Migrate Elastic Beanstalk to Python 3.8 running on Amazon Linux 2 (#287)

* Update requirements

* Remove references to Python 3.6

* Bump numpy patch version

* Install mysql in EB options config

* Switch mysql to mysql-server

* Switch mysql-client to mariadb-devel

* Source python before each container command

* Fix watershed import

* Replace deprecated skimage.draw.circle with disk

* Add app local variable

* Remove .py extension from WSGIPath

* Fix WSGIPath

* Revert to sqlalchemy 1.3 for compatibility with pytest-flask-sqlalchemy

* Add newline

.ebextensions/options.config

@@ -17,7 +17,8 @@ option_settings:
     FLASK_ENV: production
 
   aws:elasticbeanstalk:container:python:
-    WSGIPath: application.py
+    WSGIPath: application:application
 
-  aws:elasticbeanstalk:container:python:staticfiles:
-    /static/: deepcell_label/static/
+packages: 
+  yum:
+    mariadb-devel: []

.ebextensions/pip.config

@@ -1,9 +1,9 @@
 container_commands:
   01_upgrade_pip:
-    command: "python -m pip install --upgrade pip"
+    command: "source /var/app/venv/*/bin/activate && python -m pip install --upgrade pip"
     leader_only: true
-  02_upgradde_setuptools:
-    command: "python -m pip install --upgrade setuptools"
+  02_upgrade_setuptools:
+    command: "source /var/app/venv/*/bin/activate && python -m pip install --upgrade setuptools"
     leader_only: true
 
 files:

.github/ISSUE_TEMPLATE/bug_report.md

@@ -4,14 +4,14 @@ about: Create a report to help us improve
 title: ''
 labels: bug
 assignees: ''
-
 ---
 
 **Describe the bug**
 A clear and concise description of what the bug is.
 
 **To Reproduce**
 Steps to reproduce the behavior:
+
 1. Run '...'
 2. Enter '....'
 3. See error
@@ -23,9 +23,10 @@ A clear and concise description of what you expected to happen.
 If applicable, add screenshots to help explain your problem.
 
 **Desktop (please complete the following information):**
- - OS: [e.g. macOS, Ubuntu]
- - Version [e.g. 22]
- - Python Version [e.g. 3.6.7]
+
+- OS: [e.g. macOS, Ubuntu]
+- Version [e.g. 0.2]
+- Python Version [e.g. 3.8.10]
 
 **Additional context**
 Add any other context about the problem here.

.github/workflows/tests.yaml

@@ -60,7 +60,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.7, 3.8]
 
     steps:
       - uses: actions/checkout@v2

deepcell_label/label.py

@@ -11,13 +11,13 @@
 
 import numpy as np
 from matplotlib.colors import Normalize
+import skimage
 from skimage import filters
 from skimage.morphology import flood_fill, flood
-from skimage.morphology import watershed, dilation, disk, square, erosion
-from skimage.draw import circle
+from skimage.morphology import dilation, disk, square, erosion
 from skimage.exposure import rescale_intensity
 from skimage.measure import regionprops
-from skimage.segmentation import morphological_chan_vese
+from skimage.segmentation import watershed, morphological_chan_vese
 
 from deepcell_label.labelmaker import LabelInfoMaker
 
@@ -182,10 +182,10 @@ def action_handle_draw(self, trace, foreground, background, brush_size):
         img_replaced = np.where(img == background, foreground, img)
 
         for loc in trace:
-            x_loc = loc[0]
-            y_loc = loc[1]
-            brush_area = circle(y_loc, x_loc, brush_size,
-                                (self.project.height, self.project.width))
+            x = loc[0]
+            y = loc[1]
+            brush_area = skimage.draw.disk((y, x), brush_size,
+                                           shape=(self.project.height, self.project.width))
             img[brush_area] = img_replaced[brush_area]
 
         foreground_in_after = np.any(np.isin(img, foreground))

requirements.txt

@@ -1,18 +1,17 @@
-boto3==1.9.182
-flask~=1.1.4
+boto3~=1.20.20
+flask~=2.0.2
 flask-compress~=1.10.1
 flask-cors~=3.0.10
 flask-dropzone~=1.6.0
-flask-monitoringdashboard~=3.1.0
-flask-sqlalchemy~=2.5.0
-matplotlib==3.0.3
-mysqlclient~=1.4.6
-numpy>=1.16.4
-pillow>=7.1.0,<8.3.2
+flask-monitoringdashboard~=3.1.1
+flask-sqlalchemy~=2.5.1
+matplotlib~=3.5.0
+mysqlclient~=2.1.0
+numpy~=1.21.4
+pillow~=8.4.0
 python-decouple~=3.1
-python-dotenv~=0.19.1
+python-dotenv~=0.19.2
 requests~=2.26.0
-scikit-image>=0.15.0,<0.17.0
-sqlalchemy<1.4
-# TODO: drop python 3.6 and bump this requirement
-tifffile==2020.9.3
+scikit-image~=0.19.0
+sqlalchemy~=1.3.24
+tifffile~=2021.11.2