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Error https://github.com/Novartis/cellxgene-gateway/runs/5547618966?check_suite_focus=true
The issue is that jinja2-2.11.3 calls soft_unicode in markupsafe, but "soft_unicode" was removed in latest m…
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## Need
This library will be use by several different project, using different version of python. The old version used is 3.8 which is used by the cellxgene-schema-cli and the portal processing cod…
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**Describe the bug**
When I ingest multiple `h5ad` files with `tiledbsoma.io.from_h5ad` using a `registration_mapping` (generated with `tiledbsoma.io.register_h5ads`), the `from_h5ad` function didn…
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## Motivation
One of the parameters we use to gate keep datasets from the cellxgene data corpus is the size of the file on disk. At the time of writing this, the max size supported was 50GB. It was a…
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Lots of warnings from `py-build.yml`:
```
[Build Python wheel and sdist](https://github.com/chanzuckerberg/cellxgene-census/actions/runs/7820976112/job/21413441596)
Node.js 16 actions are depreca…
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Dear all,
I am trying to adapt scDist to use it with miloDE (https://www.biorxiv.org/content/10.1101/2023.03.08.531744v1).
MiloDE builds on miloR assigning cells to neighborhoods, and proceeds to …
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Investigate whether we can mine CxG Census to find all CL terms in use on CxG. If yes, build GA pipeline to mine CxG for a CL term list + ROBOT pipeline to tage CL terms with subset tag: cellxgene_su…
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Hi,
I am running the gateway with cellxgene==1.0.0 on an AWS EC2 instance using docker. If I open the .h5ad files on S3 storage, the annotation and gene-set files are created but they aren't filled…
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I have installed a conda env with mofapy.
```
> reticulate::py_config()
python: /home/roy/miniconda3/envs/mofa/bin/python
libpython: /home/roy/miniconda3/envs/mofa/lib/libpython3.10…
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Right now, if we're running the schema migration SFN in dev, and a deploy to dev occurs, we'll switch to using the newly deployed version of dev. This was a problem for the initial dev SFN run because…