From 26e51aaeb8abf14cf9ca929b2b4a3e3803e37fe4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 3 Apr 2023 18:50:44 +0000
Subject: [PATCH 1/7] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/psf/black: 23.1.0 → 23.3.0](https://github.com/psf/black/compare/23.1.0...23.3.0)
- [github.com/charliermarsh/ruff-pre-commit: v0.0.254 → v0.0.260](https://github.com/charliermarsh/ruff-pre-commit/compare/v0.0.254...v0.0.260)
- [github.com/nbQA-dev/nbQA: 1.6.3 → 1.7.0](https://github.com/nbQA-dev/nbQA/compare/1.6.3...1.7.0)
- [github.com/MarcoGorelli/cython-lint: v0.12.5 → v0.15.0](https://github.com/MarcoGorelli/cython-lint/compare/v0.12.5...v0.15.0)
---
 .pre-commit-config.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 934229ed31a..45ba371defd 100644
--- a/.pre-commit-config.yaml
+++ b/.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: v0.0.260
   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]

From 26ca605c03e135b664956b4fa75b46f5badab30e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 3 Apr 2023 18:52:43 +0000
Subject: [PATCH 2/7] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 yt/funcs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/yt/funcs.py b/yt/funcs.py
index 3f48268a063..cbbc30c96ec 100644
--- a/yt/funcs.py
+++ b/yt/funcs.py
@@ -607,7 +607,7 @@ 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):

From ecdf8ced3f5e9b684b8c3dc25fcc0d98684f00a2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Robert?= <cr52@protonmail.com>
Date: Mon, 3 Apr 2023 21:02:50 +0200
Subject: [PATCH 3/7] MNT: cleanup unused target-version option in ruff

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6ae9b5ee205..da45de8149c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -265,7 +265,6 @@ exclude = '''
 '''
 
 [tool.ruff]
-target-version = "py38"  # https://github.com/charliermarsh/ruff/issues/2039
 exclude = [
     "doc",
     "benchmarks",

From 8b539cc3bb1ecaaaf89af212be77402e26b8e2cd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Robert?= <cr52@protonmail.com>
Date: Mon, 3 Apr 2023 21:29:17 +0200
Subject: [PATCH 4/7] STY: add explicit stacklevel argument to warnings.warn
 calls (B028)

---
 yt/data_objects/construction_data_containers.py | 1 +
 yt/data_objects/static_output.py                | 3 ++-
 yt/frontends/amrvac/data_structures.py          | 1 +
 yt/loaders.py                                   | 3 ++-
 yt/utilities/answer_testing/framework.py        | 3 ++-
 yt/utilities/configure.py                       | 7 +++++--
 yt/visualization/_commons.py                    | 3 ++-
 yt/visualization/base_plot_types.py             | 3 ++-
 yt/visualization/plot_container.py              | 3 ++-
 yt/visualization/plot_modifications.py          | 5 +++--
 10 files changed, 22 insertions(+), 10 deletions(-)

diff --git a/yt/data_objects/construction_data_containers.py b/yt/data_objects/construction_data_containers.py
index e8cb0486663..016ca47f246 100644
--- a/yt/data_objects/construction_data_containers.py
+++ b/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):
diff --git a/yt/data_objects/static_output.py b/yt/data_objects/static_output.py
index 39b66ff254f..7ce7f8f1c5c 100644
--- a/yt/data_objects/static_output.py
+++ b/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)
diff --git a/yt/frontends/amrvac/data_structures.py b/yt/frontends/amrvac/data_structures.py
index 4ddbd0289da..d5c66bda339 100644
--- a/yt/frontends/amrvac/data_structures.py
+++ b/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(
diff --git a/yt/loaders.py b/yt/loaders.py
index 0974abef632..57cffd81b5c 100644
--- a/yt/loaders.py
+++ b/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)
diff --git a/yt/utilities/answer_testing/framework.py b/yt/utilities/answer_testing/framework.py
index 0e72ffe6b90..c738b408baf 100644
--- a/yt/utilities/answer_testing/framework.py
+++ b/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]),
diff --git a/yt/utilities/configure.py b/yt/utilities/configure.py
index adcf9d262b3..7894b63314f 100644
--- a/yt/utilities/configure.py
+++ b/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)
 
diff --git a/yt/visualization/_commons.py b/yt/visualization/_commons.py
index f07484cf9a9..6f87f949cba 100644
--- a/yt/visualization/_commons.py
+++ b/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)
diff --git a/yt/visualization/base_plot_types.py b/yt/visualization/base_plot_types.py
index a4e782eb228..7e6d8b6893e 100644
--- a/yt/visualization/base_plot_types.py
+++ b/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
diff --git a/yt/visualization/plot_container.py b/yt/visualization/plot_container.py
index eb2b307445f..6b5198ba28a 100644
--- a/yt/visualization/plot_container.py
+++ b/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
 
diff --git a/yt/visualization/plot_modifications.py b/yt/visualization/plot_modifications.py
index c050e35e928..2adb5487dac 100644
--- a/yt/visualization/plot_modifications.py
+++ b/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
 

From 317a22c189c8547ad0a3987e635185d786b21e2e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Robert?= <cr52@protonmail.com>
Date: Mon, 3 Apr 2023 21:34:41 +0200
Subject: [PATCH 5/7] STY: disable spurious linter warning (B018)

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index da45de8149c..62aea0b84d1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -292,6 +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
 ]
 
 

From 5ccbc32e9c9c11f99f5262d07c0281807f8cd53c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Robert?= <cr52@protonmail.com>
Date: Wed, 5 Apr 2023 10:30:23 +0200
Subject: [PATCH 6/7] MNT: upgrade ruff (get by false positives with B030)

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 45ba371defd..0943441ed39 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -39,7 +39,7 @@ repos:
         additional_dependencies: [black==23.1.0]
 
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.0.260
+  rev: v0.0.261
   hooks:
   - id: ruff
     args: [--fix]

From b3fe5fc095f68ad0836fbf9dd3b3508b0cd34fce Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 5 Apr 2023 08:37:07 +0000
Subject: [PATCH 7/7] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 yt/funcs.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/yt/funcs.py b/yt/funcs.py
index cbbc30c96ec..6be779b9257 100644
--- a/yt/funcs.py
+++ b/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 {} to {} ".format(*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):