add support for layer selection in get_values() method

.pre-commit-config.yaml

@@ -12,8 +12,8 @@ repos:
       rev: 24.10.0
       hooks:
           - id: black
-    - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v4.0.0-alpha.8
+    - repo: https://github.com/rbubley/mirrors-prettier
+      rev: v3.4.2
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs

README.md

@@ -12,9 +12,9 @@
 
 SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.
 
--   [spatialdata-io](https://github.com/scverse/spatialdata-io): load data from common spatial omics technologies into spatialdata.
--   [spatialdata-plot](https://github.com/scverse/spatialdata-plot): Static plotting library for spatialdata.
--   [napari-spatialdata](https://github.com/scverse/napari-spatialdata): napari plugin for interactive exploration and annotation of spatial data.
+- [spatialdata-io](https://github.com/scverse/spatialdata-io): load data from common spatial omics technologies into spatialdata.
+- [spatialdata-plot](https://github.com/scverse/spatialdata-plot): Static plotting library for spatialdata.
+- [napari-spatialdata](https://github.com/scverse/napari-spatialdata): napari plugin for interactive exploration and annotation of spatial data.
 
 [//]: # "numfocus-fiscal-sponsor-attribution"
 
@@ -33,16 +33,16 @@ The spatialdata project also received support by the Chan Zuckerberg Initiative.
 
 ![SpatialDataOverview](https://github.com/scverse/spatialdata/assets/1120672/cb91071f-12a7-4b8e-9430-2b3a0f65e52f)
 
--   **The library is currently under review.** We expect there to be changes as the community provides feedback. We have an announcement channel for communicating these changes, please see the contact section below.
--   The SpatialData storage format is built on top of the [OME-NGFF](https://ngff.openmicroscopy.org/latest/) specification.
+- **The library is currently under review.** We expect there to be changes as the community provides feedback. We have an announcement channel for communicating these changes, please see the contact section below.
+- The SpatialData storage format is built on top of the [OME-NGFF](https://ngff.openmicroscopy.org/latest/) specification.
 
 ## Getting started
 
 Please refer to the [documentation][link-docs]. In particular:
 
--   [API documentation][link-api].
--   [Design doc][link-design-doc].
--   [Example notebooks][link-notebooks].
+- [API documentation][link-api].
+- [Design doc][link-design-doc].
+- [Example notebooks][link-notebooks].
 
 Another useful resource to get started is the source code of the [`spatialdata-io`](https://github.com/scverse/spatialdata-io) package, which shows example of how to read data from common technologies.
 
@@ -62,20 +62,20 @@ mamba install -c conda-forge spatialdata napari-spatialdata spatialdata-io spati
 
 ## Limitations
 
--   Code only manually tested for Windows machines. Currently the framework is being developed using Linux, macOS and Windows machines, but it is automatically tested only for Linux and macOS machines.
+- Code only manually tested for Windows machines. Currently the framework is being developed using Linux, macOS and Windows machines, but it is automatically tested only for Linux and macOS machines.
 
 ## Contact
 
 To get involved in the discussion, or if you need help to get started, you are welcome to use the following options.
 
--   <ins>Chat</ins> via [`scverse` Zulip](https://scverse.zulipchat.com/#narrow/stream/315824-spatial) (public or 1 to 1).
--   <ins>Forum post</ins> in the [scverse discourse forum](https://discourse.scverse.org/).
--   <ins>Bug report/feature request</ins> via the [GitHub issue tracker][issue-tracker].
--   <ins>Zoom call</ins> as part of the SpatialData Community Meetings, held every 2 weeks on Thursday, [schedule here](https://hackmd.io/enWU826vRai-JYaL7TZaSw).
+- <ins>Chat</ins> via [`scverse` Zulip](https://scverse.zulipchat.com/#narrow/stream/315824-spatial) (public or 1 to 1).
+- <ins>Forum post</ins> in the [scverse discourse forum](https://discourse.scverse.org/).
+- <ins>Bug report/feature request</ins> via the [GitHub issue tracker][issue-tracker].
+- <ins>Zoom call</ins> as part of the SpatialData Community Meetings, held every 2 weeks on Thursday, [schedule here](https://hackmd.io/enWU826vRai-JYaL7TZaSw).
 
 Finally, especially relevant for for developers that are building a library upon `spatialdata`, please follow this channel for:
 
--   <ins>Announcements</ins> on new features and important changes [Zulip](https://imagesc.zulipchat.com/#narrow/stream/329057-scverse/topic/spatialdata.20announcements).
+- <ins>Announcements</ins> on new features and important changes [Zulip](https://imagesc.zulipchat.com/#narrow/stream/329057-scverse/topic/spatialdata.20announcements).
 
 ## Citation
 

docs/contributing.md

@@ -143,10 +143,10 @@ in the cookiecutter-scverse template.
 
 Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features:
 
--   the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
--   [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
--   Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
--   [Sphinx autodoc typehints][], to automatically reference annotated input and output types
+- the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
+- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
+- [Sphinx autodoc typehints][], to automatically reference annotated input and output types
 
 See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
 on how to write documentation.
@@ -163,10 +163,10 @@ repository.
 
 #### Hints
 
--   If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
-    if you do so can sphinx automatically create a link to the external documentation.
--   If building the documentation fails because of a missing link that is outside your control, you can add an entry to
-    the `nitpick_ignore` list in `docs/conf.py`
+- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
+  if you do so can sphinx automatically create a link to the external documentation.
+- If building the documentation fails because of a missing link that is outside your control, you can add an entry to
+  the `nitpick_ignore` list in `docs/conf.py`
 
 #### Building the docs locally