From 9bcef37c84406d491af49092248a976f6a511a77 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 20 Mar 2021 00:27:12 +0000 Subject: [PATCH 1/7] Bump jinja2 from 2.10 to 2.11.3 Bumps [jinja2](https://github.com/pallets/jinja) from 2.10 to 2.11.3. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/master/CHANGES.rst) - [Commits](https://github.com/pallets/jinja/compare/2.10...2.11.3) Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 57ea6b6..fd34780 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,7 +13,7 @@ grpcio==1.15.0 h5py==2.9.0 idna==2.7 itsdangerous==1.1.0 -Jinja2==2.10 +Jinja2==2.11.3 Keras-Applications==1.0.6 Keras-Preprocessing==1.0.5 Markdown==3.0.1 From cf797bca06152198a8245c6e770e4867fbc34f66 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 6 May 2021 19:26:53 +0000 Subject: [PATCH 2/7] Bump flask-cors from 3.0.7 to 3.0.9 Bumps [flask-cors](https://github.com/corydolphin/flask-cors) from 3.0.7 to 3.0.9. - [Release notes](https://github.com/corydolphin/flask-cors/releases) - [Changelog](https://github.com/corydolphin/flask-cors/blob/master/CHANGELOG.md) - [Commits](https://github.com/corydolphin/flask-cors/compare/3.0.7...3.0.9) Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 57ea6b6..b3255b5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ chardet==3.0.4 Click==7.0 CouchDB==1.2 Flask==1.0.2 -Flask-Cors==3.0.7 +Flask-Cors==3.0.9 Flask-Uploads==0.2.1 gast==0.2.2 grpcio==1.15.0 From 18b7d57042d78f3c84a7b6b046373b9c7aca20e5 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 1 Jun 2021 23:16:09 +0000 Subject: [PATCH 3/7] Bump urllib3 from 1.24 to 1.26.5 Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.24 to 1.26.5. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/1.24...1.26.5) --- updated-dependencies: - dependency-name: urllib3 dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 57ea6b6..c7059f1 100644 --- a/requirements.txt +++ b/requirements.txt @@ -30,7 +30,7 @@ six==1.12.0 tensorboard==1.12.2 tensorflow==1.12.0 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 From 09fc4f8242446de47e84db1784dd9154d57a6ef1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 12 Oct 2021 22:56:14 +0000 Subject: [PATCH 4/7] Bump opencv-python from 4.0.0.21 to 4.2.0.32 Bumps [opencv-python](https://github.com/skvark/opencv-python) from 4.0.0.21 to 4.2.0.32. - [Release notes](https://github.com/skvark/opencv-python/releases) - [Commits](https://github.com/skvark/opencv-python/commits) --- updated-dependencies: - dependency-name: opencv-python dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 57ea6b6..ea968b7 100644 --- a/requirements.txt +++ b/requirements.txt @@ -33,4 +33,4 @@ termcolor==1.1.0 urllib3==1.24 virtualenv==16.2.0 Werkzeug==0.14.1 -opencv-python==4.0.0.21 +opencv-python==4.2.0.32 From ff0b780565d093e0d917b2c747e64be16160d0f5 Mon Sep 17 00:00:00 2001 From: Alexandros Sigaras Date: Wed, 12 Jan 2022 13:50:48 -0500 Subject: [PATCH 5/7] Bump version to 1.2.2 --- README.md | 2 +- src/api/version.py | 5 +++-- src/static/index.html | 2 +- src/static/login.html | 2 +- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index c38b34a..5dc46eb 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ https://doi.org/10.1038/s41746-019-0096-y Classify IVF images in real time. -[![Actions Status](https://github.com/eipm/stork/workflows/Docker/badge.svg)](https://github.com/eipm/stork/actions) [![Github](https://img.shields.io/badge/github-1.2.1-green?style=flat&logo=github)](https://github.com/eipm/stork) [![EIPM Docker Hub](https://img.shields.io/badge/EIPM%20docker%20hub-1.2.1-blue?style=flat&logo=docker)](https://hub.docker.com/repository/docker/eipm/stork) [![GitHub Container Registry](https://img.shields.io/badge/GitHub%20Container%20Registry-1.2.1-blue?style=flat&logo=docker)](https://github.com/orgs/eipm/packages/container/package/stork) [![Python 2.7](https://img.shields.io/badge/python-2.7-blue.svg)](https://www.python.org/downloads/release/python-360/) [![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/stork/workflows/Docker/badge.svg)](https://github.com/eipm/stork/actions) [![Github](https://img.shields.io/badge/github-1.2.2-green?style=flat&logo=github)](https://github.com/eipm/stork) [![EIPM Docker Hub](https://img.shields.io/badge/EIPM%20docker%20hub-1.2.2-blue?style=flat&logo=docker)](https://hub.docker.com/repository/docker/eipm/stork) [![GitHub Container Registry](https://img.shields.io/badge/GitHub%20Container%20Registry-1.2.2-blue?style=flat&logo=docker)](https://github.com/orgs/eipm/packages/container/package/stork) [![Python 2.7](https://img.shields.io/badge/python-2.7-blue.svg)](https://www.python.org/downloads/release/python-360/) [![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) ## Run Stork diff --git a/src/api/version.py b/src/api/version.py index 2e20151..7bcc93f 100644 --- a/src/api/version.py +++ b/src/api/version.py @@ -1,4 +1,5 @@ -version = '1.2.1' +version = '1.2.2' + def api_version(): - return version \ No newline at end of file + return version diff --git a/src/static/index.html b/src/static/index.html index 9a30422..6450e23 100644 --- a/src/static/index.html +++ b/src/static/index.html @@ -55,7 +55,7 @@
Copyright © Englander Institute for Precision Medicine
-
Stork Version 1.2.1
+
Stork Version 1.2.2
diff --git a/src/static/login.html b/src/static/login.html index 4c8ff48..23b9f7b 100644 --- a/src/static/login.html +++ b/src/static/login.html @@ -41,7 +41,7 @@
Copyright © Englander Institute for Precision Medicine
-
Stork Version 1.2.1
+
Stork Version 1.2.2
From fbebad64c384da34dc72a9f217e21558300594c5 Mon Sep 17 00:00:00 2001 From: Alexandros Sigaras Date: Wed, 12 Jan 2022 13:51:34 -0500 Subject: [PATCH 6/7] Updated CI to include develop branch --- .github/workflows/docker-publish.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml index 014cea2..86a12ff 100644 --- a/.github/workflows/docker-publish.yml +++ b/.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: stork 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 From be992723f28433c61c384a15d233d694ff5d28b8 Mon Sep 17 00:00:00 2001 From: Alexandros Sigaras Date: Wed, 12 Jan 2022 14:12:40 -0500 Subject: [PATCH 7/7] Updated Python version and requirements.txt --- Dockerfile | 4 ++-- requirements.txt | 42 +++++++++++++++++++++--------------------- 2 files changed, 23 insertions(+), 23 deletions(-) diff --git a/Dockerfile b/Dockerfile index 68826a7..1a86ab1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.6.8-stretch +FROM python:3.7.9-buster #===============================# # Docker Image Configuration # #===============================# @@ -7,7 +7,7 @@ LABEL org.opencontainers.image.source='https://github.com/eipm/stork' \ description='STORK' \ maintainer='als2076@med.cornell.edu' \ base_image='python' \ - base_image_version='3.6.8-stretch' + base_image_version='3.7.9-buster' ENV APP_NAME='stork' \ TZ='US/Eastern' \ diff --git a/requirements.txt b/requirements.txt index a9d616c..1a5c89b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,36 +1,36 @@ -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==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==2.11.3 -Keras-Applications==1.0.6 +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==1.26.5 virtualenv==16.2.0 -Werkzeug==0.14.1 +Werkzeug==1.0.1 opencv-python==4.2.0.32