Manually fix remaining issues

Author: bouweandela

esmvalcore/_main.py

@@ -35,11 +35,15 @@
 import sys
 from importlib.metadata import entry_points
 from pathlib import Path
+from typing import TYPE_CHECKING
 
 import fire
 
 from esmvalcore.config._config import warn_if_old_extra_facets_exist
 
+if TYPE_CHECKING:
+    from esmvalcore.config import Session
+
 # set up logging
 logger = logging.getLogger(__name__)
 
@@ -80,7 +84,7 @@ def parse_resume(resume, recipe):
     return resume
 
 
-def process_recipe(recipe_file: Path, session) -> None:
+def process_recipe(recipe_file: Path, session: Session) -> None:
     """Process recipe."""
     import datetime
     import shutil
@@ -634,7 +638,7 @@ def _create_session_dir(session):
     def _run(
         self,
         recipe: Path,
-        session,
+        session: Session,
         cli_config_dir: Path | None,
     ) -> None:
         """Run `recipe` using `session`."""
@@ -697,7 +701,7 @@ def _clean_preproc(session):
             shutil.rmtree(session.preproc_dir)
 
     @staticmethod
-    def _get_recipe(recipe) -> Path:
+    def _get_recipe(recipe: str) -> Path:
         from esmvalcore.config._diagnostics import DIAGNOSTICS
 
         if not os.path.isfile(recipe):

esmvalcore/_provenance.py

@@ -194,11 +194,11 @@ def __repr__(self) -> str:
         """Return representation string (e.g., used by ``pformat``)."""
         return f"{self.__class__.__name__}: {self.filename}"
 
-    def __eq__(self, other) -> bool:
+    def __eq__(self, other: object) -> bool:
         """Check if `other` equals `self`."""
         return hasattr(other, "filename") and self.filename == other.filename
 
-    def __lt__(self, other) -> bool:
+    def __lt__(self, other: object) -> bool:
         """Check if `other` should be sorted before `self`."""
         return hasattr(other, "filename") and self.filename < other.filename
 

esmvalcore/_recipe/check.py

@@ -364,7 +364,7 @@ def _verify_span_value(span: str) -> None:
         raise RecipeError(msg)
 
 
-def _verify_groupby(groupby: Any) -> None:
+def _verify_groupby(groupby: list[str]) -> None:
     """Raise error if groupby arguments cannot be verified."""
     if not isinstance(groupby, list):
         msg = (
@@ -375,7 +375,7 @@ def _verify_groupby(groupby: Any) -> None:
         raise RecipeError(msg)
 
 
-def _verify_keep_input_datasets(keep_input_datasets: Any) -> None:
+def _verify_keep_input_datasets(keep_input_datasets: bool) -> None:
     if not isinstance(keep_input_datasets, bool):
         msg = (
             f"Invalid value encountered for `keep_input_datasets`."
@@ -385,7 +385,7 @@ def _verify_keep_input_datasets(keep_input_datasets: Any) -> None:
         raise RecipeError(msg)
 
 
-def _verify_ignore_scalar_coords(ignore_scalar_coords: Any) -> None:
+def _verify_ignore_scalar_coords(ignore_scalar_coords: bool) -> None:
     if not isinstance(ignore_scalar_coords, bool):
         msg = (
             f"Invalid value encountered for `ignore_scalar_coords`."

esmvalcore/_recipe/recipe.py

@@ -59,6 +59,8 @@
 if TYPE_CHECKING:
     from collections.abc import Iterable, Sequence
 
+    from prov.model import ProvEntity
+
     from esmvalcore._task import BaseTask
     from esmvalcore.config import Session
     from esmvalcore.io.protocol import DataElement
@@ -965,7 +967,10 @@ def _need_ncl(raw_diagnostics: dict[str, Diagnostic]) -> bool:
                     return True
         return False
 
-    def _initialize_provenance(self, raw_documentation: dict[str, Any]):
+    def _initialize_provenance(
+        self,
+        raw_documentation: dict[str, Any],
+    ) -> ProvEntity:
         """Initialize the recipe provenance."""
         doc = deepcopy(raw_documentation)
 
@@ -1381,10 +1386,10 @@ def write_html_summary(self) -> None:
                 RecipeOutput,
             )
 
-            output = self.get_output()
-
             try:
-                output = RecipeOutput.from_core_recipe_output(output)
+                output = RecipeOutput.from_core_recipe_output(
+                    self.get_output(),
+                )
             except LookupError as error:
                 # See https://github.com/ESMValGroup/ESMValCore/issues/28
                 logger.warning("Could not write HTML report: %s", error)

esmvalcore/_task.py

@@ -285,7 +285,7 @@ def flatten(self):
         tasks.add(self)
         return tasks
 
-    def run(self, input_files=None):
+    def run(self, input_files: list[str] | None = None) -> None:
         """Run task."""
         if not self.output_files:
             if input_files is None:
@@ -310,7 +310,7 @@ def run(self, input_files=None):
         return self.output_files
 
     @abc.abstractmethod
-    def _run(self, input_files):
+    def _run(self, input_files: list[str]) -> list[str]:
         """Run task."""
 
     def get_product_attributes(self) -> dict:
@@ -364,7 +364,7 @@ def __init__(self, prev_preproc_dir, preproc_dir, name):
 
         super().__init__(ancestors=None, name=name, products=products)
 
-    def _run(self, _):
+    def _run(self, _: list[str]) -> list[str]:
         """Return the result of a previous run."""
         metadata = self.get_product_attributes()
 

esmvalcore/cmor/_fixes/fix.py

@@ -8,7 +8,7 @@
 import logging
 import tempfile
 from pathlib import Path
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Any
 
 import dask
 import numpy as np
@@ -423,12 +423,12 @@ def _msg_suffix(cube: Cube) -> str:
             return f"\n(for file {cube.attributes['source_file']})"
         return f"\n(for variable {cube.var_name})"
 
-    def _debug_msg(self, cube: Cube, msg: str, *args) -> None:
+    def _debug_msg(self, cube: Cube, msg: str, *args: Any) -> None:
         """Print debug message."""
         msg += self._msg_suffix(cube)
         generic_fix_logger.debug(msg, *args)
 
-    def _warning_msg(self, cube: Cube, msg: str, *args) -> None:
+    def _warning_msg(self, cube: Cube, msg: str, *args: Any) -> None:
         """Print debug message."""
         msg += self._msg_suffix(cube)
         generic_fix_logger.warning(msg, *args)

esmvalcore/cmor/fix.py

@@ -9,7 +9,7 @@
 
 import logging
 from collections import defaultdict
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Any
 
 from iris.cube import CubeList
 
@@ -38,7 +38,7 @@ def fix_file(  # noqa: PLR0913
     add_unique_suffix: bool = False,
     session: Session | None = None,
     frequency: str | None = None,
-    **extra_facets,
+    **extra_facets: Any,
 ) -> str | Path | xr.Dataset | ncdata.NcData:
     """Fix files before loading them into a :class:`~iris.cube.CubeList`.
 
@@ -121,7 +121,7 @@ def fix_metadata(
     mip: str,
     frequency: str | None = None,
     session: Session | None = None,
-    **extra_facets,
+    **extra_facets: Any,
 ) -> CubeList:
     """Fix cube metadata if fixes are required.
 
@@ -205,7 +205,7 @@ def fix_data(
     mip: str,
     frequency: str | None = None,
     session: Session | None = None,
-    **extra_facets,
+    **extra_facets: Any,
 ) -> Cube:
     """Fix cube data if fixes are required.
 

esmvalcore/config/_config.py

@@ -94,7 +94,7 @@ def warn_if_old_extra_facets_exist() -> None:
         )
 
 
-def load_config_developer(cfg_file) -> dict:
+def load_config_developer(cfg_file: Path) -> dict:
     """Read the developer's configuration file."""
     with open(cfg_file, encoding="utf-8") as file:
         cfg = yaml.safe_load(file)

esmvalcore/config/_config_validators.py

@@ -9,7 +9,7 @@
 from functools import lru_cache, partial
 from importlib.resources import files as importlib_files
 from pathlib import Path
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, Literal
 
 from packaging import version
 
@@ -49,7 +49,11 @@ class ValidationError(ValueError):
 # to fit the needs of ESMValCore. Matplotlib is licenced under the terms of
 # the the 'Python Software Foundation License'
 # (https://www.python.org/psf/license)
-def _make_type_validator(cls: Any, *, allow_none: bool = False) -> Any:
+def _make_type_validator(
+    cls: Any,  # noqa: ANN401
+    *,
+    allow_none: bool = False,
+) -> Callable:
     """Construct a type validator for `cls`.
 
     Return a validator that converts inputs to *cls* or raises (and
@@ -363,7 +367,9 @@ def validate_extra_facets_dir(value):
     return validate_pathlist(value)
 
 
-def validate_projects(value: Any) -> Any:
+def validate_projects(
+    value: dict,
+) -> dict[str, dict[str, Any]]:
     """Validate projects mapping."""
     mapping = validate_dict(value)
     options_for_project: dict[str, Callable[[Any], Any]] = {
@@ -446,8 +452,8 @@ def _handle_deprecation(
 # TODO: remove in v2.15.0
 def deprecate_extra_facets_dir(
     validated_config: ValidatedConfig,
-    value: Any,
-    validated_value: Any,
+    value: str | Path,
+    validated_value: str | Path,
 ) -> None:
     """Deprecate ``extra_facets_dir`` option.
 
@@ -483,8 +489,8 @@ def deprecate_extra_facets_dir(
 
 def deprecate_rootpath(
     validated_config: ValidatedConfig,
-    value: Any,
-    validated_value: Any,
+    value: dict,
+    validated_value: dict,
 ) -> None:
     """Deprecate ``rootpath`` option.
 
@@ -510,8 +516,8 @@ def deprecate_rootpath(
 
 def deprecate_drs(
     validated_config: ValidatedConfig,  # noqa: ARG001
-    value: Any,  # noqa: ARG001
-    validated_value: Any,  # noqa: ARG001
+    value: dict,  # noqa: ARG001
+    validated_value: dict,  # noqa: ARG001
 ) -> None:
     """Deprecate ``drs`` option.
 
@@ -531,8 +537,8 @@ def deprecate_drs(
 
 def deprecate_download_dir(
     validated_config: ValidatedConfig,  # noqa: ARG001
-    value: Any,  # noqa: ARG001
-    validated_value: Any,  # noqa: ARG001
+    value: str | Path,  # noqa: ARG001
+    validated_value: str | Path,  # noqa: ARG001
 ) -> None:
     """Deprecate ``download_dir`` option.
 
@@ -552,8 +558,8 @@ def deprecate_download_dir(
 
 def deprecate_search_esgf(
     validated_config: ValidatedConfig,
-    value: Any,  # noqa: ARG001
-    validated_value: Any,
+    value: Literal["never", "when_missing", "always"],  # noqa: ARG001
+    validated_value: Literal["never", "when_missing", "always"],
 ) -> None:
     """Deprecate ``search_esgf`` option.
 

esmvalcore/config/_diagnostics.py

@@ -3,6 +3,7 @@
 import logging
 import os
 from pathlib import Path
+from typing import Self
 
 import yaml
 
@@ -80,7 +81,7 @@ def __init__(self, *args, **kwargs):
         self.source_file = None
 
     @classmethod
-    def from_file(cls, filename: str):
+    def from_file(cls, filename: str) -> Self:
         """Load the reference tags used for provenance recording."""
         if os.path.exists(filename):
             logger.debug("Loading tags from %s", filename)
@@ -93,7 +94,7 @@ def from_file(cls, filename: str):
             logger.debug("No tags loaded, file %s not present", filename)
             return cls()
 
-    def set_tag_value(self, section: str, tag: str, value) -> None:
+    def set_tag_value(self, section: str, tag: str, value: str) -> None:
         """Set the value of a tag in a section.
 
         Parameters
@@ -110,7 +111,7 @@ def set_tag_value(self, section: str, tag: str, value) -> None:
 
         self[section][tag] = value
 
-    def set_tag_values(self, tag_values: dict) -> None:
+    def set_tag_values(self, tag_values: dict[str, dict[str, str]]) -> None:
         """Update tags from dict.
 
         Parameters
@@ -122,7 +123,7 @@ def set_tag_values(self, tag_values: dict) -> None:
             for tag, value in tags.items():
                 self.set_tag_value(section, tag, value)
 
-    def get_tag_value(self, section: str, tag: str):
+    def get_tag_value(self, section: str, tag: str) -> str:
         """Retrieve the value of a tag from a section.
 
         Parameters
@@ -140,21 +141,19 @@ def get_tag_value(self, section: str, tag: str):
         if tag not in self[section]:
             postfix = f" of {self.source_file}" if self.source_file else ""
             msg = f"Tag '{tag}' does not exist in section '{section}'{postfix}"
-            raise ValueError(
-                msg,
-            )
+            raise ValueError(msg)
 
         return self[section][tag]
 
-    def get_tag_values(self, section: str, tags: tuple):
+    def get_tag_values(self, section: str, tags: tuple) -> tuple[str, ...]:
         """Retrieve the values for a list of tags from a section.
 
         Parameters
         ----------
-        section : str
+        section
             Name of the subsection
-        tags : tuple[str] or list[str]
-            List or tuple with tag names
+        tags
+            Tuple with tag names
         """
         return tuple(self.get_tag_value(section, tag) for tag in tags)