Split requirements.txt to a separate file

Use gunicorn and plotly_express from requirements.txt
Add requirements.txt to docker first and install to optimize docker cache hits
Add MANIFEST.in for package packaging that include the README and the requirements.txt when packaging and also any non-python files that are part of covasim(html,. R, spreadsheets, etc)

Dockerfile

@@ -3,8 +3,13 @@ FROM continuumio/anaconda3:latest
 ENV PATH="/opt/conda/bin:${PATH}"
 
 RUN apt-get -y update && apt-get install -y nginx supervisor
-RUN conda install twisted python-Levenshtein gunicorn
-RUN python3 -m pip install plotly_express
+RUN mkdir /app && \
+    conda install twisted python-Levenshtein
+
+# Add requiremments.txt first and install to maximize chances of hitting docker cache
+ADD requirements.txt /app
+RUN python3 -m pip install -r /app/requirements.txt
+
 ADD . /app
 WORKDIR /app
 

MANIFEST.in

@@ -0,0 +1,3 @@
+include requirements.txt
+include README.md
+recursive-include covasim/*

requirements.txt

@@ -0,0 +1,10 @@
+matplotlib>=2.2.2
+numpy>=1.10.1
+scipy>=1.2.0
+sciris>=0.15.8
+scirisweb>=0.15.0
+pandas
+numba
+gunicorn
+plotly_express
+#parestlib>=0.3

setup.py

@@ -2,6 +2,15 @@
 import runpy
 from setuptools import setup, find_packages
 
+# Load requirements from txt file
+with open('requirements.txt') as requirements_file:
+    # ensure EOLs are '\n' in case on windows and splits
+    requirements = []
+    for line in requirements_file.read().replace('\r\n', '\n').split('\n'):
+        if line and line[0] != '#':
+            requirements.append(line)
+
+
 # Get version
 cwd = os.path.abspath(os.path.dirname(__file__))
 versionpath = os.path.join(cwd, 'covasim', 'cova_base', 'version.py')
@@ -29,16 +38,5 @@
     classifiers=CLASSIFIERS,
     packages=find_packages(),
     include_package_data=True,
-    install_requires=[
-        "matplotlib>=2.2.2",
-        "numpy>=1.10.1",
-        "scipy>=1.2.0",
-        "sciris>=0.15.8",
-        "scirisweb>=0.15.0",
-        "pandas",
-        "numba",
-        "gunicorn",
-        "plotly_express",
-		# "parestlib>=0.3",
-    ],
+    install_requires=requirements
 )