[MAINT] run test and flake8 github actions

.github/workflows/tests.yml

@@ -18,7 +18,7 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                python-version: ['3.8', '3.9', '3.10', '3.11']
+                python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
 
         runs-on: ubuntu-latest
 
@@ -35,16 +35,20 @@ jobs:
         -   name: Install dependencies
             run: |
                 sudo apt-get update
-                python -m pip install --upgrade pip pytest jupyter nbval
+                python -m pip install --upgrade pip pytest pytest-cov
 
         -   name: Install
             run: pip install .
 
         -   name: Test
-            run: pytest --cov-report term-missing --cov=atlasreader
+            run: pytest -vvv atlasreader
+
+        -   name: Coveralls
+            uses: coverallsapp/github-action@v2
 
         -   name: Test notebooks
             run: |
+                pip install nbval 
                 for n in `ls notebooks/*ipynb`
                 do
                     pytest --nbval-lax -v -s ${n};

atlasreader/atlasreader.py

@@ -256,7 +256,7 @@ def get_subpeak_coords(clust_img, min_distance=20):
     data = check_niimg(clust_img).get_fdata()
 
     # find local maxima, excluding peaks that are on the border of the cluster
-    local_max = peak_local_max(data, exclude_border=1, indices=False)
+    local_max = peak_local_max(data, exclude_border=1)
 
     # make new clusters to check for "flat" peaks + find CoM of those clusters
     labels, nl = label(local_max)

atlasreader/info.py

@@ -25,7 +25,8 @@
 
 TESTS_REQUIRE = [
     'pytest',
-    'pytest-cov'
+    'pytest-cov',
+    'nbval'
 ]
 
 PACKAGE_DATA = {

atlasreader/tests/test_atlasreader.py

@@ -56,6 +56,9 @@
                    [-36, -19,  19, -6.21808,   648]])
 )
 
+@pytest.mark.parametrize('atlas', atlasreader._ATLASES)
+def test_check_atlases_each(atlas):
+    atlasreader.check_atlases(atlas)
 
 def test_get_atlases():
     for atlas in atlasreader._ATLASES:
@@ -64,12 +67,15 @@ def test_get_atlases():
     with pytest.raises(ValueError):
         atlasreader.get_atlas('not_an_atlas')
 
-
-def test_check_atlases():
+def test_check_atlases_all():
     atlases = atlasreader.check_atlases('all')
     assert len(atlases) == len(atlasreader._ATLASES)
+
+def test_check_atlases_default():
     atlases = atlasreader.check_atlases('default')
     assert len(atlases) == len(atlasreader._DEFAULT)
+
+def test_check_atlases_default():
     atlases = atlasreader.check_atlases(['aal', 'destrieux'])
     assert atlasreader.check_atlases(atlases) == atlases
     assert atlasreader.check_atlases(atlases[0]) == atlases[0]
@@ -113,8 +119,7 @@ def test_get_statmap_info():
     assert len(cdf) == 0
     assert len(pdf) == 0
 
-
-def test_read_atlas_preaks():
+def test_read_atlas_peaks():
     # Load a correct atlas
     atlasreader.read_atlas_peak('aal', [10, 10, 10])
     # Load a list of atlases

notebooks/.gitignore

@@ -0,0 +1,3 @@
+*.png
+*.csv
+*.nii.gz