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CHANGELOG.md

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Releases

[latest]

added

fixed

  • fixed calls to new imports matplotlib
  • fixed scanpy/muon latest
  • changed default adversarial_training = False to ensure multivi runs with scvi-tools 1.1.3 scverse/scvi-tools#2581
  • updated integration01 action to use updated scvi-tools version

dependencies

  • matplotlib 3.9.0

v1.0.0

added

  • added documentation on ingesting custom h5ad/h5mu objects

fixed

dependencies

  • pinned matplotlib 3.8 as temporary fix next release will unpin and fix get_cmap (API) and legendHandles (API)

v0.5.0

added

fixed

  • fixed error in vis
    • error occurred when only wanting to plot continuous or categorical variables (or neither), not both
  • fixed error in refmap
    • high threads was not recognised, now fixed.

dependencies

  • All the dependencies have been updated.
    • Python>=3.10 required
  • added seeds to all scvi tasks for reproducibility

v0.4.1

added

  • added example multiome submission file 10X_h5
  • added example multiome submission file cellranger
  • workflows & tutorials for qc_spatial, preprocess_spatial, and deconvolution_spatial to readthedocs
  • tutorial for vis
  • added PCA parameters in pipeline_preprocess.py for PROT modality to fix issue #120
  • added full control of dimred params for all modalities in pipeline_preprocess.py
  • more info on custom genes format files added to documentation
  • parsing summary files for cellranger multi version < 7
  • added checks for n_pcs in run_neighbors_method_choice
  • added filtering by HVF for atac

fixed

  • changed typo in tutorial paths for clustering and deconvolution
  • fix io to read cellranger outs folder for atac.
  • fixes to refmap workflow
  • typos & capitalization in the pipeline.yml files of qc_spatial, preprocess_spatial, and deconvolution_spatial, vis
  • remove assay, sample_prefix, and modalities parameters from the qc_spatial pipeline.yml
  • remove sample_prefix and modalities parameters from the preprocess_spatial pipeline.yml
  • fixed error in preprocess_spatial when filtering: run: False -> now able to run no filtering without needing to save the MuData in filtered.data before running the pipeline
  • fixed error in vis
    • change PARAMS['custom_markers_minimal'] -> PARAMS['custom_markers']['files']['minimal']
  • fix to avoid rerunning HVF and explicitly check X layer before normalization in pipeline_preprocess.py
  • fix plotting of umaps after batch correction
  • fix fetching string scvi if present in mudata for wnn
  • fixed lsi requirement for atac
  • fixed top features for atac
  • fixed filtering HVG for rna
  • moved pynndescent to PyPi dependencies

dependencies

v0.4.0

Big Change! the submission files for the ingest workflow have now changed! we require the paths to the Gene expression (RNA/GEX) and Protein (ADT) to have the following headers.

sample_id rna_path rna_filetype prot_path prot_filetype
sampleX path/to/rna 10X_h5 path/to/prot 10x_h5

See tutorials for examples of submission files.

added

  • merged PR #111:
    • LSI in panpipes_preprocess is run on the highly variable features
    • n_comp for LSI

fixed

  • changed all instances of ADT into PROT
  • changed all instances of GEX to RNA
  • changed the params to fix plotting as mentioned in issue #41
  • typo in readme
  • set default seaborn <=0.12.2 to avoid issue #104, #126

v0.3.1

  • set default matplotlib<=3.7.3 to avoid issue #104.

v0.3.0

added

  • Spatial data analysis is now included in panpipes
    • panpipes qc_spatial
    • panpipes preprocess_spatial
    • panpipes_deconvolution_spatial

fixed

  • make sure columns from individual modalities that are not in the multimodal outer obs can be used to

dependencies

  • additional dependencies: squidpy, cell2location, openpyxl

v0.2.0

  • First public version of panpipes
  • contains qc_mm, preprocess, intergration, clustering