error:
+        logging.error("Error with node installation: %s ", error)
\ No newline at end of file

From db37698de8c0040821d3cda3a9d0151eff267b31 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Tue, 6 Aug 2024 14:12:59 +0200
Subject: [PATCH 28/33] #PSYNEU-136 - Handle better errors when conda not
 present

---
 package/psyneulinkviewer/conda.py | 50 ++++++++++++++++++-------------
 1 file changed, 29 insertions(+), 21 deletions(-)

diff --git a/package/psyneulinkviewer/conda.py b/package/psyneulinkviewer/conda.py
index 7c075552..dc204307 100644
--- a/package/psyneulinkviewer/conda.py
+++ b/package/psyneulinkviewer/conda.py
@@ -14,7 +14,7 @@
 logging.basicConfig(level=logging.INFO)
 
 def activate_env():
-    logging.info("Creating conda ")
+    logging.info("Creating conda environment ")
     subprocess.run(configuration.create_env, shell=True)
 
     logging.info("Activating conda ")
@@ -37,6 +37,7 @@ def install_conda():
 
 
 def check_conda_installation():
+    conda_version = None
     try:
         conda_version = subprocess.run(
             ["conda", "--version"],
@@ -46,33 +47,40 @@ def check_conda_installation():
         if conda_version:
             conda_version = conda_version.split(" ")[1]
         logging.info("Conda version detected : %s", conda_version)
+    except Exception as error:
+        logging.error("Error with conda installation: %s ", error)
 
-        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")
+    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.splitlines()
+        ).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 is not None:
-            logging.info("Conda environment found and activated %s", env_name)
-        else:
-            activate_env()
     except Exception as error:
-        logging.error("Error with conda installation: %s ", error)
\ No newline at end of file
+        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()
\ No newline at end of file

From a4ffef91c3725eed2d0d3b552d14a349ad573178 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Tue, 6 Aug 2024 14:31:02 +0200
Subject: [PATCH 29/33] #PSYNEU-137 - Handle better lack of rossetta
 installation, catch error and proceed with installation

---
 package/psyneulinkviewer/rosetta.py | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/package/psyneulinkviewer/rosetta.py b/package/psyneulinkviewer/rosetta.py
index 1ffccc2d..3fc221bd 100644
--- a/package/psyneulinkviewer/rosetta.py
+++ b/package/psyneulinkviewer/rosetta.py
@@ -16,6 +16,7 @@ def install_rosetta():
         subprocess.run(configuration.rosetta_installation, shell=True)
 
 def check_rosetta_installation():
+    rosetta_version = None
     try:
         if platform.system() == 'Darwin':
             rosetta_version = subprocess.run(
@@ -26,15 +27,16 @@ def check_rosetta_installation():
             if rosetta_version:
                 rosetta_version = rosetta_version.split(" ")[1]
             logging.info("Rosseta version detected : %s", rosetta_version)
-
-            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()
     except Exception as error:
         logging.error("Error with rosetta installation: %s ", error)
+
+    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()
+    

From dc4b700b2d31dbbf9734f02b557678232e74a101 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Tue, 6 Aug 2024 14:34:56 +0200
Subject: [PATCH 30/33] #PSYNEU-135 - Handle better node installation when
 there's an error

---
 package/psyneulinkviewer/node.py | 33 ++++++++++++++++----------------
 1 file changed, 17 insertions(+), 16 deletions(-)

diff --git a/package/psyneulinkviewer/node.py b/package/psyneulinkviewer/node.py
index fa2b8f6c..739cfe20 100644
--- a/package/psyneulinkviewer/node.py
+++ b/package/psyneulinkviewer/node.py
@@ -14,6 +14,7 @@ def install_node():
     subprocess.run(configuration.node_installation, shell=True)
 
 def check_node_installation():
+    node_version = None
     try:
         node_version = subprocess.run(
             ["node", "--version"],
@@ -21,21 +22,21 @@ def check_node_installation():
             text = True 
         ).stdout
         logging.info("Node version detected : %s", node_version)
+    except Exception as error:
+        logging.error("Error with node installation: %s ", error)
 
-        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")
+    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()
-    except Exception as error:
-        logging.error("Error with node installation: %s ", error)
\ No newline at end of file
+        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()
\ No newline at end of file

From 87571dad040edd64f48c6866757fa9ad13c74c0c Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Tue, 6 Aug 2024 17:32:37 +0200
Subject: [PATCH 31/33] #PSYNEU-136 - Don't log error if exception is
 FileNotFoundError and continue with process, otherwise log it and exit

---
 package/psyneulinkviewer/conda.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/package/psyneulinkviewer/conda.py b/package/psyneulinkviewer/conda.py
index dc204307..5f52809b 100644
--- a/package/psyneulinkviewer/conda.py
+++ b/package/psyneulinkviewer/conda.py
@@ -46,9 +46,11 @@ def check_conda_installation():
         ).stdout
         if conda_version:
             conda_version = conda_version.split(" ")[1]
-        logging.info("Conda version detected : %s", conda_version)
+            logging.info("Conda version detected : %s", conda_version)
     except Exception as error:
-        logging.error("Error with conda installation: %s ", 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")

From 86db20363e9dc04f992295e46831b8ed2f502e2e Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Tue, 6 Aug 2024 17:51:07 +0200
Subject: [PATCH 32/33] #PSYNEU-137 - Don't log error if exception is
 FileNotFoundError and continue with process, otherwise log it and exit

---
 package/psyneulinkviewer/rosetta.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/package/psyneulinkviewer/rosetta.py b/package/psyneulinkviewer/rosetta.py
index 3fc221bd..0e882b91 100644
--- a/package/psyneulinkviewer/rosetta.py
+++ b/package/psyneulinkviewer/rosetta.py
@@ -26,9 +26,11 @@ def check_rosetta_installation():
             ).stdout
             if rosetta_version:
                 rosetta_version = rosetta_version.split(" ")[1]
-            logging.info("Rosseta version detected : %s", rosetta_version)
+                logging.info("Rosseta version detected : %s", rosetta_version)
     except Exception as error:
-        logging.error("Error with rosetta installation: %s ", 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")

From 5c37e4f29d30ae0ecc39a7cee1ed8fc607116307 Mon Sep 17 00:00:00 2001
From: jrmartin <yeshuarmartinez@gmail.com>
Date: Tue, 6 Aug 2024 17:53:19 +0200
Subject: [PATCH 33/33] #PSYNEU-135 - Don't log error if exception is
 FileNotFoundError and continue with process, otherwise log it and exit

---
 package/psyneulinkviewer/node.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/package/psyneulinkviewer/node.py b/package/psyneulinkviewer/node.py
index 739cfe20..7baf555a 100644
--- a/package/psyneulinkviewer/node.py
+++ b/package/psyneulinkviewer/node.py
@@ -21,9 +21,10 @@ def check_node_installation():
             capture_output = True,
             text = True 
         ).stdout
-        logging.info("Node version detected : %s", node_version)
     except Exception as error:
-        logging.error("Error with node installation: %s ", 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")