Giant squashed commit #237
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Fixed a bug in report generated by a previous change in saving
It seems the inclusion of 'css_files' in the build context is over-writing the default CSS stylesheets that are supposed to be there. I don't know if this is a readthedocs bug, but it used to work...
Everything seems to be working on a simulated dataset
* gaussian_kde peak to find empty drop prior, rather than mode with heuristics
* Improve cell prob plot and remove features not analyzed This was very confusing and led to what looked like a horrible bug: disagreement between the HTML report plot and the PDF plot. But it's because the report was plotting all features, not just features analyzed. The report now also plots features analyzed * Refactor sparse utils and eliminate duplication * Add multiprocessing MCKP estimation as command line option On Mac laptop this is not faster in small tests
…ilities (#202) * Implement soft constraints on cell probs
Because sometimes there are memory issues, apparently
* Mean and MAP estimator potential speedup * Save posterior as HDF5 rather than NPZ * Fix intermittent cellbender checkpoint test failure issue * Change default low_count_threshold to 5 * Attempt to preclude intermittent google workflow errors in WDL
and prevent writing the file twice
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Bringing everything up to v0.3.0