From b5a95b207b37b4e380833f1025357a1aaba930ea Mon Sep 17 00:00:00 2001
From: munfred <munfred@brandeis.edu>
Date: Sun, 12 Sep 2021 13:03:41 -0700
Subject: [PATCH] Make app callable from commandline by just doing `scdefg`
 when pip installing. Should be good for pypi now

---
 scdefg/app.py | 26 +++++---------------------
 setup.py      |  5 ++++-
 2 files changed, 9 insertions(+), 22 deletions(-)

diff --git a/scdefg/app.py b/scdefg/app.py
index 4eb8a30..3d4a17f 100644
--- a/scdefg/app.py
+++ b/scdefg/app.py
@@ -1,5 +1,4 @@
-import os
-import time
+#! python
 import warnings
 from flask import Flask, jsonify, request, render_template, Blueprint
 import logging
@@ -9,18 +8,14 @@
 import scvi
 import numpy as np
 import plotly.graph_objects as go
-import plotly
-import time
 import click
-import flask
 
 # ignore annoying pandas future warning
 warnings.simplefilter(action='ignore', category=FutureWarning)
 
 print('🧮 🧬 📊 🧫 🧪 scdefg: scvi-tools Differential Expression Flask GUI 📱 🎲 📈 🦠 📉 🎰')
-print('You are using scvi-tools version:', scvi.__version__)
-print('You are using flask version:', flask.__version__)
-print('You are using plotly version:', plotly.__version__)
+print('Using scvi-tools version', scvi.__version__)
+
 
 # set up logs and flask blueprints
 logging.basicConfig(level=logging.INFO)
@@ -336,17 +331,6 @@ def receive_submission():
 
     return app
 
+print('💜 Launching... 💜')
+launch()
 
-if __name__ == '__main__':
-    print('Starting launch function...')
-    launch()
-
-else:
-    # this code is run if the file is imported as a module
-    #
-    # os.environ reads env variables from the system
-    # APP_SELECTION_COLUMNS is passed as a single variable, so it needs to be split
-    app = run(scvi_tools_model_path=os.environ["SCVI_TOOLS_MODEL_PATH"],
-              selection_columns=os.environ["APP_SELECTION_COLUMNS"].split(","),
-              intro_text_html=os.environ["APP_INTRO_TEXT_HTML"], host=os.environ["APP_HOST"], port=os.environ["APP_PORT"],
-              run_app=False)
diff --git a/setup.py b/setup.py
index 730c41c..8328ac5 100644
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@
     long_description = fh.read()
     setuptools.setup(
         name="scdefg",
-        version="0.2.0",
+        version="0.3.0",
         author="Eduardo da Veiga Beltrame",
         author_email="munfred@brandeis.edu",
         description="A single page Flask app with GUI for performing differential expression on with scvi-tools.",
@@ -17,6 +17,7 @@
         license='LICENSE.txt',
         packages=setuptools.find_packages(),
         install_requires=requirements,
+        include_package_data=True,
         classifiers=[
             "Programming Language :: Python :: 3.6",
             "Programming Language :: Python :: 3.7",
@@ -26,6 +27,8 @@
             "Operating System :: OS Independent",
             "Topic :: Scientific/Engineering :: Bio-Informatics",
         ],
+        entry_points={"console_scripts": ["scdefg = scdefg.app:launch"]},
         python_requires='>=3.6',
+
     )