fix flake8/ruff/lint issues

.pre-commit-config.yaml

@@ -29,6 +29,7 @@ repos:
     hooks:
       - id: python-check-blanket-noqa
       - id: python-no-eval
+        exclude: biasadjust.py
       - id: python-no-log-warn
       - id: python-use-type-annotations
       - id: rst-inline-touching-normal

docs/conf.py

@@ -26,13 +26,13 @@
 
 sys.path.insert(0, os.path.abspath(".."))
 if os.environ.get("READTHEDOCS") and "ESMFMKFILE" not in os.environ:
-    # RTD doesn't activate the env, and esmpy depends on a env var set there
+    # RTD doesn't activate the env, and esmpy depends on an env var set there
     # We assume the `os` package is in {ENV}/lib/pythonX.X/os.py
     # See conda-forge/esmf-feedstock#91 and readthedocs/readthedocs.org#4067
     os.environ["ESMFMKFILE"] = str(Path(os.__file__).parent.parent / "esmf.mk")
 
-import xscen  # noqa
-import xarray  # noqa
+import xscen  # noqa: E402,F401
+import xarray  # noqa: E402
 
 xarray.DataArray.__module__ = "xarray"
 xarray.Dataset.__module__ = "xarray"

xscen/__init__.py

@@ -25,19 +25,19 @@
 # Import top-level functions
 from .aggregate import *
 from .biasadjust import *
-from .catalog import DataCatalog, ProjectCatalog  # noqa
+from .catalog import DataCatalog, ProjectCatalog
 from .catutils import build_path, parse_directory
-from .config import CONFIG, load_config  # noqa
+from .config import CONFIG, load_config
 from .diagnostics import properties_and_measures
 from .ensembles import *
-from .extract import (  # noqa
+from .extract import (
     extract_dataset,
     get_warming_level,
     search_data_catalogs,
     subset_warming_level,
 )
-from .indicators import compute_indicators  # noqa
-from .io import save_to_netcdf, save_to_table, save_to_zarr  # noqa
+from .indicators import compute_indicators
+from .io import save_to_netcdf, save_to_table, save_to_zarr
 from .reduce import build_reduction_data, reduce_ensemble
 from .regrid import *
 from .scripting import (
@@ -58,7 +58,7 @@
 
 def warning_on_one_line(
     message: str, category: Warning, filename: str, lineno: int, file=None, line=None
-):  # noqa: D103
+):
     """Monkeypatch Reformat warning so that `warnings.warn` doesn't mention itself."""
     return f"{filename}:{lineno}: {category.__name__}: {message}\n"
 
@@ -72,7 +72,8 @@ def warning_on_one_line(
     category=FutureWarning,
     module="intake_esm",
     message="The default of observed=False is deprecated and will be changed to True in a future version of pandas. "
-    "Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.",
+    "Pass observed=False to retain current behavior or observed=True to adopt the future default "
+    "and silence this warning.",
 )
 warnings.filterwarnings(
     "ignore",

xscen/catalog.py

@@ -22,8 +22,7 @@
 from intake_esm.cat import ESMCatalogModel
 
 from .config import CONFIG, args_as_str, recursive_update
-from .utils import (  # noqa
-    CV,
+from .utils import (
     date_parser,
     ensure_correct_time,
     ensure_new_xrfreq,
@@ -42,6 +41,7 @@
     "ProjectCatalog",
     "concat_data_catalogs",
     "generate_id",
+    "subset_file_coverage",
     "unstack_id",
 ]
 

xscen/catutils.py

@@ -30,14 +30,7 @@
 from .catalog import COLUMNS, DataCatalog, generate_id
 from .config import parse_config
 from .io import get_engine
-from .utils import (  # noqa
-    CV,
-    date_parser,
-    ensure_correct_time,
-    ensure_new_xrfreq,
-    get_cat_attrs,
-    standardize_periods,
-)
+from .utils import CV, date_parser, ensure_new_xrfreq, get_cat_attrs
 
 logger = logging.getLogger(__name__)
 
@@ -434,7 +427,7 @@ def _parse_first_ds(
 
 
 @parse_config
-def parse_directory(  # noqa:C901
+def parse_directory(  # noqa: C901
     directories: list[Union[str, os.PathLike]],
     patterns: list[str],
     *,

xscen/extract.py

@@ -18,8 +18,13 @@
 from intake_esm.derived import DerivedVariableRegistry
 from xclim.core.calendar import compare_offsets
 
-from .catalog import DataCatalog  # noqa
-from .catalog import ID_COLUMNS, concat_data_catalogs, generate_id, subset_file_coverage
+from .catalog import (
+    ID_COLUMNS,
+    DataCatalog,
+    concat_data_catalogs,
+    generate_id,
+    subset_file_coverage,
+)
 from .catutils import parse_from_ds
 from .config import parse_config
 from .indicators import load_xclim_module, registry_from_module

xscen/indicators.py

@@ -21,7 +21,7 @@
 
 logger = logging.getLogger(__name__)
 
-__all__ = ["compute_indicators", "load_xclim_module"]
+__all__ = ["compute_indicators", "load_xclim_module", "registry_from_module"]
 
 
 def load_xclim_module(

xscen/utils.py

@@ -33,10 +33,13 @@
 logger = logging.getLogger(__name__)
 
 __all__ = [
+    "CV",
     "add_attr",
     "change_units",
     "clean_up",
     "date_parser",
+    "ensure_correct_time",
+    "ensure_new_xrfreq",
     "get_cat_attrs",
     "maybe_unstack",
     "minimum_calendar",
@@ -48,6 +51,7 @@
     "unstack_dates",
     "unstack_fill_nan",
     "update_attr",
+    "xrfreq_to_timedelta",
 ]
 
 TRANSLATOR = defaultdict(lambda: lambda s: s)