modules list has issues with non-standard branch/path

[awgymer]

Description of the bug

Not sure if this is intended/expected but modules list with non-standard path/branch appears to have some issues finding the correct branch/path and information.

Command used and terminal output

Given modules installed with:
"modules --git-remote <repo> --branch <br> --base-path <otherpath> install mod1"


modules --git-remote <repo> list local

WARNING  Repository '<repo>' (master) does not contain the '<otherpath>' directory         
INFO     Modules installed in '.':                                                       
                                                                                         
┏━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┓
┃ Module Name ┃ Repository     ┃ Version SHA          ┃ Message       ┃ Date          ┃
┡━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━┩
│ mod1        │ repo           │  sha                 │ Not Available │ Not Available │
└─────────────┴────────────────┴──────────────────────┴───────────────┴───────────────┘

------------------------

modules --git-remote <repo> --branch <br> --base-path <otherpath> list local 

WARNING  Repository '<repo>' (master) does not contain the '<otherpath>' directory         
INFO     Modules installed in '.':                                                       
                                                                                         
┏━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┓
┃ Module Name ┃ Repository     ┃ Version SHA          ┃ Message       ┃ Date          ┃
┡━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━┩
│ mod1        │ repo           │  sha                 │ Not Available │ Not Available │
└─────────────┴────────────────┴──────────────────────┴───────────────┴───────────────┘
 
------------------------

modules --git-remote <repo> --branch <br> list local 

CRITICAL Repository '<repo>' (<br>) does not contain the 'modules' directory

System information

nf-core/tools version 2.5.dev0
python 3.9.7
macOS

[ErikDanielsson]

The issue here is that we don't support different base-paths in different branches -- the base-path is only recorded once per remote. I not sure whether the right approach is to we should scrap the --base-path option altogether, or just make the documentation clearer.

However, this also pinpoints a bigger issue: while we allow modules to be installed from a branch, we don't record what branch they were installed from and therefore other commands fail when they are unable to find the git sha recorded in the modules.json. This should be supported however, so I'll make a PR.

[awgymer]

To be clear, I only used that base-path. I did a clean install of the modules, removing any old copies and the pre-existing modules.json

[ErikDanielsson]

So the master/main branch has the same base path? Because otherwise it will fail...

[ErikDanielsson]

I've addressed a few of the minor issues causing some of the problems with --branch in #1727

[awgymer]

So the master/main branch has the same base path? Because otherwise it will fail...

Ohhhhh, I see what you meant now. Sorry. Yeah I just made a test branch with a new name for the base-path, guess that's the issue.

[ErikDanielsson]

I think the --base-path option was added without considering all the ways it could be used, so I'll make the documentation clearer on what can and can't do, and then we'll see if it survives to the next release.

[ErikDanielsson]

Closing due to merge of #1727 and follow up issue in #1728