CI only works with one step

[redur]

Currently the CI fails when we execute code over multiple steps in a given job. The reason seems to be related with the conda environment. I am not 100% sure what's the problem, but the conda environment doesnt seem to be properly passed to the next step.

The error states to do conda init before conda activate .... But even if we do so, it doesnt work. Also sourcing the bashprofile and bashrc does not help.

For now all the CI jobs work fine. But if we are to use more CI's, or move towards production, it would be great to refactor and define a setup job/step that can be reused across jobs/runners.