Manual fixes and ignores

Author: bouweandela

esmvalcore/_main.py

@@ -521,7 +521,7 @@ def _clean_preproc(session):
 
         if (
             not session["save_intermediary_cubes"]
-            and session._fixed_file_dir.exists()
+            and session._fixed_file_dir.exists()  # noqa: SLF001
         ):
             logger.debug(
                 "Removing `preproc/fixed_files` directory containing fixed "
@@ -532,7 +532,7 @@ def _clean_preproc(session):
                 "`save_intermediary_cubes` to `true` and `remove_preproc_dir` "
                 "to `false` in your configuration",
             )
-            shutil.rmtree(session._fixed_file_dir)
+            shutil.rmtree(session._fixed_file_dir)  # noqa: SLF001
 
         if session["remove_preproc_dir"] and session.preproc_dir.exists():
             logger.info(
@@ -634,7 +634,6 @@ def display(lines, out):
         logger.exception(
             "Program terminated abnormally, see stack trace "
             "below for more information:",
-            exc_info=True,
         )
         logger.info(
             "\n"

esmvalcore/_recipe/check.py

@@ -167,7 +167,7 @@ def variable(
 def _log_data_availability_errors(dataset):
     """Check if the required input data is available."""
     input_files = dataset.files
-    patterns = dataset._file_globs
+    patterns = dataset._file_globs  # noqa: SLF001
     if not input_files:
         logger.error("No input files found for %s", dataset)
         if patterns:
@@ -436,22 +436,20 @@ def _check_duration_periods(timerange):
         try:
             isodate.parse_duration(timerange[0])
         except isodate.isoerror.ISO8601Error as exc:
-            raise RecipeError(
-                "Invalid value encountered for `timerange`. "
-                f"{timerange[0]} is not valid duration according to ISO 8601."
-                + "\n"
-                + str(exc),
-            ) from exc
+            msg = (
+                f"Invalid value encountered for `timerange`. {timerange[0]} is "
+                f"not valid duration according to ISO 8601.\n{exc}"
+            )
+            raise RecipeError(msg) from exc
     elif timerange[1].startswith("P"):
         try:
             isodate.parse_duration(timerange[1])
         except isodate.isoerror.ISO8601Error as exc:
-            raise RecipeError(
-                "Invalid value encountered for `timerange`. "
-                f"{timerange[1]} is not valid duration according to ISO 8601."
-                + "\n"
-                + str(exc),
-            ) from exc
+            msg = (
+                f"Invalid value encountered for `timerange`. {timerange[1]} is "
+                f"not valid duration according to ISO 8601.\n{exc}"
+            )
+            raise RecipeError(msg) from exc
 
 
 def _check_format_years(date):
@@ -475,13 +473,14 @@ def _check_timerange_values(date, timerange):
         else:
             isodate.parse_date(date)
     except isodate.isoerror.ISO8601Error as exc:
-        raise RecipeError(
+        msg = (
             "Invalid value encountered for `timerange`. "
             "Valid value must follow ISO 8601 standard "
             "for dates and duration periods, or be "
             "set to '*' to load available years. "
-            f"Got {timerange} instead." + "\n" + str(exc),
-        ) from exc
+            f"Got {timerange} instead.\n{exc}"
+        )
+        raise RecipeError(msg) from exc
 
 
 def valid_time_selection(timerange):

esmvalcore/_recipe/to_datasets.py

@@ -425,7 +425,9 @@ def datasets_from_recipe(
     return datasets
 
 
-def _dataset_from_files(dataset: Dataset) -> list[Dataset]:
+def _dataset_from_files(  # noqa: C901
+    dataset: Dataset,
+) -> list[Dataset]:
     """Replace facet values of '*' based on available files."""
     result: list[Dataset] = []
     errors: list[str] = []
@@ -519,7 +521,7 @@ def _report_unexpanded_globs(
         )
     else:
         timerange = expanded_ds.facets.get("timerange")
-        patterns = expanded_ds._file_globs
+        patterns = expanded_ds._file_globs  # noqa: SLF001
         msg = (
             f"{msg}\nNo files found matching:\n"
             + "\n".join(str(p) for p in patterns)  # type: ignore[union-attr]

esmvalcore/cmor/_fixes/cesm/cesm2.py

@@ -16,6 +16,7 @@
 """
 
 import logging
+from typing import ClassVar
 
 from iris.cube import CubeList
 
@@ -28,7 +29,7 @@ class AllVars(NativeDatasetFix):
     """Fixes for all variables."""
 
     # Dictionary to map invalid units in the data to valid entries
-    INVALID_UNITS = {
+    INVALID_UNITS: ClassVar[dict[str, str]] = {
         "fraction": "1",
     }
 

esmvalcore/cmor/_fixes/cmip6/mcm_ua_1_0.py

@@ -26,7 +26,10 @@ def strip_cube_metadata(cube):
 class AllVars(Fix):
     """Fixes for all variables."""
 
-    def fix_metadata(self, cubes):
+    def fix_metadata(  # noqa: C901
+        self,
+        cubes,
+    ):
         """Fix metadata.
 
         Remove unnecessary spaces in metadata and rename ``var_name`` of

esmvalcore/cmor/_fixes/emac/emac.py

@@ -14,6 +14,7 @@
 import logging
 import warnings
 from shutil import copyfile
+from typing import ClassVar
 
 import dask.array as da
 import iris.analysis
@@ -36,7 +37,7 @@ class AllVars(EmacFix):
     """Fixes for all variables."""
 
     # Dictionary to map invalid units in the data to valid entries
-    INVALID_UNITS = {
+    INVALID_UNITS: ClassVar[dict[str, str]] = {
         "kg/m**2s": "kg m-2 s-1",
     }
 

esmvalcore/cmor/_fixes/fix.py

@@ -844,25 +844,21 @@ def _fix_time_units(self, cube: Cube, cube_coord: Coord) -> None:
 
                     branch_parent = "branch_time_in_parent"
                     if branch_parent in attrs:
-                        try:
+                        # Overflow happens when the time is very large.
+                        with contextlib.suppress(OverflowError):
                             attrs[branch_parent] = parent_units.convert(
                                 attrs[branch_parent],
                                 cube_coord.units,
                             )
-                        except OverflowError:
-                            # This happens when the time is very large.
-                            pass
 
                     branch_child = "branch_time_in_child"
                     if branch_child in attrs:
-                        try:
+                        # Overflow happens when the time is very large.
+                        with contextlib.suppress(OverflowError):
                             attrs[branch_child] = old_units.convert(
                                 attrs[branch_child],
                                 cube_coord.units,
                             )
-                        except OverflowError:
-                            # This happens when the time is very large.
-                            pass
 
     def _fix_time_bounds(self, cube: Cube, cube_coord: Coord) -> None:
         """Fix time bounds."""

esmvalcore/cmor/_fixes/native6/era5.py

@@ -497,7 +497,10 @@ def fix_metadata(self, cubes):
 class AllVars(Fix):
     """Fixes for all variables."""
 
-    def _fix_coordinates(self, cube):
+    def _fix_coordinates(  # noqa: C901
+        self,
+        cube,
+    ):
         """Fix coordinates."""
         # Add scalar height coordinates
         if "height2m" in self.vardef.dimensions:

esmvalcore/cmor/_fixes/native_datasets.py

@@ -3,7 +3,8 @@
 from __future__ import annotations
 
 import logging
-from typing import TYPE_CHECKING
+from contextlib import suppress
+from typing import TYPE_CHECKING, ClassVar
 
 from iris import NameConstraint
 
@@ -27,7 +28,7 @@ class NativeDatasetFix(Fix):
     """Common fix operations for native datasets."""
 
     # Dictionary to map invalid units in the data to valid entries
-    INVALID_UNITS: dict[str, str] = {}
+    INVALID_UNITS: ClassVar[dict[str, str]] = {}
 
     def fix_scalar_coords(self, cube: Cube) -> None:
         """Add missing scalar coordinate to cube (in-place).
@@ -240,10 +241,8 @@ def guess_coord_bounds(cube: Cube, coord: Coord) -> Coord:
         if isinstance(coord, str):
             coord = cube.coord(coord)
         if not coord.has_bounds():
-            try:
+            with suppress(ValueError):
                 coord.guess_bounds()
-            except ValueError:  # Coord has only 1 point
-                pass
         return coord
 
     @staticmethod

esmvalcore/cmor/check.py

@@ -3,10 +3,9 @@
 from __future__ import annotations
 
 import logging
-from collections import namedtuple
 from enum import IntEnum
 from functools import cached_property
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, NamedTuple
 
 import cf_units
 import dask
@@ -247,7 +246,9 @@ def _check_fill_value(self):
         #
         #  => Very difficult to check!
 
-    def _check_var_metadata(self):
+    def _check_var_metadata(  # noqa: C901
+        self,
+    ):
         """Check metadata of variable."""
         # Check standard_name
         if self._cmor_var.standard_name:
@@ -534,7 +535,12 @@ def _check_coords(self):
 
     def _check_coord_ranges(self, coords: list[tuple[CoordinateInfo, Coord]]):
         """Check coordinate value are inside valid ranges."""
-        Limit = namedtuple("Limit", ["name", "type", "limit", "value"])
+
+        class Limit(NamedTuple):
+            name: str
+            type: str
+            limit: float
+            value: float
 
         limits = []
         for coord_info, coord in coords:
@@ -621,7 +627,12 @@ def _check_time_bounds(self, time):
                 self._cmor_var.short_name,
             )
 
-    def _check_coord_monotonicity_and_direction(self, cmor, coord, var_name):
+    def _check_coord_monotonicity_and_direction(  # noqa: C901
+        self,
+        cmor,
+        coord,
+        var_name,
+    ):
         """Check monotonicity and direction of coordinate."""
         if coord.ndim > 1:
             return
@@ -687,7 +698,9 @@ def _check_requested_values(self, coord, coord_info, var_name):
                         str(coord.units),
                     )
 
-    def _check_time_coord(self):
+    def _check_time_coord(  # noqa: C901,PLR0912,PLR0915
+        self,
+    ):
         """Check time coordinate."""
         try:
             coord = self._cube.coord("time", dim_coords=True)