Merge pull request #20 from eipm/develop

v1.0.2

.github/workflows/docker-publish.yml

@@ -5,6 +5,7 @@ on:
     # Publish `main` as Docker `latest` image.
     branches:
       - main
+      - develop
 
     # Publish `v1.2.3` tags as releases.
     tags:
@@ -18,11 +19,9 @@ env:
   IMAGE_NAME: cnn-smoothie
 
 jobs:
-
   # Push image to GitHub Packages.
   # See also https://docs.docker.com/docker-hub/builds/
   push:
-
     runs-on: ubuntu-latest
     if: github.event_name == 'push'
 
@@ -50,6 +49,7 @@ jobs:
 
           # Use Docker `latest` tag convention
           [ "$VERSION" == "main" ] && VERSION=latest
+          [ "$VERSION" == "develop" ] && VERSION=develop
 
           echo IMAGE_ID=$IMAGE_ID
           echo VERSION=$VERSION
@@ -62,7 +62,7 @@ jobs:
         with:
           username: ${{ secrets.EIPM_DOCKER_HUB_USERNAME }}
           password: ${{ secrets.EIPM_DOCKER_HUB_TOKEN }}
-        
+
       - name: Push image to EIPM Docker Hub
         run: |
           IMAGE_ID=eipm/$IMAGE_NAME
@@ -78,6 +78,7 @@ jobs:
 
           # Use Docker `latest` tag convention
           [ "$VERSION" == "main" ] && VERSION=latest
+          [ "$VERSION" == "develop" ] && VERSION=develop
 
           echo IMAGE_ID=$IMAGE_ID
           echo VERSION=$VERSION

Dockerfile

@@ -1,13 +1,13 @@
-FROM python:3.6.8-stretch
+FROM python:3.7.9-buster
 #===============================#
-# Docker Image Configuration	#
+# Docker Image Configuration    #
 #===============================#
 LABEL org.opencontainers.image.source='https://github.com/eipm/cnn-smoothie' \
     vendor='Englander Institute for Precision Medicine' \
     description='CNN Smoothie' \
     maintainer='[email protected]' \
     base_image='python' \
-    base_image_version='3.6.8-stretch'
+    base_image_version='3.7.9-buster'
 
 ENV APP_NAME='cnn_smoothie' \
     TZ='US/Eastern' \
@@ -18,17 +18,17 @@ ENV RESULT_DIR=${CNN_SMOOTHIE}/result \
     PYTHONPATH=${PYTHONPATH}:${CNN_SMOOTHIE}:${PREDICT_DIR}
 
 #===================================#
-# Install Prerequisites         	#
+# Install Prerequisites             #
 #===================================#
 COPY requirements.txt /${APP_NAME}/requirements.txt
 RUN pip install -r /${APP_NAME}/requirements.txt
 #===================================#
-# Copy Files and set work directory	#
+# Copy Files and set work directory #
 #===================================#
 COPY src /${APP_NAME}/src/
 WORKDIR /${APP_NAME}
 #===================================#
-# Startup							#
+# Startup                           #
 #===================================#
 EXPOSE 80
 VOLUME uploads

README.md

@@ -14,7 +14,7 @@ https://doi.org/10.1016/j.ebiom.2017.12.026
 
 ![CNN Smoothie Logo](docs/images/logo.jpg)
 
-[![Actions Status](https://github.com/eipm/cnn-smoothie/workflows/Docker/badge.svg)](https://github.com/eipm/cnn-smoothie/actions) [![Github](https://img.shields.io/badge/github-1.0.1-green?style=flat&logo=github)](https://github.com/eipm/cnn-smoothie) [![EIPM Docker Hub](https://img.shields.io/badge/EIPM%20docker%20hub-1.0.1-blue?style=flat&logo=docker)](https://hub.docker.com/repository/docker/eipm/cnn-smoothie) [![GitHub Container Registry](https://img.shields.io/badge/GitHub%20Container%20Registry-1.0.1-blue?style=flat&logo=docker)](https://github.com/orgs/eipm/packages/container/package/cnn-smoothie) [![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Actions Status](https://github.com/eipm/cnn-smoothie/workflows/Docker/badge.svg)](https://github.com/eipm/cnn-smoothie/actions) [![Github](https://img.shields.io/badge/github-1.0.2-green?style=flat&logo=github)](https://github.com/eipm/cnn-smoothie) [![EIPM Docker Hub](https://img.shields.io/badge/EIPM%20docker%20hub-1.0.2-blue?style=flat&logo=docker)](https://hub.docker.com/repository/docker/eipm/cnn-smoothie) [![GitHub Container Registry](https://img.shields.io/badge/GitHub%20Container%20Registry-1.0.2-blue?style=flat&logo=docker)](https://github.com/orgs/eipm/packages/container/package/cnn-smoothie) [![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 The CNN_Smoothie pipeline presented here provides a novel framework that can be easily implemented for many different applications, including immunohistochemistry grading and detecting tumor subtypes and biomarkers. We revised the available Slim codes to fit the algorithms for running them on CPUs. For additional information and reference, please check the pre-print describing the method here:
 

requirements.txt

@@ -1,37 +1,37 @@
-absl-py==0.7.0
-astor==0.7.1
-cachetools==2.1.0
-certifi==2018.10.15
+absl-py==0.10.0
+astor==0.8.1
+cachetools==4.1.1
+certifi==2020.6.20
 chardet==3.0.4
-Click==7.0
+Click==7.1.2
 CouchDB==1.2
-Flask==1.0.2
-Flask-Cors==3.0.7
+Flask==1.1.2
+Flask-Cors==3.0.9
 Flask-Uploads==0.2.1
 gast==0.2.2
-grpcio==1.15.0
-h5py==2.9.0
-idna==2.7
+grpcio==1.32.0
+h5py==2.10.0
+idna==2.10
 itsdangerous==1.1.0
-Jinja2==2.10
-Keras-Applications==1.0.6
+Jinja2==2.11.3
+Keras-Applications==1.0.8
 Keras-Preprocessing==1.0.5
-Markdown==3.0.1
-MarkupSafe==1.1.0
-numpy==1.15.2
-protobuf==3.6.1
+Markdown==3.2.2
+MarkupSafe==1.1.1
+numpy==1.18.5
+protobuf==3.13.0
 pyasn1==0.4.4
 pyasn1-modules==0.2.2
 pytz==2018.5
-requests==2.20.0
-rsa==4.0
-selenium==3.14.1
-six==1.12.0
-tensorboard==1.12.2
-tensorflow==1.12.0
+requests==2.27.1
+rsa==4.7
+selenium==3.141.0
+six==1.15.0
+tensorboard==1.15.0
+tensorflow==1.15.4
 termcolor==1.1.0
-urllib3==1.24
+urllib3==1.26.5
 virtualenv==16.2.0
-Werkzeug==0.14.1
-opencv-python==4.0.0.21
-matplotlib==3.0.3
+Werkzeug==1.0.1
+opencv-python==4.2.0.32
+matplotlib==3.3.2

src/api/version.py

@@ -1,4 +1,5 @@
-version = '1.0.1'
+version = '1.0.2'
+
 
 def api_version():
     return version

src/static/index.html

@@ -54,7 +54,7 @@
         </div>
         <footer>
             <div>Copyright © 2019 Englander Institute for Precision Medicine</div>
-            <div>CNN Smoothie Version 1.0.1</div>
+            <div>CNN Smoothie Version 1.0.2</div>
             <img alt="logo" class="footer-logo" src="assets/LOGO_ENGLANDER_2LINE_RGB.png">
          </footer>
 

src/static/login.html

@@ -32,7 +32,7 @@ <h5 class="login-title">Log in</h5>
         </div>
         <footer>
             <div>Copyright © 2019 Englander Institute for Precision Medicine</div>
-            <div>CNN Smoothie Version 1.0.1</div>
+            <div>CNN Smoothie Version 1.0.2</div>
             <img alt="logo" class="footer-logo" src="assets/LOGO_ENGLANDER_2LINE_RGB.png">
         </footer>
         <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.2.1/jquery.min.js"></script>