Merge pull request #4395 from yt-project/pre-commit-ci-update-config

.pre-commit-config.yaml

@@ -28,7 +28,7 @@ repos:
     - id: check-yaml
 
 -   repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.3.0
     hooks:
     - id: black-jupyter
 
@@ -39,13 +39,13 @@ repos:
         additional_dependencies: [black==23.1.0]
 
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.0.254
+  rev: v0.0.261
   hooks:
   - id: ruff
     args: [--fix]
 
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.6.3
+  rev: 1.7.0
   hooks:
   - id: nbqa-ruff
     args: [--fix, --extend-ignore=E402]
@@ -56,7 +56,7 @@ repos:
     -   id: rst-backticks
 
 - repo: https://github.com/MarcoGorelli/cython-lint
-  rev: v0.12.5
+  rev: v0.15.0
   hooks:
   - id: cython-lint
     args: [--no-pycodestyle]

pyproject.toml

@@ -265,7 +265,6 @@ exclude = '''
 '''
 
 [tool.ruff]
-target-version = "py38"  # https://github.com/charliermarsh/ruff/issues/2039
 exclude = [
     "doc",
     "benchmarks",
@@ -293,6 +292,7 @@ select = [
 ignore = [
     "E501",  # line too long
     "E741",  # Do not use variables named 'I', 'O', or 'l'
+    "B018",  # Found useless expression. # disabled because ds.index is idiomatic
 ]
 
 

yt/data_objects/construction_data_containers.py

@@ -1490,6 +1490,7 @@ def _fill_fields(self, fields):
                 "This is likely due to missing ghost-zones support "
                 f"in class {type(self.ds)}",
                 category=RuntimeWarning,
+                stacklevel=1,
             )
             mylog.debug("Caught %d runtime errors.", runtime_errors_count)
         for field, v in zip(fields, ls.fields):

yt/data_objects/static_output.py

@@ -236,7 +236,8 @@ def __init_subclass__(cls, *args, **kwargs):
             warnings.warn(
                 f"Overwritting {cls.__name__}, which was previously registered. "
                 "This is expected if you're importing a yt extension with a "
-                "frontend that was already migrated to the main code base."
+                "frontend that was already migrated to the main code base.",
+                stacklevel=2,
             )
         output_type_registry[cls.__name__] = cls
         mylog.debug("Registering: %s as %s", cls.__name__, cls)

yt/frontends/amrvac/data_structures.py

@@ -97,6 +97,7 @@ def retrieve_ghost_zones(self, n_zones, fields, all_levels=False, smoothed=False
                 "ghost-zones interpolation/smoothing is not "
                 "currently supported for AMRVAC data.",
                 category=RuntimeWarning,
+                stacklevel=2,
             )
             smoothed = False
         return super().retrieve_ghost_zones(

yt/funcs.py

@@ -607,7 +607,8 @@ def fancy_download_file(url, filename, requests=None):
             iterations = int(float(total_length) / float(blocksize))
 
             pbar = get_pbar(
-                "Downloading %s to %s " % os.path.split(filename)[::-1], iterations
+                "Downloading {} to {} ".format(*os.path.split(filename)[::-1]),
+                iterations,
             )
             iteration = 0
             for chunk in response.iter_content(chunk_size=blocksize):

yt/loaders.py

@@ -1678,7 +1678,8 @@ def load_archive(
     """
 
     warnings.warn(
-        "The 'load_archive' function is still experimental and may be unstable."
+        "The 'load_archive' function is still experimental and may be unstable.",
+        stacklevel=2,
     )
 
     fn = os.path.expanduser(fn)

yt/utilities/answer_testing/framework.py

@@ -797,7 +797,8 @@ def ensure_image_comparability(a, b):
 
     warnings.warn(
         f"Images have different shapes {a.shape} and {b.shape}. "
-        "Padding nans to make them comparable."
+        "Padding nans to make them comparable.",
+        stacklevel=2,
     )
     smallest_containing_shape = (
         max(a.shape[0], b.shape[0]),

yt/utilities/configure.py

@@ -94,7 +94,8 @@ def read(self, file_names):
                     data = tomllib.load(fh)
             except tomllib.TOMLDecodeError as exc:
                 warnings.warn(
-                    f"Could not load configuration file {fname} (invalid TOML: {exc})"
+                    f"Could not load configuration file {fname} (invalid TOML: {exc})",
+                    stacklevel=2,
                 )
             else:
                 self.update(data, metadata=metadata)
@@ -117,7 +118,9 @@ def write(self, file_handler):
         else:
             pdir = file_path.parent
             if not pdir.exists():
-                warnings.warn(f"{pdir!s} does not exist, creating it (recursively)")
+                warnings.warn(
+                    f"{pdir!s} does not exist, creating it (recursively)", stacklevel=2
+                )
                 os.makedirs(pdir)
             file_path.write_text(config_as_str)
 

yt/visualization/_commons.py

@@ -96,7 +96,8 @@ def validate_image_name(filename, suffix: Optional[str] = None) -> str:
         if suffix in _get_supported_image_file_formats() and suffix != psuffix:
             warnings.warn(
                 f"Received two valid image formats {psuffix!r} (from filename) "
-                f"and {suffix!r} (from suffix). The former is ignored."
+                f"and {suffix!r} (from suffix). The former is ignored.",
+                stacklevel=2,
             )
             return f"{name}.{suffix}"
         return str(filename)

yt/visualization/base_plot_types.py

@@ -337,7 +337,8 @@ def _set_axes(self, norm: Normalize) -> None:
                         "with matplotlib versions older than 3.5\n"
                         "Please try upgrading matplotlib to a more recent version. "
                         "If the problem persists, please file a report to "
-                        "https://github.com/yt-project/yt/issues/new"
+                        "https://github.com/yt-project/yt/issues/new",
+                        stacklevel=2,
                     )
                 else:
                     raise exc

yt/visualization/plot_container.py

@@ -532,7 +532,8 @@ def save(
             if new_suffix != suffix:
                 warnings.warn(
                     f"Overriding suffix {suffix!r} with mpl_kwargs['format'] = {new_suffix!r}. "
-                    "Use the `suffix` argument directly to suppress this warning."
+                    "Use the `suffix` argument directly to suppress this warning.",
+                    stacklevel=2,
                 )
             suffix = new_suffix
 

yt/visualization/plot_modifications.py

@@ -1714,7 +1714,7 @@ def __call__(self, plot):
             dy = (yy1 - yy0) * 2 ** (0.5) * self.length
         # If the arrow is 0 length
         if dx == dy == 0:
-            warnings.warn("The arrow has zero length.  Not annotating.")
+            warnings.warn("The arrow has zero length. Not annotating.", stacklevel=2)
             return
 
         x, y, dx, dy = self._sanitize_xy_order(plot, x, y, dx, dy)
@@ -2586,7 +2586,8 @@ def __call__(self, plot):
         if self.redshift and not hasattr(plot.data.ds, "current_redshift"):
             warnings.warn(
                 f"dataset {plot.data.ds} does not have current_redshift attribute. "
-                "Set redshift=False to silence this warning."
+                "Set redshift=False to silence this warning.",
+                stacklevel=2,
             )
             self.redshift = False