⌨️🩹 Fix wrong typing using Axis instead of Axes (#314)

* 🧪⌨️ Fix typing of Axes as Axis and np.ndarray[..., Axes] as Axes * 🧰🩹 Change docformatter rev to a version compatible with pre-commit 4 🧰⬆️ Update pre-commit config 🧰✨ Add taplo to pre-commit toll for toml formatting and linting * 🚇🩹 Don't run taplo lint in pre-commit CI Pre-commit-CI doesn't support reachin out to get schema and causes a DNS error See CI run: https://results.pre-commit.ci/run/github/299106891/1734109072.qfn_wrsQS6mmHWJ4LP5PzQ
glotaran · Dec 14, 2024 · abaff2e · abaff2e
1 parent 29b37dc
commit abaff2e
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,10 +1,10 @@
 ci:
-  skip: [flake8]
+  skip: [flake8, taplo-lint]
 
 repos:
   # Formatters
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-ast
       - id: check-builtin-literals
@@ -16,14 +16,14 @@ repos:
         args: [--remove]
 
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.7.5
+    rev: 06907d0
     hooks:
       - id: docformatter
         additional_dependencies: [tomli]
         args: [--in-place, --config, ./pyproject.toml]
 
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: "2.2.4"
+    rev: "v2.5.0"
     hooks:
       - id: pyproject-fmt
 
@@ -36,17 +36,18 @@ repos:
     rev: v4.0.0-alpha.8 # Use the sha or tag you want to point at
     hooks:
       - id: prettier
+        additional_dependencies: ["[email protected]"]
 
   # Notebook tools
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
         args: [--drop-empty-cells]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.7
+    rev: v0.8.3
     hooks:
       - id: ruff
         name: "ruff sort imports notebooks"
@@ -72,7 +73,7 @@ repos:
   # Linters
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.13.0
     hooks:
       - id: mypy
         exclude: ^docs
@@ -88,7 +89,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.7
+    rev: v0.8.3
     hooks:
       - id: ruff
         name: "ruff sort imports"
@@ -127,6 +128,12 @@ repos:
         args: ["--ignore-words-list=doas"]
 
   - repo: https://github.com/rhysd/actionlint
-    rev: "v1.7.2"
+    rev: "v1.7.4"
     hooks:
       - id: actionlint
+
+  - repo: https://github.com/ComPWA/taplo-pre-commit
+    rev: v0.9.3
+    hooks:
+      - id: taplo-format
+      - id: taplo-lint
diff --git a/.ruff.toml b/.ruff.toml
@@ -36,7 +36,7 @@ select = [
   "RSE", # flake8-raise
   "RET", # flake8-return
   "SIM", # flake8-simplify
-  "TCH", # flake8-type-checking
+  "TC",  # flake8-type-checking
   "ARG", # flake8-unused-arguments
   "PTH", # flake8-use-pathlib
   "ERA", # eradicate

diff --git a/pyglotaran_extras/__init__.py b/pyglotaran_extras/__init__.py
@@ -36,38 +36,37 @@
 from pyglotaran_extras.plotting.utils import add_subplot_labels
 
 __all__ = [
+    "CONFIG",
+    "PerFunctionPlotConfig",
+    "add_subplot_labels",
+    "create_config_schema",
     "load_data",
-    "setup_case_study",
     "plot_coherent_artifact",
     "plot_concentrations",
+    "plot_config_context",
+    "plot_das",
     "plot_data_overview",
     "plot_doas",
+    "plot_fitted_traces",
     "plot_guidance",
     "plot_irf_dispersion_center",
-    "plot_overview",
-    "plot_simple_overview",
-    "plot_residual",
-    "plot_das",
-    "plot_norm_das",
-    "plot_norm_sas",
-    "plot_sas",
-    "plot_spectra",
     "plot_lsv_data",
     "plot_lsv_residual",
+    "plot_norm_das",
+    "plot_norm_sas",
+    "plot_overview",
+    "plot_residual",
     "plot_rsv_data",
     "plot_rsv_residual",
+    "plot_sas",
+    "plot_simple_overview",
+    "plot_spectra",
     "plot_sv_data",
     "plot_sv_residual",
     "plot_svd",
-    "plot_fitted_traces",
     "select_plot_wavelengths",
-    "add_subplot_labels",
-    # Config
-    "PerFunctionPlotConfig",
-    "plot_config_context",
+    "setup_case_study",
     "use_plot_config",
-    "create_config_schema",
-    "CONFIG",
 ]
 
 __version__ = "0.7.4.dev0"

diff --git a/pyglotaran_extras/io/__init__.py b/pyglotaran_extras/io/__init__.py
@@ -5,4 +5,4 @@
 from pyglotaran_extras.io.load_data import load_data
 from pyglotaran_extras.io.setup_case_study import setup_case_study
 
-__all__ = ["setup_case_study", "load_data"]
+__all__ = ["load_data", "setup_case_study"]
diff --git a/pyglotaran_extras/plotting/plot_concentrations.py b/pyglotaran_extras/plotting/plot_concentrations.py
@@ -13,13 +13,13 @@
 if TYPE_CHECKING:
     import xarray as xr
     from cycler import Cycler
-    from matplotlib.axis import Axis
+    from matplotlib.axes import Axes
 
 
 @use_plot_config(exclude_from_config=("cycler",))
 def plot_concentrations(
     res: xr.Dataset,
-    ax: Axis,
+    ax: Axes,
     center_λ: float | None,
     linlog: bool = False,
     linthresh: float = 1,
@@ -34,8 +34,8 @@ def plot_concentrations(
     ----------
     res : xr.Dataset
         Result dataset from a pyglotaran optimization.
-    ax : Axis
-        Axis to plot the traces on
+    ax : Axes
+        Axes to plot the traces on
     center_λ : float | None
         Center wavelength (λ in nm)
     linlog : bool

diff --git a/pyglotaran_extras/plotting/plot_data.py b/pyglotaran_extras/plotting/plot_data.py
@@ -3,11 +3,11 @@
 from __future__ import annotations
 
 from typing import TYPE_CHECKING
-from typing import cast
 
 import matplotlib.pyplot as plt
+import numpy as np
 from glotaran.io.prepare_dataset import add_svd_to_dataset
-from matplotlib.axis import Axis
+from matplotlib.axes import Axes
 
 from pyglotaran_extras.config.plot_config import use_plot_config
 from pyglotaran_extras.io.load_data import load_data
@@ -27,8 +27,8 @@
     import xarray as xr
     from cycler import Cycler
     from glotaran.project.result import Result
+    from matplotlib.axes import Axes
     from matplotlib.figure import Figure
-    from matplotlib.pyplot import Axes
 
     from pyglotaran_extras.types import DatasetConvertible
 
@@ -48,7 +48,7 @@ def plot_data_overview(
     vmax: float | None = None,
     svd_cycler: Cycler | None = PlotStyle().cycler,
     use_svd_number: bool = False,
-) -> tuple[Figure, Axes] | tuple[Figure, Axis]:
+) -> tuple[Figure, np.ndarray[Axes]] | tuple[Figure, Axes]:
     """Plot data as filled contour plot and SVD components.
 
     Parameters
@@ -86,7 +86,7 @@ def plot_data_overview(
 
     Returns
     -------
-    tuple[Figure, Axes] | tuple[Figure, Axis]
+    tuple[Figure, np.ndarray[Axes]] | tuple[Figure, Axes]
         Figure and axes which can then be refined by the user.
     """
     dataset = load_data(dataset, _stacklevel=3)
@@ -103,11 +103,11 @@ def plot_data_overview(
         )
 
     fig = plt.figure(figsize=figsize)
-    data_ax = cast(Axis, plt.subplot2grid((4, 3), (0, 0), colspan=3, rowspan=3, fig=fig))
+    data_ax = plt.subplot2grid((4, 3), (0, 0), colspan=3, rowspan=3, fig=fig)
     fig.subplots_adjust(hspace=0.5, wspace=0.25)
-    lsv_ax = cast(Axis, plt.subplot2grid((4, 3), (3, 0), fig=fig))
-    sv_ax = cast(Axis, plt.subplot2grid((4, 3), (3, 1), fig=fig))
-    rsv_ax = cast(Axis, plt.subplot2grid((4, 3), (3, 2), fig=fig))
+    lsv_ax = plt.subplot2grid((4, 3), (3, 0), fig=fig)
+    sv_ax = plt.subplot2grid((4, 3), (3, 1), fig=fig)
+    rsv_ax = plt.subplot2grid((4, 3), (3, 2), fig=fig)
 
     if len(data.time) > 1:
         data.plot(x="time", ax=data_ax, center=False, cmap=cmap, vmin=vmin, vmax=vmax)
@@ -146,7 +146,7 @@ def plot_data_overview(
     if linlog:
         data_ax.set_xscale("symlog", linthresh=linthresh)
         data_ax.xaxis.set_minor_locator(MinorSymLogLocator(linthresh))
-    return fig, (data_ax, lsv_ax, sv_ax, rsv_ax)
+    return fig, np.array((data_ax, lsv_ax, sv_ax, rsv_ax))
 
 
 def _plot_single_trace(
@@ -157,7 +157,7 @@ def _plot_single_trace(
     linlog: bool = False,
     linthresh: float = 1,
     figsize: tuple[float, float] = (15, 10),
-) -> tuple[Figure, Axis]:
+) -> tuple[Figure, Axes]:
     """Plot single trace data in case ``plot_data_overview`` gets passed ingle trace data.
 
     Parameters
@@ -178,7 +178,7 @@ def _plot_single_trace(
 
     Returns
     -------
-    tuple[Figure, Axis]
+    tuple[Figure, Axes]
         Figure and axis which can then be refined by the user.
     """
     fig, ax = plt.subplots(1, 1, figsize=figsize)

diff --git a/pyglotaran_extras/plotting/plot_irf_dispersion_center.py b/pyglotaran_extras/plotting/plot_irf_dispersion_center.py
@@ -7,8 +7,6 @@
 
 import matplotlib.pyplot as plt
 import xarray as xr
-from matplotlib.axis import Axis
-from matplotlib.figure import Figure
 
 from pyglotaran_extras.config.plot_config import use_plot_config
 from pyglotaran_extras.io.utils import result_dataset_mapping
@@ -20,26 +18,28 @@
     from typing import Literal
 
     from cycler import Cycler
+    from matplotlib.axes import Axes
+    from matplotlib.figure import Figure
 
     from pyglotaran_extras.types import ResultLike
 
 
 @use_plot_config(exclude_from_config=("cycler", "ax"))
 def plot_irf_dispersion_center(
     result: ResultLike,
-    ax: Axis | None = None,
+    ax: Axes | None = None,
     figsize: tuple[float, float] = (12, 8),
     cycler: Cycler | None = PlotStyle().cycler,
     irf_location: float | None = None,
-) -> tuple[Figure, Axis] | None:
+) -> tuple[Figure, Axes] | None:
     """Plot the IRF dispersion center over the spectral dimension for one or multiple datasets.
 
     Parameters
     ----------
     result : ResultLike
         Data structure which can be converted to a mapping.
-    ax : Axis | None
-        Axis to plot on. Defaults to None which means that a new figure and axis will be created.
+    ax : Axes | None
+        Axes to plot on. Defaults to None which means that a new figure and axis will be created.
     figsize : tuple[float, float]
         Size of the figure (N, M) in inches. Defaults to (12, 8).
     cycler : Cycler | None
@@ -50,51 +50,49 @@ def plot_irf_dispersion_center(
 
     Returns
     -------
-    tuple[Figure, Axis] | None
-        Figure object which contains the plots and the Axis,
+    tuple[Figure, Axes] | None
+        Figure object which contains the plots and the Axes,
         if ``ax`` is not None nothing will be returned.
     """
     result_map = result_dataset_mapping(result)
     if ax is None:
-        fig, axis = cast(tuple[Figure, Axis], plt.subplots(1, figsize=figsize))
-    else:
-        axis = ax
+        fig, ax = plt.subplots(1, figsize=figsize)
     for dataset_name, dataset in result_map.items():
         _plot_irf_dispersion_center(
             dataset,
-            axis,
+            ax,
             spectral_axis="x",
             cycler=cycler,
             label=dataset_name,
             irf_location=irf_location,
         )
-    axis.legend()
+    ax.legend()
 
     if ax is None:
         fig.suptitle("Instrument Response Functions", fontsize=16)
-        return fig, axis
+        return fig, ax
     return None
 
 
 def _plot_irf_dispersion_center(
     res: xr.Dataset,
-    ax: Axis,
+    ax: Axes,
     *,
     spectral_axis: Literal["x", "y"] = "x",
     cycler: Cycler | None = PlotStyle().cycler,
     label: str = "IRF",
     irf_location: float | None = None,
 ) -> None:
-    """Plot the IRF dispersion center on an Axis ``ax``.
+    """Plot the IRF dispersion center on an Axes ``ax``.
 
     This is an internal function to be used by higher level functions.
 
     Parameters
     ----------
     res : xr.Dataset
         Dataset containing the IRF data.
-    ax : Axis
-        Axis to plot on.
+    ax : Axes
+        Axes to plot on.
     spectral_axis : Literal["x", "y"]
         Direct of the spectral axis in the plot. Defaults to "x"
     cycler : Cycler | None

diff --git a/pyglotaran_extras/plotting/plot_residual.py b/pyglotaran_extras/plotting/plot_residual.py
@@ -16,13 +16,13 @@
 if TYPE_CHECKING:
     import xarray as xr
     from cycler import Cycler
-    from matplotlib.axis import Axis
+    from matplotlib.axes import Axes
 
 
 @use_plot_config(exclude_from_config=("cycler",))
 def plot_residual(
     res: xr.Dataset,
-    ax: Axis,
+    ax: Axes,
     linlog: bool = False,
     linthresh: float = 1,
     show_data: bool | None = False,
@@ -36,8 +36,8 @@ def plot_residual(
     ----------
     res : xr.Dataset
         Result dataset
-    ax : Axis
-        Axis to plot on.
+    ax : Axes
+        Axes to plot on.
     linlog : bool
         Whether to use 'symlog' scale or not. Defaults to False.
     linthresh : float