update isort and flake in cicd to fix pre-commit

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
       - id: check-yaml
   # isort should run before black as black sometimes tweaks the isort output
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
   # https://github.com/python/black#version-control-integration
@@ -17,10 +17,10 @@ repos:
     hooks:
       - id: black
   - repo: https://github.com/keewis/blackdoc
-    rev: v0.3.4
+    rev: v0.3.9
     hooks:
       - id: blackdoc
   - repo: https://github.com/PyCQA/flake8
-    rev: 3.8.4
+    rev: 6.1.0
     hooks:
       - id: flake8

CHANGELOG.md

@@ -14,6 +14,10 @@
 - add Zenodo integration and add citation file
   [\#195](https://github.com/EUREC4A-UK/lagtraj/pull/195) @leifdenby
 
+- update versions of flake8, black and isort in pre-commit config and resolve
+  linting issues arising from these updates
+  [\#206](https://github.com/EUREC4A-UK/lagtraj/pull/206), @leifdenby
+
 
 ## [v0.1.2](https://github.com/EUREC4A-UK/lagtraj/tree/v0.1.2)
 

lagtraj/domain/sources/era5/load.py

@@ -165,7 +165,7 @@ def _extra_var(self, v):
         return da_combined
 
     def __getitem__(self, item):
-        requested_vars = type(item) == set and item or set(item)
+        requested_vars = set(item)
         available_vars = self._selected_vars or self.data_vars
         missing_vars = requested_vars.difference(available_vars)
         if len(missing_vars) > 0:
@@ -292,7 +292,7 @@ def interp(self, kwargs, method="linear", **interp_to):
                 if np.array(interp_to[d]) in d_vals_array:
                     slices[d] = interp_to[d]
                     continue
-                if type(interp_to[d]) == xr.core.dataarray.DataArray:
+                if isinstance(interp_to[d], xr.core.dataarray.DataArray):
                     d_interp_val = interp_to[d].values
                 else:
                     d_interp_val = interp_to[d]

lagtraj/input_definitions/__init__.py

@@ -58,7 +58,7 @@ def _check_field(f_name, f_option):
         # with the fields `requires` and `choices` can be provided. `requires`
         # indicate other validations that must pass and choices are the valid
         # choices if they pass
-        if type(f_option) == dict:
+        if isinstance(f_option, dict):
             if "requires" in f_option and "choices" in f_option:
                 requirements = f_option["requires"]
                 satisfied_requirements = {}
@@ -122,7 +122,9 @@ def _check_field(f_name, f_option):
 
         # here we check whether the parameter was prescribed to have a specific
         # type and in that case whether the value provided has the correct type
-        if type(f_option) == type and type(input_params[f_name]) != f_option:
+        if isinstance(f_option, type) and not isinstance(
+            input_params[f_name], f_option
+        ):
             raise InvalidInputDefinition(
                 "Field `{}` should have type {}, but has type `{}`".format(
                     f_name, f_option, type(input_params[f_name])
@@ -138,7 +140,7 @@ def _check_field(f_name, f_option):
 
         # choices a given as a list or tuple, so we call `_check_field`
         # recursively to see if one of the options fit
-        if type(f_option) == list or type(f_option) == tuple:
+        if isinstance(f_option, list) or isinstance(f_option, tuple):
             f_options = f_option
             exceptions = []
             new_val = None

lagtraj/trajectory/create.py

@@ -73,7 +73,7 @@ def main(data_path, trajectory_name):
         da_times = _get_times_from_domain(
             trajectory_definition=traj_definition, root_data_path=data_path
         )
-    elif type(traj_definition.timestep) == datetime.timedelta:
+    elif isinstance(traj_definition.timestep, datetime.timedelta):
         da_times = _build_times_dataarray(
             origin=traj_definition.origin,
             duration=traj_definition.duration,

lagtraj/utils/xarray.py

@@ -14,7 +14,7 @@ def create_attributes_dictionary(*args, **kwargs):
     """
 
     def _serialize_item(item, prefix=""):
-        if type(item) == str:
+        if isinstance(item, str):
             yield (prefix, item)
         elif isinstance(item, float) or isinstance(item, int):
             yield (prefix, str(item))
@@ -24,17 +24,17 @@ def _serialize_item(item, prefix=""):
             yield (prefix, item.isoformat())
         else:
             sub_items = []
-            if type(item) == dict:
+            if isinstance(item, dict):
                 sub_items = item.items()
             elif (
                 isinstance(item, xr.Dataset)
                 or isinstance(item, xr.DataArray)
                 or isinstance(item, ERA5DataSet)
             ):
                 sub_items = item.attrs.items()
-            # can use isinstance because namedtuple is a kind of tuple and we
+            # can't use isinstance because namedtuple is a kind of tuple and we
             # want to save the tuple keys in that case
-            elif isinstance(item, list) or type(item) == tuple:
+            elif isinstance(item, list) or type(item) is tuple:
                 sub_items = zip(range(len(item)), item)
             else:
                 # collections.named_tuple has a `_asdict` method to turn it into a dictionary
@@ -64,5 +64,7 @@ def _serialize_item(item, prefix=""):
     ]
     for item in items:
         for (label, value) in _serialize_item(item=item):
+            if not isinstance(label, str):
+                raise ValueError(f"Expected string, got {type(label)}")
             attrs[label] = value
     return attrs

setup.cfg

@@ -42,9 +42,9 @@ dev =
 
 [flake8]
 max-line-length = 88
-extend-ignore = E203
+extend-ignore = E203, E713, E501, E701
 select = C,E,F,W,B,B950
-ignore = E203, E501, W503
+ignore = E203, E501, W503, W604
 
 [isort]
 profile=black

tests/test_cli.py

@@ -87,7 +87,7 @@ def _parse_readme_cli_commands():
 
     lines = [line.replace("$>", "").strip() for line in lines]
 
-    cli_commands = list(filter(lambda l: "python -m lagtraj" in l, lines))
+    cli_commands = list(filter(lambda line: "python -m lagtraj" in line, lines))
 
     return cli_commands