Diagnostics config common copy

[mnurisso]

PR description:

The PR proposes to add the 'diagnostics' folder to the list of folders copied/linked by the console. This is a solution that will totally replace the manual addition of individual config files done so far for all the diagnostics.

Note:

The link solution will make appear the files that are now not natively in the config folder as untracked for git. This is expected, but not very nice for the development, since it add noise to the file list.

People involved:

cc @oloapinivad

• Tests are included if a new feature is included.
• Documentation is included if a new feature is included.
• Docstrings are updated if needed.
• Changelog is updated.
• Diagnostic config files path are updated in the console if needed

[codecov]

❌ 9 Tests Failed:

Tests completed	Failed	Passed	Skipped
295	9	286	0

View the top 3 failed test(s) by shortest run time

tests/teleconnections/test_nao.py::test_class_NAO

Stack Traces | 0.024s run time

@pytest.mark.diagnostics
    def test_class_NAO():
        """
        Test that the NAO class works
        """
        telecname = 'NAO'
        model = 'IFS'
        exp = 'test-tco79'
        source = 'teleconnections'
        interface = 'teleconnections-ci'
    
>       telec = Teleconnection(model=model, exp=exp, source=source,
                               loglevel=loglevel, telecname=telecname,
                               interface=interface)

tests/teleconnections/test_nao.py:20: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
.../aqua_diagnostics/teleconnections/tc_class.py:119: in __init__
    self._load_namelist(configdir=configdir, interface=interface)
.../aqua_diagnostics/teleconnections/tc_class.py:368: in _load_namelist
    self.namelist = config.load_namelist()
.../teleconnections/tools/tools.py:43: in load_namelist
    namelist = load_yaml(self.config_file)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

infile = '....../github/home/.aqua.../teleconnections/config/teleconnections-ci.yaml'
definitions = None, jinja = True

    def load_yaml(infile, definitions=None, jinja=True):
        """
        Load yaml file with template substitution
    
        Args:
            infile (str): a file path to the yaml
            definitions (str or dict, optional): name of the section containing string template
                                                 definitions or a dictionary with the same content
            jinja: (bool): jinja2 templating is used instead of standard python templating. Default is true.
        Returns:
            A dictionary with the yaml file keys
        """
    
        if not os.path.exists(infile):
>           raise ValueError(f'ERROR: {infile} not found: you need to have this configuration file!')
E           ValueError: ERROR: ....../github/home/.aqua.../teleconnections/config/teleconnections-ci.yaml not found: you need to have this configuration file!

.../aqua/util/yaml.py:100: ValueError

tests/teleconnections/test_teleconnections.py::test_namelist

Stack Traces | 0.024s run time

@pytest.mark.diagnostics
    def test_namelist():
        """
        Test that the namelist can be loaded
        """
    
        # configdir = "..../diagnostics/teleconnections/config"
        config = TeleconnectionsConfig()
>       namelist = config.load_namelist()

tests/teleconnections/test_teleconnections.py:30: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
.../teleconnections/tools/tools.py:43: in load_namelist
    namelist = load_yaml(self.config_file)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

infile = '....../github/home/.aqua....../teleconnections/config/teleconnections-destine.yaml'
definitions = None, jinja = True

    def load_yaml(infile, definitions=None, jinja=True):
        """
        Load yaml file with template substitution
    
        Args:
            infile (str): a file path to the yaml
            definitions (str or dict, optional): name of the section containing string template
                                                 definitions or a dictionary with the same content
            jinja: (bool): jinja2 templating is used instead of standard python templating. Default is true.
        Returns:
            A dictionary with the yaml file keys
        """
    
        if not os.path.exists(infile):
>           raise ValueError(f'ERROR: {infile} not found: you need to have this configuration file!')
E           ValueError: ERROR: ....../github/home/.aqua....../teleconnections/config/teleconnections-destine.yaml not found: you need to have this configuration file!

.../aqua/util/yaml.py:100: ValueError

tests/teleconnections/test_teleconnections.py::test_regional_mean[1]

Stack Traces | 0.024s run time

months_window = 1

    @pytest.mark.diagnostics
    @pytest.mark.parametrize("months_window", [1, 3])
    def test_regional_mean(months_window):
        """
        Test that the regional_mean method works
        """
    
        filepath = "..../IFS/teleconnections/enso_test.nc"
        # configdir = "..../diagnostics/teleconnections/config"
        telecname = 'ENSO'
        interface = 'teleconnections-ci'
        rtol = approx_rel
        atol = approx_rel
    
        # 1. -- Opening yaml file
        config = TeleconnectionsConfig(interface=interface)
>       namelist = config.load_namelist()

tests/teleconnections/test_teleconnections.py:75: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
.../teleconnections/tools/tools.py:43: in load_namelist
    namelist = load_yaml(self.config_file)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

infile = '....../github/home/.aqua....../teleconnections/config/teleconnections-ci.yaml'
definitions = None, jinja = True

    def load_yaml(infile, definitions=None, jinja=True):
        """
        Load yaml file with template substitution
    
        Args:
            infile (str): a file path to the yaml
            definitions (str or dict, optional): name of the section containing string template
                                                 definitions or a dictionary with the same content
            jinja: (bool): jinja2 templating is used instead of standard python templating. Default is true.
        Returns:
            A dictionary with the yaml file keys
        """
    
        if not os.path.exists(infile):
>           raise ValueError(f'ERROR: {infile} not found: you need to have this configuration file!')
E           ValueError: ERROR: ....../github/home/.aqua....../teleconnections/config/teleconnections-ci.yaml not found: you need to have this configuration file!

.../aqua/util/yaml.py:100: ValueError

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[mnurisso]

Stanby