Fix build error with --build-template conda/micromamba:v2 for singularity

[munishchouhan]

Closes #971

Problem

Singularity builds using --build-template conda/micromamba:v2 (and conda-pixi-v1) fail with tar permission errors during the multi-stage build process. The error occurs in the
second stage when extracting the conda environment archive:

tar: conda/conda-meta: Cannot change mode to rwxrwxrwx: No such file or directory

Similar errors cascade across multiple directories (pkgs/cache, fortomp, etc.), making the build unusable.

Root Cause

The Singularity templates for conda-micromamba-v2 and conda-pixi-v1 used a two-stage build pattern:

1. Stage build: Install conda/pixi environment, then tar czf the entire environment into an archive
2. Stage final: Start from a clean base image ({{base_image}}), copy the tar archive via %files from build, then tar xzf to extract it

The tar extraction in the final stage failed because:

• File permissions and metadata from the conda environment couldn't be preserved across the stage boundary
• The tar extract encountered permission-related errors (Cannot change mode to rwxrwxrwx) when restoring files into the final stage's filesystem
• Unlike Docker multi-stage builds, Singularity's multi-stage %files from build mechanism doesn't handle complex permission structures in tar archives reliably

Solution

Convert both Singularity templates from multi-stage to single-stage builds. The conda/pixi environment is installed directly in the single stage — no tar archiving or extraction
needed.

[pditommaso]

is there any tar options that could provide an alternative solution? bit concerned about shallowing stderr in case of error (and returning

[munishchouhan]

is there any tar options that could provide an alternative solution? bit concerned about shallowing stderr in case of error (and returning

I tired multiple flags but no luck

--delay-directory-restore 
        --no-same-owner 
        --no-same-permissions 

This error could be because of proot
I think we should use single stage build for singularity builds

[munishchouhan]

because even i make a workaround where we just ignore this exception, may lead to brocker env

[munishchouhan]

and not using tar also decreases the build time

[munishchouhan]

@pditommaso should we make it single stage build for singularity or keep the multi stage build which is giving error because of proot?

[pditommaso]

Sorry I was missing this, the solution suggest

Solution:
Suppress harmless tar errors with 2>/dev/null || true. The extraction succeeds and conda environments function correctly.

is it really needed to change the build structure?

[munishchouhan]

Sorry I was missing this, the solution suggest

Solution:
Suppress harmless tar errors with 2>/dev/null || true. The extraction succeeds and conda environments function correctly.

is it really needed to change the build structure?

Apologies, I havenot changed the PR summary, its for the old solution, where we ignore atr errors
But the problem is that tar doesn't work in this case because of proot because of the permissions issue when untar the files in build stage.

So I suggested single build, I will update the pr summary

[munishchouhan]

@pditommaso I have updated the pr summary