bump ruff to 0.9 and auto-fix

ruff ignore (noqa): pymatviz/(typing|io).py:1:1: A005 Module (typing|io) shadows a Python standard-library module

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ default_install_hook_types: [pre-commit, commit-msg]
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.0
     hooks:
       - id: ruff
         args: [--fix]

assets/scripts/ptable_plotly/ptable_scatter_plotly.py

@@ -59,4 +59,4 @@
     title = f"<b>Periodic Table Scatter Plots</b><br>{mode=}"
     fig.layout.title.update(text=title, x=0.4, y=0.85, font_size=20)
     fig.show()
-    pmv.io.save_and_compress_svg(fig, f"ptable-scatter-plotly-{mode.replace('+','-')}")
+    pmv.io.save_and_compress_svg(fig, f"ptable-scatter-plotly-{mode.replace('+', '-')}")

pymatviz/classify/confusion_matrix.py

@@ -106,7 +106,7 @@ def confusion_matrix(
                 spaces = [i for i, c in enumerate(label) if c == " "]
                 if spaces:
                     split_point = min(spaces, key=lambda x: abs(x - mid))
-                    label = f"{label[:split_point]}<br>{label[split_point + 1:]}"  # noqa: PLW2901
+                    label = f"{label[:split_point]}<br>{label[split_point + 1 :]}"  # noqa: PLW2901
             formatted_labels[key] += [label]
 
     fmt_tile_vals = np.array(

pymatviz/typing.py

@@ -1,4 +1,4 @@
-"""Typing related: TypeAlias, generic types and so on."""
+"""Typing related: TypeAlias, generic types and so on."""  # noqa: A005
 
 from __future__ import annotations
 

tests/phonons/test_phonon_helpers.py

@@ -71,9 +71,9 @@ def test_phonon_bands(
     assert fig.layout.font.size == 16
 
     actual_x_labels = fig.layout.xaxis.ticktext
-    assert (
-        actual_x_labels == expected_x_labels
-    ), f"{actual_x_labels=}, {expected_x_labels=}"
+    assert actual_x_labels == expected_x_labels, (
+        f"{actual_x_labels=}, {expected_x_labels=}"
+    )
     assert fig.layout.xaxis.range is None
     assert fig.layout.yaxis.range == pytest.approx((0, 5.36385427095))
 

tests/powerups/test_both_powerups.py

@@ -291,9 +291,9 @@ def test_annotate_metrics(
         y_pred, y_true, metrics=metrics, fmt=fmt, prefix=prefix, suffix=suffix, fig=fig
     )
     anno_text_with_fixes = _extract_anno_from_fig(out_fig)
-    assert (
-        anno_text_with_fixes == prefix + expected_text + suffix
-    ), f"{anno_text_with_fixes=}"
+    assert anno_text_with_fixes == prefix + expected_text + suffix, (
+        f"{anno_text_with_fixes=}"
+    )
 
 
 def test_annotate_metrics_faceted_plotly(plotly_faceted_scatter: go.Figure) -> None:

tests/ptable/plotly/test_ptable_heatmap_plotly.py

@@ -23,12 +23,12 @@
 def test_ptable_heatmap_plotly(glass_formulas: list[str]) -> None:
     fig = pmv.ptable_heatmap_plotly(glass_formulas)
     assert isinstance(fig, go.Figure)
-    assert (
-        len(fig.layout.annotations) == 18 * 10
-    ), "not all periodic table tiles have annotations"
-    assert (
-        sum(anno.text != "" for anno in fig.layout.annotations) == 118
-    ), "no annotations should be empty"
+    assert len(fig.layout.annotations) == 18 * 10, (
+        "not all periodic table tiles have annotations"
+    )
+    assert sum(anno.text != "" for anno in fig.layout.annotations) == 118, (
+        "no annotations should be empty"
+    )
 
     # test hover_props and show_values=False
     pmv.ptable_heatmap_plotly(
@@ -134,9 +134,9 @@ def test_ptable_heatmap_plotly_kwarg_combos(
         assert fig.layout.font.size == font_size * scale
 
     if len(font_colors) == 2:
-        assert all(
-            anno.font.color in font_colors for anno in fig.layout.annotations
-        ), f"{font_colors=}"
+        assert all(anno.font.color in font_colors for anno in fig.layout.annotations), (
+            f"{font_colors=}"
+        )
     elif len(font_colors) == 1:
         assert all(
             anno.font.color == font_colors[0] for anno in fig.layout.annotations
@@ -197,12 +197,12 @@ def test_ptable_heatmap_plotly_cscale_range(
         assert trace.zmin == pytest.approx(data_min)
         assert trace.zmax == pytest.approx(data_max)
     else:
-        assert trace.zmin == pytest.approx(
-            cscale_range[0] or data_min
-        ), f"{cscale_range=}"
-        assert trace.zmax == pytest.approx(
-            cscale_range[1] or data_max
-        ), f"{cscale_range=}"
+        assert trace.zmin == pytest.approx(cscale_range[0] or data_min), (
+            f"{cscale_range=}"
+        )
+        assert trace.zmax == pytest.approx(cscale_range[1] or data_max), (
+            f"{cscale_range=}"
+        )
 
 
 def test_ptable_heatmap_plotly_cscale_range_raises() -> None:
@@ -414,35 +414,36 @@ def test_ptable_heatmap_plotly_element_symbol_map() -> None:
     # Check if custom symbols are used in tile texts
     tile_texts = [anno.text for anno in fig.layout.annotations if anno.text]
     for custom_symbol in element_symbol_map.values():
-        assert any(
-            custom_symbol in text for text in tile_texts
-        ), f"Custom symbol {custom_symbol} not found in tile texts"
+        assert any(custom_symbol in text for text in tile_texts), (
+            f"Custom symbol {custom_symbol} not found in tile texts"
+        )
 
     # Check if original element symbols are still used in hover texts
     hover_texts = fig.data[-1].text.flat
     for elem in values:
         hover_text = next(
             text for text in hover_texts if text.startswith(df_ptable.loc[elem, "name"])
         )
-        assert (
-            f"({elem})" in hover_text
-        ), f"Original symbol {elem} not found in hover text"
+        assert f"({elem})" in hover_text, (
+            f"Original symbol {elem} not found in hover text"
+        )
 
     # Test with partial mapping
     partial_map = {"Fe": "This be Iron"}
     fig = pmv.ptable_heatmap_plotly(values, element_symbol_map=partial_map)
     tile_texts = [anno.text for anno in fig.layout.annotations if anno.text]
-    assert any(
-        "This be Iron" in text for text in tile_texts
-    ), "Custom symbol not found in tile texts"
-    assert any(
-        "O</span>" in text for text in tile_texts
-    ), "Original symbol 'O' not found in tile texts"
+    assert any("This be Iron" in text for text in tile_texts), (
+        "Custom symbol not found in tile texts"
+    )
+    assert any("O</span>" in text for text in tile_texts), (
+        "Original symbol 'O' not found in tile texts"
+    )
 
     # Test with None value
     fig = pmv.ptable_heatmap_plotly(values, element_symbol_map=None)
     tile_texts = [anno.text for anno in fig.layout.annotations if anno.text]
     for elem in values:
-        assert any(
-            f"{elem}</span>" in text for text in tile_texts
-        ), f"Original symbol {elem} not found in tile texts for element_symbol_map=None"
+        assert any(f"{elem}</span>" in text for text in tile_texts), (
+            f"Original symbol {elem} not found in tile texts for "
+            "element_symbol_map=None"
+        )

tests/rdf/test_rdf_helpers.py

@@ -45,9 +45,9 @@ def test_calculate_rdf_normalization(composition: list[str], n_atoms: int) -> No
             )
 
             # Check if RDF starts from 0 at r=0
-            assert (
-                rdf[0] == 0
-            ), f"{rdf[0]=} should start from 0 at r=0 for {el1}-{el2} pair"
+            assert rdf[0] == 0, (
+                f"{rdf[0]=} should start from 0 at r=0 for {el1}-{el2} pair"
+            )
 
             # Check there are no negative values in the RDF
             assert all(rdf >= 0), f"RDF contains negative values for {el1}-{el2} pair"
@@ -61,9 +61,9 @@ def test_calculate_rdf_normalization(composition: list[str], n_atoms: int) -> No
             )
 
             # Check if the RDF has the correct number of bins
-            assert (
-                len(rdf) == n_bins
-            ), f"RDF should have {n_bins=}, got {len(rdf)} for {el1}-{el2} pair"
+            assert len(rdf) == n_bins, (
+                f"RDF should have {n_bins=}, got {len(rdf)} for {el1}-{el2} pair"
+            )
 
 
 @pytest.mark.parametrize(
@@ -156,9 +156,9 @@ def test_calculate_rdf_different_species() -> None:
     assert np.any(rdf_si_ge > 0), "Si-Ge RDF should have non-zero values"
 
     peak_index = int(4.33 / cutoff * n_bins)
-    assert (
-        rdf_si_ge[peak_index] > 0
-    ), "Expected peak in Si-Ge RDF at sqrt(3)/2 * lattice constant"
+    assert rdf_si_ge[peak_index] > 0, (
+        "Expected peak in Si-Ge RDF at sqrt(3)/2 * lattice constant"
+    )
 
 
 @pytest.mark.parametrize(

tests/rdf/test_rdf_plotly.py

@@ -93,31 +93,31 @@ def test_element_pair_rdfs_cutoff_and_bin_size(
         # Check that we have the correct number of traces (one for each element pair)
         n_elements = len({site.specie.symbol for site in struct})
         expected_traces = n_elements * (n_elements + 1) // 2
-        assert (
-            len(fig.data) == expected_traces
-        ), f"Expected {expected_traces} traces, got {len(fig.data)}"
+        assert len(fig.data) == expected_traces, (
+            f"Expected {expected_traces} traces, got {len(fig.data)}"
+        )
 
         max_cell_len = max(struct.lattice.abc)
         for trace in fig.data:
             if param == "cutoff":
                 expected_cutoff = abs(value) * max_cell_len if value < 0 else value
                 # Check that the x-axis data doesn't exceed the cutoff
-                assert np.all(
-                    trace.x <= expected_cutoff
-                ), f"X-axis data exceeds cutoff of {expected_cutoff}"
+                assert np.all(trace.x <= expected_cutoff), (
+                    f"X-axis data exceeds cutoff of {expected_cutoff}"
+                )
                 # Check that the maximum x value is close to the cutoff
-                assert max(trace.x) == pytest.approx(
-                    expected_cutoff
-                ), f"Maximum x={max(trace.x):.4} not close to cutoff {expected_cutoff}"
+                assert max(trace.x) == pytest.approx(expected_cutoff), (
+                    f"Maximum x={max(trace.x):.4} not close to cutoff {expected_cutoff}"
+                )
             elif param == "bin_size":
                 # When bin_size is specified but cutoff is None,
                 # the default cutoff is 2 * max_cell_len
                 default_cutoff = 2 * max_cell_len
                 # Check that the number of bins is approximately correct
                 expected_bins = int(default_cutoff / value)
-                assert (
-                    0.85 <= expected_bins / len(trace.x) <= 1
-                ), f"{expected_bins=}, got {len(trace.x)}"
+                assert 0.85 <= expected_bins / len(trace.x) <= 1, (
+                    f"{expected_bins=}, got {len(trace.x)}"
+                )
 
 
 def test_element_pair_rdfs_subplot_layout(structures: list[Structure]) -> None:
@@ -283,15 +283,15 @@ def test_full_rdf_cutoff_and_bin_size(
 
         if param == "cutoff":
             assert np.all(trace.x <= value), f"X-axis data exceeds cutoff of {value}"
-            assert max(trace.x) == pytest.approx(
-                value
-            ), f"Maximum x value {max(trace.x):.4} not close to cutoff {value}"
+            assert max(trace.x) == pytest.approx(value), (
+                f"Maximum x value {max(trace.x):.4} not close to cutoff {value}"
+            )
         elif param == "bin_size":
             default_cutoff = 15
             expected_bins = int(np.ceil(default_cutoff / value))
-            assert (
-                abs(len(trace.x) - expected_bins) <= 1
-            ), f"Expected around {expected_bins} bins, got {len(trace.x)}"
+            assert abs(len(trace.x) - expected_bins) <= 1, (
+                f"Expected around {expected_bins} bins, got {len(trace.x)}"
+            )
 
 
 def test_full_rdf_consistency(structures: list[Structure]) -> None:

tests/structure_viz/test_structure_viz_mpl.py

@@ -208,6 +208,6 @@ def test_structure_2d_color_schemes() -> None:
         if isinstance(patch, plt.matplotlib.patches.Wedge)
     }
 
-    assert (
-        jmol_colors != vesta_colors
-    ), f"{jmol_colors=}\n\nshould not equal\n\n{vesta_colors=}"
+    assert jmol_colors != vesta_colors, (
+        f"{jmol_colors=}\n\nshould not equal\n\n{vesta_colors=}"
+    )

tests/structure_viz/test_structure_viz_plotly.py

@@ -160,9 +160,9 @@ def test_structure_2d_plotly(kwargs: dict[str, Any]) -> None:
             vector_traces = [
                 trace for trace in fig.data if (trace.name or "").startswith("vector")
             ]
-            assert (
-                len(vector_traces) > 0
-            ), "No vector traces found when show_site_vectors is True"
+            assert len(vector_traces) > 0, (
+                "No vector traces found when show_site_vectors is True"
+            )
             for vector_trace in vector_traces:
                 assert vector_trace.mode == "lines+markers"
                 assert vector_trace.marker.symbol == "arrow"
@@ -335,14 +335,14 @@ def test_structure_3d_plotly(kwargs: dict[str, Any]) -> None:
                     text in site_trace.text for text in kwargs["site_labels"].values()
                 ), "Expected site labels not found in trace text"
             elif kwargs["site_labels"] in ("symbol", "species"):
-                assert len(site_trace.text) == len(
-                    DISORDERED_STRUCT
-                ), "Mismatch in number of site labels"
+                assert len(site_trace.text) == len(DISORDERED_STRUCT), (
+                    "Mismatch in number of site labels"
+                )
         else:
             # If site_labels is False, ensure that the trace has no text
-            assert (
-                site_trace.text is None or len(site_trace.text) == 0
-            ), "Unexpected site labels found"
+            assert site_trace.text is None or len(site_trace.text) == 0, (
+                "Unexpected site labels found"
+            )
 
     # Check for sites and arrows
     if kwargs.get("show_sites"):
@@ -355,9 +355,9 @@ def test_structure_3d_plotly(kwargs: dict[str, Any]) -> None:
             vector_traces = [
                 trace for trace in fig.data if (trace.name or "").startswith("vector")
             ]
-            assert (
-                len(vector_traces) > 0
-            ), f"No vector traces even though {show_site_vectors=}"
+            assert len(vector_traces) > 0, (
+                f"No vector traces even though {show_site_vectors=}"
+            )
             for vector_trace in vector_traces:
                 if vector_trace.type == "scatter3d":
                     assert vector_trace.mode == "lines"
@@ -526,13 +526,13 @@ def test_hover_text(
             assert "<b>" in site_hover_text, f"{site_hover_text=}"
             assert "</b>" in site_hover_text, f"{site_hover_text=}"
         elif hover_text == SiteCoords.cartesian:
-            assert re.search(
-                rf"Coordinates \({re_3_coords}\)", site_hover_text
-            ), f"{site_hover_text=}"
+            assert re.search(rf"Coordinates \({re_3_coords}\)", site_hover_text), (
+                f"{site_hover_text=}"
+            )
         elif hover_text == SiteCoords.fractional:
-            assert re.search(
-                rf"Coordinates \[{re_3_coords}\]", site_hover_text
-            ), f"{site_hover_text=}"
+            assert re.search(rf"Coordinates \[{re_3_coords}\]", site_hover_text), (
+                f"{site_hover_text=}"
+            )
         elif hover_text == SiteCoords.cartesian_fractional:
             assert re.search(
                 rf"Coordinates \({re_3_coords}\) \[{re_3_coords}\]", site_hover_text

tests/test_brillouin.py

@@ -182,15 +182,15 @@ def test_brillouin_zone_3d_trace_counts(material_id: str) -> None:
     # Assert exact counts for each trace type
     exp_mesh3d = 1
     assert trace_counts["mesh3d"] == exp_mesh3d, f"{trace_counts=}, {exp_mesh3d=}"
-    assert (
-        trace_counts["scatter3d"] == exp_scatter3d
-    ), f"{trace_counts=}, {exp_scatter3d=}"
+    assert trace_counts["scatter3d"] == exp_scatter3d, (
+        f"{trace_counts=}, {exp_scatter3d=}"
+    )
     exp_cone = 6
     assert trace_counts["cone"] == exp_cone, f"{trace_counts=}, {exp_cone=}"
     assert scatter_modes["lines"] == exp_lines, f"{scatter_modes=}, {exp_lines=}"
     exp_markers_text = 1
-    assert (
-        scatter_modes["markers+text"] == exp_markers_text
-    ), f"{scatter_modes=}, {exp_markers_text=}"
+    assert scatter_modes["markers+text"] == exp_markers_text, (
+        f"{scatter_modes=}, {exp_markers_text=}"
+    )
     exp_text = 6
     assert scatter_modes["text"] == exp_text, f"{scatter_modes=}, {exp_text=}"