diff --git a/README.md b/README.md
index 2ee18e46..5cda690e 100644
--- a/README.md
+++ b/README.md
@@ -12,10 +12,10 @@ CallFlow is structured as three components:
 
 #### Installing CallFlow
 
-The `callflow` (python package) requires [python](https://realpython.com/installing-python/) (>= 3.6) and [pip](https://pip.pypa.io/en/stable/news/) (>= 20.1.1). Other dependencies are checked/installed during the installation of `callflow` using `pip`.
+The `callflow` (python package) requires [python](https://realpython.com/installing-python/) (>= 3.6) and [pip](https://pip.pypa.io/en/stable/news/) (>= 20.1.1). Other dependencies are checked/installed during the installation of `callflow` using `setup.py`.
 
 ```
-pip install .
+python3 setup.py install
 ```
 
 #### Installing Visualization Client
diff --git a/callflow/__init__.py b/callflow/__init__.py
index 3cfd2007..e6cb9bc3 100644
--- a/callflow/__init__.py
+++ b/callflow/__init__.py
@@ -3,9 +3,6 @@
 #
 # SPDX-License-Identifier: MIT
 
-__version_info__ = ("1", "1", "0")
-__version__ = ".".join(__version_info__)
-
 # callflow.__init__.py
 from .logger import init_logger
 from logging import getLogger as get_logger
@@ -15,7 +12,6 @@
 from .datastructures.ensemblegraph import EnsembleGraph
 
 from .callflow import CallFlow
-from .notebook import _load_ipython_extension
 
 # CallFlow's public API.
 __all__ = [
@@ -25,14 +21,4 @@
     "SuperGraph",
     "EnsembleGraph",
     "CallFlow",
-    "notebook",
 ]
-
-
-def load_ipython_extension(ipython):
-    """IPython API entry point.
-    Only intended to be called by the IPython runtime.
-    See:
-      https://ipython.readthedocs.io/en/stable/config/extensions/index.html
-    """
-    _load_ipython_extension(ipython)
diff --git a/callflow/operations/argparser.py b/callflow/argparser.py
similarity index 100%
rename from callflow/operations/argparser.py
rename to callflow/argparser.py
diff --git a/callflow/operations/__init__.py b/callflow/operations/__init__.py
index cd46aa2c..a4faee18 100644
--- a/callflow/operations/__init__.py
+++ b/callflow/operations/__init__.py
@@ -7,6 +7,5 @@
 from .group import Group
 from .filter import Filter
 from .read_config import ConfigFileReader
-from .argparser import ArgParser
 
-__all__ = ["Process", "Group", "Filter", "ConfigFileReader", "ArgParser"]
+__all__ = ["Process", "Group", "Filter", "ConfigFileReader"]
diff --git a/callflow/version.py b/callflow/version.py
new file mode 100644
index 00000000..5fc6ad3a
--- /dev/null
+++ b/callflow/version.py
@@ -0,0 +1,7 @@
+# Copyright 2017-2020 Lawrence Livermore National Security, LLC and other
+# CallFlow Project Developers. See the top-level LICENSE file for details.
+#
+# SPDX-License-Identifier: MIT
+
+__version_info__ = ("1", "1", "0")
+__version__ = ".".join(__version_info__)
diff --git a/docs/getting_started.rst b/docs/getting_started.rst
index bd3252e3..627ef099 100644
--- a/docs/getting_started.rst
+++ b/docs/getting_started.rst
@@ -41,11 +41,11 @@ You can get CallFlow from its `GitHub <https://github.com/LLNL/CallFlow>`_ using
 
 Install callflow python package
 -------------------------------
-To install callflow python package, run the following command using pip. 
+To install callflow python package, run the following command using `setup.py`. 
 
 .. code-block:: console
 
-   $ pip install .
+   $ python3 setup.py install
 
 To install in the dev mode,
 
diff --git a/requirements.txt b/requirements.txt
index b956a2e3..6f57c063 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,12 +1,12 @@
-pandas
-numpy
-flask
-flask_socketio
+colorlog==4.1.0
+statsmodels==0.10.1
+hatchet==1.0.1
+matplotlib==3.1.1
+jsonschema==3.0.2
 networkx==2.2
-colorlog
-statsmodels
-matplotlib
-sklearn
-jsonschema
-eventlet
-hatchet
+scipy==1.3.1
+numpy==1.17.2
+pandas==0.23.0
+Flask_SocketIO==4.2.1
+ipython==7.18.1
+scikit_learn==0.23.2
diff --git a/server/__init__.py b/server/__init__.py
new file mode 100644
index 00000000..6b32491d
--- /dev/null
+++ b/server/__init__.py
@@ -0,0 +1,15 @@
+# Copyright 2017-2020 Lawrence Livermore National Security, LLC and other
+# CallFlow Project Developers. See the top-level LICENSE file for details.
+#
+# SPDX-License-Identifier: MIT
+
+from .notebook_server import _load_ipython_extension
+
+
+def load_ipython_extension(ipython):
+    """IPython API entry point.
+    Only intended to be called by the IPython runtime.
+    See:
+      https://ipython.readthedocs.io/en/stable/config/extensions/index.html
+    """
+    _load_ipython_extension(ipython)
diff --git a/server/main.py b/server/callflow_server.py
similarity index 99%
rename from server/main.py
rename to server/callflow_server.py
index 87bfb88b..39f45627 100644
--- a/server/main.py
+++ b/server/callflow_server.py
@@ -3,17 +3,19 @@
 #
 # SPDX-License-Identifier: MIT
 # Library imports
-from flask import Flask
-from flask_socketio import SocketIO, emit
+import os
 import json
 from networkx.readwrite import json_graph
-import os
+
+from flask import Flask
+from flask_socketio import SocketIO, emit
 
 # ------------------------------------------------------------------------------
 # CallFlow imports.
 import callflow
-from callflow import manager
-from callflow.operations import ArgParser
+from callflow.argparser import ArgParser
+from . import manager
+
 
 LOGGER = callflow.get_logger(__name__)
 _CALLFLOW_SERVER_PORT = 5000
@@ -434,8 +436,12 @@ def split_mpi_rank(data):
             emit("split_mpi_distribution", result, json=True)
 
 
-if __name__ == "__main__":
+def main():
     # if verbose, level = 1
     # else, level = 2
     callflow.init_logger(level=2)
     CallFlowServer()
+
+
+if __name__ == "__main__":
+    main()
diff --git a/callflow/manager.py b/server/manager.py
similarity index 95%
rename from callflow/manager.py
rename to server/manager.py
index 561c3cfe..b784ee32 100644
--- a/callflow/manager.py
+++ b/server/manager.py
@@ -16,7 +16,16 @@
 import errno
 import json
 import base64
-from callflow import __version__
+
+from codecs import open
+
+version = {}
+vfile = os.path.join(
+    os.path.dirname(os.path.abspath(__file__)), "..", "callflow", "version.py"
+)
+with open(vfile) as fp:
+    exec(fp.read(), version)
+__version__ = version["__version__"]
 
 # The following five types enumerate the possible return values of the
 # `start` function.
@@ -231,16 +240,19 @@ def start(args, args_string):
     Launch python server.
     """
     print("Launching Server")
+    """
     cwd = os.getcwd().split("CallFlow")[0] + "CallFlow/server/main.py"
     server_cmd = ["python3", cwd] + args_string
+    """
+    server_cmd = ["callflow_server"] + args_string
     launch_cmd(server_cmd, alias="server")
 
     """
     Launch callflow app server.
     """
     print("Launching client")
-    cwd = os.getcwd().split("CallFlow")[0] + "CallFlow/app"
-    prefix_string = ["--silent", "--prefix=" + cwd]
+    app_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "app")
+    prefix_string = ["--silent", "--prefix=" + app_path]
     client_cmd = ["npm", "run", "dev"] + prefix_string
     launch_cmd(client_cmd, alias="client")
 
diff --git a/callflow/notebook.py b/server/notebook_server.py
similarity index 98%
rename from callflow/notebook.py
rename to server/notebook_server.py
index aec0bc88..538ad178 100644
--- a/callflow/notebook.py
+++ b/server/notebook_server.py
@@ -7,12 +7,11 @@
 # through the IPython interface.
 # The code can be found at https://github.com/tensorflow/tensorboard/blob/master/tensorboard/notebook.py
 
-import shlex
 import json
-import random
 import time
 import datetime
-from callflow.operations import ArgParser
+import shlex
+import random
 
 try:
     import html
@@ -25,7 +24,8 @@
     html_escape = cgi.escape
     del cgi
 
-from callflow import manager
+from callflow.argparser import ArgParser
+from . import manager
 
 
 def _load_ipython_extension(ipython):
diff --git a/setup.py b/setup.py
index 0115c2b0..258b6444 100644
--- a/setup.py
+++ b/setup.py
@@ -1,18 +1,91 @@
 # Copyright 2017-2020 Lawrence Livermore National Security, LLC and other
-# Hatchet Project Developers. See the top-level LICENSE file for details.
+# CallFlow Project Developers. See the top-level LICENSE file for details.
 #
 # SPDX-License-Identifier: MIT
 
+import os
 from setuptools import setup, find_packages
-from callflow import __version__
 
+# ------------------------------------------------------------------------------
+# get the version safely!
+from codecs import open
+
+version = {}
+vfile = os.path.join(
+    os.path.dirname(os.path.abspath(__file__)), "callflow", "version.py"
+)
+with open(vfile) as fp:
+    exec(fp.read(), version)
+version = version["__version__"]
+
+
+# ------------------------------------------------------------------------------
+# Only allow folders in https://github.com/LLNL/CallFlow/tree/develop/data to be added.
+# For now we are hard-coding this.
+# TODO: Find a more automated solution.
+_GITHUB_DATA_FOLDERS = [
+    "caliper-cali",
+    "caliper-lulesh-json",
+    "hpctoolkit-cpi-database",
+]
+
+# Only allow jupyter notebooks in https://github.com/LLNL/CallFlow/tree/develop/example to be added.
+_GITHUB_EXAMPLE_FILES = [
+    "%callflow-ipython-magic.ipynb",
+    "CallFlow-python-interface-demo.ipynb",
+]
+
+
+# gather the data to be copied
+def list_files(directory, whitelist_files=[], whitelist_folders=[]):
+    paths = []
+    if len(whitelist_folders) > 0:
+        for item in os.listdir(directory):
+            if item in whitelist_folders:
+                for (path, directories, filenames) in os.walk(
+                    os.path.join(directory, item)
+                ):
+                    if ".callflow" not in path.split("/"):
+                        paths.append((path, [os.path.join(path, f) for f in filenames]))
+
+    if len(whitelist_files) > 0:
+        for (path, directories, filenames) in os.walk(directory):
+            paths.append(
+                (
+                    path,
+                    [os.path.join(path, f) for f in filenames if f in whitelist_files],
+                )
+            )
+    return paths
+
+
+data_files = list_files("data", whitelist_folders=_GITHUB_DATA_FOLDERS)
+example_files = list_files("examples", whitelist_files=_GITHUB_EXAMPLE_FILES)
+
+
+deps = [
+    "flask_socketio",
+    "ipython",
+    "colorlog",
+    "jsonschema",
+    "numpy",
+    "scipy",
+    "pandas",
+    "scikit_learn",
+    "statsmodels",
+    "hatchet",
+    "networkx",
+    "matplotlib",
+]
+# ------------------------------------------------------------------------------
+# now set up
 setup(
     name="CallFlow",
-    version=__version__,
+    version=version,
     license="MIT",
     description="",
     url="https://github.com/LLNL/CallFlow",
-    author="Suraj Kesavan, Huu Tan Nguyen",
+    author="Suraj Kesavan",
     author_email="spkesavan@ucdavis.edu",
     classifiers=[
         "Development Status :: 3 - Alpha",
@@ -20,15 +93,9 @@
     ],
     keywords="",
     packages=find_packages(),
-    install_requires=[
-        "numpy",
-        "pandas",
-        "tables",
-        "flask",
-        "flask_socketio",
-        "sklearn",
-        "statsmodels",
-        "networkx == 2.2",
-        "hatchet",
-    ],
+    data_files=data_files + example_files,
+    entry_points={"console_scripts": ["callflow_server = server.callflow_server:main"]},
+    install_requires=deps,
 )
+
+# ------------------------------------------------------------------------------