🚇🚀 Ready 0.7.0 release (#153)

* 🚀 Raised version from 0.6.0 to 0.7.0

* 🗑️❌ Removed pyglotaran_extras.io.boilerplate import setup_case_study
* 🗑️❌ Removed pyglotaran_extras.plotting.data
* 🗑️ Changed figure_only deprecation to warn if used
* 🚧📚 Added changes since 0.6.0 to changelog
* 🔧 Add zenodo config

Note for new users:
This package complements the `pyglotaran` package found here: https://github.com/glotaran/pyglotaran

.zenodo.json

@@ -0,0 +1,31 @@
+{
+  "title": "Convenience plotting functions for pyglotaran",
+  "creators": [
+    {
+      "name": "Joris Snellenburg",
+      "affiliation": "Vrije Universiteit Amsterdam",
+      "orcid": "0000-0002-1428-0221"
+    },
+    {
+      "name": "Sebastian Weigand",
+      "affiliation": "Technical University Berlin"
+    },
+    {
+      "name": "Ivo H.M. van Stokkum",
+      "affiliation": "Vrije Universiteit Amsterdam",
+      "orcid": "0000-0002-6143-2021"
+    }
+  ],
+  "keywords": [
+    "global analysis",
+    "target analysis",
+    "time-resolved spectroscopy",
+    "biophysics",
+    "glotaran",
+    "python",
+    "plotting"
+  ],
+  "access_right": "open",
+  "license": "MIT",
+  "upload_type": "software"
+}

changelog.md

@@ -4,8 +4,25 @@
 
 ## 0.7.0 (Unreleased)
 
+- 👌 Fix typo in internal function name (#94)
+- ✨ Add IRF dispersion center plotting (#95)
+- 👌 Improve typing (#96)
+- 👌 Shift time axis by IRF location (#99)
 - 🩹🚇 Fix 'Test pyglotaran dev' CI step (#117)
 - 👌 Add option to deactivate data/residual plotting in overview plots (#118)
+- ✨ Add coherent artifact plot functionality (#123)
+- ✨ Add a-matrix inspection function (#124)
+- ✨ Add show_zero_line option to plot_overview and plot_fitted_traces (#128)
+- 🩹 Fix SVD vector labels always starting from zero (#133)
+- 👌 Make result input for plot_coherent_artifact more generic (#134)
+- ✨ Add plot_doas function that only plots DOAS related information (#135)
+- ✨ Shift irf derivatives in plot_coherent_artifact by irf position (#136)
+- 👌 Convert plot style Enums to StrEnums for ease of use (#144)
+- 🩹 Fix heading in show_a_matrixes for multiple a-matrixes per dataset (#148)
+- 👌 Add legend_format_string argument to plot_doas (#150)
+- 👌 Make plot_data_overview able to plot single trace data (#137)
+- 👌 Improve plot_doas default legend_format_string (#151)
+- 🩹⌨️ Fix figsize typing (#152)
 - 🩹📚 Fix search in docs (#157)
 
 (changes-0_6_0)=

pyglotaran_extras/__init__.py

@@ -25,4 +25,4 @@
     "select_plot_wavelengths",
 ]
 
-__version__ = "0.6.0"
+__version__ = "0.7.0"

pyglotaran_extras/deprecation/deprecation_utils.py

@@ -5,9 +5,8 @@
 from warnings import warn
 
 FIG_ONLY_WARNING = (
-    "In the future plot functions which create figures, will return a tuple "
-    "of Figure AND the Axes. Please set ``figure_only=False`` and adjust your code.\n"
-    "This usage will be an error in version: 0.7.0."
+    "The ``figure_only`` argument was deprecated please remove it from the function call.\n"
+    "This usage will be an error in version: 0.8.0."
 )
 
 
@@ -40,7 +39,7 @@ def pyglotaran_extras_version() -> str:
     from pyglotaran_extras.
     This way all of the deprecation functionality can be used even in
     ``pyglotaran_extras.__init__.py`` without moving the import below the definition of
-    ``__version__`` or causeing a circular import issue.
+    ``__version__`` or causing a circular import issue.
 
     Returns
     -------
@@ -81,8 +80,8 @@ def parse_version(version_str: str) -> tuple[int, int, int]:
         return tuple(
             map(int, (*split_version[:2], split_version[2].partition("rc")[0]))
         )  # type:ignore[return-value]
-    except ValueError:
-        raise ValueError(error_message)
+    except ValueError as error:
+        raise ValueError(error_message) from error
 
 
 def check_overdue(deprecated_qual_name_usage: str, to_be_removed_in_version: str) -> None:

pyglotaran_extras/plotting/plot_overview.py

@@ -41,14 +41,14 @@ def plot_overview(
     main_irf_nr: int = 0,
     figsize: tuple[float, float] = (18, 16),
     cycler: Cycler | None = PlotStyle().cycler,
-    figure_only: bool = True,
+    figure_only: bool | None = None,
     nr_of_data_svd_vectors: int = 4,
     nr_of_residual_svd_vectors: int = 2,
     show_data_svd_legend: bool = True,
     show_residual_svd_legend: bool = True,
     show_irf_dispersion_center: bool = True,
     show_zero_line: bool = True,
-) -> Figure | tuple[Figure, Axes]:
+) -> tuple[Figure, Axes]:
     """Plot overview of the optimization result.
 
     Parameters
@@ -79,10 +79,8 @@ def plot_overview(
         Size of the figure (N, M) in inches. Defaults to (18, 16).
     cycler : Cycler | None
         Plot style cycler to use. Defaults to PlotStyle().cycler.
-    figure_only: bool
-        Whether or not to only return the figure.
-        This is a deprecation helper argument to transition to a consistent return value
-        consisting of the :class:`Figure` and the :class:`Axes`. Defaults to True.
+    figure_only: bool | None
+        Deprecated please remove this argument for you function calls. Defaults to None.
     nr_of_data_svd_vectors: int
         Number of data SVD vector to plot. Defaults to 4.
     nr_of_residual_svd_vectors: int
@@ -100,15 +98,15 @@ def plot_overview(
 
     Returns
     -------
-    Figure|tuple[Figure, Axes]
-        If ``figure_only`` is True, Figure object which contains the plots (deprecated).
-        If ``figure_only`` is False, Figure object which contains the plots and the Axes.
+    tuple[Figure, Axes]
     """
     res = load_data(result, _stacklevel=3)
 
     if res.coords["time"].values.size == 1:
         fig, axes = plot_guidance(res)
-        return fig if figure_only is True else (fig, axes)
+        if figure_only is not None:
+            warn(PyglotaranExtrasApiDeprecationWarning(FIG_ONLY_WARNING), stacklevel=2)
+        return fig, axes
     # Plot dimensions
     M = 4
     N = 3
@@ -153,18 +151,17 @@ def plot_overview(
         show_irf_dispersion_center=show_irf_dispersion_center,
         irf_location=irf_location,
     )
-    if figure_only is False:
-        return fig, axes
-    warn(PyglotaranExtrasApiDeprecationWarning(FIG_ONLY_WARNING), stacklevel=2)
-    return fig
+    if figure_only is not None:
+        warn(PyglotaranExtrasApiDeprecationWarning(FIG_ONLY_WARNING), stacklevel=2)
+    return fig, axes
 
 
 def plot_simple_overview(
     result: DatasetConvertible | Result,
     title: str | None = None,
     figsize: tuple[float, float] = (12, 6),
     cycler: Cycler | None = PlotStyle().cycler,
-    figure_only: bool = True,
+    figure_only: bool | None = None,
     show_irf_dispersion_center: bool = True,
     show_data: bool | None = False,
 ) -> Figure | tuple[Figure, Axes]:
@@ -180,10 +177,8 @@ def plot_simple_overview(
         Size of the figure (N, M) in inches. Defaults to (18, 16).
     cycler : Cycler | None
         Plot style cycler to use. Defaults to PlotStyle().cycler.
-    figure_only: bool
-        Whether or not to only return the figure.
-        This is a deprecation helper argument to transition to a consistent return value
-        consisting of the :class:`Figure` and the :class:`Axes`. Defaults to True.
+    figure_only: bool | None
+        Deprecated please remove this argument for you function calls. Defaults to None.
     show_irf_dispersion_center: bool
         Whether to show the the IRF dispersion center as overlay on the residual/data plot.
         Defaults to True.
@@ -193,9 +188,7 @@ def plot_simple_overview(
 
     Returns
     -------
-    Figure|tuple[Figure, Axes]
-        If ``figure_only`` is True, Figure object which contains the plots (deprecated).
-        If ``figure_only`` is False, Figure object which contains the plots and the Axes.
+    tuple[Figure, Axes]
     """
     res = load_data(result, _stacklevel=3)
 
@@ -228,10 +221,9 @@ def plot_simple_overview(
         irf_location=irf_location,
     )
 
-    if figure_only is not True:
-        return fig, axes
-    warn(PyglotaranExtrasApiDeprecationWarning(FIG_ONLY_WARNING), stacklevel=2)
-    return fig
+    if figure_only is not None:
+        warn(PyglotaranExtrasApiDeprecationWarning(FIG_ONLY_WARNING), stacklevel=2)
+    return fig, axes
 
 
 if __name__ == "__main__":
@@ -241,7 +233,7 @@ def plot_simple_overview(
     res = load_data(result_path)
     print(res)
 
-    fig, axes = plot_overview(res, figure_only=False)
+    fig, axes = plot_overview(res)
     if len(sys.argv) > 2:
         fig.savefig(sys.argv[2], bbox_inches="tight")
         print(f"Saved figure to: {sys.argv[2]}")