Fix diagnostic filter

[jvegreg]

There is an issue with the diagnostics filter if you try to filter only one diagnostic (see #712 )

This pull request fixes it

Tasks

• Create an issue to discuss what you are going to do, if you haven't done so already (and add the link at the bottom)
• This pull request has a descriptive title that can be used in a changelog
• Add unit tests
• Public functions should have a numpy-style docstring so they appear properly in the API documentation. For all other functions a one line docstring is sufficient.
• If writing a new/modified preprocessor function, please update the documentation
• Circle/CI tests pass. Status can be seen below your pull request. If the tests are failing, click the link to find out why.
• Codacy code quality checks pass. Status can be seen below your pull request. If there is an error, click the link to find out why. If you suspect Codacy may be wrong, please ask by commenting.
• Please use yamllint to check that your YAML files do not contain mistakes
• If you make backward incompatible changes to the recipe format, make a new pull request in the ESMValTool repository and add the link below

If you need help with any of the tasks above, please do not hesitate to ask by commenting in the issue or pull request.

---

Closes #712

[schlunma]

Tested successfully, thanks for the quick fix! 🎉 I think you should merge this in master and not v2.0.0, Bouwe will cherry-pick this from master once this is merged.

[bouweandela]

I tried to test this, but how do I select two tasks?

I ran

$ esmvaltool run examples/recipe_python.yml --diagnostics diagnostic1/pr diagnostic1/script1

and the output was:

ERROR: Config file /home/bandela/src/esmvalgroup/esmvalcore/diagnostic1/script1 does not exist
ERROR:esmvalcore._main:Program terminated abnormally, see stack trace below for more information
Traceback (most recent call last):
  File "/home/bandela/src/esmvalgroup/esmvalcore/esmvalcore/_main.py", line 430, in run
    fire.Fire(ESMValTool())
  File "/home/bandela/conda/envs/esmvaltool/lib/python3.8/site-packages/fire/core.py", line 138, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/home/bandela/conda/envs/esmvaltool/lib/python3.8/site-packages/fire/core.py", line 463, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/home/bandela/conda/envs/esmvaltool/lib/python3.8/site-packages/fire/core.py", line 672, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/home/bandela/src/esmvalgroup/esmvalcore/esmvalcore/_main.py", line 366, in run
    cfg = read_config_user_file(config_file, recipe_name, kwargs)
  File "/home/bandela/src/esmvalgroup/esmvalcore/esmvalcore/_config.py", line 42, in read_config_user_file
    with open(config_file, 'r') as file:
FileNotFoundError: [Errno 2] No such file or directory: '/home/bandela/src/esmvalgroup/esmvalcore/diagnostic1/script1'

It looks like the second task is somehow interpreted as the config-user file?

[jvegreg]

how do I select two tasks?

Like this,

$ esmvaltool run examples/recipe_python.yml --diagnostics '("diagnostic1/pr", "diagnostic1/script")'

but I am going to modify it a bit so it also accepts

$ esmvaltool run examples/recipe_python.yml --diagnostics 'diagnostic1/pr diagnostic1/script'

[bouweandela]

Thanks! Could you also document that syntax somewhere?

[jvegreg]

Thanks! Could you also document that syntax somewhere?

Yes.

Can you please test the branch locally? The tests run fine on my computer but fail in CircleCI, and I do not understand why

[bouweandela]

I think it's an old Python issue #719

[bouweandela]

Merging this now, because I want to make the release today. Can you please make a new pull request to document how to use the feature?