From d5941cbf0eb86395d1bfd98bcbf9d703c068e314 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Tue, 7 Jan 2025 17:45:59 +0000 Subject: [PATCH] Fix OME-Zarr spelling --- docs/contributing.md | 2 +- docs/index.md | 8 ++++---- docs/tutorial.py | 6 +++--- src/ome_zarr_models/v04/coordinate_transformations.py | 2 +- src/ome_zarr_models/v04/hcs.py | 2 +- src/ome_zarr_models/v04/image.py | 6 +++--- src/ome_zarr_models/v04/image_label.py | 4 ++-- src/ome_zarr_models/v04/image_label_types.py | 2 +- src/ome_zarr_models/v04/labels.py | 2 +- src/ome_zarr_models/v04/multiscales.py | 2 +- src/ome_zarr_models/v04/omero.py | 2 +- src/ome_zarr_models/v04/plate.py | 2 +- src/ome_zarr_models/v04/well.py | 2 +- src/ome_zarr_models/v04/well_types.py | 2 +- 14 files changed, 22 insertions(+), 22 deletions(-) diff --git a/docs/contributing.md b/docs/contributing.md index 23f6cd0..f57b6ed 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -6,7 +6,7 @@ Below are some different ways you can contribute. ## Suggesting new features -We're super open to helper functionality for working with OME-zarr metadata using our package! +We're super open to helper functionality for working with OME-Zarr metadata using our package! To suggest a new feature, please open a ticket on [our issue tracker](https://github.com/ome-zarr-models/ome-zarr-models-py). ## Reporting issues diff --git a/docs/index.md b/docs/index.md index 65a2490..4d9f8b3 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,6 +1,6 @@ # ome-zarr-models -A Python package that provides validation and a Pythonic interface for OME-zarr datasets. +A Python package that provides validation and a Pythonic interface for OME-Zarr datasets. ## Installing @@ -19,9 +19,9 @@ Useful places to get started are: This package has been designed with the following guiding principles: -- Strict adherence to the [OME-zarr specification](https://ngff.openmicroscopy.org/), with the goal of being a reference implementation. -- A usable set of Python classes for reading, writing, and interacting with OME-zarr metadata. -- The ability to work with multiple versions of the OME-zarr spec at the same time. +- Strict adherence to the [OME-Zarr specification](https://ngff.openmicroscopy.org/), with the goal of being a reference implementation. +- A usable set of Python classes for reading, writing, and interacting with OME-Zarr metadata. +- The ability to work with multiple versions of the OME-Zarr spec at the same time. - Array reading and writing operations are out of scope. ## Getting help diff --git a/docs/tutorial.py b/docs/tutorial.py index bf5affa..4fdfd98 100644 --- a/docs/tutorial.py +++ b/docs/tutorial.py @@ -10,8 +10,8 @@ # ## Loading datasets # -# OME-zarr datasets are just zarr groups with special metadata. -# To open an OME-zarr dataset, we first open the zarr group. +# OME-Zarr datasets are just zarr groups with special metadata. +# To open an OME-Zarr dataset, we first open the zarr group. zarr_group = zarr.open( "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr", mode="r" @@ -33,7 +33,7 @@ # No errors, which means the metadata is valid 🎉 # # ## Accessing metadata -# To access the OME-zarr metadata, use the `.attributes` property: +# To access the OME-Zarr metadata, use the `.attributes` property: metadata = ome_zarr_image.attributes pprint(metadata) diff --git a/src/ome_zarr_models/v04/coordinate_transformations.py b/src/ome_zarr_models/v04/coordinate_transformations.py index 9cc266d..9be6202 100644 --- a/src/ome_zarr_models/v04/coordinate_transformations.py +++ b/src/ome_zarr_models/v04/coordinate_transformations.py @@ -1,5 +1,5 @@ """ -For reference, see the [coordinate transformations section of the OME-zarr specification](https://ngff.openmicroscopy.org/0.4/#trafo-md). +For reference, see the [coordinate transformations section of the OME-Zarr specification](https://ngff.openmicroscopy.org/0.4/#trafo-md). """ from __future__ import annotations diff --git a/src/ome_zarr_models/v04/hcs.py b/src/ome_zarr_models/v04/hcs.py index 3270abe..fe2861a 100644 --- a/src/ome_zarr_models/v04/hcs.py +++ b/src/ome_zarr_models/v04/hcs.py @@ -22,7 +22,7 @@ class HCSAttrs(BaseAttrs): class HCS(GroupSpec[HCSAttrs, ArraySpec | GroupSpec], BaseGroupv04): # type: ignore[misc] """ - An OME-zarr high-content screening (HCS) dataset representing a single plate. + An OME-Zarr high-content screening (HCS) dataset representing a single plate. """ @model_validator(mode="after") diff --git a/src/ome_zarr_models/v04/image.py b/src/ome_zarr_models/v04/image.py index 638c174..d27ada5 100644 --- a/src/ome_zarr_models/v04/image.py +++ b/src/ome_zarr_models/v04/image.py @@ -61,7 +61,7 @@ def _check_arrays_compatible(data: Image) -> Image: class ImageAttrs(BaseAttrs): """ - Model for the metadata of OME-zarr data. + Model for the metadata of OME-Zarr data. See https://ngff.openmicroscopy.org/0.4/#image-layout. """ @@ -76,7 +76,7 @@ class ImageAttrs(BaseAttrs): class Image(GroupSpec[ImageAttrs, ArraySpec | GroupSpec], BaseGroupv04): # type: ignore[misc] """ - An OME-zarr multiscale dataset. + An OME-Zarr multiscale dataset. """ _check_arrays_compatible = model_validator(mode="after")(_check_arrays_compatible) @@ -84,7 +84,7 @@ class Image(GroupSpec[ImageAttrs, ArraySpec | GroupSpec], BaseGroupv04): # type @classmethod def from_zarr(cls, group: zarr.Group) -> Self: """ - Create an instance of an OME-zarr image from a `zarr.Group`. + Create an instance of an OME-Zarr image from a `zarr.Group`. Parameters ---------- diff --git a/src/ome_zarr_models/v04/image_label.py b/src/ome_zarr_models/v04/image_label.py index 419a06a..fd63f9d 100644 --- a/src/ome_zarr_models/v04/image_label.py +++ b/src/ome_zarr_models/v04/image_label.py @@ -1,5 +1,5 @@ """ -For reference, see the [image label section of the OME-zarr specification](https://ngff.openmicroscopy.org/0.4/index.html#label-md). +For reference, see the [image label section of the OME-Zarr specification](https://ngff.openmicroscopy.org/0.4/index.html#label-md). """ from __future__ import annotations @@ -47,7 +47,7 @@ class ImageLabel(GroupSpec[ImageLabelAttrs, ArraySpec | GroupSpec], BaseGroupv04 @classmethod def from_zarr(cls, group: zarr.Group) -> Self: """ - Create an instance of an OME-zarr image from a `zarr.Group`. + Create an instance of an OME-Zarr image from a `zarr.Group`. Parameters ---------- diff --git a/src/ome_zarr_models/v04/image_label_types.py b/src/ome_zarr_models/v04/image_label_types.py index fdb2df6..adbb516 100644 --- a/src/ome_zarr_models/v04/image_label_types.py +++ b/src/ome_zarr_models/v04/image_label_types.py @@ -1,5 +1,5 @@ """ -For reference, see the [image label section of the OME-zarr specification](https://ngff.openmicroscopy.org/0.4/index.html#label-md). +For reference, see the [image label section of the OME-Zarr specification](https://ngff.openmicroscopy.org/0.4/index.html#label-md). """ from __future__ import annotations diff --git a/src/ome_zarr_models/v04/labels.py b/src/ome_zarr_models/v04/labels.py index 3e00862..f37e808 100644 --- a/src/ome_zarr_models/v04/labels.py +++ b/src/ome_zarr_models/v04/labels.py @@ -21,5 +21,5 @@ class LabelsAttrs(BaseAttrs): class Labels(GroupSpec[LabelsAttrs, ArraySpec | GroupSpec], BaseGroupv04): # type: ignore[misc] """ - An OME-zarr labels dataset. + An OME-Zarr labels dataset. """ diff --git a/src/ome_zarr_models/v04/multiscales.py b/src/ome_zarr_models/v04/multiscales.py index 5fa70eb..cb6ebb2 100644 --- a/src/ome_zarr_models/v04/multiscales.py +++ b/src/ome_zarr_models/v04/multiscales.py @@ -1,5 +1,5 @@ """ -For reference, see the [multiscales section of the OME-zarr specification](https://ngff.openmicroscopy.org/0.4/#multiscale-md). +For reference, see the [multiscales section of the OME-Zarr specification](https://ngff.openmicroscopy.org/0.4/#multiscale-md). """ from __future__ import annotations diff --git a/src/ome_zarr_models/v04/omero.py b/src/ome_zarr_models/v04/omero.py index ef7251a..e589c6e 100644 --- a/src/ome_zarr_models/v04/omero.py +++ b/src/ome_zarr_models/v04/omero.py @@ -1,5 +1,5 @@ """ -For reference, see the [omero section of the OME-zarr specification](https://ngff.openmicroscopy.org/0.4/#omero-md). +For reference, see the [omero section of the OME-Zarr specification](https://ngff.openmicroscopy.org/0.4/#omero-md). """ from typing import Annotated diff --git a/src/ome_zarr_models/v04/plate.py b/src/ome_zarr_models/v04/plate.py index ec4c7a0..3c885bd 100644 --- a/src/ome_zarr_models/v04/plate.py +++ b/src/ome_zarr_models/v04/plate.py @@ -1,5 +1,5 @@ """ -For reference, see the [plate section of the OME-zarr specification](https://ngff.openmicroscopy.org/0.4/index.html#plate-md). +For reference, see the [plate section of the OME-Zarr specification](https://ngff.openmicroscopy.org/0.4/index.html#plate-md). """ from collections import Counter diff --git a/src/ome_zarr_models/v04/well.py b/src/ome_zarr_models/v04/well.py index 82678fa..8ef95dc 100644 --- a/src/ome_zarr_models/v04/well.py +++ b/src/ome_zarr_models/v04/well.py @@ -1,5 +1,5 @@ """ -For reference, see the [well section of the OME-zarr specification](https://ngff.openmicroscopy.org/0.4/#well-md). +For reference, see the [well section of the OME-Zarr specification](https://ngff.openmicroscopy.org/0.4/#well-md). """ from collections.abc import Generator diff --git a/src/ome_zarr_models/v04/well_types.py b/src/ome_zarr_models/v04/well_types.py index e5bfcc4..1472789 100644 --- a/src/ome_zarr_models/v04/well_types.py +++ b/src/ome_zarr_models/v04/well_types.py @@ -1,5 +1,5 @@ """ -For reference, see the [well section of the OME-zarr specification](https://ngff.openmicroscopy.org/0.4/#well-md). +For reference, see the [well section of the OME-Zarr specification](https://ngff.openmicroscopy.org/0.4/#well-md). """ from collections import defaultdict