TissueImageAnalytics · shaneahmed · Oct 21, 2022 · Oct 21, 2022 · Oct 21, 2022 · Oct 21, 2022
diff --git a/README.md b/README.md
@@ -18,6 +18,10 @@
             <img src="https://shields.io/conda/dn/conda-forge/tiatoolbox"  alt="conda-forge downloads"/>
     </a>
   <br>
+  <a href="https://tia-toolbox.readthedocs.io/en/latest/?badge=latest">
+    <img src="https://readthedocs.org/projects/tia-toolbox/badge/?version=latest" alt="Documentation Status" />
+  </a>
+  <br>
   <a href="https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/LICENSE">
     <img alt="GitHub license" src="https://img.shields.io/github/license/TissueImageAnalytics/tiatoolbox"></a>
   <br>
@@ -31,9 +35,6 @@
   <a href="https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml">
     <img src="https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml/badge.svg"  alt="GitHub Workflow passing"/>
   </a>
-  <a href="https://tia-toolbox.readthedocs.io/en/latest/?badge=latest">
-    <img src="https://readthedocs.org/projects/tia-toolbox/badge/?version=latest" alt="Documentation Status" />
-  </a>
   <a href="https://codecov.io/gh/TissueImageAnalytics/tiatoolbox">
       <img src="https://codecov.io/gh/TissueImageAnalytics/tiatoolbox/branch/master/graph/badge.svg?token=7UZEMacQHm" alt="Code Coverage"/>
   </a>

diff --git a/tests/test_tileserver.py b/tests/test_tileserver.py
@@ -68,7 +68,6 @@ def _fill_store(
 @pytest.fixture()
 def app(sample_ndpi, tmp_path, fill_store) -> TileServer:
     """Create a testing TileServer WSGI app."""
-
     # Make a low-res .jpg of the right shape to be used as
     # a low-res overlay.
     wsi = WSIReader.open(Path(sample_ndpi))
@@ -168,12 +167,12 @@ def test_cli_name_multiple_flag():
 
     @cli_name()
     def dummy_fn():
-        """it's empty because its a dummy function"""
+        """It is empty because it's a dummy function"""
 
     assert "Multiple" not in dummy_fn.__click_params__[0].help
 
     @cli_name(multiple=True)
     def dummy_fn():
-        """it's empty because its a dummy function"""
+        """It is empty because it's a dummy function"""
 
     assert "Multiple" in dummy_fn.__click_params__[0].help
diff --git a/tiatoolbox/cli/show_wsi.py b/tiatoolbox/cli/show_wsi.py
@@ -25,7 +25,6 @@
 )
 def show_wsi(img_input, name, colour_by, colour_map):  # pragma: no cover
     """Show a slide together with any overlays."""
-
     from tiatoolbox.utils.visualization import AnnotationRenderer
     from tiatoolbox.visualization.tileserver import TileServer
 

diff --git a/tiatoolbox/tools/registration/wsi_registration.py b/tiatoolbox/tools/registration/wsi_registration.py
@@ -235,7 +235,6 @@ def match_histograms(
             - :class:`numpy.ndarray` - A normalized grayscale image.
 
     """
-
     image_a, image_b = np.squeeze(image_a), np.squeeze(image_b)
     if len(image_a.shape) == 3 or len(image_b.shape) == 3:
         raise ValueError("The input images should be grayscale images.")

diff --git a/tiatoolbox/utils/metrics.py b/tiatoolbox/utils/metrics.py
@@ -87,7 +87,6 @@ def dice(gt_mask, pred_mask):
             A dice overlap
 
     """
-
     if gt_mask.shape != pred_mask.shape:
         raise ValueError(f'{"Shape mismatch between the two masks."}')
 

diff --git a/tiatoolbox/utils/misc.py b/tiatoolbox/utils/misc.py
@@ -1020,7 +1020,6 @@ def add_from_dat(
             The x and y coordinates to use as the origin for the annotations.
 
     """
-
     data = joblib.load(fp)
     props = list(data[list(data.keys())[0]].keys())
     if "contour" not in props:
-Original file line number
+Diff line change
@@ Expand Up / @@ -87,7 +87,6 @@ def dice(gt_mask, pred_mask): @@
                 A dice overlap
         """
         if gt_mask.shape != pred_mask.shape:
             raise ValueError(f'{"Shape mismatch between the two masks."}')
@@ Expand Down @@