v1.1.0

[dbdimitrov]

1.1.0 (12.04.2024)

• Added a check for the subset of cell types in li.multi.dea_to_lr. Related to Add a check that for the subset of cell types in li.multi.dea_to_lr #92.

• Split Local and Global Bivariate metrics. Specifically, I reworked completely the underlying code, though the API should remain relatively unchanged. With the exceptions of: 1) lr_bivar is now removed and bivar has been renamed to bivariate. This allowed me to remove a lot of redundancies between the two functions. 2) nz_threshold has been renamed to nz_prop for consistency with expr_prop in the remainder of the package. Related to Split global from local scores #44.

• li.mt.bivariate parameter mod_added has been renamed to key_added due to this now refer to both .obsm and .mod - depedening whether an AnnData or MuData object is passed.

• Added Global Lee's statistic, along with a note on weighted product that upon z-scaling it is equivalent to Lee's local statistic.

• The Global L statistic and Global Moran's R are themselves basically identical. See Eq.22 from Lee and Eq.1 in Supps of SpatialDM.

• Changed the li.mt.bivar parameter function_name to local_name for consistency and to avoid ambiguity with the newly-added global_name parameter.

• Added bumpversion to manage versioning. Related to Add bumpversion + metadata #73.

• Added max_runs and stable_runs parameters to enable the inference of robust causal networks with CORNETO. Related to Generate Union of Causal Net Predictions #82.

• Optimized MISTy such that the matrix multiplication by weights is done only once, rather than for each target. Users can now obtain the weighted matrix via the misty.get_weighted_matrix function.

• MISTy models are now passed externally, rather than being hardcoded. This allows for more flexibility in the models used. As an example, I also added a RobustLinearModel from statsmodels. Related to External + GPU-enabled MISTy models #74.

• Removed forced conversion to sparse csr_matrix matrices in MISTy. Related to By default do not convert views to csr_matrix when building MistyData. #57.