From fb7b00f0e83d84a21088eb9b54f2f8b5d72c3d41 Mon Sep 17 00:00:00 2001
From: Ryuichi Arafune <ryuichi.arafune@gmail.com>
Date: Mon, 18 Mar 2024 18:13:49 +0900
Subject: [PATCH 01/10] =?UTF-8?q?=F0=9F=92=AC=20=20Update=20type=20hints?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 pyproject.toml                 | 2 +-
 src/arpes/utilities/jupyter.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index e707d81e..cee87c78 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -98,7 +98,7 @@ lint.ignore = [
   "NPY201", #  Numpy 2.0, 
 ]
 lint.select = ["ALL"]
-target-version = "py310"
+target-version = "py312"
 line-length = 100
 indent-width = 4
 
diff --git a/src/arpes/utilities/jupyter.py b/src/arpes/utilities/jupyter.py
index 52684ae5..cccf956b 100644
--- a/src/arpes/utilities/jupyter.py
+++ b/src/arpes/utilities/jupyter.py
@@ -118,7 +118,7 @@ def get_full_notebook_information() -> NoteBookInfomation | None:
             if not url.startswith(("http:", "https:")):
                 msg = "URL must start with 'http:' or 'https:'"
                 raise ValueError(msg)
-            sessions = json.load(urllib.request.urlopen(url))
+            sessions = json.load(urllib.request.urlopen(url))  # noqa: S310
             for sess in sessions:
                 if sess["kernel"]["id"] == kernel_id:
                     return {

From 115bcf068ee3052374273faa0a39f9a26e72bd8b Mon Sep 17 00:00:00 2001
From: Ryuichi Arafune <ryuichi.arafune@gmail.com>
Date: Tue, 19 Mar 2024 10:04:16 +0900
Subject: [PATCH 02/10] =?UTF-8?q?=F0=9F=92=AC=20=20Add=20Incomplete=20to?=
 =?UTF-8?q?=20type=20unknown=20args.?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 pyproject.toml                                 |  2 +-
 src/arpes/analysis/band_analysis.py            | 11 ++++++++---
 src/arpes/analysis/mask.py                     | 14 +++++++-------
 src/arpes/bootstrap.py                         |  4 ++--
 .../corrections/fermi_edge_corrections.py      |  2 +-
 src/arpes/deep_learning/interpret.py           |  2 +-
 src/arpes/fits/broadcast_common.py             |  2 +-
 src/arpes/models/band.py                       |  5 +++--
 src/arpes/plotting/bz.py                       | 10 +++++-----
 .../bz_tool/RangeOrSingleValueWidget.py        |  4 ++--
 src/arpes/plotting/dynamic_tool.py             |  4 ++--
 src/arpes/plotting/utils.py                    | 10 +++++-----
 src/arpes/utilities/bz.py                      | 12 +++++++-----
 src/arpes/utilities/jupyter.py                 |  2 +-
 src/arpes/utilities/ui.py                      | 14 +++++++-------
 src/arpes/widgets.py                           | 18 +++++++++---------
 16 files changed, 62 insertions(+), 54 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 18c3c64d..7db833d8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -98,7 +98,7 @@ lint.ignore = [
   "NPY201", #  Numpy 2.0, 
 ]
 lint.select = ["ALL"]
-target-version = "py310"
+target-version = "py311"
 line-length = 100
 
 exclude = ["scripts", "docs", "conda"]
diff --git a/src/arpes/analysis/band_analysis.py b/src/arpes/analysis/band_analysis.py
index d712ba6e..280e5e29 100644
--- a/src/arpes/analysis/band_analysis.py
+++ b/src/arpes/analysis/band_analysis.py
@@ -435,8 +435,9 @@ def fit_bands(
     Args:
         arr(xr.DataArray):
         band_description: A description of the bands to fit in the region
-        background
-        direction
+        background:
+        direction:
+        step:
 
     Returns:
         Fitted bands.
@@ -543,7 +544,11 @@ def fit_bands(
     return band_results, unpacked_bands, residual  # Memo bunt_result is xr.DataArray
 
 
-def _interpolate_intersecting_fragments(coord, coord_index, points):
+def _interpolate_intersecting_fragments(
+    coord: Incomplete,
+    coord_index: int,
+    points: Incomplete,
+) -> Incomplete:
     """Finds all consecutive pairs of points in `points`.
 
     [TODO:description]
diff --git a/src/arpes/analysis/mask.py b/src/arpes/analysis/mask.py
index 65e77002..b1597b56 100644
--- a/src/arpes/analysis/mask.py
+++ b/src/arpes/analysis/mask.py
@@ -50,8 +50,8 @@ def raw_poly_to_mask(poly: Incomplete) -> dict[str, Incomplete]:
 
 def polys_to_mask(
     mask_dict: dict[str, Incomplete],
-    coords,
-    shape,
+    coords: Incomplete,
+    shape: Incomplete,
     radius: float = 0,
     *,
     invert: bool = False,
@@ -66,9 +66,9 @@ def polys_to_mask(
     waypoints are given in unitful values rather than index values.
 
     Args:
-        mask_dict
-        coords
-        shape
+        mask_dict (TODO)
+        coords:
+        shape:
         radius (float): Additional margin on the path in coordinates of *points*.
         invert (bool):
 
@@ -108,7 +108,7 @@ def apply_mask_to_coords(
     dims: list[str],
     *,
     invert: bool = True,
-):
+) -> Incomplete:
     """Performs broadcasted masking along a given dimension.
 
     Args:
@@ -139,7 +139,7 @@ def apply_mask(
     data: xr.DataArray,
     mask: dict[str, Incomplete],
     replace: float = np.nan,
-    radius=None,
+    radius: Incomplete = None,
     *,
     invert: bool = False,
 ) -> xr.DataArray:
diff --git a/src/arpes/bootstrap.py b/src/arpes/bootstrap.py
index 50778a71..f231e0e8 100644
--- a/src/arpes/bootstrap.py
+++ b/src/arpes/bootstrap.py
@@ -249,7 +249,7 @@ def draw_samples(self, n_samples: int = Distribution.DEFAULT_N_SAMPLES) -> NDArr
         return scipy.stats.norm.rvs(self.center, scale=self.stderr, size=n_samples)
 
     @classmethod
-    def from_param(cls: type, model_param: lf.Model.Parameter):
+    def from_param(cls: type, model_param: lf.Model.Parameter) -> Incomplete:
         """Generates a Normal from an `lmfit.Parameter`."""
         return cls(center=model_param.value, stderr=model_param.stderr)
 
@@ -353,7 +353,7 @@ def bootstrapped(
         n: int = 20,
         prior_adjustment: int = 1,
         **kwargs: Incomplete,
-    ):
+    ) -> Incomplete:
         # examine args to determine which to resample
         resample_indices = [
             i
diff --git a/src/arpes/corrections/fermi_edge_corrections.py b/src/arpes/corrections/fermi_edge_corrections.py
index 4f166fa4..b95054ad 100644
--- a/src/arpes/corrections/fermi_edge_corrections.py
+++ b/src/arpes/corrections/fermi_edge_corrections.py
@@ -167,7 +167,7 @@ def build_direct_fermi_edge_correction(
     others = [d for d in arr.dims if d not in exclude_axes]
     edge_fit = broadcast_model(GStepBModel, arr.sum(others).sel(eV=energy_range), along).results
 
-    def sieve(_, v) -> bool:
+    def sieve(_: Incomplete, v: Incomplete) -> bool:
         return v.item().params["center"].stderr < 0.001  # noqa: PLR2004
 
     corrections = edge_fit.G.filter_coord(along, sieve).G.map(
diff --git a/src/arpes/deep_learning/interpret.py b/src/arpes/deep_learning/interpret.py
index 42882654..92db5d62 100644
--- a/src/arpes/deep_learning/interpret.py
+++ b/src/arpes/deep_learning/interpret.py
@@ -137,7 +137,7 @@ def items(self) -> list[InterpretationItem]:
     def top_losses(self, *, ascending: bool = False) -> list[InterpretationItem]:
         """Orders the items by loss."""
 
-        def key(item):
+        def key(item: Incomplete) -> Incomplete:
             return item.loss if ascending else -item.loss
 
         return sorted(self.items, key=key)
diff --git a/src/arpes/fits/broadcast_common.py b/src/arpes/fits/broadcast_common.py
index f7a928d1..76f6e6f6 100644
--- a/src/arpes/fits/broadcast_common.py
+++ b/src/arpes/fits/broadcast_common.py
@@ -38,7 +38,7 @@ def unwrap_params(
 
     def transform_or_walk(
         v: dict | xr.DataArray | Iterable[float],
-    ):
+    ) -> Incomplete:
         """[TODO:summary].
 
         [TODO:description]
diff --git a/src/arpes/models/band.py b/src/arpes/models/band.py
index fb6c85df..54cc3187 100644
--- a/src/arpes/models/band.py
+++ b/src/arpes/models/band.py
@@ -13,6 +13,7 @@
 
 if TYPE_CHECKING:
     import lmfit as lf
+    from _typeshed import Incomplete
     from numpy.typing import NDArray
 
     from arpes._typing import DataType
@@ -144,7 +145,7 @@ def amplitude(self) -> xr.DataArray:
         return self.get_dataarray("amplitude", clean=True)
 
     @property
-    def indexes(self):
+    def indexes(self) -> Incomplete:
         """Fetches the indices of the originating data (after fit reduction)."""
         assert isinstance(self._data, xr.DataArray | xr.Dataset)
         return self._data.center.indexes
@@ -165,7 +166,7 @@ def dims(self) -> tuple[str, ...]:
 class MultifitBand(Band):
     """Convenience class that reimplements reading data out of a composite fit result."""
 
-    def get_dataarray(self, var_name: str):
+    def get_dataarray(self, var_name: str) -> Incomplete:
         """Converts the underlying data into an array representation."""
         assert isinstance(self._data, xr.DataArray | xr.Dataset)
         full_var_name = self.label + var_name
diff --git a/src/arpes/plotting/bz.py b/src/arpes/plotting/bz.py
index c5f23d03..bbd91518 100644
--- a/src/arpes/plotting/bz.py
+++ b/src/arpes/plotting/bz.py
@@ -230,7 +230,7 @@ def plot_data_to_bz(
     data: DataType,
     cell: Sequence[Sequence[float]] | NDArray[np.float_],
     **kwargs: Incomplete,
-):
+) -> Path | tuple[Figure, Axes]:
     """A dimension agnostic tool used to plot ARPES data onto a Brillouin zone."""
     if len(data) == TWO_DIMENSION + 1:
         return plot_data_to_bz3d(data, cell, **kwargs)
@@ -368,7 +368,7 @@ def bz3d_plot(
             stacklevel=2,
         )
         msg = "You will need to install ASE before using Brillouin Zone plotting"
-        raise ImportError(msg)
+        logger.exception(msg)
 
     class Arrow3D(FancyArrowPatch):
         def __init__(
@@ -382,7 +382,7 @@ def __init__(
             FancyArrowPatch.__init__(self, (0, 0), (0, 0), *args, **kwargs)
             self._verts3d = xs, ys, zs
 
-        def draw(self, renderer) -> None:
+        def draw(self, renderer: Incomplete) -> None:
             xs3d, ys3d, zs3d = self._verts3d
             xs, ys, zs = proj3d.proj_transform(xs3d, ys3d, zs3d, renderer.M)
             self.set_positions((xs[0], ys[0]), (xs[1], ys[1]))
@@ -537,7 +537,7 @@ def annotate_special_paths(
     cell: NDArray[np.float_] | Sequence[Sequence[float]] | None = None,
     offset: dict[str, Sequence[float]] | None = None,
     special_points: dict[str, NDArray[np.float_]] | None = None,
-    labels=None,
+    labels: Incomplete = None,
     **kwargs: Incomplete,
 ) -> None:
     """Annotates user indicated paths in k-space by plotting lines (or points) over the BZ."""
@@ -650,7 +650,7 @@ def bz2d_segments(
     return segments_x, segments_y
 
 
-def twocell_to_bz1(cell: NDArray[np.float_]):
+def twocell_to_bz1(cell: NDArray[np.float_]) -> Incomplete:
     from ase.dft.bz import bz_vertices
 
     # 2d in x-y plane
diff --git a/src/arpes/plotting/bz_tool/RangeOrSingleValueWidget.py b/src/arpes/plotting/bz_tool/RangeOrSingleValueWidget.py
index e2d12b74..af46de2f 100644
--- a/src/arpes/plotting/bz_tool/RangeOrSingleValueWidget.py
+++ b/src/arpes/plotting/bz_tool/RangeOrSingleValueWidget.py
@@ -61,10 +61,10 @@ def __init__(
 
         self.recompute()
 
-    def mode_changed(self, event, source) -> None:
+    def mode_changed(self, event: Incomplete, source: Incomplete) -> None:
         """Unused, currently."""
 
-    def value_changed(self, event, source) -> None:
+    def value_changed(self, event: Incomplete, source: Incomplete) -> None:
         """Responds to changes in the internal value."""
         if self._prevent_change_events:
             return
diff --git a/src/arpes/plotting/dynamic_tool.py b/src/arpes/plotting/dynamic_tool.py
index 17aada75..62a2e786 100644
--- a/src/arpes/plotting/dynamic_tool.py
+++ b/src/arpes/plotting/dynamic_tool.py
@@ -87,8 +87,8 @@ def update_data(self) -> None:
         try:
             mapped_data = self._function(self.data, **self.current_arguments)
             self.views["f(xy)"].setImage(mapped_data.fillna(0))
-        except Exception as err:
-            logger.debug(f"Exception occurs. {err=}, {type(err)=}")
+        except Exception:
+            logger.exception("Exception occurs.")
 
     def add_controls(self) -> None:
         specification = self.calculate_control_specification()
diff --git a/src/arpes/plotting/utils.py b/src/arpes/plotting/utils.py
index 94409cf1..3a002ff7 100644
--- a/src/arpes/plotting/utils.py
+++ b/src/arpes/plotting/utils.py
@@ -1102,8 +1102,8 @@ def remove_colorbars(fig: Figure | None = None) -> None:
                     ax.remove()
         else:
             remove_colorbars(plt.gcf())
-    except Exception as err:
-        logger.debug(f"Exception occurs: {err=}, {type(err)=}")
+    except Exception:
+        logger.exception("Exception occurs")
 
 
 def generic_colorbarmap_for_data(
@@ -1168,7 +1168,7 @@ class AnchoredHScaleBar(mpl.offsetbox.AnchoredOffsetbox):
     as alternate to the one provided through matplotlib.
     """
 
-    def __init__(
+    def __init__(  # noqa: PLR0913
         self,
         size: float = 1,
         extent: float = 0.03,
@@ -1235,14 +1235,14 @@ def load_data_for_figure(p: str | Path) -> None:
         raise ValueError(msg)
 
     with Path(pickle_file).open("rb") as f:
-        return pickle.load(f)
+        return pickle.load(f)  # noqa: S301
 
 
 def savefig(
     desired_path: str | Path,
     dpi: int = 400,
     data: list[XrTypes] | tuple[XrTypes, ...] | set[XrTypes] | None = None,
-    save_data=None,
+    save_data: Incomplete = None,
     *,
     paper: bool = False,
     **kwargs: Incomplete,
diff --git a/src/arpes/utilities/bz.py b/src/arpes/utilities/bz.py
index f6bbc6d3..610abc42 100644
--- a/src/arpes/utilities/bz.py
+++ b/src/arpes/utilities/bz.py
@@ -12,7 +12,7 @@
 import itertools
 import re
 from collections import Counter
-from typing import TYPE_CHECKING, Literal, NamedTuple
+from typing import TYPE_CHECKING, Literal, NamedTuple, TypeVar
 
 import matplotlib.path
 import numpy as np
@@ -57,6 +57,8 @@
     "hex": {"G", "X", "BX"},
 }
 
+T = TypeVar("T")
+
 
 class SpecialPoint(NamedTuple):
     name: str
@@ -400,7 +402,7 @@ def build_2dbz_poly(
     return raw_poly_to_mask(points_2d)
 
 
-def bz_symmetry(flat_symmetry_points) -> Literal["rect", "square", "hex"] | None:
+def bz_symmetry(flat_symmetry_points: Incomplete) -> Literal["rect", "square", "hex"] | None:
     """Determines symmetry from a list of the symmetry points.
 
     Args:
@@ -701,7 +703,7 @@ def reduced_bz_selection(data: DataType) -> DataType:
     return data
 
 
-def bz_cutter(symmetry_points, *, reduced: bool = True):
+def bz_cutter(symmetry_points: Incomplete, *, reduced: bool = True) -> Incomplete:
     """Cuts data so that it areas outside the Brillouin zone are masked away.
 
     Args:
@@ -711,7 +713,7 @@ def bz_cutter(symmetry_points, *, reduced: bool = True):
     TODO: UNFINISHED, Test
     """
 
-    def build_bz_mask(data) -> None:
+    def build_bz_mask(data: Incomplete) -> None:
         """[TODO:summary].
 
         Args:
@@ -721,7 +723,7 @@ def build_bz_mask(data) -> None:
             [TODO:description]
         """
 
-    def cutter(data, cut_value: float = np.nan):
+    def cutter(data: Incomplete, cut_value: float = np.nan) -> Incomplete:
         """[TODO:summary].
 
         Args:
diff --git a/src/arpes/utilities/jupyter.py b/src/arpes/utilities/jupyter.py
index 52684ae5..cccf956b 100644
--- a/src/arpes/utilities/jupyter.py
+++ b/src/arpes/utilities/jupyter.py
@@ -118,7 +118,7 @@ def get_full_notebook_information() -> NoteBookInfomation | None:
             if not url.startswith(("http:", "https:")):
                 msg = "URL must start with 'http:' or 'https:'"
                 raise ValueError(msg)
-            sessions = json.load(urllib.request.urlopen(url))
+            sessions = json.load(urllib.request.urlopen(url))  # noqa: S310
             for sess in sessions:
                 if sess["kernel"]["id"] == kernel_id:
                     return {
diff --git a/src/arpes/utilities/ui.py b/src/arpes/utilities/ui.py
index d41d638f..8cce7847 100644
--- a/src/arpes/utilities/ui.py
+++ b/src/arpes/utilities/ui.py
@@ -465,7 +465,7 @@ def _wrap_text(str_or_widget: str | QLabel) -> QLabel:
     return label(str_or_widget) if isinstance(str_or_widget, str) else str_or_widget
 
 
-def _unwrap_subject(subject_or_widget):
+def _unwrap_subject(subject_or_widget: Incomplete) -> Incomplete:
     try:
         return subject_or_widget.subject
     except AttributeError:
@@ -495,7 +495,7 @@ def submit(gate: str, keys: list[str], ui: dict[str, QWidget]) -> rx.Observable:
     )
 
 
-def _try_unwrap_value(v):
+def _try_unwrap_value(v: Incomplete) -> Incomplete:
     try:
         return v.value
     except AttributeError:
@@ -590,16 +590,16 @@ def bind_dataclass(dataclass_instance: Incomplete, prefix: str, ui: dict[str, QW
             )
             inverse_mapping = {v: k for k, v in forward_mapping.items()}
 
-            def extract_field(v):
+            def extract_field(v: Incomplete) -> Incomplete:
                 try:
                     return v.value
                 except AttributeError:
                     return v
 
-            def translate_to_field(x):
+            def translate_to_field(x: Incomplete) -> Incomplete:
                 return forward_mapping[x]
 
-            def translate_from_field(x):
+            def translate_from_field(x: Incomplete) -> Incomplete:
                 return inverse_mapping[extract_field(x)]
 
         current_value = translate_from_field(getattr(dataclass_instance, field_name))
@@ -609,8 +609,8 @@ def translate_from_field(x):
         w.subject.on_next(current_value)
 
         # close over the translation function
-        def build_setter(translate, name):
-            def setter(value) -> None:
+        def build_setter(translate: Incomplete, name: Incomplete) -> Callable[..., None]:
+            def setter(value: Incomplete) -> None:
                 try:
                     value = translate(value)
                 except ValueError:
diff --git a/src/arpes/widgets.py b/src/arpes/widgets.py
index 7b9e0cde..97e7dd6e 100644
--- a/src/arpes/widgets.py
+++ b/src/arpes/widgets.py
@@ -161,8 +161,8 @@ def onselect(self, verts: NDArray[np.float_]) -> None:
 
             if self._on_select is not None:
                 self._on_select(self.ind)
-        except Exception as err:
-            logger.debug(f"Exception occurs: {err=}, {type(err)=}")
+        except Exception:
+            logger.exception("Exception occurs.")
 
     def disconnect(self) -> None:
         self.lasso.disconnect_events()
@@ -222,7 +222,7 @@ class DataArrayView:
     Look some more into holoviews for different features. https://github.com/pyviz/holoviews/pull/1214
     """
 
-    def __init__(
+    def __init__(  # noqa: PLR0913
         self,
         ax: Axes,
         data: xr.DataArray | None = None,
@@ -280,7 +280,7 @@ def handle_select(self, event_click: MouseEvent, event_release: MouseEvent) -> N
 
         self._inner_on_select(region)
 
-    def attach_selector(self, on_select) -> None:
+    def attach_selector(self, on_select: Incomplete) -> None:
         # data should already have been set
         """[TODO:summary].
 
@@ -404,7 +404,7 @@ def mask(self):  # noqa: ANN202
         return self._mask
 
     @mask.setter
-    def mask(self, new_mask) -> None:
+    def mask(self, new_mask: Incomplete) -> None:
         """[TODO:summary].
 
         Args:
@@ -510,7 +510,7 @@ def compute_parameters() -> dict:
         ]
         return dict(itertools.chain(*[list(d.items()) for d in renamed]))
 
-    def on_add_new_peak(selection) -> None:
+    def on_add_new_peak(selection: Incomplete) -> None:
         """[TODO:summary].
 
         Args:
@@ -727,15 +727,15 @@ def clamp(x: int, low: int, high: int) -> int:
             assert val_x != val_y
 
             set_axes(val_x, val_y)
-        except Exception as err:
-            logger.debug(f"Exception occurs: {err=}, {type(err)=}")
+        except Exception:
+            logger.exception("Exception occurs.")
 
     context["axis_button"] = Button(ax_widget_1, "Change Decomp Axes")
     context["axis_button"].on_clicked(on_change_axes)
     context["axis_X_input"] = TextBox(ax_widget_2, "Axis X:", initial=str(initial_values[0]))
     context["axis_Y_input"] = TextBox(ax_widget_3, "Axis Y:", initial=str(initial_values[1]))
 
-    def on_select_summed(region) -> None:
+    def on_select_summed(region: Incomplete) -> None:
         """[TODO:summary].
 
         Args:

From 3cb3c71ff9093be4cb2ce5c5196785c1b71313e7 Mon Sep 17 00:00:00 2001
From: Ryuichi Arafune <ryuichi.arafune@gmail.com>
Date: Tue, 19 Mar 2024 10:28:01 +0900
Subject: [PATCH 03/10] =?UTF-8?q?=F0=9F=92=AC=20=20Update=20type=20hints?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/arpes/plotting/bz.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/arpes/plotting/bz.py b/src/arpes/plotting/bz.py
index 8c4db346..b622ac43 100644
--- a/src/arpes/plotting/bz.py
+++ b/src/arpes/plotting/bz.py
@@ -507,10 +507,12 @@ def draw(self, renderer: Incomplete) -> None:
             for name, point in zip(names, points, strict=True):
                 x, y, z = point
                 if name == "G":
-                    name = "\\Gamma"
+                    name_tex = "\\Gamma"
                 elif len(name) > 1:
-                    name = name[0] + "_" + name[1]
-                ax.text(x, y, z, "$" + name + "$", ha="center", va="bottom", color="r")
+                    name_tex = name[0] + "_" + name[1]
+                else:
+                    name_tex = name
+                ax.text(x, y, z, f"${name_tex}$", ha="center", va="bottom", color="r")
 
     if kpoints is not None:
         for p in kpoints:

From 5973903c0dd40d40ba6fe6d34dbdb24bdf272a60 Mon Sep 17 00:00:00 2001
From: Ryuichi Arafune <ryuichi.arafune@gmail.com>
Date: Tue, 19 Mar 2024 11:09:44 +0900
Subject: [PATCH 04/10] =?UTF-8?q?=F0=9F=92=AC=20=20Change=20target=20pytho?=
 =?UTF-8?q?n=20version.?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index cee87c78..ddb04c60 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -96,9 +96,10 @@ lint.ignore = [
   "G004",   # logging-f-string
   #
   "NPY201", #  Numpy 2.0, 
+  "ISC001", # single-line-implicit-string-concatenation
 ]
 lint.select = ["ALL"]
-target-version = "py312"
+target-version = "py311"
 line-length = 100
 indent-width = 4
 

From b62366c07f86f19e3055cd2da4e8d0bdb8c4fcfe Mon Sep 17 00:00:00 2001
From: Ryuichi Arafune <ryuichi.arafune@gmail.com>
Date: Tue, 19 Mar 2024 11:10:05 +0900
Subject: [PATCH 05/10] =?UTF-8?q?=F0=9F=92=AC=20=20Update=20type=20hints?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/arpes/deep_learning/interpret.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/arpes/deep_learning/interpret.py b/src/arpes/deep_learning/interpret.py
index 8e8e3e3e..92db5d62 100644
--- a/src/arpes/deep_learning/interpret.py
+++ b/src/arpes/deep_learning/interpret.py
@@ -137,7 +137,7 @@ def items(self) -> list[InterpretationItem]:
     def top_losses(self, *, ascending: bool = False) -> list[InterpretationItem]:
         """Orders the items by loss."""
 
-        def key(item: Incomplete):
+        def key(item: Incomplete) -> Incomplete:
             return item.loss if ascending else -item.loss
 
         return sorted(self.items, key=key)

From e8159fc9ba06c9af266b5494f1caea9a8424cff3 Mon Sep 17 00:00:00 2001
From: Ryuichi Arafune <ryuichi.arafune@gmail.com>
Date: Tue, 19 Mar 2024 11:19:17 +0900
Subject: [PATCH 06/10] =?UTF-8?q?=F0=9F=92=AC=20=20Update=20type=20hints?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/arpes/analysis/band_analysis.py     | 13 +++++++++++++
 src/arpes/plotting/fit_tool/__init__.py |  2 +-
 src/arpes/plotting/qt_tool/__init__.py  |  2 +-
 src/arpes/plotting/stack_plot.py        |  4 ++--
 src/arpes/utilities/widgets.py          |  2 +-
 5 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/src/arpes/analysis/band_analysis.py b/src/arpes/analysis/band_analysis.py
index cbc6113a..e2b979b8 100644
--- a/src/arpes/analysis/band_analysis.py
+++ b/src/arpes/analysis/band_analysis.py
@@ -7,6 +7,7 @@
 import functools
 import itertools
 from itertools import pairwise
+from logging import DEBUG, INFO, Formatter, StreamHandler, getLogger
 from typing import TYPE_CHECKING, Any, Literal
 
 import numpy as np
@@ -36,6 +37,18 @@
     "fit_for_effective_mass",
 )
 
+LOGLEVELS = (DEBUG, INFO)
+LOGLEVEL = LOGLEVELS[1]
+logger = getLogger(__name__)
+fmt = "%(asctime)s %(levelname)s %(name)s :%(message)s"
+formatter = Formatter(fmt)
+handler = StreamHandler()
+handler.setLevel(LOGLEVEL)
+logger.setLevel(LOGLEVEL)
+handler.setFormatter(formatter)
+logger.addHandler(handler)
+logger.propagate = False
+
 
 def fit_for_effective_mass(
     data: xr.DataArray,
diff --git a/src/arpes/plotting/fit_tool/__init__.py b/src/arpes/plotting/fit_tool/__init__.py
index 6d805cc3..f9c7c22c 100644
--- a/src/arpes/plotting/fit_tool/__init__.py
+++ b/src/arpes/plotting/fit_tool/__init__.py
@@ -266,7 +266,7 @@ def configure_image_widgets(self) -> None:
                 layout=self.content_layout,
             )
 
-    def generate_fit_marginal_for(
+    def generate_fit_marginal_for(  # noqa: PLR0913
         self,
         dimensions: tuple[int, ...],
         column_row: tuple[int, int],
diff --git a/src/arpes/plotting/qt_tool/__init__.py b/src/arpes/plotting/qt_tool/__init__.py
index f27c32f5..8f210789 100644
--- a/src/arpes/plotting/qt_tool/__init__.py
+++ b/src/arpes/plotting/qt_tool/__init__.py
@@ -552,7 +552,7 @@ def set_data(self, data: xr.DataArray) -> None:
 def _qt_tool(data: XrTypes, **kwargs: Incomplete) -> None:
     """Starts the qt_tool using an input spectrum."""
     with contextlib.suppress(TypeError):
-        data = dill.loads(data)
+        data = dill.loads(data)  # noqa: S301
 
     tool = QtTool()
     tool.set_data(data)
diff --git a/src/arpes/plotting/stack_plot.py b/src/arpes/plotting/stack_plot.py
index 8d611012..e6606137 100644
--- a/src/arpes/plotting/stack_plot.py
+++ b/src/arpes/plotting/stack_plot.py
@@ -65,7 +65,7 @@
 
 
 @save_plot_provenance
-def offset_scatter_plot(
+def offset_scatter_plot(  # noqa: PLR0913
     data: xr.Dataset,
     name_to_plot: str = "",
     stack_axis: str = "",
@@ -133,7 +133,7 @@ def offset_scatter_plot(
     skip_colorbar = True
     if cbarmap is None:
         skip_colorbar = False
-        cbar: colorbar.Colorbar | Callable[..., colorbar.Colorbar]
+        cbar: Callable[..., colorbar.Colorbar]
         cmap: Callable[..., ColorType] | Callable[..., Callable[..., ColorType]]
         try:
             cbar, cmap = colorbarmaps_for_axis[stack_axis]
diff --git a/src/arpes/utilities/widgets.py b/src/arpes/utilities/widgets.py
index 04b0c2cc..ec432501 100644
--- a/src/arpes/utilities/widgets.py
+++ b/src/arpes/utilities/widgets.py
@@ -138,7 +138,7 @@ def __init__(self, *args: QWidget | None) -> None:
         self.toggled.connect(lambda: self.subject.on_next(self.isChecked()))
         self.subject.subscribe(self.update_ui)
 
-    def update_ui(self, value: bool) -> None:
+    def update_ui(self, *, value: bool) -> None:
         """Forwards value change to the UI."""
         self.setChecked(value)
 

From 39c076918281f1069b7d7002527f05e2c6ecf2f3 Mon Sep 17 00:00:00 2001
From: Ryuichi Arafune <ryuichi.arafune@gmail.com>
Date: Tue, 19 Mar 2024 11:46:16 +0900
Subject: [PATCH 07/10] =?UTF-8?q?=F0=9F=92=AC=20=20Update=20type=20hints?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/arpes/deep_learning/transforms.py | 35 ++++++++++++++++++++++++---
 src/arpes/plotting/spin.py            | 11 +++------
 src/arpes/utilities/qt/app.py         |  2 +-
 3 files changed, 37 insertions(+), 11 deletions(-)

diff --git a/src/arpes/deep_learning/transforms.py b/src/arpes/deep_learning/transforms.py
index c96313d1..2f286526 100644
--- a/src/arpes/deep_learning/transforms.py
+++ b/src/arpes/deep_learning/transforms.py
@@ -15,15 +15,44 @@ class Identity:
     """Represents a reversible identity transform."""
 
     def encodes(self, x: Incomplete) -> Incomplete:
+        """[TODO:summary].
+
+        Args:
+            x: [TODO:description]
+
+        Returns:
+            [TODO:description]
+        """
         return x
 
     def __call__(self, x: Incomplete) -> Incomplete:
+        """[TODO:summary].
+
+        Args:
+            x: [TODO:description]
+
+        Returns:
+            [TODO:description]
+        """
         return x
 
     def decodes(self, x: Incomplete) -> Incomplete:
+        """[TODO:summary].
+
+        Args:
+            x: [TODO:description]
+
+        Returns:
+            [TODO:description]
+        """
         return x
 
     def __repr__(self) -> str:
+        """[TODO:summary].
+
+        Returns:
+            [TODO:description]
+        """
         return "Identity()"
 
 
@@ -54,9 +83,9 @@ def __post_init__(self) -> None:
         for t in self.transforms:
             if isinstance(t, tuple | list):
                 xt, yt = t
-                t = [xt or _identity, yt or _identity]
-
-            safe_transforms.append(t)
+                safe_transforms.append([xt or _identity, yt or _identity])
+            else:
+                safe_transforms.append(t)
 
         self.original_transforms = self.transforms
         self.transforms = safe_transforms
diff --git a/src/arpes/plotting/spin.py b/src/arpes/plotting/spin.py
index f2f77291..f372b15a 100644
--- a/src/arpes/plotting/spin.py
+++ b/src/arpes/plotting/spin.py
@@ -163,11 +163,9 @@ def spin_polarized_spectrum(  # noqa: PLR0913
         counts = spin_dr
         pol = to_intensity_polarization(counts)
 
-    ax_left = ax[0]
-    ax_right = ax[1]
+    ax_left, ax_right = ax[0], ax[1]
 
-    up = counts.down.data
-    down = counts.up.data
+    down, up = counts.down.data, counts.up.data
 
     energies = spin_dr.coords["eV"].values
     min_e, max_e = np.min(energies), np.max(energies)
@@ -194,8 +192,7 @@ def spin_polarized_spectrum(  # noqa: PLR0913
     ax_left.set_xlabel(r"\textbf{Kinetic energy} (eV)")
     ax_left.set_xlim(min_e, max_e)
 
-    max_up = np.max(up)
-    max_down = np.max(down)
+    max_up, max_down = np.max(up), np.max(down)
     ax_left.set_ylim(0, max(max_down, max_up) * 1.2)
 
     # Plot the polarization and associated statistical error bars
@@ -296,7 +293,7 @@ def hue_brightness_plot(
     assert isinstance(ax, Axes)
     assert isinstance(fig, Figure)
     x, y = data.coords[data.intensity.dims[0]].values, data.coords[data.intensity.dims[1]].values
-    extent = [y[0], y[-1], x[0], x[-1]]
+    extent = (y[0], y[-1], x[0], x[-1])
     ax.imshow(
         polarization_intensity_to_color(data, **kwargs),
         extent=extent,
diff --git a/src/arpes/utilities/qt/app.py b/src/arpes/utilities/qt/app.py
index dc06d009..1cfffb36 100644
--- a/src/arpes/utilities/qt/app.py
+++ b/src/arpes/utilities/qt/app.py
@@ -143,7 +143,7 @@ def set_colormap(self, colormap: Colormap | str) -> None:
             if isinstance(view, DataArrayImageView):
                 view.setColorMap(cmap)
 
-    def generate_marginal_for(
+    def generate_marginal_for(  # noqa: PLR0913
         self,
         dimensions: tuple[int, ...],
         column: int,

From 945f3d25f06781cbcc87e611b661bc19b3c65b71 Mon Sep 17 00:00:00 2001
From: Ryuichi Arafune <ryuichi.arafune@gmail.com>
Date: Tue, 19 Mar 2024 13:03:18 +0900
Subject: [PATCH 08/10] =?UTF-8?q?=F0=9F=92=AC=20=20Update=20type=20hints?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/arpes/analysis/band_analysis.py     | 13 ++++++-------
 src/arpes/fits/utilities.py             |  2 +-
 src/arpes/plotting/annotations.py       |  3 ++-
 src/arpes/plotting/fit_tool/__init__.py |  2 +-
 src/arpes/xarray_extensions.py          |  9 +++++----
 5 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/src/arpes/analysis/band_analysis.py b/src/arpes/analysis/band_analysis.py
index e2b979b8..abe3049f 100644
--- a/src/arpes/analysis/band_analysis.py
+++ b/src/arpes/analysis/band_analysis.py
@@ -261,7 +261,7 @@ def dataarray_for_value(param_name: str, i: int = i, *, is_value: bool) -> xr.Da
 
 
 @update_provenance("Fit bands from pattern")
-def fit_patterned_bands(
+def fit_patterned_bands(  # noqa: PLR0913
     arr: xr.DataArray,
     band_set: dict[Incomplete, Incomplete],
     fit_direction: str = "",
@@ -293,10 +293,9 @@ def fit_patterned_bands(
         band_set: dictionary with bands and points along the spectrum
         fit_direction (str):
         stray (float, optional):
-        orientation: edc or mdc
-        direction_normal
-        preferred_k_direction
-        dataset: if True, return as Dataset
+        background (bool):
+        interactive(bool):
+        dataset(bool): if true, return as xr.Dataset.
 
     Returns:
         Dataset or DataArray, as controlled by the parameter "dataset"
@@ -309,7 +308,7 @@ def fit_patterned_bands(
     free_directions = list(arr.dims)
     free_directions.remove(fit_direction)
 
-    def resolve_partial_bands_from_description(
+    def resolve_partial_bands_from_description(  # noqa: PLR0913
         coord_dict: dict[str, Incomplete],
         name: str = "",
         band: Incomplete = None,
@@ -525,7 +524,7 @@ def fit_bands(
         # be stable
         closest_model_params = initial_fits  # fix me
         dist = float("inf")
-        frozen_coordinate = tuple(coordinate[k] for k in template.dims)
+        frozen_coordinate = tuple(coordinate[str(k)] for k in template.dims)
         for c, v in all_fit_parameters.items():
             delta = np.array(c) - frozen_coordinate
             current_distance = delta.dot(delta)
diff --git a/src/arpes/fits/utilities.py b/src/arpes/fits/utilities.py
index bee785e6..d31ec0dd 100644
--- a/src/arpes/fits/utilities.py
+++ b/src/arpes/fits/utilities.py
@@ -230,7 +230,7 @@ def broadcast_model(  # noqa: PLR0913
         def unwrap(result_data: str) -> object:  # (Unpickler)
             # using the lmfit deserialization and serialization seems slower than double pickling
             # with dill
-            return dill.loads(result_data)
+            return dill.loads(result_data)  # noqa: S301
 
         exe_results = [(unwrap(res), residual, cs) for res, residual, cs in exe_results]
 
diff --git a/src/arpes/plotting/annotations.py b/src/arpes/plotting/annotations.py
index 4672b121..06eca149 100644
--- a/src/arpes/plotting/annotations.py
+++ b/src/arpes/plotting/annotations.py
@@ -201,7 +201,7 @@ def annotate_cuts(
 def annotate_point(
     ax: Axes | Axes3D,
     location: Sequence[float],
-    delta: tuple[float, ...] = (),
+    delta: tuple[float, float] | tuple[float, float, float] | None = None,
     **kwargs: Unpack[MPLTextParam],
 ) -> None:
     """Annotates a point or high symmetry location into a plot."""
@@ -220,6 +220,7 @@ def annotate_point(
             -0.05,
             0.05,
         )
+    assert isinstance(delta, tuple)
     if "color" not in kwargs:
         kwargs["color"] = "red"
 
diff --git a/src/arpes/plotting/fit_tool/__init__.py b/src/arpes/plotting/fit_tool/__init__.py
index f9c7c22c..11ad2839 100644
--- a/src/arpes/plotting/fit_tool/__init__.py
+++ b/src/arpes/plotting/fit_tool/__init__.py
@@ -500,7 +500,7 @@ def set_data(self, data: xr.Dataset) -> None:
 def _fit_tool(data: xr.Dataset) -> None:
     """Starts the fitting inspection tool using an input fit result Dataset."""
     with contextlib.suppress(TypeError):
-        data = dill.loads(data)
+        data = dill.loads(data)  # noqa: S301
 
     # some sanity checks that we were actually passed a collection of fit results
     assert isinstance(data, xr.Dataset)
diff --git a/src/arpes/xarray_extensions.py b/src/arpes/xarray_extensions.py
index 7b8e780c..4bcde284 100644
--- a/src/arpes/xarray_extensions.py
+++ b/src/arpes/xarray_extensions.py
@@ -1196,7 +1196,7 @@ def unpack_dim(dim_name: str) -> str:
             # remove missing dimensions from selection for permissiveness
             # and to transparent composing of regions
             region = {k: process_region_selector(v, k) for k, v in region.items() if k in obj.dims}
-            obj = obj.sel(**region)
+            obj = obj.sel(region)
 
         return obj
 
@@ -2520,13 +2520,14 @@ def iterate_axis(
         self,
         axis_name_or_axes: list[str] | str,
     ) -> Generator[tuple[dict[str, float], XrTypes], str, None]:
-        """[TODO:summary].
+        """Generator to extract data for along the specified axis.
 
         Args:
             axis_name_or_axes: [TODO:description]
 
-        Returns:
-            [TODO:description]
+        Returns: (tuple[dict[str, float], XrTypes])
+            dict object represents the axis(dim) name and it's value.
+            XrTypes object the corresponding data.
         """
         assert isinstance(self._obj, xr.DataArray | xr.Dataset)
         if isinstance(axis_name_or_axes, str):

From 8e230e05c3fc425e6727d9c9d73f493aca25ccef Mon Sep 17 00:00:00 2001
From: Ryuichi Arafune <ryuichi.arafune@gmail.com>
Date: Tue, 19 Mar 2024 13:25:13 +0900
Subject: [PATCH 09/10] =?UTF-8?q?=F0=9F=9A=A8=20=20Introduce=20helper=20fu?=
 =?UTF-8?q?nction.?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/arpes/endstations/__init__.py | 57 +++++++++++++++++--------------
 1 file changed, 31 insertions(+), 26 deletions(-)

diff --git a/src/arpes/endstations/__init__.py b/src/arpes/endstations/__init__.py
index 277ef4cb..7a64373d 100644
--- a/src/arpes/endstations/__init__.py
+++ b/src/arpes/endstations/__init__.py
@@ -278,7 +278,7 @@ def concatenate_frames(
         frames.sort(key=lambda x: x.coords[scan_coord])
         return xr.concat(frames, scan_coord)
 
-    def resolve_frame_locations(self, scan_desc: ScanDesc | None = None) -> list[Path | str]:
+    def resolve_frame_locations(self, scan_desc: ScanDesc | None = None) -> list[Path]:
         """Determine all files and frames associated to this piece of data.
 
         This always needs to be overridden in subclasses to handle data appropriately.
@@ -358,31 +358,12 @@ def postprocess_final(
         coord_names: tuple[str, ...] = tuple(sorted([str(c) for c in data.dims if c != "cycle"]))
         spectrum_type = _spectrum_type(coord_names)
 
-        if "phi" not in data.coords:
-            data.coords["phi"] = 0
-            for s in data.S.spectra:
-                s.coords["phi"] = 0
-
-        if spectrum_type is not None:
-            data.attrs["spectrum_type"] = spectrum_type
-            if "spectrum" in data.data_vars:
-                data.spectrum.attrs["spectrum_type"] = spectrum_type
-
-        ls = [data, *data.S.spectra]
-        for a_data in ls:
-            for k, key_fn in self.ATTR_TRANSFORMS.items():
-                if k in a_data.attrs:
-                    transformed = key_fn(a_data.attrs[k])
-                    if isinstance(transformed, dict):
-                        a_data.attrs.update(transformed)
-                    else:
-                        a_data.attrs[k] = transformed
-
-        for a_data in ls:
-            for k, v in self.MERGE_ATTRS.items():
-                a_data.attrs.setdefault(k, v)
-
-        for a_data in [_ensure_coords(a_data, self.ENSURE_COORDS_EXIST) for a_data in ls]:
+        modified_data = [
+            self._modify_a_data(a_data, spectrum_type) for a_data in [data, *data.S.spectra]
+        ]
+        for a_data in [
+            _ensure_coords(a_data, self.ENSURE_COORDS_EXIST) for a_data in modified_data
+        ]:
             if "chi" in a_data.coords and "chi_offset" not in a_data.attrs:
                 a_data.attrs["chi_offset"] = a_data.coords["chi"].item()
 
@@ -449,6 +430,30 @@ def load(self, scan_desc: ScanDesc | None = None, **kwargs: Incomplete) -> xr.Da
 
         return concatted
 
+    def _modify_a_data(self, a_data: DataType, spectrum_type: str | None) -> DataType:
+        """Helper function to modify the Dataset and DataArray that are contained in the Dataset.
+
+        Args:
+            a_data: [TODO:description]
+            spectrum_type: [TODO:description]
+
+        Returns:
+            [TODO:description]
+        """
+        if "phi" not in a_data.coords:
+            a_data.coords["phi"] = 0
+        a_data.attrs["spectrum_type"] = spectrum_type
+        for k, key_fn in self.ATTR_TRANSFORMS.items():
+            if k in a_data.attrs:
+                transformed = key_fn(a_data.attrs[k])
+                if isinstance(transformed, dict):
+                    a_data.attrs.update(transformed)
+                else:
+                    a_data.attrs[k] = transformed
+        for k, v in self.MERGE_ATTRS.items():
+            a_data.attrs.setdefault(k, v)
+        return a_data
+
 
 def _spectrum_type(
     coord_names: Sequence[str],

From fa7b283dcbf12d45c1586c1cb3ca971177cb9a5f Mon Sep 17 00:00:00 2001
From: Ryuichi Arafune <ryuichi.arafune@gmail.com>
Date: Tue, 19 Mar 2024 14:18:39 +0900
Subject: [PATCH 10/10] =?UTF-8?q?=F0=9F=9A=A8=20=20Remove=20ruff=20Warning?=
 =?UTF-8?q?=20in=20xarray=5Fextensions.py=20=20=20=20=20-=20=20PLW2901=20?=
 =?UTF-8?q?=F0=9F=92=AC=20=20Update=20type=20hints?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/arpes/analysis/mask.py                    | 14 +++---
 src/arpes/endstations/nexus_utils.py          |  3 +-
 src/arpes/endstations/plugin/ANTARES.py       | 31 +++++++++----
 src/arpes/endstations/plugin/BL10_SARPES.py   |  2 +-
 .../plugin/Elettra_spectromicroscopy.py       | 23 ++++++++--
 src/arpes/endstations/plugin/HERS.py          | 11 ++++-
 src/arpes/endstations/plugin/IF_UMCS.py       |  5 ++-
 src/arpes/endstations/plugin/MAESTRO.py       |  6 ++-
 src/arpes/endstations/plugin/kaindl.py        |  4 +-
 src/arpes/endstations/plugin/merlin.py        |  4 +-
 src/arpes/plotting/bz.py                      | 45 +++++++++----------
 .../bz_tool/CoordinateOffsetWidget.py         | 17 ++++++-
 .../bz_tool/RangeOrSingleValueWidget.py       |  2 +
 src/arpes/provenance.py                       |  2 +
 src/arpes/utilities/collections.py            |  4 +-
 src/arpes/utilities/conversion/core.py        |  8 ++--
 src/arpes/xarray_extensions.py                | 21 ++++++---
 17 files changed, 136 insertions(+), 66 deletions(-)

diff --git a/src/arpes/analysis/mask.py b/src/arpes/analysis/mask.py
index ae4e8121..ec94e8b8 100644
--- a/src/arpes/analysis/mask.py
+++ b/src/arpes/analysis/mask.py
@@ -55,7 +55,7 @@ def polys_to_mask(
     radius: float = 0,
     *,
     invert: bool = False,
-) -> NDArray[np.float_] | NDArray[np.bool_]:
+) -> NDArray[np.bool_]:
     """Converts a mask definition in terms of the underlying polygon to a True/False mask array.
 
     Uses the coordinates and shape of the target data in order to determine which pixels
@@ -120,18 +120,20 @@ def apply_mask_to_coords(
     Returns:
         The masked data.
     """
-    p = Path(mask["poly"])
-
     as_array = np.stack([data.data_vars[d].values for d in dims], axis=-1)
     shape = as_array.shape
     dest_shape = shape[:-1]
     new_shape = [np.prod(dest_shape), len(dims)]
+    mask_array = (
+        Path(np.array(mask["poly"]))
+        .contains_points(as_array.reshape(new_shape))
+        .reshape(dest_shape)
+    )
 
-    mask = p.contains_points(as_array.reshape(new_shape)).reshape(dest_shape)
     if invert:
-        mask = np.logical_not(mask)
+        mask_array = np.logical_not(mask_array)
 
-    return mask
+    return mask_array
 
 
 @update_provenance("Apply boolean mask to data")
diff --git a/src/arpes/endstations/nexus_utils.py b/src/arpes/endstations/nexus_utils.py
index 26f06542..aad506d9 100644
--- a/src/arpes/endstations/nexus_utils.py
+++ b/src/arpes/endstations/nexus_utils.py
@@ -15,6 +15,7 @@
 if TYPE_CHECKING:
     from collections.abc import Callable
 
+    from _typeshed import Incomplete
     import xarray as xr
 
 __all__ = ("read_data_attributes_from",)
@@ -63,7 +64,7 @@ class Target:
 
     value: Any = None
 
-    def read_h5(self, g, path) -> None:
+    def read_h5(self, g: Incomplete, path: Incomplete) -> None:
         self.value = None
         self.value = self.read(read_group_data(g))
 
diff --git a/src/arpes/endstations/plugin/ANTARES.py b/src/arpes/endstations/plugin/ANTARES.py
index 0248bd57..668d8d88 100644
--- a/src/arpes/endstations/plugin/ANTARES.py
+++ b/src/arpes/endstations/plugin/ANTARES.py
@@ -73,7 +73,11 @@
 }
 
 
-def parse_axis_name_from_long_name(name: str, keep_segments: int = 1, separator: str = "_") -> str:
+def parse_axis_name_from_long_name(
+    name: str,
+    keep_segments: int = 1,
+    separator: str = "_",
+) -> str:
     segments = name.split("/")[-keep_segments:]
     segments = [s.replace("'", "") for s in segments]
     return separator.join(segments)
@@ -99,14 +103,18 @@ def infer_scan_type_from_data(group: dict) -> str:
     raise NotImplementedError(scan_name)
 
 
-class ANTARESEndstation(HemisphericalEndstation, SynchrotronEndstation, SingleFileEndstation):
+class ANTARESEndstation(
+    HemisphericalEndstation,
+    SynchrotronEndstation,
+    SingleFileEndstation,
+):
     """Implements data loading for ANTARES at SOLEIL.
 
     There's not too much metadata here except what comes with the analyzer settings.
     """
 
     PRINCIPAL_NAME = "ANTARES"
-    ALIASES: ClassVar[list] = []
+    ALIASES: ClassVar[list[str]] = []
 
     _TOLERATED_EXTENSIONS: ClassVar[set[str]] = {".nxs"}
 
@@ -120,14 +128,12 @@ def load_top_level_scan(
     ) -> xr.Dataset:
         """Reads a spectrum from the top level group in a NeXuS scan format.
 
-        [TODO:description]
-
         Args:
             group ([TODO:type]): [TODO:description]
             scan_desc: [TODO:description]
             spectrum_index ([TODO:type]): [TODO:description]
 
-        Returns:
+        Returns (xr.Dataset):
             [TODO:description]
         """
         if scan_desc:
@@ -177,7 +183,10 @@ def get_coords(self, group: Incomplete, scan_name: str, shape: Incomplete):
                 (
                     name
                     if set_names[name] == 1
-                    else parse_axis_name_from_long_name(actuator_long_names[i], keep_segments)
+                    else parse_axis_name_from_long_name(
+                        actuator_long_names[i],
+                        keep_segments,
+                    )
                 )
                 for i, name in enumerate(actuator_names)
             ]
@@ -241,13 +250,17 @@ def take_last(vs):
         energy = data[e_keys[0]][0], data[e_keys[1]][0], data[e_keys[2]][0]
         angle = data[ang_keys[0]][0], data[ang_keys[1]][0], data[ang_keys[2]][0]
 
-        def get_first(item):
+        def get_first(item: NDArray[np.float_] | float):
             if isinstance(item, np.ndarray):
                 return item.ravel()[0]
 
             return item
 
-        def build_axis(low: float, high: float, step_size: float) -> tuple[NDArray[np.float_], int]:
+        def build_axis(
+            low: float,
+            high: float,
+            step_size: float,
+        ) -> tuple[NDArray[np.float_], int]:
             # this might not work out to be the right thing to do, we will see
             low, high, step_size = get_first(low), get_first(high), get_first(step_size)
             est_n: int = int((high - low) / step_size)
diff --git a/src/arpes/endstations/plugin/BL10_SARPES.py b/src/arpes/endstations/plugin/BL10_SARPES.py
index 55e6801b..da58da44 100644
--- a/src/arpes/endstations/plugin/BL10_SARPES.py
+++ b/src/arpes/endstations/plugin/BL10_SARPES.py
@@ -121,7 +121,7 @@ def load_single_region(
         """Loads a single region for multi-region scans."""
         from arpes.load_pxt import read_single_pxt
 
-        name, _ = Path(region_path).stem
+        name = Path(region_path).stem
         num = name[-3:]
 
         pxt_data = read_single_pxt(region_path, allow_multiple=True)
diff --git a/src/arpes/endstations/plugin/Elettra_spectromicroscopy.py b/src/arpes/endstations/plugin/Elettra_spectromicroscopy.py
index 08b04674..aeaf5e60 100644
--- a/src/arpes/endstations/plugin/Elettra_spectromicroscopy.py
+++ b/src/arpes/endstations/plugin/Elettra_spectromicroscopy.py
@@ -109,7 +109,10 @@ def unwrap_bytestring(
     )
 
 
-class SpectromicroscopyElettraEndstation(HemisphericalEndstation, SynchrotronEndstation):
+class SpectromicroscopyElettraEndstation(
+    HemisphericalEndstation,
+    SynchrotronEndstation,
+):
     """Data loading for the nano-ARPES beamline "Spectromicroscopy Elettra".
 
     Information available on the beamline can be accessed
@@ -145,7 +148,12 @@ def files_for_search(cls: type, directory: str | Path) -> list[Path]:
             else:
                 base_files = [*base_files, Path(file)]
 
-        return list(filter(lambda f: Path(f).suffix in cls._TOLERATED_EXTENSIONS, base_files))
+        return list(
+            filter(
+                lambda f: Path(f).suffix in cls._TOLERATED_EXTENSIONS,
+                base_files,
+            )
+        )
 
     ANALYZER_INFORMATION: ClassVar[dict[str, str | float | bool]] = {
         "analyzer": "Custom: in vacuum hemispherical",
@@ -228,7 +236,10 @@ def concatenate_frames(
 
         return xr.Dataset({"spectrum": xr.concat(fs, scan_coord)})
 
-    def resolve_frame_locations(self, scan_desc: ScanDesc | None = None) -> list[Path]:
+    def resolve_frame_locations(
+        self,
+        scan_desc: ScanDesc | None = None,
+    ) -> list[Path]:
         """Determines all files associated with a given scan.
 
         This beamline saves several HDF files in scan associated folders, so this
@@ -269,7 +280,11 @@ def load_single_frame(
 
             return xr.Dataset(arrays)
 
-    def postprocess_final(self, data: xr.Dataset, scan_desc: ScanDesc | None = None) -> xr.Dataset:
+    def postprocess_final(
+        self,
+        data: xr.Dataset,
+        scan_desc: ScanDesc | None = None,
+    ) -> xr.Dataset:
         """Performs final postprocessing of the data.
 
         This mostly amounts to:
diff --git a/src/arpes/endstations/plugin/HERS.py b/src/arpes/endstations/plugin/HERS.py
index 8e3e7ef2..4a1868fb 100644
--- a/src/arpes/endstations/plugin/HERS.py
+++ b/src/arpes/endstations/plugin/HERS.py
@@ -23,7 +23,10 @@
 __all__ = ("HERSEndstation",)
 
 
-class HERSEndstation(SynchrotronEndstation, HemisphericalEndstation):
+class HERSEndstation(
+    SynchrotronEndstation,
+    HemisphericalEndstation,
+):
     """Implements data loading at the ALS HERS beamline.
 
     This should be unified with the FITs endstation code, but I don't have any projects at BL10
@@ -33,7 +36,11 @@ class HERSEndstation(SynchrotronEndstation, HemisphericalEndstation):
     PRINCIPAL_NAME = "ALS-BL1001"
     ALIASES: ClassVar[list[str]] = ["ALS-BL1001", "HERS", "ALS-HERS", "BL1001"]
 
-    def load(self, scan_desc: ScanDesc | None = None, **kwargs: Incomplete) -> xr.Dataset:
+    def load(
+        self,
+        scan_desc: ScanDesc | None = None,
+        **kwargs: Incomplete,
+    ) -> xr.Dataset:
         """Loads HERS data from FITS files. Shares a lot in common with Lanzara group formats.
 
         Args:
diff --git a/src/arpes/endstations/plugin/IF_UMCS.py b/src/arpes/endstations/plugin/IF_UMCS.py
index 3e663617..72d77b7f 100644
--- a/src/arpes/endstations/plugin/IF_UMCS.py
+++ b/src/arpes/endstations/plugin/IF_UMCS.py
@@ -23,7 +23,10 @@
 __all__ = ("IF_UMCS",)
 
 
-class IF_UMCS(HemisphericalEndstation, SingleFileEndstation):  # noqa: N801
+class IF_UMCS(  # noqa: N801
+    HemisphericalEndstation,
+    SingleFileEndstation,
+):
     """Implements loading xy text files from the Specs Prodigy software."""
 
     PRINCIPAL_NAME = "IF_UMCS"
diff --git a/src/arpes/endstations/plugin/MAESTRO.py b/src/arpes/endstations/plugin/MAESTRO.py
index 833182e7..25112acd 100644
--- a/src/arpes/endstations/plugin/MAESTRO.py
+++ b/src/arpes/endstations/plugin/MAESTRO.py
@@ -29,7 +29,11 @@
 __all__ = ("MAESTROMicroARPESEndstation", "MAESTRONanoARPESEndstation")
 
 
-class MAESTROARPESEndstationBase(SynchrotronEndstation, HemisphericalEndstation, FITSEndstation):
+class MAESTROARPESEndstationBase(
+    SynchrotronEndstation,
+    HemisphericalEndstation,
+    FITSEndstation,
+):
     """Common code for the MAESTRO ARPES endstations at the Advanced Light Source."""
 
     PRINCIPAL_NAME = ""
diff --git a/src/arpes/endstations/plugin/kaindl.py b/src/arpes/endstations/plugin/kaindl.py
index 73103a2a..251cfdc5 100644
--- a/src/arpes/endstations/plugin/kaindl.py
+++ b/src/arpes/endstations/plugin/kaindl.py
@@ -180,8 +180,8 @@ def concatenate_frames(
 
                 frames.sort(key=lambda x: x.coords[axis_name])
                 return xr.concat(frames, axis_name)
-            except Exception as err:
-                logger.info(f"Exception occurs. {err=}, {type(err)=}")
+            except Exception:
+                logger.exception("Exception occurs.")
         return None
 
     def postprocess_final(self, data: xr.Dataset, scan_desc: ScanDesc | None = None) -> xr.Dataset:
diff --git a/src/arpes/endstations/plugin/merlin.py b/src/arpes/endstations/plugin/merlin.py
index 5144d0f0..8bce7e8b 100644
--- a/src/arpes/endstations/plugin/merlin.py
+++ b/src/arpes/endstations/plugin/merlin.py
@@ -202,9 +202,7 @@ def load_single_frame(
             scan_desc["path"] = frame_path
             return self.load_SES_nc(scan_desc=scan_desc, **kwargs)
 
-        original_data_loc: Path | str = scan_desc.get("path", scan_desc.get("file"))
-
-        p = Path(original_data_loc)
+        p = Path(scan_desc.get("path", scan_desc.get("file", "")))
 
         # find files with same name stem, indexed in format R###
         regions = find_ses_files_associated(p, separator="R")
diff --git a/src/arpes/plotting/bz.py b/src/arpes/plotting/bz.py
index b622ac43..88c24aa5 100644
--- a/src/arpes/plotting/bz.py
+++ b/src/arpes/plotting/bz.py
@@ -188,7 +188,7 @@ def apply_transformations(
 def plot_plane_to_bz(
     cell: Sequence[Sequence[float]] | NDArray[np.float_],
     plane: str | list[NDArray[np.float_]],
-    ax: Axes,
+    ax: Axes3D,
     special_points: dict[str, NDArray[np.float_]] | None = None,
     facecolor: ColorType = "red",
 ) -> None:
@@ -209,7 +209,7 @@ def plot_plane_to_bz(
     if isinstance(plane, str):
         plane_points: list[NDArray[np.float_]] = process_kpath(
             plane,
-            cell,
+            np.array(cell),
             special_points=special_points,
         )[0]
     else:
@@ -226,7 +226,7 @@ def plot_plane_to_bz(
 
 
 def plot_data_to_bz(
-    data: DataType,
+    data: xr.DataArray,
     cell: Sequence[Sequence[float]] | NDArray[np.float_],
     **kwargs: Incomplete,
 ) -> Path | tuple[Figure, Axes]:
@@ -313,10 +313,10 @@ def plot_data_to_bz2d(  # noqa: PLR0913
 
 
 def plot_data_to_bz3d(
-    data: DataType,
+    data: xr.DataArray,
     cell: Sequence[Sequence[float]] | NDArray[np.float_],
     **kwargs: Incomplete,
-) -> None:
+) -> Path | tuple[Figure, Axes]:
     """Plots ARPES data onto a 3D Brillouin zone."""
     msg = "plot_data_to_bz3d is not implemented yet."
     logger.debug(f"id of data: {data.attrs.get('id', None)}")
@@ -533,7 +533,7 @@ def draw(self, renderer: Incomplete) -> None:
 
 def annotate_special_paths(
     ax: Axes,
-    paths: list[str] | str,
+    paths: list[str] | str = "",
     cell: NDArray[np.float_] | Sequence[Sequence[float]] | None = None,
     offset: dict[str, Sequence[float]] | None = None,
     special_points: dict[str, NDArray[np.float_]] | None = None,
@@ -541,17 +541,11 @@ def annotate_special_paths(
     **kwargs: Incomplete,
 ) -> None:
     """Annotates user indicated paths in k-space by plotting lines (or points) over the BZ."""
-    logger.debug(f"annotate-ax: {ax}")
-    logger.debug(f"annotate-paths: {paths}")
-    logger.debug(f"annotate-cell: {cell}")
-    logger.debug(f"annotate-offset: {offset}")
-    logger.debug(f"annotate-special_points: {special_points}")
-    logger.debug(f"annotate-labels: {labels}")
     if kwargs:
         for k, v in kwargs.items():
             logger.debug(f"kwargs: kyes: {k}, value: {v}")
 
-    if paths == "":
+    if not paths:
         msg = "Must provide a proper path."
         raise ValueError(msg)
 
@@ -668,7 +662,7 @@ def twocell_to_bz1(cell: NDArray[np.float_]) -> Incomplete:
 
 
 def bz2d_plot(
-    cell: Sequence[Sequence[float]],
+    cell: Sequence[Sequence[float]] | NDArray[np.float_],
     paths: str | list[float] | None = None,
     points: Sequence[float] | None = None,
     repeat: tuple[int, int] | None = None,
@@ -687,16 +681,8 @@ def bz2d_plot(
 
     Plots a Brillouin zone corresponding to a given unit cell
     """
-    logger.debug(f"bz2d_plot-cell: {cell}")
-    logger.debug(f"bz2d_plot-paths: {paths}")
-    logger.debug(f"bz2d_plot-points: {points}")
-    logger.debug(f"bz2d_plot-repeat: {repeat}")
-    logger.debug(f"bz2d_plot-transformations: {transformations}")
-    logger.debug(f"bz2d_plot-hide_ax: {hide_ax}")
-    logger.debug(f"bz2d_plot-vectors: {vectors}")
-    logger.debug(f"bz2d_plot-set_equal_aspect: {set_equal_aspect}")
     kpoints = points
-    bz1, icell, cell = twocell_to_bz1(cell)
+    bz1, icell, cell = twocell_to_bz1(np.array(cell))
     logger.debug(f"bz1 : {bz1}")
     if ax is None:
         ax = plt.axes()
@@ -710,6 +696,12 @@ def bz2d_plot(
         path_string = cell_structure.special_path if paths == "all" else paths
         paths = []
         for names in parse_path_string(path_string):
+            """
+            >>> parse_path_string('GX')
+            [['G', 'X']]
+            >>> parse_path_string('GX,M1A')
+            [['G', 'X'], ['M1', 'A']]
+            """
             points = []
             for name in names:
                 points.append(np.dot(icell.T, special_points[name]))
@@ -774,7 +766,12 @@ def bz2d_plot(
         )
 
     if paths is not None:
-        annotate_special_paths(ax, paths, offset=offset, transformations=transformations)
+        annotate_special_paths(
+            ax,
+            paths,
+            offset=offset,
+            transformations=transformations,
+        )
 
     if kpoints is not None:
         for p in kpoints:
diff --git a/src/arpes/plotting/bz_tool/CoordinateOffsetWidget.py b/src/arpes/plotting/bz_tool/CoordinateOffsetWidget.py
index 642a8d57..7a6324e2 100644
--- a/src/arpes/plotting/bz_tool/CoordinateOffsetWidget.py
+++ b/src/arpes/plotting/bz_tool/CoordinateOffsetWidget.py
@@ -3,10 +3,24 @@
 from __future__ import annotations
 
 from functools import partial
+from logging import DEBUG, INFO, Formatter, StreamHandler, getLogger
 from typing import TYPE_CHECKING
 
 from PySide6 import QtWidgets
 
+LOGLEVELS = (DEBUG, INFO)
+LOGLEVEL = LOGLEVELS[1]
+logger = getLogger(__name__)
+fmt = "%(asctime)s %(levelname)s %(name)s :%(message)s"
+formatter = Formatter(fmt)
+handler = StreamHandler()
+handler.setLevel(LOGLEVEL)
+logger.setLevel(LOGLEVEL)
+handler.setFormatter(formatter)
+logger.addHandler(handler)
+logger.propagate = False
+
+
 if TYPE_CHECKING:
     from _typeshed import Incomplete
     from PySide6.QtCore import QEvent
@@ -28,7 +42,7 @@ def __init__(
     ) -> None:
         """Configures utility label, an inner control, and a linked spinbox for text entry."""
         super().__init__(title=coordinate_name, parent=parent)
-
+        logger.debug(f"value = {value} has not been used.")
         self.layout: QGridLayout = QtWidgets.QGridLayout(self)
 
         self.label = QtWidgets.QLabel("Value: ")
@@ -56,6 +70,7 @@ def value_changed(
         if self._prevent_change_events:
             return
 
+        logger.debug(f"event={event} has not been used.")
         self._prevent_change_events = True
         self.slider.setValue(source.value())
         self.spinbox.setValue(source.value())
diff --git a/src/arpes/plotting/bz_tool/RangeOrSingleValueWidget.py b/src/arpes/plotting/bz_tool/RangeOrSingleValueWidget.py
index 81b7e411..8f0885f9 100644
--- a/src/arpes/plotting/bz_tool/RangeOrSingleValueWidget.py
+++ b/src/arpes/plotting/bz_tool/RangeOrSingleValueWidget.py
@@ -53,6 +53,7 @@ def __init__(
         """
         super().__init__(title=coordinate_name, parent=parent)
 
+        logger.debug(f"value = {value} has not been used.")
         self.layout: QGridLayout = QtWidgets.QGridLayout(self)
 
         self.label = QtWidgets.QLabel("Value: ")
@@ -83,6 +84,7 @@ def value_changed(self, event: Incomplete, source: Incomplete) -> None:
         if self._prevent_change_events:
             return
 
+        logger.debug(f"event={event} has not been used.")
         self._prevent_change_events = True
         self.slider.setValue(source.value())
         self.spinbox.setValue(source.value())
diff --git a/src/arpes/provenance.py b/src/arpes/provenance.py
index c1fa5215..5736aeaf 100644
--- a/src/arpes/provenance.py
+++ b/src/arpes/provenance.py
@@ -80,6 +80,8 @@ class Provenance(TypedDict, total=False):
     new_axis: str
     transformed_vars: list[str]
     #
+    #
+    parant_id: tuple[str, str]
     occupation_ratio: float
     #
     correlation: bool
diff --git a/src/arpes/utilities/collections.py b/src/arpes/utilities/collections.py
index 7a5e6a0f..a6d5cf2a 100644
--- a/src/arpes/utilities/collections.py
+++ b/src/arpes/utilities/collections.py
@@ -19,8 +19,8 @@ def deep_update(destination: dict[str, T], source: dict[str, T]) -> dict[str, T]
     Instead recurse down from the root and update as appropriate.
 
     Args:
-        destination:
-        source:
+        destination: dict object to be updated.
+        source: source dict
 
     Returns:
         The destination item
diff --git a/src/arpes/utilities/conversion/core.py b/src/arpes/utilities/conversion/core.py
index 69cf1dfe..bf89ba89 100644
--- a/src/arpes/utilities/conversion/core.py
+++ b/src/arpes/utilities/conversion/core.py
@@ -658,12 +658,12 @@ def _extract_symmetry_point(
     """[TODO:summary].
 
     Args:
-        name (str): [TODO:description]
-        arr (xr.DataArray): [TODO:description]
+        name (str):  Name of the symmetry points, such as G, X, L.
+        arr (xr.DataArray): ARPES data.
         extend_to_edge (bool): [TODO:description]
 
-    Returns:
-        [TODO:description]
+    Returns: dict(Hashable, float)
+        Return dict object as the symmetry point
     """
     raw_point: dict[Hashable, float] = arr.attrs["symmetry_points"][name]
     G = arr.attrs["symmetry_points"]["G"]
diff --git a/src/arpes/xarray_extensions.py b/src/arpes/xarray_extensions.py
index 4bcde284..cc2c4474 100644
--- a/src/arpes/xarray_extensions.py
+++ b/src/arpes/xarray_extensions.py
@@ -684,9 +684,15 @@ def symmetry_points(
 
         The original version was something complicated, but the coding seemed to be in
         process and the purpose was unclear, so it was streamlined considerably.
+
+
+        Returns (dict[str, dict[str, float]]):
+            Dict object representing the symmpetry points in the ARPES data.
+
+        Examples:
+            example of "symmetry_points": symmetry_points = {"G": {"phi": 0.405}}
         """
         symmetry_points: dict[str, dict[str, float]] = {}
-        # An example of "symmetry_points": symmetry_points = {"G": {"phi": 0.405}}
         our_symmetry_points = self._obj.attrs.get("symmetry_points", {})
 
         symmetry_points.update(our_symmetry_points)
@@ -1191,12 +1197,17 @@ def unpack_dim(dim_name: str) -> str:
             return dim_name
 
         for region in regions:
-            region = {unpack_dim(k): v for k, v in normalize_region(region).items()}
-
             # remove missing dimensions from selection for permissiveness
             # and to transparent composing of regions
-            region = {k: process_region_selector(v, k) for k, v in region.items() if k in obj.dims}
-            obj = obj.sel(region)
+            obj = obj.sel(
+                {
+                    k: process_region_selector(v, k)
+                    for k, v in {
+                        unpack_dim(k): v for k, v in normalize_region(region).items()
+                    }.items()
+                    if k in obj.dims
+                },
+            )
 
         return obj