Alan O'Callaghan

BiocParallel doesn't propagate warnings

3

This is not ideal imo, means that warnings silently disappear. Would be fine (ish) if at least a message showed up saying we encountered some warnings ```r library(BiocParallel) fun [[1]]...

Cellnote hoverinfo

2

Make hoverinfo work with cellnote #76 Also change argument specification so that only required arguments are missing. add label_format_fun to the plotly heatmap fun

Discrepancy with Bioconductor version

1

The [methylclock paper](https://academic.oup.com/bioinformatics/article/37/12/1759/5909987?login=false) and the [bioc package page](https://bioconductor.org/packages/release/bioc/html/methylclock.html) both point to this repo, but the version of the package on Bioc is completely different to the version hosted here. Is...

Linux tar should not be nested

1

My fault for [trying to write a valid tar from memory](https://xkcd.com/1168/) but the current linux build ends up as a tar.xz that contains the build/dist/QuPath directory, rather than the top...

Switch from leiden to leidenbase

5

The Leiden implementation provided by `leiden` is absurdly slow, way more than I'd expect from the overhead of calling reticulate. This switches for the (mostly) equivalent `leidenbase`. Tests pass locally...

I get an error currently: ``` Error in py_module_import(module, convert = convert) : ModuleNotFoundError: No module named 'kaleido' Run `reticulate::py_last_error()` for details. ``` but webshot doesn't work atm and orca...

## Description Sorry if this is trivial, but when I notice them I feel obliged to report. ## Pull request recommendations: - [x] Name your pull request _your-development-type/short-description_. Ex: _feature/read-tiff-files_...

environment.yml is missing

4

``` alan@pop-os:~/Documents/github/imaging/squidpy_notebooks/ (main) $ grep -r environment.yml tutorials/tutorial_mibitof.ipynb: "`environment.yml `_." tutorials/tutorial_seqfish.ipynb: "`environment.yml `_." tutorials/tutorial_visium_hne.ipynb: "`environment.yml `_." tutorials/tutorial_visium_fluo.ipynb: "`environment.yml `_." tutorials/tutorial_slideseqv2.ipynb: "`environment.yml `_." tutorials/tutorial_imc.ipynb: "`environment.yml `_." tutorials/tutorial_fouri.ipynb: "`environment.yml `_." tutorials/tutorial_merfish.ipynb: "`environment.yml...