Can't install modules when `version_naming` is set

[muffato]

Describe the bug

Sorry I couldn't chime in during #679, I got sick. I'm now trying to test the feature but can't make it work.

The problem I'm facing is that <module_base>/<container_path>/<version> is meant to be a directory under which shpc creates the bin directory with all the wrapper scripts.
With version_naming set to true, shpc now also assumes with path to be a file to write the content of the TCL module, hence a clash. cc @Amjadhpc

To Reproduce

With the default settings (version_naming set to false):

$ rm -r modules
$ shpc config get version_naming
False
$ shpc install python:3.9.2-alpine
Module python:3.9.2-alpine was created.

With the option turned on

$ shpc config set version_naming True
Updated version_naming to be True
$ shpc config get version_naming
True
$ rm -r modules
$ shpc install python:3.9.2-alpine
Traceback (most recent call last):
  File "/software/treeoflife/conda/users/envs/team328/mm49/shpc/bin/shpc", line 8, in <module>
    sys.exit(run_shpc())
             ^^^^^^^^^^
  File "/nfs/users/nfs_m/mm49/workspace/tol-it/central_software/singularity-hpc/shpc/client/__init__.py", line 556, in run_shpc
    main(args=args, parser=parser, extra=extra, subparser=helper)
  File "/nfs/users/nfs_m/mm49/workspace/tol-it/central_software/singularity-hpc/shpc/client/install.py", line 27, in main
    cli.install(
  File "/nfs/users/nfs_m/mm49/workspace/tol-it/central_software/singularity-hpc/shpc/main/modules/base.py", line 485, in install
    self.container.install(module_path, template, module, kwargs.get("features"))
  File "/nfs/users/nfs_m/mm49/workspace/tol-it/central_software/singularity-hpc/shpc/main/container/singularity.py", line 233, in install
    utils.write_file(module_path, out)
  File "/nfs/users/nfs_m/mm49/workspace/tol-it/central_software/singularity-hpc/shpc/utils/fileio.py", line 176, in write_file
    with open(filename, mode) as filey:
         ^^^^^^^^^^^^^^^^^^^^
IsADirectoryError: [Errno 21] Is a directory: '/nfs/users/nfs_m/mm49/workspace/tol-it/central_software/singularity-hpc/modules/python/3.9.2-alpine'

Expected behavior

I believe shpc install python:3.9.2-alpine should succeed out of the box, especially as I didn't see any indication the new option could only be used in certain conditions.

Also, I wonder how it works in the test case: https://github.com/singularityhub/singularity-hpc/pull/679/files#diff-9ef112d1d82a448d99f2cf48d7718defdde5618f6657ab2a99e6f6f5d7941729 . Am I doing anything different ?

Version of Singularity and Singularity Registry HPC Client

$ git show
commit 0848c8747042240f36f99cfa886a13724443578f (HEAD -> main, tag: 0.1.31, origin/main, origin/HEAD)
Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Date:   Sat Jan 11 13:59:13 2025 -0700

    Automated deployment to update contributors 2025-01-11 (#684)
    
    Co-authored-by: github-actions <github-actions@users.noreply.github.com>

$ git diff
diff --git a/shpc/settings.yml b/shpc/settings.yml
index ed80a5715..4f68cbf56 100644
--- a/shpc/settings.yml
+++ b/shpc/settings.yml
@@ -5,7 +5,7 @@
 # set a default module system
 # Currently lmod and tcl are supported. To request an additional system,
 # please open an issue https://github.com/singularityhub/singularity-hpc
-module_sys: lmod
+module_sys: tcl
 
 # config editor
 config_editor: vim

[vsoch]

I'll revert until this is addressed: #686

[Amjadhpc]

@muffato , correct me if i am wrong, you are just deleting the modules file with
rm -r modules ?
Can you please use shpc uninstall instead of rm ?

shpc uninstall python:3.9.2-alpine
python:3.9.2-alpine? (yes/no)? yes
$container_base/python:3.9.2-alpine and all subdirectories have been removed.
$module_base/python:3.9.2-alpine and all subdirectories have been removed.
$wrapper_base/python:3.9.2-alpine and all subdirectories have been removed.
singularity-hpc]# shpc config set version_naming True
Updated version_naming to be True
singularity-hpc]# shpc install python:3.9.2-alpine
singularity-hpc]#Module python:3.9.2-alpine was created.

[muffato]

Same error when doing shpc uninstall because all the files involved were in modules/ and shpc uninstall merely does a rm -r under the hood. But that made me understand the difference and the problem better !

In default settings, module_base == wrapper_base == $root_dir/modules. That's essentially what's causing my bug.
If I set wrapper_base to a different location, then the wrapper script directory doesn't clash anymore with the module directory. In other words, version_naming requires wrapper_base to be set to a different path from module_base.