Lukas Heumos

@Imipenem could it be that you're reading old h5ad files here and these trigger the AnnData warnings?

Also ```tests/anndata/test_anndata_ext.py::TestAnndataExt::test_move_to_x tests/anndata/test_anndata_ext.py::TestAnndataExt::test_move_to_x_move_to_obs tests/anndata/test_anndata_ext.py::TestAnndataExt::test_move_to_x_move_to_obs /home/zeth/miniconda3/envs/ehrapy/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. warnings.warn( ``` must be resolved. Edit: I did this.

I got rid of quite many of them. Let's have another pass in the future.

I've added a section in the troubleshooting docs: https://ewels.github.io/MegaQC/docs/troubleshooting.html#installation-setup I've encountered the same issue back when I was setting it up for the first time and can confirm that this...

Before suggesting anything I have a couple of questions: Could you please check whether you have a postgres DB called `megaqc`? > Error - MultiQC megaqc_url not set Do you...

Article that explains email confirmation with Flask really well https://realpython.com/handling-email-confirmation-in-flask/

@ewels it helps if we (like nf-core) don't hard pin every requirement, but only the most important. However, users may then run into issues which we did not expect, because...

https://github.com/ewels/MegaQC/pull/157 solved most of these. But e.g. superagent is still 3.5.2 and therefore < 3.7.0

So I cannot pin superagent in `package-lock.json` . Whenever I run `npm install` it just overwrites everything again. https://github.com/holidayextras/jsonapi-client the jsonapi-client library is not maintained anymore. @TMiguelT is there like...

@TMiguelT The distributions page is this one: https://github.com/ewels/MegaQC/blob/master/megaqc/templates/public/distributions.html Which one do you mean with report page? https://github.com/ewels/MegaQC/blob/master/megaqc/templates/public/report_plot.html https://github.com/ewels/MegaQC/blob/master/megaqc/templates/public/reports_management.html Both?