rose stem fails with "fatal: Could not read from remote repository."

[MichaelWhitall]

Hi all,

I can't get rose stem to work from my git clone as per the instructions in the working practices.

I'm running from a clone pointing at a UM vn14.0 branch:
$cylc vip -z group=ex1a_ga_comorph,azspice_ga_comorph -n vn14.0_comorph_refact ./rose-stem

This successfully launches, but the extract_source task immediately fails when trying to fetch the JULES source (full error message copied below). The error message makes it sound like I haven't got ssh key access to MetOffice organisation repositories setup, but I definitely have got this setup (I wouldn't have been able to push / commit to my branch in my fork without this right?)

Any ideas what's going wrong / how to fix it? Note I also tried with -S USE_MIRRORS=true; this also failed in the extract_source task but with a different error to the one below.

Full error message from the extract_source task below.
Cheers!
Mike

[FAIL] Command failed: git -C /home/users/michael.whitall/cylc-run/vn14.0_comorph_refact/run1/share/source/jules fetch origin 2025.12.1
Error: ERROR: The 'MetOffice' organization has enabled or enforced SAML SSO.
To access this repository, you must use the HTTPS remote with a personal access token or SSH with an SSH key and passphrase that has been authorized for this organization.
Visit https://docs.github.com/articles/authenticating-to-a-github-organization-with-saml-single-sign-on/ for more information.

fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Traceback (most recent call last):
File "/data/scratch/michael.whitall/cylc-run/vn14.0_comorph_refact/run1/work/1/extract_source/rose_stem_extract_source.py", line 84, in
main()
File "/data/scratch/michael.whitall/cylc-run/vn14.0_comorph_refact/run1/work/1/extract_source/rose_stem_extract_source.py", line 74, in main
clone_repo(values["source"], values["ref"], loc)
File "/data/scratch/michael.whitall/cylc-run/vn14.0_comorph_refact/run1/work/1/extract_source/get_git_sources.py", line 122, in clone_repo
run_command(command)
File "/data/scratch/michael.whitall/cylc-run/vn14.0_comorph_refact/run1/work/1/extract_source/get_git_sources.py", line 52, in run_command
raise subprocess.CalledProcessError(
subprocess.CalledProcessError: Command '['git', '-C', '/home/users/michael.whitall/cylc-run/vn14.0_comorph_refact/run1/share/source/jules', 'fetch', 'origin', '2025.12.1']' returned non-zero exit status 128.
[FAIL] python3 rose_stem_extract_source.py # return-code=1
2026-01-21T15:11:54Z CRITICAL - failed/ERR

[MichaelWhitall]

OK I've now managed to get past this error :) It stopped happening after I:
a) Re-did the setup of MFA on github using an authenticator app (I previously had this setup on github to use SMS for MFA, but this seems to've got disabled at some point so I no longer had MFA).
b) Re-did the authorizing of my ssh key for Single Sign-On as described here: https://docs.github.com/en/enterprise-cloud@latest/authentication/authenticating-with-single-sign-on/authorizing-an-ssh-key-for-use-with-single-sign-on

I'm confused that my ssh key was still working fine for doing push / commit to my branches, but wouldn't work for extracting source from the repository to compile things in rose stem, but hey ho!

Mike