Fix bugs in base Dockerfile

[samsrabin]

I'm unable to build the base/centos8/Dockerfile as currently set up (main branch, commit c48f872). This PR:

• Resolves CentOS8 is dead... #13 by switching to oraclelinux 9.
• Resolves Outdated links in base Dockerfile #14 by pointing to Github release links.

Builds successfully and works for building the CTSM documentation.

[jedwards4b]

Is this using the gnu compiler? Try adding flag -fallow-argument-mismatch

[samsrabin]

Yep, tried that after posting but no luck (commit b455099). Updating to 1.12.2 fixed it, though (commit c111b56).

[jedwards4b]

Note that the latest pnetcdf version is 1.13.0

[samsrabin]

Yep, and some of the other packages have more recent versions too. I figured minimal changes would be best at first, just to get the container to build. Then once I know what sort of testing is required, I can look into upgrading the dependencies.

[samsrabin]

Unfortunately, the CTSM docs fail to build like they should when calling ./build_docs -b ../../ctsm-docs/versions/master -d -c:

Running Sphinx v7.4.7
WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English).
loading translations [en]... done
making output directory... done
Converting `source_suffix = ['.rst', '.md']` to `source_suffix = {'.rst': 'restructuredtext', '.md': 'restructuredtext'}`.
WARNING: The pre-Sphinx 1.0 'intersphinx_mapping' format is deprecated and will be removed in Sphinx 8. Update to the current format as described in the documentation. Hint: `intersphinx_mapping = {'<name>': ('https://docs.python.org/', None)}`.https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#confval-intersphinx_mapping
WARNING: while setting up extension sphinx_rtd_theme: extension 'sphinx_rtd_theme' has no setup() function; is it really a Sphinx extension module?

Theme error:
no theme named 'sphinx_rtd_theme' found (missing theme.toml?)
make: *** [Makefile:41: html] Error 2
Traceback (most recent call last):
  File "/Users/samrabin/Documents/git_repos/CTSM_myfork/doc/./doc-builder/build_docs", line 14, in <module>
    build_docs.main()
  File "/Users/samrabin/Documents/git_repos/CTSM_myfork/doc/doc-builder/doc_builder/build_docs.py", line 176, in main
    run_build_command(build_command=build_command)
  File "/Users/samrabin/Documents/git_repos/CTSM_myfork/doc/doc-builder/doc_builder/build_docs.py", line 108, in run_build_command
    subprocess.check_call(build_command)
  File "/opt/homebrew/Caskroom/mambaforge/base/envs/vscode-restructuredtext/lib/python3.12/subprocess.py", line 413, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['docker', 'run', '--name', 'build_docs_ujyjqlzn', '--mount', 'type=bind,source=/Users/samrabin,target=/home/user/mounted_home', '--workdir', '/home/user/mounted_home/Documents/git_repos/CTSM_myfork/doc', '-t', '--rm', 'samsrabin/escomp-base-ctsm-docs:base-update-202410-930606e', 'make', 'BUILDDIR=/home/user/mounted_home/Documents/git_repos/ctsm-docs/versions/master', '-j', '4', 'html']' returned non-zero exit status 2.

I think this is due to the version-dropdown-with-fixes branch being too outdated. Upgrading that is above my pay grade.

[samsrabin]

I think I've fixed the CTSM docs build issue with changes in other repos (ESMCI/doc-builder and ESCOMP/CTSM).

[samsrabin]

@briandobbins will work on a different update of the container, which will allow this PR to be closed.

Brian, while you're at it, it'd be great if you could add the sphinx_mdinclude python module. You might also want to consider breaking up the HDF5/netCDF/PnetCDF installation as in ae71e60, which makes troubleshooting easier. Thanks!