When using setup-micromamba and micromamba, then the Install MDAnalysis version step of a typical MDAKit workflow fails. The first indication is that the Uninstall pre-existing versions step does not find the conda executable (eg https://github.com/MDAnalysis/PathSimAnalysis/actions/runs/29975869290/job/89107396571?pr=31 from MDAnalysis/PathSimAnalysis#31 ):
/Users/runner/work/_temp/8e80427b-4f65-4028-aed2-026b3dc094e0.sh: line 6: conda: command not found
/Users/runner/work/_temp/8e80427b-4f65-4028-aed2-026b3dc094e0.sh: line 7: conda: command not found
Thus, the conda package is not properly uninstalled with micromamba uninstall. Instead we use pip and that leaves something behind that prevents the next step (Install with conda from actually installing the desired MDAnalysis version:
All requested packages already installed
The Get final version step fails silently with
Run pyver=$(python -c 'import MDAnalysis; print(MDAnalysis.__version__)')
Traceback (most recent call last):
File "<string>", line 1, in <module>
import MDAnalysis; print(MDAnalysis.__version__)
^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'MDAnalysis'
We should not hard-code conda for the removal step but use the selected package manager.
When using setup-micromamba and
micromamba, then the Install MDAnalysis version step of a typical MDAKit workflow fails. The first indication is that the Uninstall pre-existing versions step does not find thecondaexecutable (eg https://github.com/MDAnalysis/PathSimAnalysis/actions/runs/29975869290/job/89107396571?pr=31 from MDAnalysis/PathSimAnalysis#31 ):Thus, the conda package is not properly uninstalled with
micromamba uninstall. Instead we usepipand that leaves something behind that prevents the next step (Install with conda from actually installing the desired MDAnalysis version:The Get final version step fails silently with
We should not hard-code
condafor the removal step but use the selected package manager.