🩹 Fix incompatibility of plot_data_and_fits with matplotlib>=3.8

.github/workflows/test.yml

@@ -149,11 +149,55 @@ jobs:
       - name: Run tests
         run: python -m pytest --nbval --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml tests
 
+      - name: Codecov Upload
+        continue-on-error: true
+        uses: codecov/codecov-action@v4
+        with:
+          file: ./coverage.xml
+          name: test-pyglotaran-dev
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  test-min-versions:
+    name: Test dependency min versions
+    runs-on: ubuntu-latest
+    needs: [pre-commit, docs]
+
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip wheel
+          python -m pip install -r requirements_min.txt
+          python -m pip install -e ".[test]"
+
+      - name: Show installed dependencies
+        run: pip freeze
+
+      - name: Run tests
+        run: python -m pytest --nbval --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml tests
+
+      - name: Codecov Upload
+        continue-on-error: true
+        uses: codecov/codecov-action@v4
+        with:
+          file: ./coverage.xml
+          name: test-min-versions
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
   deploy:
     name: Deploy to PyPi
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-    needs: test
+    needs: [test, test-pyglotaran-dev, test-min-versions]
     permissions:
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:

changelog.md

@@ -1,5 +1,13 @@
 # Changelog
 
+(changes-0_7_3)=
+
+## 0.7.3 (Unreleased)
+
+- 🩹 Fix incompatibility of plot_data_and_fits with matplotlib>=3.8 (#275)
+- 🩹 Fix deprecation warning for using xr.Dataset.dim (#267)
+- 🩹 Fix very slow data/residual plots (#239)
+
 (changes-0_7_2)=
 
 ## 0.7.2 (2023-12-07)

pyglotaran_extras/plotting/plot_traces.py

@@ -15,6 +15,7 @@
 from pyglotaran_extras.plotting.utils import add_unique_figure_legend
 from pyglotaran_extras.plotting.utils import extract_dataset_scale
 from pyglotaran_extras.plotting.utils import extract_irf_location
+from pyglotaran_extras.plotting.utils import get_next_cycler_color
 from pyglotaran_extras.plotting.utils import select_plot_wavelengths
 
 __all__ = ["select_plot_wavelengths", "plot_fitted_traces"]
@@ -96,7 +97,7 @@ def plot_data_and_fits(
             (result_data.data / scale).plot(x="time", ax=axis, label=f"{dataset_name}_data")
             (result_data.fitted_data / scale).plot(x="time", ax=axis, label=f"{dataset_name}_fit")
         else:
-            [next(axis._get_lines.prop_cycler) for _ in range(2)]
+            [get_next_cycler_color(axis) for _ in range(2)]
     if linlog:
         axis.set_xscale("symlog", linthresh=linthresh)
         axis.xaxis.set_minor_locator(MinorSymLogLocator(linthresh))

pyglotaran_extras/plotting/utils.py

@@ -28,6 +28,7 @@
     from matplotlib.pyplot import Axes
 
     from pyglotaran_extras.types import BuiltinSubPlotLabelFormatFunctionKey
+    from pyglotaran_extras.types import CyclerColor
     from pyglotaran_extras.types import ResultLike
     from pyglotaran_extras.types import SubPlotLabelCoord
 
@@ -215,6 +216,28 @@ def add_unique_figure_legend(fig: Figure, axes: Axes) -> None:
     fig.legend(*zip(*unique, strict=True))
 
 
+def get_next_cycler_color(ax: Axes) -> CyclerColor:
+    """Get next color from cycler assigned to ``ax``.
+
+    Note
+    ----
+    This will advance the cycler to the next state.
+
+    Parameters
+    ----------
+    ax : Axes
+        Axes to get the color from.
+
+    Returns
+    -------
+    CyclerColor
+    """
+    # Matplotlib<3.8 compat
+    if hasattr(ax._get_lines, "prop_cycler"):
+        return next(ax._get_lines.prop_cycler)
+    return {"color": ax._get_lines.get_next_color()}
+
+
 def select_plot_wavelengths(
     result: ResultLike,
     axes_shape: tuple[int, int] = (4, 4),

pyglotaran_extras/types.py

@@ -5,12 +5,17 @@
 from collections.abc import Mapping
 from collections.abc import Sequence
 from pathlib import Path
+from typing import TYPE_CHECKING
 from typing import Literal
 from typing import TypeAlias
+from typing import TypedDict
 
 import xarray as xr
 from glotaran.project.result import Result
 
+if TYPE_CHECKING:
+    from pyglotaran_extras.plotting.style import ColorCode
+
 
 class UnsetType:
     """Type for the ``Unset`` singleton."""
@@ -26,6 +31,13 @@ def __repr__(self) -> str:  # noqa: DOC
 This way we can prevent regressions.
 """
 
+
+class CyclerColor(TypedDict):
+    """Color value returned by a cycler."""
+
+    color: str | ColorCode
+
+
 DatasetConvertible: TypeAlias = xr.Dataset | xr.DataArray | str | Path
 """Types of data which can be converted to a dataset."""
 ResultLike: TypeAlias = (

pyproject.toml

@@ -33,7 +33,7 @@ dynamic = [
 dependencies = [
   "cycler>=0.10",
   "matplotlib>=3.3",
-  "numpy>=1.21.2",
+  "numpy>=1.22",
   "pyglotaran>=0.7",
   "tabulate>=0.8.9",
   "xarray>=2022.3",

requirements_min.txt

@@ -0,0 +1,8 @@
+# Minimum versions runtime dependencies
+
+cycler==0.10
+numpy==1.22
+matplotlib==3.3
+pyglotaran==0.7.2
+tabulate==0.8.9
+xarray==2022.3

tests/plotting/test_utils.py

@@ -17,6 +17,7 @@
 from pyglotaran_extras.plotting.utils import calculate_ticks_in_units_of_pi
 from pyglotaran_extras.plotting.utils import ensure_axes_array
 from pyglotaran_extras.plotting.utils import format_sub_plot_number_upper_case_letter
+from pyglotaran_extras.plotting.utils import get_next_cycler_color
 from pyglotaran_extras.plotting.utils import not_single_element_dims
 
 if TYPE_CHECKING:
@@ -42,11 +43,9 @@ def test_add_cycler_if_not_none_single_axis(cycler: Cycler | None, expected_cycl
     ax = plt.subplot()
     add_cycler_if_not_none(ax, cycler)
 
-    ax_cycler = iter(ax._get_lines._cycler_items)
-
     for _ in range(10):
         expected = next(expected_cycler)
-        assert next(ax_cycler) == expected
+        assert get_next_cycler_color(ax) == expected
 
 
 @pytest.mark.parametrize(
@@ -58,13 +57,10 @@ def test_add_cycler_if_not_none_multiple_axes(cycler: Cycler | None, expected_cy
     _, axes = plt.subplots(1, 2)
     add_cycler_if_not_none(axes, cycler)
 
-    ax0_cycler = iter(axes[0]._get_lines._cycler_items)
-    ax1_cycler = iter(axes[1]._get_lines._cycler_items)
-
     for _ in range(10):
         expected = next(expected_cycler)
-        assert next(ax0_cycler) == expected
-        assert next(ax1_cycler) == expected
+        assert get_next_cycler_color(axes[0]) == expected
+        assert get_next_cycler_color(axes[1]) == expected
 
 
 @pytest.mark.parametrize(