Shifting from setup.py to pyproject.toml

.gitignore

@@ -32,3 +32,4 @@ test_database/dicom_leica
 dpyproject.toml
 mask_ihc.ipynb
 pyproject.toml
+test_output

build.sh

@@ -8,8 +8,7 @@ else
     exit 1
 fi
 
-python setup.py sdist
-python setup.py bdist_wheel
+python -m build
 
 echo -e "\nTo upload to PyPI, run the following command:\n"
 echo -e "\ttwine upload dist/*\n"

pathopatch/utils/patch_util.py

@@ -184,14 +184,14 @@ def target_mpp_to_downsample(
             rescaling_factor = 1.0
         else:
             logger.warning(
-                f"Requested mpp resolution ({target_mpp}) is not a power of the base resultion {base_mpp}. "
+                f"Requested mpp resolution ({target_mpp}) is not a power of the base resolution {base_mpp}. "
                 "We perform rescaling, but this may not be accurate and is very slow!"
             )
             downsample = int(np.floor(target_mpp / base_mpp))
             rescaling_factor = target_mpp / (base_mpp * downsample)
     else:
         logger.warning(
-            f"Requested mpp resolution ({target_mpp}) is not a power of the base resultion {base_mpp}. "
+            f"Requested mpp resolution ({target_mpp}) is not a power of the base resolution {base_mpp}. "
             "We perform rescaling, but this may not be accurate and is very slow!"
         )
         downsample = 1

test_database/input/example_config.yaml

@@ -0,0 +1,6 @@
+wsi_paths: ./test_database/input/WSI/JP2K-33003-1.svs
+output_path: ./test_output
+patch_size: 512
+target_mag: 10
+processes: 2
+overwrite: True