Updates to several container and module bases

[vsoch]

This PR include several bug fixes or updates, specially:

• Add test for docker and podman to fix shpc test fails with podman and docker #392
• various module template updates to close Minimal comments on Podman/Docker support #391
• namespace as format string for command named renamed to repository to address Rename namespace to repository  #378
• updates to comment in settings to close Notation for Lua/Tcl module languages #396
• shpc test/uninstall should be run for all tests
• bug with uninstall fixes shpc uninstall fails with docker/podman #393
• adding user and group ids to docker and podman commands to close Enforce host user when using Docker as runtime #394
• remove conflict with entire module name, should only be for aliases to close to close Question on conflict modules in generated modulefiles #395
• ensuring shpc edit works when error in settings.yml Cannot "shpc config edit" if there's a bug in settings.yaml #398
• renaming "namespace" in format string to "repository"

Signed-off-by: vsoch vsoch@users.noreply.github.com

[marcodelapierre]

On module name conflict, as I mentioned in #395, It's probably good to leave the full name, as it prevents from accidentally loading two versions of the same SHPC container module. So ... can it be added for Lua, too?

On the Docker/Podman optional env variables (as in my comment to #391), I was wondering ... instead of using DOCKER for Podman, too ... how about using PODMAN for Docker ...? too daring ...? after all SHPC is more focused on HPC, Docker is kind of a free add-on feature

[marcodelapierre]

{{ namespace }} should be changed to {{ repository }} also in the comment in settings.yaml

[vsoch]

On module name conflict, as I mentioned in #395, It's probably good to leave the full name, as it prevents from accidentally loading two versions of the same SHPC container module. So ... can it be added for Lua, too?

Added back! For Lua I didn't add {{ name }} because I thought that myModuleName() would translate to that. But if it does not (?) I definitely can.

On the Docker/Podman optional env variables (as in my comment to #391), I was wondering ... instead of using DOCKER for Podman, too ... how about using PODMAN for Docker ...? too daring ...? after all SHPC is more focused on HPC, Docker is kind of a free add-on feature

Let's be daring!

[marcodelapierre]

Testing related GH issues, and new features.

All good but this one:

Help block in Podman modulefile:

• -v ${PWD} -w ${PWD} missing in <tool>-run and <tool>-shell
• --entrypoint /bin/sh missing for <tool>-shell (I guess that /bin/sh is actually a variable taken from settings.yaml)

[marcodelapierre]

Note that issues #378 and #398 are also solved by this PR :-)

[vsoch]

@marcodelapierre I don't see those issues in either docker.tcl or docker.lua - could you comment directly on the code here to point them out?

[marcodelapierre]

@vsoch it's only for Lua, in lines from 18 on of docker.lua:

 - {|module_name|}-run:
       {{ command }} run -i{% if tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if envfile %}--env-file {{ module_dir }}/{{ envfile }}{% endif %} {% if bindpaths %}-v {{ bindpaths }} -v ${PWD} -w ${PWD} {% endif %}<container> "$@"
 - {|module_name|}-shell:
       {{ command }} run -i{% if tty %}t{% endif %} -u `id -u`:`id -g` --rm {% if envfile %}--env-file {{ module_dir }}/{{ envfile }}{% endif %} {% if bindpaths %}-v {{ bindpaths }} --entrypoint {{ shell }} -v ${PWD} -w ${PWD} {% endif %}<container>
 - {|module_name|}-exec:
       {{ command }} run -i{% if tty %}t{% endif %} -u `id -u`:`id -g` --rm --entrypoint "" {% if envfile %}--env-file {{ module_dir }}/{{ envfile }}{% endif %} {% if bindpaths %}-v {{ bindpaths }} {% endif %} -v ${PWD} -w ${PWD} <container> "$@"

For shell and exec,
There's a misplaced {% endif %} that should go straight after {% if bindpaths %}-v {{ bindpaths }}

[marcodelapierre]

In the TCL module files for Podman, I actually notice other issues (had not checked before):

help screen:

• missing --rm for alias commands
• for <tool-exec> entrypoint should NOT be --entrypoint /bin/sh but instead --entrypoint ""

actual command definitions:

• set execCmd misses -v $workdir -w $workdir
• alias commands should have NOTHING after ${containerPath} (right now the command is repeated, but it's already in the entrypoint)

[vsoch]

alias commands should have NOTHING after ${containerPath} (right now the command is repeated, but it's already in the entrypoint)

This is because some aliases have other arguments following the executable. If it's repeated it's a bug with deriving alias.entrypoing vs. alias.args, let me take a look. (Update, can confirm it was using alias.command instead of alias args, will fix!)