Update container

[jasonb5]

Description

• Migrates from conda to spack
• Fix mixed perl environment (conda/system)
• Moves to UV to manage python
• Simplifies usage and testing workflow

Checklist

• My code follows the style guidelines of this project (black formatting)
• I have performed a self-review of my own code
• My changes generate no new warnings
• I have added tests that exercise my feature/fix and existing tests continue to pass
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding additions and changes to the documentation

[jedwards4b]

There is a variable user_home which it seems like should replace the hardcoded
/home/cime throughout - but then you are also handling a case of root running so I'm a little lost as to the intent.

[Copilot]

Pull request overview

Updates the project’s container image and CI entrypoint behavior to improve dependency handling (notably Perl), move inputdata download into the entrypoint logic, and adjust GitHub Actions to explicitly source the container entrypoint.

Changes:

• Switch Docker base image reference to quay.io/condaforge/miniforge3 and adjust OS-level package installs (Perl + gosu).
• Refactor docker/entrypoint.sh to handle HOME/.cime setup in CI/root scenarios and add helper functions (e.g., inputdata download, cprnc build).
• Update CI workflow steps to manually source /entrypoint.sh and remove old .cime copy logic (plus a temporary debug listing).

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 5 comments.

File	Description
docker/entrypoint.sh	Adds CI/root HOME handling, .cime relocation, and new helper functions; changes environment setup behavior.
docker/cime.yaml	Adds editor dependency and enables HDF5 OpenMPI build in the conda env spec.
docker/Dockerfile	Updates base image source, installs Perl/gosu via apt, and runs inputdata download via sourced entrypoint during build.
.github/workflows/testing.yml	Sources /entrypoint.sh in jobs and removes legacy .cime copy; includes a temporary debug ls.

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[Copilot]

The Docker build step calls download_input_data, but the image no longer installs wget (or curl) via apt and it’s not guaranteed to be available in the base conda env. This can make the build fail when wget is missing. Install wget/curl in the image layer before this RUN step, or invoke the downloader via conda run -n <env> / an explicit path to the env’s wget.

[jasonb5]

Added wget/curl/subversion to dockerfile.

[Copilot]

The generated .bashrc prepends /usr/bin to PATH after conda activation. This can cause system tools (e.g., python/cmake/mpirun) to be picked over the conda environment versions, breaking builds/tests. If the intent is only to force system Perl, use a more targeted approach (e.g., set PERL=/usr/bin/perl, hash -p /usr/bin/perl perl, or adjust only perl resolution) rather than reordering the entire PATH.

Suggested change

	# Clobber PATH so system perl is used instead of conda perl
	echo "export PATH=/usr/bin:\$PATH"
	# Ensure system perl is used instead of conda perl without changing PATH order
	echo "hash -p /usr/bin/perl perl"

[jasonb5]

Used both hash and PERL variable.

[Copilot]

Use $(...) instead of legacy backticks for command substitution (easier to read/nest, less error-prone).

[Copilot]

Remove the temporary debug ls -la "${HOME}" step (and the TODO) before merging; it adds noise to CI logs and can inadvertently expose environment details in logs.

Suggested change

	# TODO remove just for testing
	ls -la "${HOME}"

[github-actions]

You can preview documentation at https://esmci.github.io/cime/branch/fix-containers/html/index.html

[rljacob]

@jayeshkrishna can you comment on these versions?

[jasonb5]

@jedwards4b @billsacks I don't think the CESM failure is caused by this PR, probably related to this change. If it is I'll just merge this PR. Thanks!

[billsacks]

@jasonb5 - Thanks - I agree that the CESM failure is due to a CICE change - we just saw that in our recent testing as well without this CIME change.