TACCO 0.4.0 (2024-07-16)¶

Fixes¶

Adapted to work with anndata>=0.9.0 and pandas>=2.0.0. This involves changes in the handling of dtypes and (floating point) precision, which leads to “small” numerical changes in the results.
Stronger preservation of input dtype in tacco.utils.split_beads() with downstream effects on tacco.tools.split_observations() and tacco.preprocessing.normalize_platform().
tacco.tools.enrichments(), tacco.tools.get_contributions(), tacco.tools.get_compositions(): Always work with float64 to avoid rounding errors as far as possible.

tacco.tools.annotate(): Report clear error message for using bisectioning with integer data
tacco.utils.row_scale(),:func:tacco.utils.col_scale: Report clear error message for rescaling integer data inplace with floating rescaling factors
tacco.tools.enrichments(), tacco.tools.get_contributions(): Deprecate on-the-fly sample split in favour of explicit use of tacco.utils.split_spatial_samples().
Handeled pandas FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
Handeled anndata FutureWarning: The dtype argument is deprecated and will be removed in late 2024. Requires anndata>=0.9.0
Handeled anndata FutureWarning: Use anndata.concat instead of AnnData.concatenate, AnnData.concatenate is deprecated and will be removed in the future. See the tutorial for concat at: https://anndata.readthedocs.io/en/latest/concatenation.html
Handeled sklearn FutureWarning: The default value of `dual will change from True to ‘auto’ in 1.5. Set the value of dual explicitly to suppress the warning.`