Dave Bunten

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icon company University of Colorado Anschutz Medical Campus icon location Denver, CO icon location Research Software Engineer with the Department of Biomedical Informatics at the University of Colorado Anschutz Medical Campus

Results 95 comments of Dave Bunten

`SingleCells` parameter `sqlite_file` string results in AttributeError: 'Connection' object has no attribute 'cursor' with updated Pandas versions

Confirming this is still not working with later revisions of Pandas (specifically just tested Pandas 2.2.3). It may be worth exploring this solution within Pycytominer to gain compatibility https://stackoverflow.com/a/38333100 .

`SingleCells` parameter `sqlite_file` string results in AttributeError: 'Connection' object has no attribute 'cursor' with updated Pandas versions

I believe this is now resolved (was able to run tests with Pandas 2.2.3 today).

Add new check for ambiguous`LIMIT` or `OFFSET` without `ORDER BY` (non-deterministic results)

Hi @WittierDinosaur - thanks for the outreach and help here! I've just removed the `lcov` file (apologies about this - it was added by accident when troubleshooting the coverage messages...

Add new check for ambiguous`LIMIT` or `OFFSET` without `ORDER BY` (non-deterministic results)

Thanks @WittierDinosaur for the review on this! I wanted to double check just in case: it looks like this is planned to be merged at some point via auto-merge. Do...

Add new check for ambiguous`LIMIT` or `OFFSET` without `ORDER BY` (non-deterministic results)

Thanks @WittierDinosaur and no worries! I've made a change in an attempt to cover the 1 line.

FeatureRequest: Automated identification and removal of non-biologically variant features

Thank you @hwarden162 for opening this issue and for the description of the enhancement! Looking into this further, it seems like this capability might relate to a parameter called `blocklist_file`...

FeatureRequest: Automated identification and removal of non-biologically variant features

Thanks for those additional thoughts @hwarden162 ! Based on what you mentioned it made me think about [`pycytominer.operations.variance_threshold()`](https://pycytominer.readthedocs.io/en/stable/pycytominer.operations.html#pycytominer.operations.variance_threshold.variance_threshold) (which available for use via [`pycytominer.feature_select()`](https://pycytominer.readthedocs.io/en/stable/pycytominer.html#module-pycytominer.feature_select)). I don't know that it'd meet...

hv.save() yields increasing side margins in exported png when using datashader

Thanks all for the discussion here and for the workarounds. I ended up using @cdeciampa's solution (thank you!) regarding `hv.save(center=False)` to workaround the very large widths. For my scenario I...

Adding DOI to the code base

I think adding the software DOI somewhere it can be easily found is a good idea. This would help us follow [FAIR practices](https://www.go-fair.org/fair-principles/) (making it "Findable"). The GitHub integration with...

Adding DOI to the code base

Maybe we could use "credit redirection" to help address some of this issue's discussion: https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#credit-redirection . That section of the `CITATION.cff` observes that sometimes we want to cite a different...