Merge pull request #248 from scverse/add-tests-datasets

new test datasets

Author: LucaMarconato

.github/workflows/prepare_test_data.yaml

@@ -18,15 +18,30 @@ jobs:
               run: |
                   mkdir -p ./data
                   cd ./data
+
+                  # 10x Genomics Xenium 2.0.0
                   curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Breast_2fov/Xenium_V1_human_Breast_2fov_outs.zip
                   curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Lung_2fov/Xenium_V1_human_Lung_2fov_outs.zip
 
+                  # 10x Genomics Xenium 3.0.0 (5K) Mouse ileum, multimodal cell segmentation
+                  # this file seems to be corrupted; skipping it for now
+                  # curl -O https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny.zip
+
+                  # 10x Genomics Xenium 3.0.0 (5K) Mouse ileum, nuclear expansion
+                  curl -O https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_Mouse_Ileum_tiny/Xenium_Prime_Mouse_Ileum_tiny_outs.zip
+
+                  # Spatial Genomics seqFISH v2
+                  curl -O https://s3.embl.de/spatialdata/raw_data/seqfish-2-test-dataset.zip
+
             - name: Unzip files
               run: |
-                  unzip ./data/Xenium_V1_human_Breast_2fov_outs.zip -d ./data/Xenium_V1_human_Breast_2fov_outs
-                  unzip ./data/Xenium_V1_human_Lung_2fov_outs.zip -d ./data/Xenium_V1_human_Lung_2fov_outs
-                  rm ./data/Xenium_V1_human_Breast_2fov_outs.zip
-                  rm ./data/Xenium_V1_human_Lung_2fov_outs.zip
+                  cd ./data
+                  for file in *.zip; do
+                      dir="${file%.zip}"
+                      mkdir -p "$dir"
+                      unzip "$file" -d "$dir"
+                      rm "$file"
+                  done
 
             - name: Upload artifacts
               uses: actions/upload-artifact@v3

CHANGELOG.md

@@ -10,138 +10,138 @@ 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
+- (Visium/Visium HD) lowres and hires images now mapped also to the 'global' coordinate system #230
+- (Macsima) added support @berombau #224
 
 ## [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

README.md

@@ -12,27 +12,27 @@
 
 This package contains reader functions to load common spatial omics formats into SpatialData. Currently, we provide support for:
 
--   10x Genomics Visium®
--   10x Genomics Visium HD®
--   10x Genomics Xenium®
--   Akoya PhenoCycler® (formerly CODEX®)
--   Curio Seeker®
--   DBiT-seq
--   MCMICRO (output data)
--   NanoString CosMx®
--   Spatial Genomics GenePS® (seqFISH)
--   Steinbock (output data)
--   STOmics Stereo-seq®
--   Vizgen MERSCOPE® (MERFISH)
--   MACSima® (MACS® iQ View output)
+- 10x Genomics Visium®
+- 10x Genomics Visium HD®
+- 10x Genomics Xenium®
+- Akoya PhenoCycler® (formerly CODEX®)
+- Curio Seeker®
+- DBiT-seq
+- MCMICRO (output data)
+- NanoString CosMx®
+- Spatial Genomics GenePS® (seqFISH)
+- Steinbock (output data)
+- STOmics Stereo-seq®
+- Vizgen MERSCOPE® (MERFISH)
+- MACSima® (MACS® iQ View output)
 
 Note: all mentioned technologies are registered trademarks of their respective companies.
 
 ## Known limitations
 
 Contributions for addressing the below limitations are very welcomed.
 
--   Only Stereo-seq 7.x is supported, 8.x is not currently supported. https://github.com/scverse/spatialdata-io/issues/161
+- Only Stereo-seq 7.x is supported, 8.x is not currently supported. https://github.com/scverse/spatialdata-io/issues/161
 
 ### How to Contribute
 
@@ -46,7 +46,7 @@ Contributions for addressing the below limitations are very welcomed.
 
 Please refer to the [documentation][link-docs]. In particular, the
 
--   [API documentation][link-api].
+- [API documentation][link-api].
 
 ## Installation
 
@@ -76,10 +76,10 @@ If you found a bug, please use the [issue tracker][issue-tracker].
 
 Technologies that can be read into `SpatialData` objects using third-party libraries:
 
--   METASPACE (MALDI, ...): [metaspace-converter](https://github.com/metaspace2020/metaspace-converter)
--   PhenoCycler®: [SOPA](https://github.com/gustaveroussy/sopa)
--   MACSima®: [SOPA](https://github.com/gustaveroussy/sopa)
--   Hyperion® (Imaging Mass Cytometry): [SOPA](https://github.com/gustaveroussy/sopa)
+- METASPACE (MALDI, ...): [metaspace-converter](https://github.com/metaspace2020/metaspace-converter)
+- PhenoCycler®: [SOPA](https://github.com/gustaveroussy/sopa)
+- MACSima®: [SOPA](https://github.com/gustaveroussy/sopa)
+- Hyperion® (Imaging Mass Cytometry): [SOPA](https://github.com/gustaveroussy/sopa)
 
 ## Disclaimer
 

docs/contributing.md

@@ -138,10 +138,10 @@ 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.
@@ -158,10 +158,10 @@ 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