Ausbeth upgrade

[Ausbeth]

About shpc upgrade software

If software is not installed yet: ask user to "install" it (achieved)
Else, follow this logic: (achieved)

For each version already installed:
If version == latest:
currently just skip, in the future check the checksum of the container
Else:
ask the user about uninstalling it
If latest version was not installed yet:
install the latest

Also needs:

--all option to do the above for all software (achieved)
--dry-run option to show which versions would be uninstalled and installed (achieved as "--preview")

Note - The following are considered to be invalid syntax:

  shpc upgrade software:version
  shpc upgrade software --all
  shpc upgrade software --preview
  shpc upgrade software --all --preview
  shpc upgrade --all --preview      

[gq1]

$ shpc upgrade
Incomplete command.
For upgrade help description, please use shpc upgrade --help or shpc upgrade -h.

Can you do similar things like shpc install to give the usage and error message?

$ shpc install
usage: shpc install [-h] [--keep-path] [--no-view] [--force] [--module-sys {lmod,tcl}]
                    [--container-tech {singularity,podman,docker}]
                    install_recipe [container_image]
shpc install: error: the following arguments are required: install_recipe

When the installed list is empty, still no usage being printed and with a different error message, can you make it consistent?

$ shpc upgrade
Cannot perform shpc upgrade because you currently do not have any software installed.

[muffato]

Hi @Ausbeth . I think that's almost the end for me ! Everything's getting there

[Ausbeth]

Hi @Ausbeth . I think that's almost the end for me ! Everything's getting there

Hi @muffato , thanks a lot for your review and contributions! I have committed the changes you suggested.

[muffato]

All good for me 👏🏼
(please wait for @gq1's approval before merging)

[gq1]

If you have conda installed, you can follow these steps to fix the format problem in your local:

singularity-hpc/.github/workflows/main.yml

Lines 27 to 29 in 52a80f8

	source activate black
	pip install -r .github/dev-requirements.txt
	pre-commit run --all-files

If not, all the fixes and errors reported here:
https://github.com/sanger-tol/singularity-hpc/actions/runs/11050810144/job/30699369537

[gq1]

More format to fix: https://github.com/sanger-tol/singularity-hpc/actions/runs/11053323799/job/30707425335?pr=3

[Ausbeth]

More format to fix: https://github.com/sanger-tol/singularity-hpc/actions/runs/11053323799/job/30707425335?pr=3

Hi @gq1 , upon fixing this issue, the following files were modified by black:

and pyproject.toml had to be modified by me to make black work

[Ausbeth]

Hmmm, its still failing on the GitHub repo but working locally

[gq1]

Make sure the all Github CI jobs pass.

[gq1]

Can you squash merge? And then make a PR to the upstream.