LucaMarconato

Benchmark geopandas query methods

1

> A solution would be to benchmark the polygon query and bounding box implementation for points and shapes and see if one is significantly faster than the other. Ideally the...

Opening this issue after a comment from @Felicie-Giraud-Sauveur at the scverse conference. The interpolation options for `rasterize()` and `transform()`, respectively handled here https://github.com/scverse/spatialdata/blob/3988452f433a565b0b64224d02d7e0562637f149/src/spatialdata/_core/operations/rasterize.py#L576 and here https://github.com/scverse/spatialdata/blob/3988452f433a565b0b64224d02d7e0562637f149/src/spatialdata/_core/operations/transform.py#L365 are not exposed to...

Update pyproject.toml

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When [trying to solve](https://dev.azure.com/conda-forge/feedstock-builds/_build/results?buildId=1172956&view=logs&j=7b6f2c87-f3a7-5133-8d84-7c03a75d9dfc&t=9eb77fd2-8ddd-5444-8fc0-71cb28dcb736) a conda env for `multiscale-spatial-image` I got the following error: ``` Solving environment (_test_env): ...working... failed WARNING: failed to get package records, retrying. exception was: Unsatisfiable...

Reintroduce Python 3.13 support. Closes #104 The CI will fail because at the moment I cannot regenerate the lock file (see my comment here https://github.com/spatial-image/multiscale-spatial-image/pull/105#issuecomment-2649134616).

Support for Python 3.13

3

Hi, I noticed that `multiscale-spatial-image` does not support Python 3.13 (in the sense that the following `requires-python = ">=3.10,

Even after the [latest fix](https://github.com/scverse/napari-spatialdata/pull/349), some [tests sometimes fail](https://github.com/scverse/napari-spatialdata/actions/runs/14579292539/job/40892220813) due to improper cleanup. Probably because the fix was not extended to those tests. In this PR, I fix only the...

Legend (categorical obs column) for scatterplot widget not consistent

1

Originally discovered here: https://github.com/scverse/napari-spatialdata/issues/328#issuecomment-2464885435. To reproduce: ```python import numpy as np import scanpy as sc from spatialdata.datasets import blobs np.random.seed(10) sdata = blobs(length=1000, n_channels=3) sc.pp.pca( sdata["table"], copy=False, ) sc.pp.neighbors( sdata["table"],...

See the problem in action here. This CI run failed: https://github.com/scverse/napari-spatialdata/actions/runs/12379528925/attempts/1?pr=285, I re-run it as it was, and it worked: https://github.com/scverse/napari-spatialdata/actions/runs/12379528925?pr=285. The problem has been discussed here https://github.com/scverse/napari-spatialdata/pull/270#discussion_r1731494552, and this...

Next steps after the scatterplot PR

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#270 is now merged! 🥳 Thanks again @fjorka and @melonora. In the PR discussion were some open points to consider in follow-up PRs. I moved the points here, to make...

We currently have a the custom implementation for reading matrices (copied from `scanpy`) in https://github.com/scverse/spatialdata-io/blob/main/src/spatialdata_io/readers/_utils/_read_10x_h5.py. I would remove that code and use directly `scanpy`, which is already a dependency. I...