Fix code snippets in documentation for doctest

conftest.py

@@ -0,0 +1,6 @@
+# Root level conftest to ignore scripts folder in doctests.
+def pytest_ignore_collect(path):
+    if "scripts/" in str(path):
+        return True
+    if "docs/" in str(path):
+        return True

pyaerocom/_lowlevel_helpers.py

@@ -337,7 +337,7 @@ class ConstrainedContainer(BrowseDict):
 
     This class enables to create dict-like objects that have a fixed set of
     keys and value types (once assigned). Optional values may be instantiated
-    as None, in which case the first time instantiation definecs its type.
+    as None, in which case the first time instantiation defines its type.
 
     Note
     ----
@@ -346,12 +346,11 @@ class ConstrainedContainer(BrowseDict):
 
     Example
     -------
-    class MyContainer(ConstrainedContainer):
-        def __init__(self):
-            self.val1 = 1
-            self.val2 = 2
-            self.option = None
-
+    >>> class MyContainer(ConstrainedContainer):
+    ...    def __init__(self):
+    ...        self.val1 = 1
+    ...        self.val2 = 2
+    ...        self.option = None
     >>> mc = MyContainer()
     >>> mc['option'] = 42
     """

pyaerocom/aeroval/config/emep/emep4no_base_config.py

@@ -29,32 +29,32 @@ def get_CFG(year: int, model_dir: str, *, file_pattern: str = r"^RERUN2022_{freq
     >>> import pathlib
     >>>
     >>> if __name__ == "__main__":
-    >>>     import matplotlib.pyplot as plt
-    >>>     import pyaerocom as pya
-    >>>     from pyaerocom import const
-    >>>     from pyaerocom.aeroval import EvalSetup, ExperimentProcessor
-    >>>
-    >>>     # Customize cache dir to avoid disk quota issues.
-    >>>     # cdir = pathlib.Path("./cache")
-    >>>     # cdir.mkdir(exist_ok=True)
-    >>>     # const.CACHEDIR = str(cdir)
-    >>>
-    >>>     cfg = get_CFG(2022, "/lustre/storeB/project/fou/kl/emep/ModelRuns/EMEP4NO/EMEP4NO_rerun_2022/")
-    >>>
-    >>>     # Change any experiment details.
-    >>>     cfg.update(
-    >>>         {
-    >>>             #"proj_id": "<project name>",
-    >>>             #"exp_id": "<experiment name>",
-    >>>             #"json_basedir": "/lustre/storeB/users/thlun8736/python/aeroval/data",
-    >>>             #"coldata_basedir": "/lustre/storeB/users/thlun8736/python/aeroval/coldata",
-    >>>         }
-    >>>     )
-    >>>
-    >>>     # Run the experiment.
-    >>>     stp = EvalSetup(**cfg)
-    >>>     ana = ExperimentProcessor(stp)
-    >>>     res = ana.run()
+    ...     import matplotlib.pyplot as plt
+    ...     import pyaerocom as pya
+    ...     from pyaerocom import const
+    ...     from pyaerocom.aeroval import EvalSetup, ExperimentProcessor
+    ...
+    ...     # Customize cache dir to avoid disk quota issues.
+    ...     # cdir = pathlib.Path("./cache")
+    ...     # cdir.mkdir(exist_ok=True)
+    ...     # const.CACHEDIR = str(cdir)
+    ...
+    ...     cfg = get_CFG(2022, "/lustre/storeB/project/fou/kl/emep/ModelRuns/EMEP4NO/EMEP4NO_rerun_2022/")
+    ...
+    ...     # Change any experiment details.
+    ...     cfg.update(
+    ...         {
+    ...             #"proj_id": "<project name>",
+    ...             #"exp_id": "<experiment name>",
+    ...             #"json_basedir": "/lustre/storeB/users/thlun8736/python/aeroval/data",
+    ...             #"coldata_basedir": "/lustre/storeB/users/thlun8736/python/aeroval/coldata",
+    ...         }
+    ...     )
+    ...
+    ...     # Run the experiment.
+    ...     stp = EvalSetup(**cfg)
+    ...     ana = ExperimentProcessor(stp)
+    ...     res = ana.run()
     """
     cfg = get_EMEP_CFG(None, year, model_dir)
 

pyaerocom/griddeddata.py

@@ -2171,17 +2171,6 @@ def interpolate(self, sample_points=None, scheme="nearest", collapse_scalar=True
         -------
         GriddedData
             new data object containing interpolated data
-
-        Examples
-        --------
-
-            >>> from pyaerocom import GriddedData
-            >>> data = GriddedData()
-            >>> data._init_testdata_default()
-            >>> itp = data.interpolate([("longitude", (10)),
-            ...                         ("latitude" , (35))])
-            >>> print(itp.shape)
-            (365, 1, 1)
         """
         if isinstance(scheme, str):
             scheme = str_to_iris(scheme)

pyaerocom/io/file_conventions.py

@@ -105,12 +105,15 @@ def from_file(self, file):
         >>> from pyaerocom.io import FileConventionRead
         >>> filename = 'aerocom3_CAM5.3-Oslo_AP3-CTRL2016-PD_od550aer_Column_2010_monthly.nc'
         >>> print(FileConventionRead().from_file(filename))
+        <BLANKLINE>
         pyaeorocom FileConventionRead
         name: aerocom3
         file_sep: _
         year_pos: -2
         var_pos: -4
         ts_pos: -1
+        vert_pos: -3
+        data_id_pos: 1
         """
 
         if basename(file).count("_") >= 4:
@@ -295,6 +298,9 @@ def get_info_from_file(self, file: str) -> dict:
         ('year', 2010)
         ('var_name', 'od550aer')
         ('ts_type', 'monthly')
+        ('vert_code', 'Column')
+        ('is_at_stations', False)
+        ('data_id', 'CAM5.3-Oslo_AP3-CTRL2016-PD')
         """
         if self.name == "aerocom3":
             return self._info_from_aerocom3(file)

pyaerocom/io/read_aeronet_invv3.py

@@ -105,7 +105,7 @@ def read_file(self, filename, vars_to_retrieve=None, vars_as_series=False):
         Example
         -------
         >>> import pyaerocom.io as pio
-        >>> obj = pio.read_aeronet_invv2.ReadAeronetInvV2()
+        >>> obj = pio.read_aeronet_invv3.ReadAeronetInvV3()
         >>> files = obj.get_file_list()
         >>> filedata = obj.read_file(files[0])
         """

pyaerocom/io/readungridded.py

@@ -773,12 +773,12 @@ def read(
 
         Example
         -------
-        >>> import pyaerocom.io.readungridded as pio
-        >>> from pyaerocom import const
-        >>> obj = pio.ReadUngridded(data_id=const.AERONET_SUN_V3L15_AOD_ALL_POINTS_NAME)
-        >>> obj.read()
-        >>> print(obj)
-        >>> print(obj.metadata[0.]['latitude'])
+        >>> import pyaerocom.io.readungridded as pio # doctest: +SKIP
+        >>> from pyaerocom import const # doctest: +SKIP
+        >>> obj = pio.ReadUngridded(data_ids=const.AERONET_SUN_V3L15_AOD_ALL_POINTS_NAME) # doctest: +SKIP
+        >>> obj.read() # doctest: +SKIP
+        >>> print(obj) # doctest: +SKIP
+        >>> print(obj.metadata[0.]['latitude']) # doctest: +SKIP
 
         """
         if data_ids is None:

pyaerocom/io/utils.py

@@ -36,14 +36,12 @@ def browse_database(model_or_obs, verbose=False):
     Example
     -------
     >>> import pyaerocom as pya
-    >>> pya.io.browse_database('AATSR*ORAC*v4*')
+    >>> pya.io.utils.browse_database('AATSR*ORAC*v4*')
+    <BLANKLINE>
     Pyaerocom ReadGridded
     ---------------------
-    Model ID: AATSR_ORAC_v4.01
-    Data directory: /lustre/storeA/project/aerocom/aerocom-users-database/CCI-Aerosol/CCI_AEROSOL_Phase2/AATSR_ORAC_v4.01/renamed
-    Available variables: ['abs550aer', 'ang4487aer', 'clt', 'landseamask', 'od550aer', 'od550dust', 'od550gt1aer', 'od550lt1aer', 'pixelcount']
-    Available years: [2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012]
-    Available time resolutions ['daily']
+    Data ID: AATSR_ORAC_v4.02
+    ...
 
     """
     if not verbose:

pyaerocom/mathutils.py

@@ -188,7 +188,7 @@ def numbers_in_str(input_string):
     Example
     -------
     >>> numbers_in_str('Bla42Blub100')
-    [42, 100]
+    ['42', '100']
     """
     numbers = []
     IN_NUM = False
@@ -227,7 +227,7 @@ def exponent(num):
     -------
     >>> from pyaerocom.mathutils import exponent
     >>> exponent(2340)
-    3
+    np.int64(3)
     """
     return np.floor(np.log10(abs(np.asarray(num)))).astype(int)
 
@@ -251,11 +251,11 @@ def range_magnitude(low, high):
     -------
 
     >>> range_magnitude(0.1, 100)
-    3
+    np.int64(3)
     >>> range_magnitude(100, 0.1)
-    -3
+    np.int64(-3)
     >>> range_magnitude(1e-3, 1e6)
-    9
+    np.int64(9)
 
     """
     return exponent(high) - exponent(low)

pyaerocom/plot/config.py

@@ -64,7 +64,10 @@ class ColorTheme:
     pyaerocom ColorTheme
     name : dark
     cmap_map : viridis
+    cmap_map_div : PuOr_r
+    cmap_map_div_shifted : True
     color_coastline : #e6e6e6
+    color_map_text : r
     """
 
     def __init__(

pyaerocom/plot/helpers.py

@@ -114,20 +114,13 @@ def calc_pseudolog_cmaplevels(vmin, vmax, add_zero=False):
     Example
     -------
     >>> vmin, vmax = 0.02, 0.75
-    >>> vals = calc_pseudolog_cmaplevels(vmin, vmax, num_per_mag=10, add_zero=True)
+    >>> vals = calc_pseudolog_cmaplevels(vmin, vmax, add_zero=True)
     >>> for val in vals: print("%.4f" %val)
     0.0000
-    0.0100
-    0.0126
-    0.0158
     0.0200
-    0.0251
-    0.0316
-    0.0398
-    0.0501
-    0.0631
-    0.0794
-    0.1000
+    ...
+    0.7000
+    0.7500
 
     """
     warnings.warn(

pyaerocom/ungriddeddata.py

@@ -2034,10 +2034,9 @@ def filter_by_meta(self, negate=None, **filter_attributes):
         Example
         -------
         >>> import pyaerocom as pya
-        >>> r = pya.io.ReadUngridded(['AeronetSunV2Lev2.daily',
-                                      'AeronetSunV3Lev2.daily'], 'od550aer')
+        >>> r = pya.io.ReadUngridded(['AeronetSunV3Lev2.daily'], 'od550aer')
         >>> data = r.read()
-        >>> data_filtered = data.filter_by_meta(data_id='AeronetSunV2Lev2.daily',
+        >>> data_filtered = data.filter_by_meta(data_id='AeronetSunV3Lev2.daily',
         ...                                     longitude=[-30, 30],
         ...                                     latitude=[20, 70],
         ...                                     altitude=[0, 1000])
@@ -3083,16 +3082,16 @@ def __and__(self, other):
 
         Example
         -------
-        >>> from pyaerocom.io import ReadAeronetSdaV2
-        >>> read = ReadAeronetSdaV2()
+        >>> from pyaerocom.io import ReadAeronetSdaV3
+        >>> read = ReadAeronetSdaV3()
 
         >>> d0 = read.read(last_file=10)
         >>> d1 = read.read(first_file=10, last_file=20)
 
         >>> merged = d0 & d1
 
         >>> print(d0.shape, d1.shape, merged.shape)
-        (7326, 11) (9894, 11) (17220, 11)
+        (9868, 12) (12336, 12) (22204, 12)
         """
         return self.merge(other, new_obj=True)
 

pyaerocom/utils.py

@@ -65,12 +65,14 @@ def create_varinfo_table(
 
     Example
     -------
-    >>> from pyaerocom import create_varinfo_table
+    >>> from pyaerocom import create_varinfo_table # doctest: +ELLIPSIS
     >>> models = ['INCA-BCext_CTRL2016-PD',
-                  'GEOS5-freegcm_CTRL2016-PD']
+    ...           'GEOS5-freegcm_CTRL2016-PD']
     >>> vars = ['ang4487aer', 'od550aer', 'ec*']
-    >>> df = create_varinfo_table(models, vars)
-    >>> print(df)
+    >>> create_varinfo_table(models, vars)
+    At model: INCA-BCext_CTRL2016-PD (0 of 2)
+    At model: GEOS5-freegcm_CTRL2016-PD (1 of 2)
+    ...
     """
     if isinstance(model_ids, str):
         model_ids = [model_ids]

pyproject.toml

@@ -212,7 +212,7 @@ commands_pre =
     python --version
     python -m pip freeze --all
 commands =
-    python -m pytest -ra -q {posargs:--cov --no-cov-on-fail}
+    python -m pytest . -ra -q {posargs:--cov --no-cov-on-fail}
 extras =
     test
 setenv =