ruff fixes (#196)

* ruff fixes

* fix s101 use of assert

* globally ignore SLF001, access private class member

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add todo tag

* put docstring and global ignore on top

* fix py017, properly capture exception

* Fix PT011, exception capture without match

* add TODO tag for #195 (comment)

* fix NPY201, np trapz

* use warn over print to fix T201

* add comments for globally ignored ruff rules

* guard type check only import when possible

* remove ISC001 from ignore

* add todo tag

* reduce duration items shown to 20

* import Self from typing extension

* remove global ignore of S311 as there're only 2 violation

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* replace random with numpy, which also fixes S311

* fix "PT006",   # pytest-parametrize-names-wrong-type

* guard type check only import

* fix "COM812",  # trailing comma missing

* remove no type check mark

* Revert "fix "COM812",  # trailing comma missing"

This reverts commit 5ab3390.

* fix unit test of io

* NEED confirm: change width from 457 to 458

* clean up branch condition

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* use native array size arg

* revert accidental elem -> element rename

* fix random array generation

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix random array generate in asset maker

* revert test_io value to 457, reason unknown

* skip eslint for now #197

* format pre-commit config

* remove eslint skip mark in CI

* fix indentation in pyproject.toml

* drop quotes in test.yml string

* fix typo in filename

* fix shaded_ys type

* remove overwriting pytest duration

* pyproject whitespace

---------

Co-authored-by: Janosh Riebesell <[email protected]>

Author: DanielYang59

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 ci:
   autoupdate_schedule: quarterly
-  skip: [pyright, eslint]
+  skip: [pyright]
 
 default_stages: [commit]
 
@@ -76,6 +76,7 @@ repos:
     rev: v9.9.1
     hooks:
       - id: eslint
+        stages: [manual] # TODO: skip eslint for now
         types: [file]
         args: [--fix, --config, site/eslint.config.js]
         files: \.(js|ts|svelte)$

examples/dataset_exploration/ricci_carrier_transport/convert_dtype+add_strucs.py renamed to examples/dataset_exploration/ricci_carrier_transport/convert_dtype+add_structs.py

@@ -1,3 +1,6 @@
+# ruff: noqa: RUF001
+"""Unprocessed data in data/carrier_transport.json.gz obtained from https://git.io/JOMwY."""
+
 # %%
 import pandas as pd
 from matminer.datasets import load_dataset
@@ -6,12 +9,6 @@
 from pymatviz.enums import Key
 
 
-"""
-Unprocessed data in data/carrier_transport.json.gz obtained from https://git.io/JOMwY.
-"""
-# ruff: noqa: RUF001
-
-
 # %%
 df_carrier = load_dataset("ricci_boltztrap_mp_tabular")
 

examples/make_assets/phonons.py

@@ -11,6 +11,7 @@
 from pymatviz.enums import Key
 
 
+# TODO: ffonons not working properly (see #195)
 try:
     import ffonons  # noqa: F401
 except ImportError:

examples/make_assets/ptable/ptable_matplotlib.py

@@ -1,6 +1,4 @@
 # %%
-import random
-
 import numpy as np
 from matminer.datasets import load_dataset
 from pymatgen.core.periodic_table import Element
@@ -137,11 +135,10 @@
 
 
 # %% Evenly-split tile plots laid out as a periodic table
+rng = np.random.default_rng()
 for n_splits in (2, 3, 4):
     data_dict = {
-        elem.symbol: [
-            random.randint(10 * n_splits, 20 * (n_splits + 1)) for _ in range(n_splits)
-        ]
+        elem.symbol: rng.integers(10 * n_splits, 20 * (n_splits + 1), size=n_splits)
         for elem in Element
     }
 

pymatviz/bar.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 from collections.abc import Sequence
-from typing import Any, Literal, cast
+from typing import TYPE_CHECKING, cast
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -19,6 +19,10 @@
 from pymatviz.utils import PLOTLY, Backend, crystal_sys_from_spg_num, si_fmt_int
 
 
+if TYPE_CHECKING:
+    from typing import Any, Literal
+
+
 def spacegroup_bar(
     data: Sequence[int | str | Structure] | pd.Series,
     *,

pymatviz/cumulative.py

@@ -2,13 +2,15 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING
 
 import matplotlib.pyplot as plt
 import numpy as np
 
 
 if TYPE_CHECKING:
+    from typing import Any
+
     from numpy.typing import ArrayLike
 
 

pymatviz/enums.py

@@ -10,8 +10,11 @@
 
 
 if TYPE_CHECKING:
-    from typing import Any, Self
+    from typing import Any
 
+    from typing_extensions import Self
+
+# TODO: remove following definition of StrEnum once Python 3.11+
 if sys.version_info >= (3, 11):
     from enum import StrEnum
 else:

pymatviz/histogram.py

@@ -2,7 +2,8 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Literal
+import warnings
+from typing import TYPE_CHECKING
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -17,15 +18,18 @@
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
+    from typing import Any, Literal
 
     from pymatviz.utils import ElemValues
 
 
 def spacegroup_hist(*args: Any, **kwargs: Any) -> plt.Axes | go.Figure:
     """Alias for spacegroup_bar."""
-    print(  # noqa: T201
+    warnings.warn(
         "spacegroup_hist() is deprecated and will be removed in a future version. "
-        "use pymatviz.bar.spacegroup_bar() instead."
+        "use pymatviz.bar.spacegroup_bar() instead.",
+        category=DeprecationWarning,
+        stacklevel=2,
     )
     return spacegroup_bar(*args, **kwargs)
 

pymatviz/io.py

@@ -5,10 +5,11 @@
 import copy
 import os
 import subprocess
+import warnings
 from pathlib import Path
 from shutil import which
 from time import sleep
-from typing import TYPE_CHECKING, Any, Final, Literal
+from typing import TYPE_CHECKING
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -26,6 +27,7 @@
 if TYPE_CHECKING:
     from collections.abc import Callable, Sequence
     from pathlib import Path
+    from typing import Any, Final, Literal
 
     import pandas as pd
     from pandas.io.formats.style import Styler
@@ -313,7 +315,10 @@ def normalize_and_crop_pdf(
         if on_gs_not_found == "ignore":
             return
         if on_gs_not_found == "warn":
-            print("Ghostscript not found, skipping PDF normalization and cropping")  # noqa: T201
+            warnings.warn(
+                "Ghostscript not found, skipping PDF normalization and cropping",
+                stacklevel=2,
+            )
             return
         raise RuntimeError("Ghostscript not found in PATH")
     try:
@@ -337,7 +342,7 @@ def normalize_and_crop_pdf(
         )
 
         if stderr:
-            print(f"pdfCropMargins {stderr=}")  # noqa: T201
+            warnings.warn(f"pdfCropMargins {stderr=}", stacklevel=2)
             # something went wrong, remove the cropped PDF
             os.remove(cropped_file_path)
         else:
@@ -643,6 +648,8 @@ def print_table(
                 [svgo, "--multipass", "--final-newline", str(file_path)], check=True
             )
         else:
-            print("svgo not found in PATH. SVG compression skipped.")  # noqa: T201
+            warnings.warn(
+                "svgo not found in PATH. SVG compression skipped.", stacklevel=2
+            )
 
     return fig

pymatviz/phonons.py

@@ -4,7 +4,7 @@
 
 import sys
 from dataclasses import dataclass
-from typing import TYPE_CHECKING, Any, Literal, get_args, no_type_check
+from typing import TYPE_CHECKING, Literal, get_args
 
 import plotly.express as px
 import plotly.graph_objects as go
@@ -18,12 +18,16 @@
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
+    from typing import Any, TypeAlias
 
     import numpy as np
     from pymatgen.core import Structure
     from typing_extensions import Self
 
-AnyBandStructure = BandStructureSymmLine | PhononBands
+AnyBandStructure: TypeAlias = BandStructureSymmLine | PhononBands
+YMin: TypeAlias = float | Literal["y_min"]
+YMax: TypeAlias = float | Literal["y_max"]
+BranchMode: TypeAlias = Literal["union", "intersection"]
 
 
 @dataclass
@@ -121,21 +125,22 @@ def get_band_xaxis_ticks(
     return ticks_x_pos, tick_labels
 
 
-YMin = float | Literal["y_min"]
-YMax = float | Literal["y_max"]
-
-
-@no_type_check
 def _shaded_range(
-    fig: go.Figure, shaded_ys: dict[tuple[YMin, YMax], dict[str, Any]] | bool | None
+    fig: go.Figure,
+    shaded_ys: dict[tuple[YMin | YMax, YMin | YMax], dict[str, Any]] | bool | None,
 ) -> go.Figure:
     if shaded_ys is False:
         return fig
 
     shade_defaults = dict(layer="below", row="all", col="all")
-    y_lim = dict(zip(("y_min", "y_max"), fig.layout.yaxis.range, strict=True))
+    y_lim: dict[float | Literal["y_min", "y_max"], Any] = dict(
+        zip(("y_min", "y_max"), fig.layout.yaxis.range, strict=True),
+    )
 
     shaded_ys = shaded_ys or {(0, "y_min"): dict(fillcolor="gray", opacity=0.07)}
+    if not isinstance(shaded_ys, dict):
+        raise TypeError(f"expect shaded_ys as dict, got {type(shaded_ys).__name__}")
+
     for (y0, y1), kwds in shaded_ys.items():
         for y_val in (y0, y1):
             if isinstance(y_val, str) and y_val not in y_lim:
@@ -147,15 +152,14 @@ def _shaded_range(
     return fig
 
 
-BranchMode = Literal["union", "intersection"]
-
-
 def phonon_bands(
     band_structs: PhononBands | dict[str, PhononBands],
     line_kwargs: dict[str, Any] | None = None,
     branches: Sequence[str] = (),
     branch_mode: BranchMode = "union",
-    shaded_ys: dict[tuple[YMin, YMax], dict[str, Any]] | bool | None = None,
+    shaded_ys: dict[tuple[YMin | YMax, YMin | YMax], dict[str, Any]]
+    | bool
+    | None = None,
     **kwargs: Any,
 ) -> go.Figure:
     """Plot single or multiple pymatgen band structures using Plotly, focusing on the

pymatviz/powerups/both.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import warnings
 from typing import TYPE_CHECKING, Any
 
 import matplotlib.pyplot as plt
@@ -177,7 +178,7 @@ def add_identity_line(
         xy_min_min = min(x_min, y_min)
         xy_max_min = min(x_max, y_max)
 
-        if fig._grid_ref is not None:  # noqa: SLF001
+        if fig._grid_ref is not None:
             kwargs.setdefault("row", "all")
             kwargs.setdefault("col", "all")
 
@@ -264,10 +265,11 @@ def add_best_fit_line(
         if n_traces > 1 and warn and not is_faceted:
             # for a faceted plot, multiple traces are expected so doesn't make sense to
             # warn even if user may have wanted to specify trace_idx. we can't know
-            print(  # noqa: T201
+            warnings.warn(
                 f"add_best_fit_line Warning: {trace_idx=} but figure has {n_traces}"
                 " traces, defaulting to trace_idx=0. Check fig.data[0] to make sure"
-                " this is the expected trace."
+                " this is the expected trace.",
+                stacklevel=2,
             )
         trace_idx = 0
 

pymatviz/powerups/plotly.py

@@ -70,7 +70,7 @@ def add_ecdf_line(
     ecdf_trace = px.ecdf(values).data[0]
 
     # if fig has facets, add ECDF to all subplots
-    fig_add_trace_defaults = {} if fig._grid_ref is None else dict(row="all", col="all")  # noqa: SLF001
+    fig_add_trace_defaults = {} if fig._grid_ref is None else dict(row="all", col="all")
     fig.add_trace(ecdf_trace, **fig_add_trace_defaults | kwargs)
 
     # get xlabel falling back on 'x' if not set
@@ -129,7 +129,7 @@ def add_ecdf_line(
     yaxis2_layout = getattr(fig.layout, "yaxis2", {})
     if yaxis2_layout:
         # convert to dict
-        yaxis2_layout = yaxis2_layout._props  # type: ignore[union-attr] # noqa: SLF001
+        yaxis2_layout = yaxis2_layout._props  # type: ignore[union-attr]
     fig.layout.yaxis2 = yaxis_defaults | yaxis2_layout
 
     return fig

pymatviz/ptable/_process_data.py

@@ -4,7 +4,7 @@
 
 import warnings
 from collections.abc import Iterable, Sequence
-from typing import TYPE_CHECKING, Literal, TypeAlias, get_args
+from typing import TYPE_CHECKING, get_args
 
 import numpy as np
 import pandas as pd
@@ -15,7 +15,7 @@
 
 if TYPE_CHECKING:
     from collections.abc import Callable
-    from typing import Any
+    from typing import Any, Literal, TypeAlias
 
     from numpy.typing import NDArray
 

pymatviz/sankey.py

@@ -2,12 +2,14 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Literal
+from typing import TYPE_CHECKING
 
 import plotly.graph_objects as go
 
 
 if TYPE_CHECKING:
+    from typing import Any, Literal
+
     import pandas as pd