Fix some typos with codespell (#1284)

* Fix some typos with codespell

* format

Author: fm3

cluster_tools/pyproject.toml

@@ -38,7 +38,7 @@ include = ["cluster_tools*"]
 exclude = ["cluster_tools.tests"]
 
 # This is a fix for an issue in setuptools. See: https://github.com/pypa/setuptools/issues/4759
-# This shoulde be removed when the issue is resolved.
+# This should be removed when the issue is resolved.
 [tool.setuptools]
 license-files = []
 

cluster_tools/tests/test_all.py

@@ -41,7 +41,7 @@ def raise_if(msg: str, _bool: bool) -> None:
 # Most of the specs in this module should be executed with multiple executors. Some tests
 # should be called with all executors (including the pickling variants) and some with a subset (i.e., without the pickling variants).
 # In order to avoid redundant parameterization of each test, pytest_generate_tests is defined here.
-# If a spec uses an `exc_with_pickling` fixture (defined as a function parameter), that test is automatically parameterized with all executors. Analoguous, parameterization happens with `exc`.
+# If a spec uses an `exc_with_pickling` fixture (defined as a function parameter), that test is automatically parameterized with all executors. Analogous, parameterization happens with `exc`.
 # Regarding how this works in details: This function is called for each test and has access to the fixtures supplied
 # to the test and most importantly can parametrize those fixtures.
 def pytest_generate_tests(metafunc: Any) -> None:

docs/overrides/main.html

@@ -56,8 +56,8 @@
 </script>
 {% endblock libs %}
 
-## Add a custom footer to every page highlight help otions, such as the community forums
+## Add a custom footer to every page, highlighting help options, such as the community forums
 {% block content %}
 {{ super() }}
 {% include "partials/page_content_footer.html" %}
-{% endblock %}
+{% endblock %}

webknossos/Changelog.md

@@ -304,8 +304,8 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Breaking Changes
 - `RemoteDataset.display_name` is deprecated. To change the name of a dataset use the `name` property instead.
 - `Dataset.get_remote_datasets()` returns a mapping. The keys of this mapping changed from datasets name to datasets id.
-- `Task.create()` needs a `dataset_id` now instead of a `dataset_name`. Alternativly a `RemoteDataset` object can be used. The `dataset_name` is marked as deprecated. As `dataset_name` is an optional argument now its position has changed, this is important if `create()` is called only with positional arguments.
-- When uploading an Annotation the organization_id is neccessary now. The organization_id might be stored in the Annotation object or it is inferred from the current webknossos_context. [#1155](https://github.com/scalableminds/webknossos-libs/pull/1155)
+- `Task.create()` needs a `dataset_id` now instead of a `dataset_name`. Alternatively a `RemoteDataset` object can be used. The `dataset_name` is marked as deprecated. As `dataset_name` is an optional argument now its position has changed, this is important if `create()` is called only with positional arguments.
+- When uploading an Annotation the organization_id is necessary now. The organization_id might be stored in the Annotation object or it is inferred from the current webknossos_context. [#1155](https://github.com/scalableminds/webknossos-libs/pull/1155)
 
 ### Added
 - `Dataset` method `get_remote_datasets()` accepts `name` and `folder_id` as arguments now to filter remote datasets.
@@ -510,7 +510,7 @@ Removed the CZI installation extra from `pip install webknossos[all]` by default
 - Added a pixel level heuristic for distinguishing color and segmentation layers when importing image data with the `from_images` or `add_layer_from_images` method. [#1007](https://github.com/scalableminds/webknossos-libs/pull/1007)
 - Added .ims as supported suffix. [#1085](https://github.com/scalableminds/webknossos-libs/pull/1085)
 - Added suffixes supported by bioformats for Zeiss CZI, Leica LOF, Zeiss LSM (laser scanning microscope), Zeiss LSM (Laser Scanning Microscope) 510/710, Leica XLEF and Zeiss AxioVision ZVI (Zeiss Vision Image). [#1086](https://github.com/scalableminds/webknossos-libs/pull/1086)
-- Added suport for setting a default ID mapping for segmentation layers. [#1118](https://github.com/scalableminds/webknossos-libs/pull/1118)
+- Added support for setting a default ID mapping for segmentation layers. [#1118](https://github.com/scalableminds/webknossos-libs/pull/1118)
 
 ### Changed
 - Moved functional parts of merge volume annotation CLI to Dataset and Annotation classes. [#1055](https://github.com/scalableminds/webknossos-libs/pull/1055)

webknossos/pyproject.toml

@@ -189,7 +189,7 @@ requires = ["setuptools>=70.0", "wheel; python_version>='3.12'"]
 build-backend = "setuptools.build_meta"
 
 # This is a fix for an issue in setuptools. See: https://github.com/pypa/setuptools/issues/4759
-# This shoulde be removed when the issue is resolved.
+# This should be removed when the issue is resolved.
 [tool.setuptools]
 license-files = []
 

webknossos/tests/conftest.py

@@ -126,7 +126,7 @@ def use_replay_proxay(request: Any) -> Generator:
     if "use_proxay" in request.keywords:
         os.environ["HTTP_PROXY"] = "http://localhost:3000"
         os.environ["http_proxy"] = (
-            "http://localhost:3000"  # for tensorstore. env var names are case-senstive on Linux
+            "http://localhost:3000"  # for tensorstore. env var names are case-sensitive on Linux
         )
         httpx.post("http://localhost:3000/__proxay/tape", json={"tape": testname})
     yield

webknossos/webknossos/cli/_utils.py

@@ -243,6 +243,6 @@ def prepare_shard_shape(
     else:
         if shard_shape % chunk_shape != Vec3Int.zeros():
             raise ValueError(
-                f"The shard_shape {shard_shape} must be cleanly divisble by the chunk_shape {chunk_shape}."
+                f"The shard_shape {shard_shape} must be cleanly divisible by the chunk_shape {chunk_shape}."
             )
         return shard_shape

webknossos/webknossos/geometry/vec_int.py

@@ -69,9 +69,7 @@ def __new__(
             if isinstance(args[0], VecInt):
                 return args[0]
             if isinstance(args[0], np.ndarray):
-                assert np.count_nonzero(args[0] % 1) == 0, (
-                    _value_error(args) + "Thsi error!"
-                )
+                assert np.count_nonzero(args[0] % 1) == 0, _value_error(args)
             if isinstance(args[0], str):
                 return cls.from_str(args[0])
             if isinstance(args[0], Iterable):