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nadeemlab / SPT

Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images
https://oncopathtk.org
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Library dependency updates #322

Closed jimmymathews closed 6 months ago

jimmymathews commented 6 months ago

This PR makes changes for consistency with the most recent releases of all dependency libraries. The most significant change was to the squidpy metric tests (current version 1.5.0), as it seems that the neighborhood enrichment and auto-correlation implementations have changed from 1.3.0 to 1.5.0.

All tests pass, though possibly some functionality not directly tested by the test suite is affected, like deployment scripts, uploaders or workflows on current data.

Although this was done in branch issue177, this PR does not close #177.

jimmymathews commented 6 months ago

I am also provisionally deprecating the graph-plugin-dockerized workflow test, as it takes too long at around 10 minutes. To restore it we will need to fix this (it should not take this long).

jimmymathews commented 6 months ago

Before merge the last thing to update is the re-analysis scripts. It is expected that the results related to autocorrelation and neighborhood enrichment will need to be updated.

jimmymathews commented 6 months ago

This includes a re-creation of all of those cached computations (cached during application usage) requested by the analysis scripts, and this was a successful test of the recent infrastructure configuration changes.