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…landing page, as designed by the UI V2 group
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
…ctory Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Embedding plots (tSNE/UMAP/PCA) get the full 12 columns; other displays use the widest width used by at least 25% of their placements in saved collections. Tiles are packed into rows by width. Debug logging is left commented out. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
… existing bioregistry.io ones (issue #394)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
… and update HTML documentation for required files
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Mainly merging now to introduce identifiers.org support
This pull request introduces several improvements and refactorings to the spatial data upload handlers, enhances error reporting for missing files, and adds a new utility for determining display widths in auto-arranged layouts. It also updates documentation to use modern systemctl commands. The most important changes are grouped below.
Spatial Data Handler Improvements and Validation:
_raise_if_missing_inputsinlib/gear/spatialhandler.pyto check for required files after tarball extraction, providing clear error messages listing all missing user-facing files for each platform. This improves user feedback and reduces confusion about required file naming and placement.CosMxHandler,CurioHandler,VisiumHandler,VisiumHDHandler,XeniumHandler) to use_raise_if_missing_inputsfor validating required input files, replacing ad hoc file existence checks and improving consistency and clarity of error messages. [1] [2] [3] [4] [5]Auto Layout Display Width Utility:
get_auto_layout_widthtolib/geardb.py, which determines the optimal grid width for a display in an auto-arranged layout using a set of rules (embedding plots get full width, otherwise the most common wide usage is preferred), improving the automatic layout experience for users.get_auto_layout_widthintests/python/helpers/fake_geardb.pyto support testing. [1] [2]Documentation Updates:
docs/developer/setup/apache.mdto usesystemctlinstead of the deprecatedservicecommand, aligning instructions with modern best practices. [1] [2] [3] [4]Minor Codebase Improvements:
lib/gear/spatialhandler.py(e.g., addedglobandVisiumKeysimports, removed unnecessary exception checks). [1] [2] [3]These changes collectively improve user experience, maintainability, and error reporting for spatial data uploads and display layout management.