Update Scanpy to v1.11.5 and add support for interactive vitessce plots #7588
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pavanvidem
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nilchia
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Jan 19, 2026
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nilchia
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nilchia
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Thanks Pavan! Looks really cool
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| <requirement type="package" version="0.10.3">anndata</requirement> | ||
| <requirement type="package" version="1.26.4">numpy</requirement> | ||
| <requirement type="package" version="2.2.2">pandas</requirement> | ||
| <requirement type="package" version="1.14.1">scipy</requirement> | ||
| <requirement type="package" version="0.14.2">statsmodels</requirement> | ||
| <requirement type="package" version="0.3.5">fa2</requirement> |
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Are these not required anymore?
| </token> | ||
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| <xml name="param_interactive_plot"> | ||
| <param name="interactive_plot" type="boolean" checked="false" label="Make an interactive plot?" help="Creates an vitessce configuration file using easy_vitessce for interactive visualization"/> |
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Suggested change
| <param name="interactive_plot" type="boolean" checked="false" label="Make an interactive plot?" help="Creates an vitessce configuration file using easy_vitessce for interactive visualization"/> | |
| <param name="interactive_plot" type="boolean" checked="false" label="Make an interactive plot?" help="Creates a vitessce configuration file using easy_vitessce for interactive visualization"/> |
| <expand macro="pl_figsize"/> | ||
| </when> | ||
| <when value="pl.pca"> | ||
| <expand macro="param_interactive_plot"/> |
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It is not included in the if logic in the command.
| <filter>advanced_common['show_log']</filter> | ||
| </data> | ||
| <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"> | ||
| <filter>advanced_common['output_anndata']</filter> |
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why not just this?
advanced_common['output_anndata']
| <data name="vitessce_config" format="vitessce.json" from_work_dir="config.json" label="${tool.name} (${method.method}) on ${on_string}: Vitessce interactive visualization"> | ||
| <filter>method['method'] in ['pl.umap', 'pl.tsne', 'pl.diffmap', 'pl.violin', 'pl.dotplot', 'pl.heatmap'] and method['interactive_plot']</filter> | ||
| </data> | ||
| <data name="anndata_config" format="json" from_work_dir="anndata.ref.json" label="${tool.name} (${method.method}) on ${on_string}: Anndata configuration"> |
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is this defined in the script? anndata.ref.json
or automatically generated by the tool?
bgruening
reviewed
Jan 19, 2026
| anndata_out_id = "${__app__.security.encode_id($anndata_out.id)}" | ||
| anndata_config_id = "${__app__.security.encode_id($anndata_config.id)}" | ||
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| config_dict = widget.config.to_dict(base_url="") |
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what can we do with base_url?
Is that helping here: https://python-docs.vitessce.io/notebooks/widget_brain_with_base_dir.html?highlight=base_url_placeholder
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changes in the releases after 1.10.2:
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FOR CONTRIBUTOR: