type test functions, update commit hooks incl. mypy, setup.cfg set implicit_optional=true which defaults to false in newer mypys

github.com/python/mypy/pull/13401

Author: janosh

.pre-commit-config.yaml

@@ -7,29 +7,29 @@ default_install_hook_types: [pre-commit, commit-msg]
 
 repos:
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.11.4
     hooks:
       - id: isort
 
   - repo: https://github.com/psf/black
-    rev: 22.8.0
+    rev: 22.12.0
     hooks:
       - id: black-jupyter
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
+    rev: 6.0.0
     hooks:
       - id: flake8
         additional_dependencies: [flake8-bugbear]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.38.2
+    rev: v3.3.1
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.981
+    rev: v0.991
     hooks:
       - id: mypy
         additional_dependencies: [types-requests]
@@ -40,7 +40,7 @@ repos:
       - id: format-ipy-cells
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
       - id: check-case-conflict
       - id: check-symlinks
@@ -52,14 +52,14 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.1
+    rev: v2.2.2
     hooks:
       - id: codespell
         stages: [commit, commit-msg]
         exclude_types: [csv, svg, html, yaml, jupyter]
 
   - repo: https://github.com/PyCQA/autoflake
-    rev: v1.6.1
+    rev: v2.0.0
     hooks:
       - id: autoflake
 
@@ -70,12 +70,12 @@ repos:
         exclude: tests
 
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.5.0
+    rev: v1.5.1
     hooks:
       - id: docformatter
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.5.2
+    rev: 1.5.3
     hooks:
       - id: nbqa-pyupgrade
         args: [--py38-plus]

pymatviz/histograms.py

@@ -286,7 +286,7 @@ def hist_elemental_prevalence(
     log: bool = False,
     keep_top: int = None,
     ax: plt.Axes = None,
-    bar_values: Literal["percent", "count", None] = "percent",
+    bar_values: Literal["percent", "count"] | None = "percent",
     h_offset: int = 0,
     v_offset: int = 10,
     rotation: int = 45,

pymatviz/ptable.py

@@ -117,7 +117,7 @@ def ptable_heatmap(
     zero_color: str = "#DDD",  # light gray
     infty_color: str = "lightskyblue",
     na_color: str = "white",
-    heat_mode: Literal["value", "fraction", "percent", None] = "value",
+    heat_mode: Literal["value", "fraction", "percent"] | None = "value",
     precision: str = None,
     text_color: str | tuple[str, str] = "auto",
     exclude_elements: Sequence[str] = (),
@@ -367,7 +367,7 @@ def ptable_heatmap_plotly(
     count_mode: CountMode = "element_composition",
     colorscale: str | Sequence[str] | Sequence[tuple[float, str]] | None = None,
     showscale: bool = True,
-    heat_mode: Literal["value", "fraction", "percent", None] = "value",
+    heat_mode: Literal["value", "fraction", "percent"] | None = "value",
     precision: str = None,
     hover_props: Sequence[str] | dict[str, str] | None = None,
     hover_data: dict[str, str | int | float] | pd.Series | None = None,
@@ -418,7 +418,7 @@ def ptable_heatmap_plotly(
         hover_data (dict[str, str | int | float] | pd.Series): Map from element symbols
             to additional data to display in the hover tooltip. {"Fe": "this shows up in
             the hover tooltip on a new line below the element name"}. Defaults to None.
-        font_colors (list[str]): One or two color strings [min_color, max_color].
+        font_colors (list[str]): One color name or two for [min_color, max_color].
             min_color is applied to annotations for heatmap values
             < (max_val - min_val) / 2. Defaults to ["black"].
         gap (float): Gap in pixels between tiles of the periodic table. Defaults to 5.

readme.md

@@ -6,9 +6,9 @@ A toolkit for visualizations in materials informatics.
 
 [![Tests](https://github.com/janosh/pymatviz/actions/workflows/test.yml/badge.svg)](https://github.com/janosh/pymatviz/actions/workflows/test.yml)
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/janosh/pymatviz/main.svg)](https://results.pre-commit.ci/latest/github/janosh/pymatviz/main)
-[![This project supports Python 3.8+](https://img.shields.io/badge/Python-3.8+-blue.svg?logo=python)](https://python.org/downloads)
-[![PyPI](https://img.shields.io/pypi/v/pymatviz?logo=PyPI)](https://pypi.org/project/pymatviz)
-[![PyPI Downloads](https://img.shields.io/pypi/dm/pymatviz)](https://pypistats.org/packages/pymatviz)
+[![This project supports Python 3.8+](https://img.shields.io/badge/Python-3.8+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads)
+[![PyPI](https://img.shields.io/pypi/v/pymatviz?logo=pypi&logoColor=white)](https://pypi.org/project/pymatviz)
+[![PyPI Downloads](https://img.shields.io/pypi/dm/pymatviz?logo=icloud&logoColor=white)](https://pypistats.org/packages/pymatviz)
 
 </h4>
 

setup.cfg

@@ -75,9 +75,7 @@ disallow_untyped_defs = true
 warn_redundant_casts = true
 warn_unused_ignores = true
 show_error_codes = true
-
-[mypy-tests.*]
-disallow_untyped_defs = false
+implicit_optional = true
 
 [codespell]
 ignore-words-list = hist

tests/test_cumulative.py

@@ -13,7 +13,7 @@ def test_cumulative_error(alpha: float) -> None:
     assert isinstance(ax, plt.Axes)
 
 
-def test_cumulative_residual():
+def test_cumulative_residual() -> None:
     ax = cumulative_residual(abs(y_true - y_pred))
     assert isinstance(ax, plt.Axes)
     assert len(ax.lines) == 3

tests/test_ptable.py

@@ -1,5 +1,7 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING, Literal, Sequence
+
 import matplotlib.pyplot as plt
 import pandas as pd
 import plotly.graph_objects as go
@@ -17,6 +19,10 @@
 from pymatviz.utils import df_ptable
 
 
+if TYPE_CHECKING:
+    from pymatviz.ptable import CountMode
+
+
 @pytest.fixture
 def glass_formulas() -> list[str]:
     """Output of:
@@ -26,10 +32,10 @@ def glass_formulas() -> list[str]:
     load_dataset("matbench_glass").composition.head(20)
     """
     return (
-        "Al,Al(NiB)2,Al10Co21B19,Al10Co23B17,Al10Co27B13,Al10Co29B11,Al10Co31B9,"
-        "Al10Co33B7,Al10Cr3Si7,Al10Fe23B17,Al10Fe27B13,Al10Fe31B9,Al10Fe33B7,"
-        "Al10Ni23B17,Al10Ni27B13,Al10Ni29B11,Al10Ni31B9,Al10Ni33B7,Al11(CrSi2)3"
-    ).split(",")
+        "Al Al(NiB)2 Al10Co21B19 Al10Co23B17 Al10Co27B13 Al10Co29B11 Al10Co31B9 "
+        "Al10Co33B7 Al10Cr3Si7 Al10Fe23B17 Al10Fe27B13 Al10Fe31B9 Al10Fe33B7 "
+        "Al10Ni23B17 Al10Ni27B13 Al10Ni29B11 Al10Ni31B9 Al10Ni33B7 Al11(CrSi2)3"
+    ).split()
 
 
 @pytest.fixture
@@ -64,13 +70,13 @@ def steel_elem_counts(steel_formulas: pd.Series[Composition]) -> pd.Series[int]:
         ("reduced_composition", {"Fe": 13, "O": 27, "P": 3}),
     ],
 )
-def test_count_elements(count_mode, counts):
+def test_count_elements(count_mode: CountMode, counts: dict[str, float]) -> None:
     series = count_elements(["Fe2 O3"] * 5 + ["Fe4 P4 O16"] * 3, count_mode=count_mode)
     expected = pd.Series(counts, index=df_ptable.index, name="count").fillna(0)
     assert series.equals(expected)
 
 
-def test_count_elements_by_atomic_nums():
+def test_count_elements_by_atomic_nums() -> None:
     series_in = pd.Series(1, index=range(1, 119))
     el_cts = count_elements(series_in)
     expected = pd.Series(1, index=df_ptable.index, name="count")
@@ -79,7 +85,7 @@ def test_count_elements_by_atomic_nums():
 
 
 @pytest.mark.parametrize("range_limits", [(-1, 10), (100, 200)])
-def test_count_elements_bad_atomic_nums(range_limits):
+def test_count_elements_bad_atomic_nums(range_limits: tuple[int, int]) -> None:
     with pytest.raises(ValueError, match="assumed to represent atomic numbers"):
         count_elements({idx: 0 for idx in range(*range_limits)})
 
@@ -88,7 +94,7 @@ def test_count_elements_bad_atomic_nums(range_limits):
         count_elements({str(idx): 0 for idx in range(*range_limits)})
 
 
-def test_hist_elemental_prevalence(glass_formulas):
+def test_hist_elemental_prevalence(glass_formulas: list[str]) -> None:
     ax = hist_elemental_prevalence(glass_formulas)
     assert isinstance(ax, plt.Axes)
 
@@ -99,7 +105,9 @@ def test_hist_elemental_prevalence(glass_formulas):
     hist_elemental_prevalence(glass_formulas, keep_top=10, bar_values="count")
 
 
-def test_ptable_heatmap(glass_formulas, glass_elem_counts):
+def test_ptable_heatmap(
+    glass_formulas: list[str], glass_elem_counts: pd.Series[int]
+) -> None:
     ax = ptable_heatmap(glass_formulas)
     assert isinstance(ax, plt.Axes)
 
@@ -139,8 +147,11 @@ def test_ptable_heatmap(glass_formulas, glass_elem_counts):
 
 
 def test_ptable_heatmap_ratio(
-    steel_formulas, glass_formulas, steel_elem_counts, glass_elem_counts
-):
+    steel_formulas: list[str],
+    glass_formulas: list[str],
+    steel_elem_counts: pd.Series[int],
+    glass_elem_counts: pd.Series[int],
+) -> None:
     # composition strings
     ax = ptable_heatmap_ratio(glass_formulas, steel_formulas)
     assert isinstance(ax, plt.Axes)
@@ -153,7 +164,7 @@ def test_ptable_heatmap_ratio(
     ptable_heatmap_ratio(glass_elem_counts, steel_formulas)
 
 
-def test_ptable_heatmap_plotly(glass_formulas):
+def test_ptable_heatmap_plotly(glass_formulas: list[str]) -> None:
     fig = ptable_heatmap_plotly(glass_formulas)
     assert isinstance(fig, go.Figure)
     assert (
@@ -194,10 +205,16 @@ def test_ptable_heatmap_plotly(glass_formulas):
 )
 @pytest.mark.parametrize("showscale", [False, True])
 @pytest.mark.parametrize("font_size", [None, 14])
-@pytest.mark.parametrize("font_colors", [None, ("black", "white")])
+@pytest.mark.parametrize("font_colors", [["red"], ("black", "white")])
 def test_ptable_heatmap_plotly_kwarg_combos(
-    glass_formulas, exclude_elements, heat_mode, showscale, font_size, font_colors, log
-):
+    glass_formulas: list[str],
+    exclude_elements: Sequence[str],
+    heat_mode: Literal["value", "fraction", "percent"] | None,
+    showscale: bool,
+    font_size: int,
+    font_colors: tuple[str] | tuple[str, str],
+    log: bool,
+) -> None:
     fig = ptable_heatmap_plotly(
         glass_formulas,
         exclude_elements=exclude_elements,
@@ -211,8 +228,10 @@ def test_ptable_heatmap_plotly_kwarg_combos(
 
 
 @pytest.mark.parametrize(
-    "clr_scl", ["YlGn", ["blue", "red"], [(0, "blue"), (1, "red")]]
+    "colorscale", ["YlGn", ["blue", "red"], [(0, "blue"), (1, "red")]]
 )
-def test_ptable_heatmap_plotly_colorscale(glass_formulas, clr_scl):
-    fig = ptable_heatmap_plotly(glass_formulas, colorscale=clr_scl)
+def test_ptable_heatmap_plotly_colorscale(
+    glass_formulas: list[str], colorscale: str | list[tuple[float, str]] | list[str]
+) -> None:
+    fig = ptable_heatmap_plotly(glass_formulas, colorscale=colorscale)
     assert isinstance(fig, go.Figure)

tests/test_utils.py

@@ -15,7 +15,7 @@
 from tests.conftest import y_pred, y_true
 
 
-def test_add_mae_r2_box():
+def test_add_mae_r2_box() -> None:
     text_box = add_mae_r2_box(y_pred, y_true)
 
     assert isinstance(text_box, AnchoredText)
@@ -65,7 +65,7 @@ def test_add_identity_line(
     assert line["line"]["color"] == line_kwds["color"] if line_kwds else "gray"
 
 
-def test_df_to_arrays():
+def test_df_to_arrays() -> None:
     df = pd.DataFrame([y_true, y_pred]).T
     x1, y1 = df_to_arrays(None, y_true, y_pred)
     x_col, y_col = df.columns[:2]