List view organization

[vsoch]

Feedback:

• Comment: the output of list is currently organised by tool, and then for each of these a comma-list of versions is given; I was wondering about an alternative output format that is easier to copy-paste or parse for use, e.g. listing one tool/version identifier per line

Yes this is a great idea! Could you provide an example here to get me started?

[marcodelapierre]

Sure, let me explain.

Here is an example of production use, with a few container modules installed:

$ shpc list
quay.io/biocontainers/bbmap: 38.90--he522d1c_1
marco/zio: v21
biocontainers/fastqc: v0.11.9_cv8, v0.11.5
biocontainers/samtools: v1.9-4-deb_cv1

Now, suppose I want to interact with one of these modules using the shpc commands. It can be any sub-command, let's take shpc inspect as an example.

Now, I am a lazy person and want to copy-paste the identifier of an installed module from the list above.
Right now I have to do it in two chunks, 1st copy-paste the module name, and 2nd copy-paste the version, because:

1. there's always a space after the colon
2. when there are multiple versions of a module, they're listed in a comma-separated way

Then, for this lazy copy-paste habit, I would find this output handier:

$ shpc list
quay.io/biocontainers/bbmap:38.90--he522d1c_1
marco/zio:v21
biocontainers/fastqc:v0.11.9_cv8
biocontainers/fastqc:v0.11.5
biocontainers/samtools:v1.9-4-deb_cv1

One disadvantage is that the list gets longer because you have one entry per version, rather than per tool.
Not sure whether this is a legitimate official use for the command, though :-D

Looking at the other open issues, one way to work around this would be enabling the autocompletion feature, so that one can tab-complete installed module identifiers (#363 ).

[vsoch]

okay, here is an easier to read, and easier to copy paste solution! The default now shows all the containers and tags, one per line:

$ shpc list
        biocontainers/samtools:v1.9-4-deb_cv1
                        python:3.9.5-alpine
                        python:3.9.2-slim
                        python:3.9.2-alpine
                      dinosaur:fork
                 vanessa/salad:latest
                         salad:latest
      ghcr.io/autamus/prodigal:latest
      ghcr.io/autamus/samtools:latest
        ghcr.io/autamus/clingo:5.5.0

I added the left padding so the ":" would line up in the middle to make it easier to compare. If the user adds --short, then the original listing is shown:

$ shpc list --short
        biocontainers/samtools: v1.9-4-deb_cv1
                        python: 3.9.2-slim, 3.9.5-alpine, 3.9.2-alpine
                      dinosaur: fork
                 vanessa/salad: latest
                         salad: latest
      ghcr.io/autamus/prodigal: latest
      ghcr.io/autamus/samtools: latest
        ghcr.io/autamus/clingo: 5.5.0

That's probably the best of both worlds. This is also added to #367. And just in case it's not known, LMOD at least does support tab completion once you start typing the name!

[marcodelapierre]

Looks great! thanks for thinking of the --short option, too