CI
1c07203f14
Build pipeline: openpipelines-bio.openpipeline-spatial.v0.5-chjp2
Source commit: 56d3738b53
Source message: Merge remote-tracking branch 'origin/main' into v0.5
126 lines
4.7 KiB
Markdown
126 lines
4.7 KiB
Markdown
# openpipeline_spatial 0.5.0
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## NEW FUNCTIONALITY
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* `dataflow/concatenate_spatialdata`: Concatenate two or more SpatialData objects (PR #49).
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* `dataflow/move_layer_spatialdata`: Move/rename a layer in a SpatialData object (PR #50).
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* `convert/from_h5mu_to_seurat_with_fov`: Added converter component for H5MU data to Seurat objects with spatial FOV (PR #51).
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## MAJOR CHANGES
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* Pin OpenPipeline dependency to v4.1.0 (PR #56).
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## MINOR CHANGES
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* Pin ome-zarr to 0.13.0 to avoid a chunk shape incompatibility with zarr 3.x (PR #48).
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* Bump Viash to 0.9.7 (PR #57).
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* Bump anndata to 0.12.16 (PR #57).
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* Bump mudata to 0.3.8 (PR #57).
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* Bump scanpy to 1.11.4 (PR #57)
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* Testing: bump viashpy to 0.10.0 (PR #57).
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## BUG FIXES
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* `convert/from_h5mu_to_spatialdata`: Make sure the AnnData table is properly parsed before inserting into the new SpatialData object (PR #53).
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* `convert/from_h5mu_to_spatialexperiment`: Add `libuv1-dev` to the test image so reticulate imports successfully (#54).
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* `nichecompass/gene_program_mask`: Bump container base image to `nvidia/cuda:12.6.3-cudnn-devel-ubuntu24.04` and pin `decoupler>=2.1.6` to pick up the updated HCOP orthology download URL (PR #55).
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# openpipeline_spatial 0.4.0
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## NEW FUNCTIONALITY
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* `feature_annotation/spatial_autocorr`: Added a spatial autocorrelation component (PR #45).
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* `feature_annotation/xenium_spatial_statistics`: Added a component to calculate spatial statistics on Xenium-ingested data (PR #46).
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* `neighbors/join_graphs`: Combine spatial and expression neighborhood graphs into a single graph (PR #47).
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# openpipeline_spatial 0.3.0
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## NEW FUNCTIONALITY
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* `convert/from_h5mu_to_spatialdata`: Added a converter component to convert from H5MU to SpatialData (PR #40)
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* `nichecompass/gene_program_mask`: Added a component to create a prior knowledge gene program mask for NicheCompass analysis (PR #27).
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## MINOR CHANGES
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* Bump squidpy to 1.8.1 and spatialdata to 0.7.2 (PR #41).
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* Update openpipeline dependencies to v4.0.3 (PR #42, PR #44).
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# openpipeline_spatial 0.2.0
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## NEW FUNCTIONALITY
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* `neighbors/spatial_neighborhood_graph`: Calculate the spatial neighborhood graph (PR #29).
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* `convert/from_spaceranger_to_h5mu`: Added converter component for convert Spaceranger output to H5MU files (PR #33).
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* `workflows/ingestion/spaceranger_mapping`: Added a workflow to ingest Visium data using Spaceranger and convert the count matrix to an H5MU file (PR #33).
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## MINOR CHANGES
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* Add `scope` to component and workflow configurations (PR #22).
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* `convert/from_xenium_to_spatialexperiment`: Add arrow with zstd codec support to handle I/O of zstd-compressed Xenium parquet files (PR #30).
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* `mapping/spaceranger_count`: Allow providing individual FASTQ files instead of directories (PR #32).
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* Bump anndata to 0.12.7 and mudata to 0.3.2 (PR #34).
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* Bump spatialdata to 0.6.1 and spatialdata-io to 0.5.1 (PR #24, #34).
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* Bump squidpy to 1.7.0 (PR #36).
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* Update openpipeline dependencies to v4.0.0 (PR #37).
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## BUG FIXES
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* `convert/from_cosmx_to_h5mu`: Fixed an issue where parent directories of the cosmx output bundle were duplicated when reading in data (PR #25).
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* `mapping/spaceranger_count`: Fixed issue with long temporary folder paths causing write failures (PR #31).
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# openpipeline_spatial 0.1.1
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## MINOR CHANGES
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* Add a README (PR #21).
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## NEW FUNCTIONALITY
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* `convert`: Updated multiple components to accept spatial output bundles in .zip format (for CosMx, Xenium and Aviti) as input (PR #19, PR #20).
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* `convert/from_cosmx_to_h5mu`: Updated component to handle CosMx output bundles generated with AtoMx SIP versions < v1.3.2 (PR #25).
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# openpipeline_spatial 0.1.0
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## NEW FUNCTIONALITY
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* `filter/subset_cosmx`: Added a component to subset COSMX data (PR #3, PR #9).
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* `convert/from_cosmx_to_h5mu`: Added converter component for COSMX data (PR #3, PR #9).
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* `mapping/spaceranger_count`: Added a spaceranger count component (PR #2).
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* `convert/from_spatialdata_to_h5mu`, `convert/from_xenium_to_spatialdata`, `convert/from_xenium_to_h5mu`: Added converter components for xenium data (PR #1, #10).
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* `convert/from_xenium_to_spatialexperiment`, `convert/from_cosmx_to_spatialexperiment`: Added converter components for Xenium or CosMx data to SpatialExperiment objects (PR #9).
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* `convert/from_cells2stats_to_h5mu`: Added a component to convert data resulting from Aviti Teton sequencers processed by Cells2Stats into an H5MU file (PR #15).
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* `workflows/qc/qc`: Added a pipeline for calculating qc metrics of spatial omics samples (PR #5).
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* `workflows/multiomics/spatial_process_samples`: Added a pipeline to pre-process multiple spatial omics samples (PR #7).
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* `convert/from_h5mu_to_spatialexperiment`: Added converter component for H5MU data to SpatialExperiment objects (PR #15).
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