441 inconsistency between yaml libs bugfix

jo-basevi commented 3 months ago

As suggested in this issue #441,

Add warnings when reading config.yaml files with duplicate keys (as PyYAML library silently over-writes the value with the subsequent value)
When adding restarts to config.yaml when creating a new git branch, allow duplicate keys but still warn that they will get deleted when the config.yaml file gets modified (note the subsequent key will get deleted). Ruamel yaml library is used for modifying the config files as it can preserve multi-line strings and comments.
Added a test for testing the warnings above

Closes #441

By default warnings are formatted with a line of the source code, e.g. the line warnings.warn( in

/home/189/jb4202/payu_fork/payu/fsops.py:83: UserWarning: Duplicate key found in config.yaml: key 'model' with value 'mom6' (original value: '')
  warnings.warn(

In fb45911983e399befc52e03feb9394a74c796f93, I have just patched the warnings used globally it doesn't include the line of source code. This is to avoid logs with like warnings.warn( with unclosed brackets.

pep8speaks commented 3 months ago

Hello @jo-basevi! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! :beers:

Comment last updated at 2024-08-20 02:16:51 UTC

coveralls commented 3 months ago

coverage: 52.758% (+0.5%) from 52.281% when pulling cddbef651ae7d474fcfe378ce426b47e9eca742b on ACCESS-NRI:441-inconsistency-between-yaml-libs-bugfix into 83001a2b45ef786e178894f77dd9fbc0878e73c1 on payu-org:master.

payu-org / payu

441 inconsistency between yaml libs bugfix #480

Comment last updated at 2024-08-20 02:16:51 UTC