Robrecht Cannoodt

Update: nevermind, not even the current version is returning this info (https://github.com/dynverse/ti_slingshot/blob/master/package/R/ti_slingshot.R#L193). I'll fix this asap. However, please note that this only affects the `plot_dimred` visualisation ; other downstream analyses...

## Review checklist for @rcannood ### Conflict of interest - [x] I confirm that I have read the [JOSS conflict of interest (COI) policy](https://github.com/openjournals/joss/blob/master/COI.md) and that: I have no COIs...

I made my suggestions in https://github.com/scverse/anndata/issues/769, waiting for the authors to get back to us.

Update: this PR works on [ubuntu-latest](https://github.com/rcannood/zellkonverter/actions/runs/3282938619/jobs/5407035435) but not on : * [windows-latest](https://github.com/rcannood/zellkonverter/actions/runs/3282938619/jobs/5407035641)): Same error as #45 and others; Error log ``` ═══════════════════════════════════════════════════════════════ ── Error ('test-read.R:111'): Conversion of raw works ──────────────────────────...

Sorry that I was away the past few days, there were a few important deadlines and I lost track of my mails. Thanks for making the necessary changes to get...

I see! This is indeed a problem :) The issue is that reticulate has a set of `py_to_r` and `r_to_py` converters. Since `anndata` the R package adds (amongst others) `py_to_r.anndata._core.anndata.AnnData`,...

3. A clean but tedious solution would be to use `anndata

Hmm... Simply converting an AnnDataR6 to a `anndata._core.anndata.AnnData` (as in https://github.com/theislab/zellkonverter/compare/master...rcannood:zellkonverter:fix/compat_anndatar6?expand=1 ) doesn't work straight out of the box because anndata (the R package) also adds converters for other Python...

I see! I agree option 3 would be a lot cleaner. One think I'm wondering about is whether to set `convert` to `TRUE` or `FALSE` in `SCE2AnnData` since that object...

Agh! Setting `convert = TRUE` in `SCE2AnnData(...)` breaks the symmetry with `AnnData2SCE(...)`. That is, running `AnnData2SCE(SCE2AnnData(...))` doesn't work. Perhaps it makes more sense to add `convert` as a parameter to...