Unable to build Augur in podman due to `--chmod`

[MoralCode]

Description:
Due to some current bugs relating to podman's support of both symbolic notation in the --chmod argument to the dockerfile COPY instruction, and the handling of the X (only apply executable permission to directories) portion of the flag, Augur is unable to be built using podman tooling.

How to reproduce:

1. Clone the augur repo in an environment with podman set up
2. follow instructions at https://oss-augur.readthedocs.io/en/main/docker/quick-start.html to build the container, substituting docker for podman in commands as needed

Expected behavior:
Since Podman is generally a drop-in replacement for docker, it should work the same

Actual behavior:

The podman build fails during a COPY step with an error like this:

Error: building at STEP "COPY --chmod=u=rw,u+X,go=r,go+X ./README.md .": Error parsing chmod u=rw,u+X,go=r,go+X

Outstanding questions
I would be curious whether this is the intention of augur to support podman or not.

On one hand, I wasn't able to see any statements that podman is officially supported in the README and it seems like all the CI jobs use docker for the tests.

That said, an issue that's related to this bug (see the references section below) was intending to fix support for openshift, leading me to believe that supporting that ecosystem of tooling* is something desirable for augur. Additionally, it seems like systems (Fedora) that are more closely related to RHEL or other enterprise distributions seem to either preinstall or make it easier to use podman (compared to the process of installing the docker daemon on linux and fixing the permissions) - but maybe that's my personal preference for podman kicking in

Log files
N/A

Software versions:

• Augur: v0.89.3
• OS: Fedora 41
• Browser: N/A

Affected Versions:

The PR that caused this issue was merged immediately after v0.86.1 was tagged (the tag points to commit d55dfe5 in case it gets updated in the future), so all versions after v0.86.1 are likely affected.

References:

Upstream podman issue: containers/buildah#6066

Issue/PR that caused this issue in augur: #3107

* i think this ecosystem includes podman but I'm not sure how strong that coupling is

[MoralCode]

based on my testing, using the octal notation resolves the issue with building in podman, however this comes at the cost of not-quite-identical semantics with regard to the X value affecting recursive copies (i.e. only make directories being copied executable, not every file within them).

enabling podman to support this symbolic format for --chmod arguments seems to be the best path forward for resolving this, however it may be more effort than the current desire to support podman is worth, so worst case I hope this issue just serves as documentation for the next person who runs into this

I also think, once this is fixed, it may be useful to add tests that cover the podman builds in a similar way to the current docker based CI jobs (even if their failure doesn't block a PR) just to create a point of additional information about whether future PRs cause issues for podman so issues can be fixed in code review

[JohnStrunk]

It may also be possible to resolve this by replacing the copy's chmod with a fancy RUN find ... after the copy to properly search and set the permissions.