From 2e15fff332e3824211e72c21b09661be7cdc5536 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 3 Jan 2025 20:09:39 +0000 Subject: [PATCH] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- CHANGELOG.md | 102 +++++++++++++++++++++++++-------------------------- 1 file changed, 51 insertions(+), 51 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0eb3b81e..eb370cb4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,140 +10,140 @@ and this project adheres to [Semantic Versioning][]. ## incoming release -- (Visium/Visium HD) lowres and hires images now mapped also to the 'global' coordinate system #230 -- (Macsima) added support @berombau #224 -- (seqFISH) support for v2 instrument #227 -- (Visium HD) added argument `annotate_table_by_labels` to rasterize the bins as labels #211 @ArneDefauw +- (Visium/Visium HD) lowres and hires images now mapped also to the 'global' coordinate system #230 +- (Macsima) added support @berombau #224 +- (seqFISH) support for v2 instrument #227 +- (Visium HD) added argument `annotate_table_by_labels` to rasterize the bins as labels #211 @ArneDefauw ## [0.1.6] - 2024-11-26 -- (MERSCOPE) added `feature_key` attribute for points (i.e., the `'gene'` column) #210 -- (Visium HD) get transformation matrices even when only images are parsed #215 -- Support for `xarray.DataTree` (which was moved from `datatree.DataTree`) #232 +- (MERSCOPE) added `feature_key` attribute for points (i.e., the `'gene'` column) #210 +- (Visium HD) get transformation matrices even when only images are parsed #215 +- Support for `xarray.DataTree` (which was moved from `datatree.DataTree`) #232 ## [0.1.5] - 2024-09-25 ### Added -- (Xenium) added `dims` parameter for more control in `xenium_aligned_image()` +- (Xenium) added `dims` parameter for more control in `xenium_aligned_image()` ### Fixed -- Passing `rgb=None` to image model parser for both visium and visiumhd, leading to 3-4 channel images being - interpreted as RGB(A) -- Fix header bug Visium data #200 -- (Visium HD) Fix path parsing when images are missing #204 #206 +- Passing `rgb=None` to image model parser for both visium and visiumhd, leading to 3-4 channel images being + interpreted as RGB(A) +- Fix header bug Visium data #200 +- (Visium HD) Fix path parsing when images are missing #204 #206 ## [0.1.4] - 2024-08-07 ### Changed -- (Xenium) changed default target of table to labels; radii of circles computed from cells, not nuclei #179 -- (Visium HD) changed default geometry to squares from circles for the bins; added parameter to choose #183 -- (CosMx) dropping points element with zero-length from the cosmx reader #191 +- (Xenium) changed default target of table to labels; radii of circles computed from cells, not nuclei #179 +- (Visium HD) changed default geometry to squares from circles for the bins; added parameter to choose #183 +- (CosMx) dropping points element with zero-length from the cosmx reader #191 ## [0.1.3] - 2024-07-03 ### Added -- (Xenium) support reading multi-polygon selection files from the Xenium Explorer -- (ISS) An experimental loader to load elemental ISS data objects, e.g. raw.tif, label.tif and anndata.h5ad -- (Stereo-seq) Added reader @LLehner @timtreis @florianingelfinger #70 -- (MERSCOPE) Optional rioxarray backend for MERSCOPE data (reads chunks) -- (MERSCOPE) Can choose which elements should be loaded +- (Xenium) support reading multi-polygon selection files from the Xenium Explorer +- (ISS) An experimental loader to load elemental ISS data objects, e.g. raw.tif, label.tif and anndata.h5ad +- (Stereo-seq) Added reader @LLehner @timtreis @florianingelfinger #70 +- (MERSCOPE) Optional rioxarray backend for MERSCOPE data (reads chunks) +- (MERSCOPE) Can choose which elements should be loaded ### Fixed -- (Visium) Fixed issue with joining a SpatialElement with a table due to index values not being unique. - obs_names_make_unique is now called internally to enforce unique index values allowing for join operations. +- (Visium) Fixed issue with joining a SpatialElement with a table due to index values not being unique. + obs_names_make_unique is now called internally to enforce unique index values allowing for join operations. ### Changed -- (MERSCOPE) "global" coordinate system is used as a default instead of "microns" +- (MERSCOPE) "global" coordinate system is used as a default instead of "microns" ## [0.1.2] - 2024-03-30 ### Added -- (Visium HD) added reader, coauthored by @LLehner +- (Visium HD) added reader, coauthored by @LLehner ### Fixed -- (Xenium) reader for 1.0.1 (paper data) and unknown versions -- (Xenium) fix in reading "minimalistic" Xenium datasets #132 +- (Xenium) reader for 1.0.1 (paper data) and unknown versions +- (Xenium) fix in reading "minimalistic" Xenium datasets #132 ## [0.1.1] - 2024-03-24 ### Added -- (Xenium) support for post-xenium aligned images (IF, HE) -- (Xenium) reader for the selection coordinates file from the Xenium Explorer -- (Xenium) support for the new Xenium 2.0.0 (multimodal segmentation) -- (Xenium) reading multiscale labels from cells.zarr.zip -- (MCMICRO) support for TMAs (such as the data of exemplar-002) -- (DBiT-seq) reader -- converter functions `experimental.to_legacy_anndata()` and `experimental.from_legacy_anndata()` -- (Visium) support for raw reads (capture locations not under tissue) +- (Xenium) support for post-xenium aligned images (IF, HE) +- (Xenium) reader for the selection coordinates file from the Xenium Explorer +- (Xenium) support for the new Xenium 2.0.0 (multimodal segmentation) +- (Xenium) reading multiscale labels from cells.zarr.zip +- (MCMICRO) support for TMAs (such as the data of exemplar-002) +- (DBiT-seq) reader +- converter functions `experimental.to_legacy_anndata()` and `experimental.from_legacy_anndata()` +- (Visium) support for raw reads (capture locations not under tissue) ### Fixed -- (Xenium) fixed index (fail on write) -- (Xenium) renamed cells_as_shapes to cells_as_circles; set default to True -- (MERSCOPE) don't try to load unexisting elements #87 -- (Visium) fixed axes ordering +- (Xenium) fixed index (fail on write) +- (Xenium) renamed cells_as_shapes to cells_as_circles; set default to True +- (MERSCOPE) don't try to load unexisting elements #87 +- (Visium) fixed axes ordering ## [0.0.9] - 2023-11-06 ### Fixed -- (Xenium) bug when converting feature_name #81, from @fbnrst -- (Visium) visium() supports file counts without dataset_id #91 +- (Xenium) bug when converting feature_name #81, from @fbnrst +- (Visium) visium() supports file counts without dataset_id #91 ## [0.0.8] - 2023-10-02 ### Fixed -- (Xenium) coerce cell id to str #64 -- (MERSCOPE) fix coordinate transformation #68 -- (MERSCOPE) Improvements/fixes: merscope reader #73 +- (Xenium) coerce cell id to str #64 +- (MERSCOPE) fix coordinate transformation #68 +- (MERSCOPE) Improvements/fixes: merscope reader #73 ## [0.0.7] - 2023-07-23 ### Fixed -- Bugs in Xenium and MERSCOPE +- Bugs in Xenium and MERSCOPE ## [0.0.5] - 2023-06-21 ### Added -- MERFISH reader (from @quentinblampey) -- CODEX reader (from @LLehner) +- MERFISH reader (from @quentinblampey) +- CODEX reader (from @LLehner) ### Fixed -- Issues on Visium reader (thanks @ilia-kats) and Xenium reader +- Issues on Visium reader (thanks @ilia-kats) and Xenium reader ## [0.0.4] - 2023-05-23 ### Added -- Curio reader +- Curio reader ## [0.0.3] - 2023-05-22 ### Merged -- Merge pull request #40 from scverse/fix/categories +- Merge pull request #40 from scverse/fix/categories ## [0.0.2] - 2023-05-04 ### Changed -- Revert version regex (#37) +- Revert version regex (#37) ## [0.0.1] - 2023-05-04 ### Tested -- Test installation from pypi +- Test installation from pypi