Enable ruff pydocstyle linter rule (#2547)

Co-authored-by: Manuel Schlund <[email protected]>

esmvalcore/cmor/_fixes/__init__.py

@@ -1,5 +1,5 @@
 """
-Automatic fixes for input data
+Automatic fixes for input data.
 
 Module to apply automatic fixes at different levels to input data for known
 errors.

esmvalcore/cmor/_fixes/cmip5/gfdl_cm3.py

@@ -9,7 +9,7 @@ class AllVars(BaseAllVars):
 
 
 class Areacello(Fix):
-    """Fixes for areacello"""
+    """Fixes for areacello."""
 
     def fix_metadata(self, cubes):
         """
@@ -56,7 +56,7 @@ def fix_data(self, cube):
 
 
 class Tos(Fix):
-    """Fixes for tos"""
+    """Fixes for tos."""
 
     def fix_metadata(self, cubes):
         """

esmvalcore/cmor/_fixes/cmip5/gfdl_esm2g.py

@@ -37,7 +37,7 @@ def fix_metadata(self, cubes):
 
 
 class Areacello(Fix):
-    """Fixes for areacello"""
+    """Fixes for areacello."""
 
     def fix_metadata(self, cubes):
         """
@@ -116,6 +116,7 @@ def fix_metadata(self, cubes):
         Parameters
         ----------
         cubes: iris.cube.CubeList
+
         Returns
         -------
         iris.cube.CubeList
@@ -137,6 +138,7 @@ def fix_metadata(self, cubes):
         Parameters
         ----------
         cubes: iris.cube.CubeList
+
         Returns
         -------
         iris.cube.CubeList

esmvalcore/cmor/_fixes/cmip5/gfdl_esm2m.py

@@ -9,7 +9,7 @@ class AllVars(BaseAllVars):
 
 
 class Areacello(Fix):
-    """Fixes for areacello"""
+    """Fixes for areacello."""
 
     def fix_metadata(self, cubes):
         """

pyproject.toml

@@ -34,6 +34,7 @@ line-length = 79
 [tool.ruff.lint]
 select = [
     "B",
+    "D",       # pydocstyle
     "E",       # pycodestyle
     "F",       # pyflakes
     "I",       # isort
@@ -42,10 +43,19 @@ select = [
 ]
 ignore = [
     "E501",  # Disable line-too-long as this is taken care of by the formatter.
+    "D105",  # Disable Missing docstring in magic method as these are well defined.
 ]
 [tool.ruff.lint.per-file-ignores]
 "tests/**.py" = [
     "B011",  # `assert False` is valid test code.
+    # Docstrings in tests are only needed if the code is not self-explanatory.
+    "D100",  # Missing docstring in public module
+    "D101",  # Missing docstring in public class
+    "D102",  # Missing docstring in public method
+    "D103",  # Missing docstring in public function
+    "D104",  # Missing docstring in public package
 ]
 [tool.ruff.lint.isort]
 known-first-party = ["esmvalcore"]
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"

tests/__init__.py

@@ -19,11 +19,7 @@ class Test(unittest.TestCase):
     """Provides esmvaltool specific testing functionality."""
 
     def _remove_testcase_patches(self):
-        """
-        Helper method to remove per-testcase patches installed by
-        :meth:`patch`.
-
-        """
+        """Remove per-testcase patches installed by :meth:`patch`."""
         # Remove all patches made, ignoring errors.
         for patch in self.testcase_patches:
             patch.stop()

tests/conftest.py

@@ -8,7 +8,7 @@
 
 @pytest.fixture
 def cfg_default(mocker):
-    """Configuration object with defaults."""
+    """Create a configuration object with default values."""
     cfg = deepcopy(CFG)
     cfg.load_from_dirs([])
     return cfg

tests/integration/cmor/_fixes/cmip5/test_bnu_esm.py

@@ -29,7 +29,7 @@ def setUp(self):
         self.fix = Cl(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         fix = Fix.get_fixes("CMIP5", "BNU-ESM", "Amon", "cl")
         assert fix == [Cl(None), GenericFix(None)]
 

tests/integration/cmor/_fixes/cmip5/test_cnrm_cm5.py

@@ -19,7 +19,7 @@ def setUp(self):
         self.fix = Msftmyz(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "CNRM-CM5", "Amon", "msftmyz"),
             [Msftmyz(None), GenericFix(None)],
@@ -41,7 +41,7 @@ def setUp(self):
         self.fix = Msftmyzba(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "CNRM-CM5", "Amon", "msftmyzba"),
             [Msftmyzba(None), GenericFix(None)],

tests/integration/cmor/_fixes/cmip5/test_ec_earth.py

@@ -28,7 +28,7 @@ def setUp(self):
         self.fix = Sic(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "EC-EARTH", "Amon", "sic"),
             [Sic(None), GenericFix(None)],
@@ -50,7 +50,7 @@ def setUp(self):
         self.fix = Sftlf(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "EC-EARTH", "Amon", "sftlf"),
             [Sftlf(None), GenericFix(None)],
@@ -68,7 +68,6 @@ class TestTas(unittest.TestCase):
 
     def setUp(self):
         """Prepare tests."""
-
         height_coord = DimCoord(
             2.0,
             standard_name="height",
@@ -99,15 +98,14 @@ def setUp(self):
         self.fix = Tas(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "EC-EARTH", "Amon", "tas"),
             [Tas(None), GenericFix(None)],
         )
 
     def test_tas_fix_metadata(self):
         """Test metadata fix."""
-
         out_cube_without = self.fix.fix_metadata(self.cube_without)
 
         # make sure this does not raise an error
@@ -131,7 +129,6 @@ class TestAreacello(unittest.TestCase):
 
     def setUp(self):
         """Prepare tests."""
-
         latitude = Cube(
             np.ones((2, 2)),
             standard_name="latitude",
@@ -163,15 +160,14 @@ def setUp(self):
         self.fix = Areacello(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "EC-EARTH", "Omon", "areacello"),
             [Areacello(None), GenericFix(None)],
         )
 
     def test_areacello_fix_metadata(self):
         """Test metadata fix."""
-
         out_cube = self.fix.fix_metadata(self.cubes)
         assert len(out_cube) == 1
 
@@ -184,7 +180,6 @@ class TestPr(unittest.TestCase):
 
     def setUp(self):
         """Prepare tests."""
-
         wrong_time_coord = AuxCoord(
             points=[1.0, 2.0, 1.0, 2.0, 3.0],
             var_name="time",
@@ -226,15 +221,14 @@ def setUp(self):
         self.fix = Pr(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "EC-EARTH", "Amon", "pr"),
             [Pr(None), GenericFix(None)],
         )
 
     def test_pr_fix_metadata(self):
         """Test metadata fix."""
-
         out_wrong_cube = self.fix.fix_metadata(self.wrong_cube)
         out_correct_cube = self.fix.fix_metadata(self.correct_cube)
 

tests/integration/cmor/_fixes/cmip5/test_fio_esm.py

@@ -31,7 +31,7 @@ def setUp(self):
         self.fix = Ch4(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "FIO-ESM", "Amon", "ch4"),
             [Ch4(None), GenericFix(None)],
@@ -53,7 +53,7 @@ def setUp(self):
         self.fix = Co2(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "FIO-ESM", "Amon", "co2"),
             [Co2(None), GenericFix(None)],

tests/integration/cmor/_fixes/cmip5/test_gfdl_cm2p1.py

@@ -44,7 +44,7 @@ def setUp(self):
         self.fix = Sftof(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "GFDL-CM2P1", "fx", "sftof"),
             [Sftof(None), AllVars(None), GenericFix(None)],
@@ -67,7 +67,7 @@ def setUp(self):
         self.fix = Areacello(self.vardef)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "GFDL-CM2P1", "Amon", "areacello"),
             [
@@ -114,7 +114,7 @@ def setUp(self):
         self.fix = Sit(self.var_info_mock)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "GFDL-CM2P1", "OImon", "sit"),
             [Sit(self.var_info_mock), AllVars(None), GenericFix(None)],

tests/integration/cmor/_fixes/cmip5/test_gfdl_cm3.py

@@ -20,7 +20,7 @@ def setUp(self):
         self.fix = Sftof(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "GFDL-CM3", "fx", "sftof"),
             [Sftof(None), AllVars(None), GenericFix(None)],
@@ -43,7 +43,7 @@ def setUp(self):
         self.fix = Areacello(self.vardef)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "GFDL-CM3", "Amon", "areacello"),
             [

tests/integration/cmor/_fixes/cmip5/test_gfdl_esm2g.py

@@ -79,7 +79,7 @@ def setUp(self):
         self.fix = Co2(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "GFDL-ESM2G", "Amon", "co2"),
             [Co2(None), AllVars(None), GenericFix(None)],
@@ -102,7 +102,7 @@ def setUp(self):
         self.fix = Usi(self.vardef)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "GFDL-ESM2G", "day", "usi"),
             [Usi(self.vardef), AllVars(self.vardef), GenericFix(self.vardef)],
@@ -124,7 +124,7 @@ def setUp(self):
         self.fix = Vsi(self.vardef)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "GFDL-ESM2G", "day", "vsi"),
             [Vsi(self.vardef), AllVars(self.vardef), GenericFix(self.vardef)],
@@ -146,7 +146,7 @@ def setUp(self):
         self.fix = Areacello(self.vardef)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "GFDL-ESM2G", "fx", "areacello"),
             [

tests/integration/cmor/_fixes/cmip5/test_gfdl_esm2m.py

@@ -25,7 +25,7 @@ def setUp(self):
         self.fix = Sftof(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "GFDL-ESM2M", "fx", "sftof"),
             [Sftof(None), AllVars(None), GenericFix(None)],
@@ -47,7 +47,7 @@ def setUp(self):
         self.fix = Co2(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "GFDL-ESM2M", "Amon", "co2"),
             [Co2(None), AllVars(None), GenericFix(None)],
@@ -70,7 +70,7 @@ def setUp(self):
         self.fix = Areacello(self.vardef)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "GFDL-ESM2M", "fx", "areacello"),
             [

tests/integration/cmor/_fixes/cmip5/test_hadgem2_cc.py

@@ -11,7 +11,7 @@ class TestAllVars(unittest.TestCase):
     """Test allvars fixes."""
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "HADGEM2-CC", "Amon", "tas"),
             [AllVars(None), GenericFix(None)],
@@ -22,7 +22,7 @@ class TestO2(unittest.TestCase):
     """Test o2 fixes."""
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "HADGEM2-CC", "Amon", "o2"),
             [O2(None), AllVars(None), GenericFix(None)],

tests/integration/cmor/_fixes/cmip5/test_miroc_esm_chem.py

@@ -19,7 +19,7 @@ def setUp(self):
         self.fix = Tro3(None)
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "MIROC-ESM-CHEM", "Amon", "tro3"),
             [Tro3(None), GenericFix(None)],

tests/integration/cmor/_fixes/cmip5/test_mri_esm1.py

@@ -11,7 +11,7 @@ class TestMsftmyz(unittest.TestCase):
     """Test msftmyz fixes."""
 
     def test_get(self):
-        """Test fix get"""
+        """Test fix get."""
         self.assertListEqual(
             Fix.get_fixes("CMIP5", "MRI-ESM1", "Amon", "msftmyz"),
             [Msftmyz(None), GenericFix(None)],

tests/integration/cmor/_fixes/cmip5/test_noresm1_me.py

@@ -72,7 +72,7 @@ def test_tas(cubes_in, cubes_out):
 
 
 def test_get():
-    """Test fix get"""
+    """Test fix get."""
     assert Fix.get_fixes("CMIP5", "NORESM1-ME", "Amon", "tas") == [
         Tas(None),
         GenericFix(None),