[giacomofiorin]

Summary

This PR replaces Apptainer-format containers with Docker-format ones for use in CI jobs. The change is breaking for existing branches because they pull containers expecting them in Apptainer format. However, one can still use the containers with Apptainer by specifying that they are in Docker format.

The container images are now compatible with all major container software (Docker, Podman, Apptainer), and updated instructions for each are in the README.

Also included some small CI fixes and improvements:

• Fixed the cache keys in a couple of jobs
• Reduced the maximum ccache size per job, allowing more caches for more branches within the repo's allotted quota.
• Switched the order of testing in backends CI jobs (interface tests now run first, because they take less and are arguably less redundant than the stand-alone library tests)
• The website is now updated as part of the Version Maintenance job, i.e. it will only be updated after merging to master

Related issue(s)

Installing Apptainer from PPA sporadically fails, and it adds some extra time at startup. Using Docker is better integrated with GHA, but we can still use Apptainer offline.

Affected engine(s)

Author(s)

@giacomofiorin

Licensing

By submitting this pull request, I agree that my contribution will be included in Colvars repository and redistributed under the GNU Lesser General Public License (LGPL) version 3.

Note: NAMD, VMD and TinkerHP follow more restrictive licenses, e.g. the UIUC license. However, the terms of the LGPLv3 remain in effect for the copies of the Colvars code distributed alongside those packages.

Artificial Intelligence (AI)

Copilot converted the Apptainer definition files to Dockerfiles; it also drafted the fix for MathJax code, which I reviewed very quickly.

Further information / links

[Copilot]

🟡 Changes recommended

Unconditional app-token generation blocks public backend builds on forks without private credentials, while unexpanded workspace paths break diagnostic uploads and cache configuration.

2 open issues

• Artifact paths use an unexpanded workspace variable · New
• oneAPI cache uses a relative literal workspace path · New

10 resolved since last review

• Use python3 for documentation generation
• Allow repeated HTML repairs when a backup already exists
• Use DNF5 syntax to add the repository
• Use the ARM64 CMake distribution on ARM64 runners
• Use HTTPS credentials for website publishing
• Scope the app token to the website repository
• Create the Colvars target before configuring Lepton
• Create private-repository tokens only for NAMD/VMD jobs
• Use GitHub Actions expressions for workspace paths
• Update cache cleanup to match the new key prefix

_{Review effort: Balanced}