Merge pull request #150 from fmi-faim/typos

Add typos pre-commit hook

.pre-commit-config.yaml

@@ -15,6 +15,14 @@ repos:
     rev: 24.4.2
     hooks:
       - id: black
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.22.9
+    hooks:
+      - id: typos
+        files: \.(py|md|rst|yaml|toml)
+        # empty to do not write fixes
+        args: []
+        exclude: pyproject.toml
 # mypy will force you to type your code ;)
 #  - repo: https://github.com/pre-commit/mirrors-mypy
 #    rev: v0.910-1

pyproject.toml

@@ -119,3 +119,12 @@ exclude_lines = [
 
 [tool.setuptools_scm]
 write_to = "src/faim_ipa/_version.py"
+
+[tool.typos.default]
+extend-ignore-words-re = [
+  # Hexadecimal identifiers in file names
+  "^[A-F0-9]*$",
+]
+
+[tool.typos.default.extend-words]
+ome = "ome"

src/faim_ipa/dask_utils.py

@@ -40,8 +40,8 @@ def __init__(
 
     def _get_scheduler_address(self):
         if self._scheduler_address is None:
-            scheduler_adress = self._queue.get()
-            self._scheduler_address = scheduler_adress
+            scheduler_address = self._queue.get()
+            self._scheduler_address = scheduler_address
             self._queue.close()
             self._queue = None
 

tests/hcs/imagexpress/test_ImageXpress.py

@@ -32,7 +32,7 @@ def single_plane_acquisition(acquisition_dir):
     return SinglePlaneAcquisition(acquisition_dir, alignment=TileAlignmentOptions.GRID)
 
 
-def test_single_plane_acquistion(single_plane_acquisition: PlateAcquisition):
+def test_single_plane_acquisition(single_plane_acquisition: PlateAcquisition):
     wells = single_plane_acquisition.get_well_acquisitions()
 
     assert wells is not None
@@ -99,7 +99,7 @@ def stack_acquisition(acquisition_dir):
     return StackAcquisition(acquisition_dir, alignment=TileAlignmentOptions.GRID)
 
 
-def test_stack_acquistion(stack_acquisition: PlateAcquisition):
+def test_stack_acquisition(stack_acquisition: PlateAcquisition):
     wells = stack_acquisition.get_well_acquisitions()
 
     assert wells is not None
@@ -290,7 +290,7 @@ def single_channel_acquisition(acquisition_dir_single_channel):
     )
 
 
-def test_single_channel_acquistion(single_channel_acquisition: PlateAcquisition):
+def test_single_channel_acquisition(single_channel_acquisition: PlateAcquisition):
     wells = single_channel_acquisition.get_well_acquisitions()
 
     assert wells is not None
@@ -343,7 +343,7 @@ def time_lapse_acquisition(acquisition_dir_time_lapse):
     )
 
 
-def test_time_lapse_acquistion(time_lapse_acquisition: PlateAcquisition):
+def test_time_lapse_acquisition(time_lapse_acquisition: PlateAcquisition):
     wells = time_lapse_acquisition.get_well_acquisitions()
     for well in wells:
         assert isinstance(well, WellAcquisition)
@@ -357,7 +357,7 @@ def test_time_lapse_acquistion(time_lapse_acquisition: PlateAcquisition):
             assert tile.shape == (256, 256)
 
 
-def test_single_field_stack_acquistion(stack_acquisition: PlateAcquisition):
+def test_single_field_stack_acquisition(stack_acquisition: PlateAcquisition):
     # Regular z spacing in dataset
     files = stack_acquisition._parse_files()
     z_step = stack_acquisition._compute_z_spacing(files)

tests/hcs/test_acquisition.py

@@ -236,7 +236,7 @@ def test_raise_not_implemented_errors(dummy_well):
         dummy_well.get_z_spacing()
 
 
-def test_get_coordiante_transformations_3d(dummy_well):
+def test_get_coordinate_transformations_3d(dummy_well):
     dummy_well.get_z_spacing = lambda: 1.0
     dummy_well.get_yx_spacing = lambda: (2.0, 3.0)
     ct = dummy_well.get_coordinate_transformations(
@@ -280,7 +280,7 @@ def test_get_coordiante_transformations_3d(dummy_well):
     ]
 
 
-def test_get_coordiante_transformations_2d(dummy_well):
+def test_get_coordinate_transformations_2d(dummy_well):
     dummy_well.get_z_spacing = lambda: None
     dummy_well.get_yx_spacing = lambda: (2.0, 3.0)
     ct = dummy_well.get_coordinate_transformations(max_layer=2, yx_binning=1, ndim=3)