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Make app callable from commandl ine by just doing scdefg after pip installing. #3

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Make app callable from commandl ine by just doing scdefg after pip installing. #3

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26 changes: 5 additions & 21 deletions scdefg/app.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
import os
import time
#! python
import warnings
from flask import Flask, jsonify, request, render_template, Blueprint
import logging
Expand All @@ -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)
Expand Down Expand Up @@ -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)
5 changes: 4 additions & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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="[email protected]",
description="A single page Flask app with GUI for performing differential expression on with scvi-tools.",
Expand All @@ -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",
Expand All @@ -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',

)