From f9aad01c1491be45ccb36647e6c049eea23b9c79 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 6 Jan 2025 18:16:13 +0000 Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/pre-commit/mirrors-mypy: v1.14.0 → v1.14.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.14.0...v1.14.1) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 46c41f2f..bcf129f3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,7 +23,7 @@ repos: hooks: - id: isort - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.14.0 + rev: v1.14.1 hooks: - id: mypy additional_dependencies: [numpy, types-PyYAML] From 0a909588c6ad8dcaaab9e7d4a6248b3119e3810e Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 6 Jan 2025 18:19:40 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- README.md | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index f3dd6fca..41beda62 100644 --- a/README.md +++ b/README.md @@ -86,15 +86,18 @@ Technologies that can be read into `SpatialData` objects using third-party libra This library is community maintained and is not officially endorsed by the aforementioned spatial technology companies. As such, we cannot offer any warranty of the correctness of the representation. Furthermore, we cannot ensure the correctness of the readers for every data version as the technologies evolve and update their formats. If you find a bug or notice a misrepresentation of the data please report it via our [Bug Tracking System](https://github.com/scverse/spatialdata-io/issues?q=sort%3Aupdated-desc+is%3Aissue+is%3Aopen) so that it can be addressed either by the maintainers of this library or by the community. ## Solutions to common problems + ### Problem: I cannot visualize the data, everything is slow -Solution: after parsing the data with `spatialdata-io` readers, you need to write it to Zarr and read it again. Otherwise the performance advantage given by the SpatialData Zarr format will not available. + +Solution: after parsing the data with `spatialdata-io` readers, you need to write it to Zarr and read it again. Otherwise the performance advantage given by the SpatialData Zarr format will not available. + ```python from spatialdata_io import xenium from spatialdata import read_zarr -sdata = xenium('raw_data') -sdata.write('data.zarr') -sdata = read_zarr('sdata.zarr') +sdata = xenium("raw_data") +sdata.write("data.zarr") +sdata = read_zarr("sdata.zarr") ``` ## Citation