* Tidy up

  🔥  - Remove the class and functions in corrections/**init**.py (HashableDict, reference_key, correc…
  ➕  add dependency about notebook (v7 or later is required.)

Changes.md

@@ -59,6 +59,8 @@ Major Changes from 3.0.1
   - Remove condensed_attrs: We should not enfoce camelcase on attributes, while original version did. Rather, the snake_case would be better from the modern pythonic viewpoint.
   - Remove `trace` arg for debugging. This technique may be sharp, but not so well fitted the current python trend; typing oriented.
 
+  - Remove the class and functions in corrections/**init**.py (HashableDict, reference_key, correction_from_reference_set), which have not used.
+
 Fix from 3.0.1
 
 - bug of concatenating in broadcast_model

README.rst

@@ -68,19 +68,17 @@ If you use PyARPES in your work, please support the development of scientific so
 Installation
 ============
 
-PyARPES can be installed from source.   Python version 3.11 or newer is strongly recommmended.
+PyARPES (>= V.4.0) can be installed from source.   Python version 3.11 or newer is strongly recommmended.
 
-The current version has been largely revised from the original version which are in PyPI and conda site. 
-Unfortunately, I don't have the right the updated version to these site, and I would not like to take over it from the original author.
+The current version has been largely revised from the original version which are in PyPI and conda site.
+Unfortunately, I don't have the right the upload the current version to these site, and I would not like to take over it from the original author.
 
-The main purpose of revision of the package is to make this be reliable. Actually, the original version outputs wrong results in many
+The main purpose of revision of the package is to make this be reliable for us. Actually, the original version outputs the wrong results in many
 case, especially for angle-momentum conversion.
 
-
 Thus, the current package can be installed only through the github.
 
 
-
 Pip installation
 ----------------
 
@@ -96,6 +94,7 @@ If you want to modify the source for PyARPES as you use it, you might prefer a l
 Details can be found on `the documentation site`_.
 
 
+
 Suggested steps
 ---------------
 
@@ -108,6 +107,8 @@ Suggested steps
 Contact
 =======
 
+Very unfortunately, we cannot get any responses from the original author.  The comment below does not make sense at present.
+
 Questions, difficulties, and suggestions can be directed to Conrad Stansbury ([email protected])
 or added to the repository as an issue. In the case of trouble, also check the `FAQ`_.
 

pyproject.toml

@@ -10,7 +10,7 @@ readme = "README.rst"
 requires-python = ">= 3.10"
 
 dependencies = [
-  "holoviews",
+  "holoviews>=1.16.0",
   "astropy>=5.3",
   "xarray>=2023.5.0",
   "lmfit>=1.2.1",
@@ -28,6 +28,7 @@ dependencies = [
   "scikit-image>=0.20.0",
   "netcdf4>=1.6.4",
   "rx>=3.2.0",
+  "notebook>=7.0",
   "ipywidgets",
 ]
 
@@ -94,8 +95,8 @@ lint.ignore = [
   #
   "NPY201", #  Numpy 2.0, 
 ]
-target-version = "py310"
 lint.select = ["ALL"]
+target-version = "py310"
 line-length = 100
 
 exclude = ["scripts", "docs", "conda"]

src/arpes/analysis/decomposition.py

@@ -5,13 +5,14 @@
 from functools import wraps
 from typing import TYPE_CHECKING
 
+import xarray as xr
+
 from arpes.constants import TWO_DIMENSION
 from arpes.provenance import PROVENANCE, provenance
 from arpes.utilities import normalize_to_spectrum
 
 if TYPE_CHECKING:
     import sklearn
-    import xarray as xr
     from _typeshed import Incomplete
 
 __all__ = (

src/arpes/analysis/mask.py

@@ -5,13 +5,13 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
+import xarray as xr
 from matplotlib.path import Path
 
 from arpes.provenance import update_provenance
 from arpes.utilities import normalize_to_spectrum
 
 if TYPE_CHECKING:
-    import xarray as xr
     from _typeshed import Incomplete
     from numpy.typing import NDArray
 

src/arpes/analysis/moire.py

@@ -2,6 +2,7 @@
 
 All of the moirés discussed here are on hexagonal crystal systems.
 """
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Any
@@ -119,7 +120,7 @@ def calculate_bz_vertices_from_direct_cell(cell: NDArray[np.float_]) -> list:
         assert all(abs(cell[2][0:2]) < RTOL)
         assert all(abs(cell.T[2][0:2]) < RTOL)
     else:
-        cell = [[*list(c), 0] for c in cell] + [[0, 0, 1]]
+        cell = np.array([[*list(c), 0] for c in cell] + [[0, 0, 1]])
 
     icell = np.linalg.inv(cell).T
     try:
@@ -167,7 +168,7 @@ def calc_commensurate_moire_cell(
     if swap_angle:
         moire_angle = -moire_angle
 
-    moire_cell = hex_cell_2d(moire_a)
+    moire_cell = hex_cell_2d(float(moire_a))
     moire_cell = [[*list(c), 0] for c in moire_cell] + [[0, 0, 1]]
     moire_cell = Rotation.from_rotvec([0, 0, moire_angle]).apply(moire_cell)
     moire_icell = np.linalg.inv(moire_cell).T

src/arpes/corrections/__init__.py

@@ -11,13 +11,6 @@
 
 from __future__ import annotations
 
-from collections import OrderedDict
-from typing import TYPE_CHECKING
-
-import xarray as xr
-
-from arpes.utilities import deep_equals, normalize_to_dataset
-
 from .fermi_edge_corrections import (
     apply_direct_fermi_edge_correction,
     apply_photon_energy_fermi_edge_correction,
@@ -27,40 +20,3 @@
     build_quadratic_fermi_edge_correction,
     find_e_fermi_linear_dos,
 )
-
-if TYPE_CHECKING:
-    from arpes._typing import XrTypes
-
-__all__ = (
-    "reference_key",
-    "correction_from_reference_set",
-)
-
-
-class HashableDict(OrderedDict):
-    """Implements hashing for ordered dictionaries.
-
-    The dictionary must be ordered for the hash to be stable.
-    """
-
-    def __hash__(self):
-        return hash(frozenset(self.items()))
-
-
-def reference_key(data: xr.DataArray) -> HashableDict:
-    """Calculates a key/hash for data determining reference/correction equality."""
-    data_array = data if isinstance(data, xr.DataArray) else normalize_to_dataset(data)
-    assert isinstance(data_array, xr.DataArray)
-    return HashableDict(data_array.S.reference_settings)
-
-
-def correction_from_reference_set(data: xr.DataArray, reference_set):
-    """Determines which correction to use from a set of references."""
-    data_array = data if isinstance(data, xr.DataArray) else normalize_to_dataset(data)
-    correction = None
-    for k, corr in reference_set.items():
-        if deep_equals(dict(reference_key(data_array)), dict(k)):
-            correction = corr
-            break
-
-    return correction

src/arpes/endstations/__init__.py

@@ -9,7 +9,7 @@
 import warnings
 from logging import DEBUG, INFO, Formatter, StreamHandler, getLogger
 from pathlib import Path
-from typing import TYPE_CHECKING, ClassVar, Literal, TypedDict, reveal_type
+from typing import TYPE_CHECKING, ClassVar, Literal, TypedDict
 
 import h5py
 import numpy as np

src/arpes/endstations/nexus_utils.py

@@ -2,10 +2,12 @@
 
 Currently we assume that the raw file format is actually HDF.
 """
+
 from __future__ import annotations
 
 import contextlib
 from dataclasses import dataclass, field
+from logging import DEBUG, INFO, Formatter, StreamHandler, getLogger
 from typing import TYPE_CHECKING, Any
 
 import numpy as np
@@ -17,6 +19,18 @@
 
 __all__ = ["read_data_attributes_from"]
 
+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 read_group_data(group: dict, attribute_name: str = "") -> xr.Dataset:
     if attribute_name:
@@ -65,7 +79,7 @@ class DebugTarget(Target):
     name = "debug"
 
     def read_h5(self, g, path) -> None:
-        print(path, self.read(read_group_data(g)))
+        logger.info(f"path {path}, group_data {self.read(read_group_data(g))}")
 
 
 @dataclass

src/arpes/plotting/fermi_surface.py

@@ -98,10 +98,10 @@ def magnify_circular_regions_plot(
         data: [TODO:description]
         magnified_points: [TODO:description]
         mag: [TODO:description]
-        radius: [TODO:description]
+        radius (float): [TODO:description]
         cmap: [TODO:description]
         color: [TODO:description]
-        edgecolor: [TODO:description]
+        edgecolor (ColorType): [TODO:description]
         out: [TODO:description]
         ax: [TODO:description]
         kwargs: [TODO:description]

src/arpes/utilities/conversion/core.py

@@ -179,6 +179,7 @@ def slice_along_path(  # noqa: PLR0913
         for x in interpolation_points
     ]
 
+    logger.debug(f"parsed_interpolation_points: {parsed_interpolation_points}")
     free_coordinates = list(arr.dims)
     seen_coordinates = collections.defaultdict(set)
     for point in parsed_interpolation_points:
@@ -659,7 +660,7 @@ def _extract_symmetry_point(
     arr: xr.DataArray,
     *,
     extend_to_edge: bool = False,
-) -> dict:
+) -> dict[Hashable, float]:
     """[TODO:summary].
 
     Args:

src/arpes/utilities/excepthook.py

@@ -1,30 +1,37 @@
 """A utility excepthook for Qt applications which ensures errors are visible in Jupyter."""
+
 from __future__ import annotations
 
 import traceback
-from collections import namedtuple
+from typing import TYPE_CHECKING, NamedTuple
+
+if TYPE_CHECKING:
+    from types import FrameType, TracebackType
 
 __all__ = ("patched_excepthook",)
 
 
-def patched_excepthook(exc_type, exc_value, exc_tb) -> None:
+def patched_excepthook(
+    exc_type: type[BaseException] | None,
+    exc_value: BaseException | None,
+    exc_tb: TracebackType | FakeTB | None,
+) -> None:
     """Prints the traceback instead of dying silently. Useful for debugging Qt apps in Jupyter."""
     enriched_tb = _add_missing_frames(exc_tb) if exc_tb else exc_tb
     traceback.print_exception(exc_type, exc_value, enriched_tb)
 
 
-def _add_missing_frames(tb):
-    result = fake_tb(tb.tb_frame, tb.tb_lasti, tb.tb_lineno, tb.tb_next)
+def _add_missing_frames(tb: TracebackType | FakeTB) -> FakeTB:
+    result = FakeTB(tb.tb_frame, tb.tb_lasti, tb.tb_lineno, tb.tb_next)
     frame = tb.tb_frame.f_back
     while frame:
-        result = fake_tb(frame, frame.f_lasti, frame.f_lineno, result)
+        result = FakeTB(frame, frame.f_lasti, frame.f_lineno, result)
         frame = frame.f_back
     return result
 
 
-fake_tb = namedtuple("fake_tb", ("tb_frame", "tb_lasti", "tb_lineno", "tb_next"))
-# class fake_tb(NamedTuple):
-#    tb_frame
-#    tb_lasti
-#    tb_lineno
-#    tb_next
+class FakeTB(NamedTuple):
+    tb_frame: FrameType
+    tb_lasti: int
+    tb_lineno: int
+    tb_next: TracebackType | FakeTB | None

src/arpes/utilities/qt/windows.py

@@ -149,4 +149,4 @@ def toggle_help(self, event: QKeyEvent) -> None:
 
     def window_print(self, *args: Incomplete, **kwargs: Incomplete) -> None:
         """Forward prints to the application instance so they end up in Jupyter."""
-        print(*args, **kwargs)
+        logger.info(f"args: {args}, kwargs: {kwargs}")

tests/conftest.py

@@ -5,17 +5,16 @@
 from pathlib import Path
 from typing import TYPE_CHECKING, TypedDict
 
-import pytest
-
 import arpes.config
 import arpes.endstations
+import pytest
+
 from tests.utils import cache_loader
 
 if TYPE_CHECKING:
     from collections.abc import Callable, Generator
 
     import xarray as xr
-
     from arpes._typing import SCANINFO, WORKSPACETYPE
 
 

tests/test_basic_data_loading.py

@@ -5,11 +5,10 @@
 import contextlib
 from typing import TYPE_CHECKING, Any, ClassVar
 
+import arpes.xarray_extensions  # pylint: disable=unused-import, redefined-outer-name  # noqa: F401
 import numpy as np
 import pytest
 import xarray as xr
-
-import arpes.xarray_extensions  # pylint: disable=unused-import, redefined-outer-name  # noqa: F401
 from arpes.utilities.conversion import convert_to_kspace
 
 if TYPE_CHECKING:

tests/test_bz.py

@@ -1,7 +1,6 @@
 """Test for utilitiy.bz."""
 
 import numpy as np
-
 from arpes.utilities import bz
 
 

tests/test_bz_spec.py

@@ -1,6 +1,5 @@
 """Test for utilitiy.bz."""
 import numpy as np
-
 from arpes.utilities import bz_spec
 
 

tests/test_curve_fitting.py

@@ -1,7 +1,6 @@
 """Unit test for curve fitting."""
 
 import numpy as np
-
 from arpes.analysis import rebin
 from arpes.fits import AffineBroadenedFD, broadcast_model
 from arpes.io import example_data

tests/test_derivative_analysis.py

@@ -5,7 +5,6 @@
 
 import numpy as np
 import pytest
-
 from arpes.analysis.derivative import dn_along_axis
 from arpes.analysis.filters import gaussian_filter_arr
 

tests/test_direct_and_example_data_loading.py

@@ -6,7 +6,6 @@
 
 import numpy as np
 import xarray as xr
-
 from arpes.endstations.plugin.ALG_main import ALGMainChamber
 from arpes.io import load_data, load_example_data