CWL: demonstrate use of conda suggestions

[mr-c]

Allows each step to use a different conda environment and the selection
of conda packages that are not co-installable.

I can also send a PR to replace prepare_paper_macros.cwl with an inline file creation as part of compile_paper.cwl, if desired

[joergfunger]

Thanks a lot for the comments. Could you adapt the github actions such that the different conda environments are directly tested. In particular for paraview, there might be some modifications required.

[mr-c]

FYI, for best results, perhaps there should be materials testing & research version of biocontainers.org ; a service that automatically creates software containers based upon (bio)conda packages (and other sources). Everything is open source and I'd be happy to introduce you all to the team

[dglaeser]

FYI, for best results, perhaps there should be materials testing & research version of biocontainers.org ; a service that automatically creates software containers based upon (bio)conda packages (and other sources). Everything is open source and I'd be happy to introduce you all to the team

@mr-c, so you mean instead of using the conda actions in the CI, we may use that service to automatically let them create and host images for us (and use these in the CI)? This sounds interesting!

[mr-c]

@dglaeser My guess is that there is something in the GitHub Actions environment for Ubuntu causing problems;

A colleague suggested using https://github.com/mxschmitt/action-tmate to debug the situation by enabling SSHing into the runner itself.

just make sure to also secure it if you don't want people watching you 😉
(limit-acces-to-actor)

It will be a bit tricky, as there isn't much debugging output for using --beta-conda-dependencies

[dglaeser]

@joergfunger, the actions work now. I am ok with the PR, but there are two open threads that were raised by you. Would you mind double-checking them? !