Payu setup -r handle empty manifest

[Qian-HuiChen]

Closes #704 as part of this payu setup repro check issue.

When manifest is empty (e.g., OM2 initial experiment), payu setup -r does not error immediately. It only errors when a new restart manifests file is created.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 63.70%. Comparing base (c37e75c) to head (5c7f176).
⚠️ Report is 3 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #707      +/-   ##
==========================================
+ Coverage   63.68%   63.70%   +0.01%     
==========================================
  Files          67       67              
  Lines        5557     5554       -3     
==========================================
- Hits         3539     3538       -1     
+ Misses       2018     2016       -2     

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[jo-basevi]

Thanks for adding this fix in! I've just had a super quick review

[Qian-HuiChen]

Hi @jo-basevi , I am not 100% confident that I understand the issue, or whether my update solve the issue as desired. Please let me know if this is not what we are looking for.

[jo-basevi]

Hi @jo-basevi , I am not 100% confident that I understand the issue, or whether my update solve the issue as desired. Please let me know if this is not what we are looking for.

Removing that check which fails when manifests are empty was the main issue.

We want to be able to run reproduce checks on all files even if one of the manifests is expected to have no files. So for example one way to manually test this would be to get one of the ACCESS-OM2 configurations which cold start (don't start from restarts so has a empty restart manifest), and run payu setup -r. Then to test an expected failure, set restart: /path/to/an/actual/restartN in config.yaml, and run payu setup -r.

[jo-basevi]

Looks good to me