fix: citation, relational query index, python 3.12 tests (#569)

* fix citation, fix relational query index

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix test

* fix tests

* testing against 3.12

* fix docs

* restoring tests against 3.10 instead of 3.12

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

docs/index.md

@@ -12,7 +12,7 @@ SpatialData is a data framework that comprises a FAIR storage format and a colle
 -   `spatialdata-plot`: Static plotting library for `spatialdata` ([repository][spatialdata-plot-repo], [documentation][spatialdata-plot-docs]).
 -   `napari-spatialdata-repo`: napari plugin for interactive exploration and annotation of `spatialdata` ([repository][napari-spatialdata-repo], [documentation][napari-spatialdata-docs]).
 
-Please see our preprint {cite}`Marconato2023.05.05.539647` for citation and to learn more.
+Please see our publication {cite}`marconatoSpatialDataOpenUniversal2024` for citation and to learn more.
 
 ```{eval-rst}
 .. note::

docs/references.bib

@@ -27,3 +27,14 @@ @article {Marconato2023.05.05.539647
 	eprint = {https://www.biorxiv.org/content/early/2023/05/08/2023.05.05.539647.full.pdf},
 	journal = {bioRxiv}
 }
+
+@article{marconatoSpatialDataOpenUniversal2024,
+  title = {{{SpatialData}}: An Open and Universal Data Framework for Spatial Omics},
+  author = {Marconato, Luca and Palla, Giovanni and Yamauchi, Kevin A. and Virshup, Isaac and Heidari, Elyas and Treis, Tim and Vierdag, Wouter-Michiel and Toth, Marcella and Stockhaus, Sonja and Shrestha, Rahul B. and Rombaut, Benjamin and Pollaris, Lotte and Lehner, Laurens and V{\"o}hringer, Harald and Kats, Ilia and Saeys, Yvan and Saka, Sinem K. and Huber, Wolfgang and Gerstung, Moritz and Moore, Josh and Theis, Fabian J. and Stegle, Oliver},
+  year = {2024},
+  month = mar,
+  journal = {Nature Methods},
+  issn = {1548-7105},
+  doi = {10.1038/s41592-024-02212-x},
+  abstract = {Spatially resolved omics technologies are transforming our understanding of biological tissues. However, the handling of uni- and multimodal spatial omics datasets remains a challenge owing to large data volumes, heterogeneity of data types and the lack of flexible, spatially aware data structures. Here we introduce SpatialData, a framework that establishes a unified and extensible multiplatform file-format, lazy representation of larger-than-memory data, transformations and alignment to common coordinate systems. SpatialData facilitates spatial annotations and cross-modal aggregation and analysis, the utility of which is illustrated in the context of multiple vignettes, including integrative analysis on a multimodal Xenium and Visium breast cancer study.}
+}

src/spatialdata/_core/query/relational_query.py

@@ -248,6 +248,8 @@ def _get_masked_element(
     if match_rows == "right":
         mask_values = _match_rows(table_instance_key_column, mask, element_indices, match_rows)
 
+    if isinstance(element, DaskDataFrame):
+        return element.map_partitions(lambda df: df.loc[mask_values], meta=element)
     return element.loc[mask_values, :]
 
 

src/spatialdata/dataloader/datasets.py

@@ -61,7 +61,7 @@ class ImageTilesDataset(Dataset):
     tile_scale
         This parameter is used to determine the size (width and height) of the tiles.
         Each tile will have size in units equal to tile_scale times the diameter of the circle that approximates (=same
-         area) the region that defines the tile.
+        area) the region that defines the tile.
 
         For example, suppose the regions to be multiscale labels; this is how the tiles are created:
 

tests/core/query/test_relational_query.py

@@ -704,6 +704,7 @@ def test_points_table_joins(full_sdata):
     element_dict, table = join_spatialelement_table(
         sdata=full_sdata, spatial_element_names="points_0", table_name="table", how="inner"
     )
+
     assert len(element_dict["points_0"]) == 100
     assert all(table.obs["instance_id"] == list(reversed(range(100))))