Add testing for python 3.9 and 3.10 (#288)

* Test Python 3.9 and 3.10

* Make 3.10 a string

* Bump pytest version for Python 3.10

* Switch from pep8 to flake8

* Add flake8 to requirements-test.txt with pinned version

* Make changes to conform to flake8

* Add quotes to all Python versions

.github/workflows/tests.yaml

@@ -60,7 +60,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.7, 3.8]
+        python-version: ['3.7', '3.8', '3.9', '3.10']
 
     steps:
       - uses: actions/checkout@v2
@@ -89,7 +89,7 @@ jobs:
 
       - name: Run PyTest
         run: |
-          pytest deepcell_label --cov deepcell_label --pep8
+          pytest deepcell_label --cov deepcell_label --flake8
 
       - name: Coveralls
         if: env.COVERALLS_REPO_TOKEN != null

convert.py

@@ -80,7 +80,8 @@ def main():
             dest = file.parent / file.stem
         data_utils.trks_to_trk_folder(str(file), str(dest))
     else:
-        raise NotImplemented
+        raise NotImplementedError
+
 
 if __name__ == "__main__":
     main()

deepcell_label/__init__.py

@@ -3,10 +3,7 @@
 from __future__ import division
 from __future__ import print_function
 
-import logging
-
 from flask import Flask
-from flask.logging import default_handler
 from flask_cors import CORS
 from flask_compress import Compress
 from flask_dropzone import Dropzone

deepcell_label/blueprints_test.py

@@ -86,7 +86,7 @@ def test_redo(client):
 
 def test_create_project(client, mocker):
     mocker.patch('deepcell_label.blueprints.loaders.URLLoader', lambda *args: DummyLoader())
-    response = client.post(f'/api/project')
+    response = client.post('/api/project')
     assert response.status_code == 200
 
 
@@ -95,7 +95,7 @@ def test_create_project_dropped_npz(client):
     np.savez(npz, X=np.zeros((1, 1, 1, 1)), y=np.ones((1, 1, 1, 1)))
     npz.seek(0)
     data = {'file': (npz, 'test.npz')}
-    response = client.post(f'/api/project/dropped', data=data, content_type='multipart/form-data')
+    response = client.post('/api/project/dropped', data=data, content_type='multipart/form-data')
     assert response.status_code == 200
 
 
@@ -105,7 +105,7 @@ def test_create_project_dropped_tiff(client):
         writer.save(np.zeros((1, 1, 1, 1)))
         tifffile.seek(0)
     data = {'file': (tifffile, 'test.tiff')}
-    response = client.post(f'/api/project/dropped', data=data, content_type='multipart/form-data')
+    response = client.post('/api/project/dropped', data=data, content_type='multipart/form-data')
     assert response.status_code == 200
 
 
@@ -115,7 +115,7 @@ def test_create_project_dropped_png(client):
     img.save(png, format="png")
     png.seek(0)
     data = {'file': (png, 'test.png')}
-    response = client.post(f'/api/project/dropped', data=data, content_type='multipart/form-data')
+    response = client.post('/api/project/dropped', data=data, content_type='multipart/form-data')
     assert response.status_code == 200
 
 

deepcell_label/exporters_test.py

@@ -1,6 +1,5 @@
 """Tests for exporters.py"""
 
-import pytest
 import io
 
 from deepcell_label import models

deepcell_label/imgutils_test.py

@@ -4,7 +4,6 @@
 
 from skimage.io import imread
 import numpy as np
-import pytest
 
 from deepcell_label import imgutils
 from deepcell_label import models

deepcell_label/label_test.py

@@ -66,7 +66,6 @@ def test_action_new_single_cell(self, app):
         cell = 1
         feature = 0
         expected_new_label = 2
-        frame = 0
 
         with app.app_context():
             edit.action_new_single_cell(cell)
@@ -474,5 +473,5 @@ def test_action_new_track(self, app):
             assert cell not in edit.frame[..., feature]
             assert expected_new_cell in edit.frame[..., feature]
             assert expected_new_cell in edit.labels.cell_ids[feature]
-            assert prev_track['frames'] == (tracks[cell]['frames'] +
-                                            tracks[expected_new_cell]['frames'])
+            assert prev_track['frames'] == (tracks[cell]['frames']
+                                            + tracks[expected_new_cell]['frames'])

deepcell_label/labelmaker_test.py

@@ -1,7 +1,6 @@
 """Tests for labelmaker.py"""
 
 import numpy as np
-import pytest
 
 from deepcell_label.labelmaker import LabelInfoMaker
 

deepcell_label/loaders_test.py

@@ -5,14 +5,12 @@
 import io
 import zipfile
 
-import pytest
-
 import numpy as np
 import responses
 from PIL import Image
 from tifffile import TiffWriter
 
-from deepcell_label.loaders import URLLoader, FileLoader
+from deepcell_label.loaders import URLLoader
 
 
 @responses.activate

pytest.ini

@@ -25,7 +25,7 @@ norecursedirs=
 # E731 do not assign a lambda expression, use a def
 # W503 line break occurred before a binary operator
 
-pep8ignore=* E731
+flake8-ignore=* E731 W503
 
-# Enable line length testing with maximum line length of 80
-pep8maxlinelength = 100
+# Enable line length testing with maximum line length of 100
+flake8-max-line-length = 100

requirements-test.txt

@@ -1,11 +1,12 @@
-pytest>=5.2,<6
+pytest~=6.2.5 
 pytest-cov==2.5.1
 pytest-mock
-pytest-pep8
+pytest-flake8
 pytest-flask
 pytest-flask-sqlalchemy
 pytest-lazy-fixture
 fakeredis
+flake8<4 # Pin flake8 to version 3 to prevent StringIO error (see tholo/pytest-flake8#81)
 six>=1.12
 coveralls>3,<3.3.0
 responses