Julianus Pfeuffer

More signature error on macOS

6

From GitHub discussions: Thank you for the quick response! I ended up being able to convert it with ProteoWizard to mzML. I'm trying to get `FileInfo` to work anyway, just...

Move to Cython3 or activate binding=True for pyOpenMS

9

To have better introspection. https://cython.readthedocs.io/en/latest/src/userguide/migrating_to_cy30.html

Weird build names for pyopenms on CDash

4

This causes the links generated and presented at the end of a GHA run to be wrong/ambiguous (I ended up on a Win build when clicking on the link presented...

Download pipelines with authenticated GH API calls

3

For repos that follow the nf-core template but need authentication. ## PR checklist - [x] This comment contains a description of changes (with reason) - [ ] `CHANGELOG.md` is updated...

recipe linter does not support valid conda-build jinja functions!

1

And not even the existing ones are registered correctly. Pin_compatible also has a upper and lower bound argument. This is a huge blocker for our recipe: https://github.com/bioconda/bioconda-utils/blob/961c43bfcc55393a6c0122fbf5d5b4dd5041e7f7/bioconda_utils/recipe.py#L138-L143 https://docs.conda.io/projects/conda-build/en/stable/resources/define-metadata.html#conda-build-specific-jinja2-functions

I think this project needs a relatively urgent update of dependencies and actions. At least pyo3 needs to be updated to get rid of the linting errors. Unfortunately, pyo3 updates...

We can already plan ahead for the 2026 roadmap - workflow outputs - strict syntax - topics for modules https://nf-co.re/blog/2025/retreat-2025#adopting-new-nextflow-syntax

- MSStats+ - MSStatsBig

Remove (c)bgen dependency for unpack_variables?

5

Hi! Thanks for creating sgkit. Very useful package. We are using it for performing calculations on a dataset that was converted from bgen. For reading, our code uses something like...

### Checklist - [x] I added a descriptive title - [x] I searched open reports and couldn't find a duplicate ### What happened? My meta.yaml: ```yaml {% set name =...