minor typo fixes

.pre-commit-config.yaml

@@ -17,7 +17,8 @@ repos:
     rev: typos-dict-v0.11.20
     hooks:
       - id: typos
-        args: [--force-exclude]  # omitting --write-changes
+        #args: [--force-exclude]  # omitting --write-changes
+        args: [--force-exclude, --write-changes]
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     rev: v0.4.8

src/ngio/core/label_handler.py

@@ -184,7 +184,7 @@ def __init__(
         else:
             self._group: zarr.Group = group["labels"]
 
-        self._imgage_ref = image_ref
+        self._image_ref = image_ref
 
     def list(self) -> list[str]:
         """List all labels in the group."""
@@ -246,14 +246,14 @@ def derive(
         # create the new label
         new_label_group = self._group.create_group(name, overwrite=overwrite)
 
-        if self._imgage_ref is None:
+        if self._image_ref is None:
             label_0 = self.get(list_of_labels[0])
             metadata = label_0.metadata
             on_disk_shape = label_0.on_disk_shape
             chunks = label_0.array.chunks
             dataset = label_0.dataset
         else:
-            label_0 = self._imgage_ref
+            label_0 = self._image_ref
             metadata = label_0.metadata
             channel_index = metadata.index_mapping.get("c", None)
             if channel_index is not None:

src/ngio/core/ngff_image.py

@@ -1,6 +1,6 @@
 """Abstract class for handling OME-NGFF images."""
 
-from typing import Any, Protocol, TypeVar
+from typing import Protocol, TypeVar
 
 import numpy as np
 

src/ngio/core/utils.py

@@ -3,7 +3,6 @@
 import math
 from typing import Any
 
-from ngio.core.image_handler import Image
 from ngio.io import StoreLike
 from ngio.ngff_meta import (
     create_image_metadata,
@@ -106,7 +105,7 @@ def create_empty_ome_zarr_image(
             dimension_separator="/",
         )
 
-        # Todo redo this with when a proper build of pyramid id implemente
+        # Todo redo this with when a proper build of pyramid is implemented
         shape = [int(s / sc) for s, sc in zip(shape, scaling_factor, strict=True)]
 
         if chunks is not None:
@@ -184,7 +183,7 @@ def create_empty_ome_zarr_label(
             dimension_separator="/",
         )
 
-        # Todo redo this with when a proper build of pyramid id implemente
+        # Todo redo this with when a proper build of pyramid is implemented
         _shape = []
         for s, sc in zip(shape, scaling_factor, strict=True):
             if math.floor(s / sc) % 2 == 0:

src/ngio/io/_zarr.py

@@ -5,8 +5,8 @@
 import zarr
 from packaging.version import Version
 
-zarr_verison = version("zarr")
-ZARR_PYTHON_V = 2 if Version(zarr_verison) < Version("3.0.0a") else 3
+zarr_version = version("zarr")
+ZARR_PYTHON_V = 2 if Version(zarr_version) < Version("3.0.0a") else 3
 
 # Zarr v3 Imports
 # import zarr.store

src/ngio/ngff_meta/utils.py

@@ -98,7 +98,7 @@ def create_image_metadata(
             for the pyramid building.
         z_scaling_factor: The scaling factor for the z axis, to be used for the
             pyramid building. Note that several tools may not support scaling
-            diffent than 1.0 for the z axis.
+            different than 1.0 for the z axis.
         time_spacing: The time spacing (If the time axis is present).
         time_units: The units of the time spacing (If the time axis is present).
         num_levels: The number of levels in the pyramid.
@@ -146,10 +146,10 @@ def create_image_metadata(
             )
 
     channels = []
-    for label, wavelenghts, kwargs in zip(
+    for label, wavelengths, kwargs in zip(
         channel_labels, channel_wavelengths, channel_kwargs, strict=True
     ):
-        channels.append(Channel(label=label, wavelength_id=wavelenghts, **kwargs))
+        channels.append(Channel(label=label, wavelength_id=wavelengths, **kwargs))
 
     omero_kwargs = {} if omero_kwargs is None else omero_kwargs
     omero = Omero(channels=channels, **omero_kwargs)
@@ -185,7 +185,7 @@ def create_label_metadata(
             for the pyramid building.
         z_scaling_factor: The scaling factor for the z axis, to be used for the
             pyramid building. Note that several tools may not support scaling
-            diffent than 1.0 for the z axis.
+            different than 1.0 for the z axis.
         time_spacing: The time spacing (If the time axis is present).
         time_units: The units of the time spacing (If the time axis is present).
         num_levels: The number of levels in the pyramid.

src/ngio/pipes/data_pipe.py

@@ -9,11 +9,11 @@ class DataTransformPipe:
     """A class to handle a pipeline of data transforms.
 
     For example, a pipeline of transforms can be:
-        - Selecte a subset of the data
+        - Select a subset of the data
         - Shuffle the axes of the data
         - Normalize the data
 
-    All these in reverse order will be applied to the data when seting a patch.
+    All these in reverse order will be applied to the data when setting a patch.
 
     """
 

src/ngio/tables/_utils.py

@@ -51,21 +51,21 @@ def _safe_to_df(data_frame: pd.DataFrame, index_key: str) -> pd.DataFrame:
 def df_to_andata(
     data_frame: pd.DataFrame,
     index_key: str = "label",
-    inplicit_conversion: bool = False,
+    implicit_conversion: bool = False,
 ) -> ad.AnnData:
     """Convert a pandas DataFrame representing a fractal table to an AnnData object.
 
     Args:
         data_frame: A pandas DataFrame representing a fractal table.
         index_key: The column name to use as the index of the DataFrame.
             Default is 'label'.
-        inplicit_conversion: If True, the function will convert the data frame
+        implicit_conversion: If True, the function will convert the data frame
             to an AnnData object as it. If False, the function will check the data frame
             for compatibility.
             And correct correctly formatted data frame to AnnData object.
             Default is False.
     """
-    if inplicit_conversion:
+    if implicit_conversion:
         return ad.AnnData(data_frame)
 
     return _safe_to_df(data_frame, index_key)

src/ngio/tables/v1/feature_tables.py

@@ -37,13 +37,13 @@ class FeatureTableV1:
     https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/
     """
 
-    def __init__(self, group: zarr.Group, inplicit_conversion: bool = False):
+    def __init__(self, group: zarr.Group, implicit_conversion: bool = False):
         """Initialize the class from an existing group.
 
         Args:
             group (zarr.Group): The group containing the
                 ROI table.
-            inplicit_conversion (bool): If True, the anndata object will be
+            implicit_conversion (bool): If True, the anndata object will be
                 converted to a DataFrame without any checks. If False, the
                 anndata object will be checked for compatibility and converted
                 to a DataFrame. Default is False.
@@ -139,7 +139,7 @@ def write(self) -> None:
     @staticmethod
     def _write(group: zarr.Group, table: DataFrame, meta: FeatureTableV1Meta) -> None:
         ad_table = df_to_andata(
-            table, index_key=meta.instance_key, inplicit_conversion=False
+            table, index_key=meta.instance_key, implicit_conversion=False
         )
 
         path = Path(group.store.path) / group.path

src/ngio/tables/v1/roi_tables.py

@@ -119,7 +119,7 @@ def _create_new(
             table = DataFrame(columns=columns)
         else:
             cls._validate_roi_table(table=table)
-        # this should be possibe to do duing initialization
+        # this should be possible to do duing initialization
         # but for now this works
         table = table.set_index("FieldIndex")
         cls._write(group=table_group, table=table)

tests/core/conftest.py

@@ -6,8 +6,8 @@
 from packaging.version import Version
 from pytest import fixture
 
-zarr_verison = version("zarr")
-ZARR_PYTHON_V = 2 if Version(zarr_verison) < Version("3.0.0a") else 3
+zarr_version = version("zarr")
+ZARR_PYTHON_V = 2 if Version(zarr_version) < Version("3.0.0a") else 3
 
 
 @fixture

tests/io/conftest.py

@@ -5,8 +5,8 @@
 from packaging.version import Version
 from pytest import fixture
 
-zarr_verison = version("zarr")
-ZARR_PYTHON_V = 2 if Version(zarr_verison) < Version("3.0.0a") else 3
+zarr_version = version("zarr")
+ZARR_PYTHON_V = 2 if Version(zarr_version) < Version("3.0.0a") else 3
 
 
 def _create_zarr(tempdir, zarr_format=2):

tests/ngff_meta/conftest.py

@@ -6,8 +6,8 @@
 from packaging.version import Version
 from pytest import fixture
 
-zarr_verison = version("zarr")
-ZARR_PYTHON_V = 2 if Version(zarr_verison) < Version("3.0.0a") else 3
+zarr_version = version("zarr")
+ZARR_PYTHON_V = 2 if Version(zarr_version) < Version("3.0.0a") else 3
 
 
 @fixture

tests/tables/conftest.py

@@ -6,8 +6,8 @@
 from packaging.version import Version
 from pytest import fixture
 
-zarr_verison = version("zarr")
-ZARR_PYTHON_V = 2 if Version(zarr_verison) < Version("3.0.0a") else 3
+zarr_version = version("zarr")
+ZARR_PYTHON_V = 2 if Version(zarr_version) < Version("3.0.0a") else 3
 
 
 @fixture