Fix a bunch of code smells and a Py<3.8 error

Stoner/HDF5.py

@@ -37,7 +37,7 @@ def get_hdf_loader(f, default_loader=lambda *args, **kargs: None):
             Callable function that can produce an object of an appropriate class.
     """
     if "type" not in f.attrs:
-        StonerLoadError("HDF5 Group does not specify the type attribute used to check we can load it.")
+        raise StonerLoadError("HDF5 Group does not specify the type attribute used to check we can load it.")
     typ = bytes2str(f.attrs.get("type", ""))
     if (typ not in globals() or not isinstance(globals()[typ], type)) and "module" not in f.attrs:
         raise StonerLoadError(
@@ -84,8 +84,8 @@ def __init__(self, filename, mode="r"):
             if not mode.startswith("w"):
                 with h5py.File(filename, "r"):
                     pass
-        except (IOError, OSError):
-            raise StonerLoadError(f"{filename} not at HDF5 File")
+        except (IOError, OSError) as err:
+            raise StonerLoadError(f"{filename} not at HDF5 File") from err
         self.filename = filename
 
     def __enter__(self):
@@ -108,7 +108,7 @@ def __enter__(self):
             raise StonerLoadError("Note a resource that can be handled with HDF")
         return self.handle
 
-    def __exit__(self, type, value, traceback):
+    def __exit__(self, _type, _value, _traceback):
         """Ensure we close the hdf file no matter what."""
         if self.file is not None and self.close:
             self.file.close()

Stoner/Image/core.py

@@ -251,7 +251,6 @@ def __new__(cls, *args, **kargs):
         We're using __new__ rather than __init__ to imitate a numpy array as
         close as possible.
         """
-
         array_arg_keys = ["dtype", "copy", "order", "subok", "ndmin", "mask"]  # kwargs for array setup
         array_args = {k: kargs.pop(k) for k in array_arg_keys if k in kargs.keys()}
         user_metadata = kargs.get("metadata", {})
@@ -671,6 +670,10 @@ def __delitem__(self, index):
         else:
             super().__delitem__(index)
 
+    def save(self, filename=None, **kargs):
+        """Stub method for a save function."""
+        raise NotImplementedError(f"Save is not implemented in {self.__class__}")
+
 
 @class_modifier(
     [

Stoner/Image/folders.py

@@ -249,7 +249,7 @@ def from_tiff(cls, filename, **kargs):
                 except (TypeError, ValueError, IOError):
                     metadata = []
             else:
-                raise TypeError(f"Cannot load as an ImageFolder due to lack of description tag")
+                raise TypeError("Cannot load as an ImageFolder due to lack of description tag")
             imglist = []
             for ix, md in enumerate(metadata):
                 img.seek(ix)

Stoner/Image/kerr.py

@@ -83,6 +83,10 @@ def tesseractable(self):
         """Do a test call to tesseract to see if it is there and cache the result."""
         return _tesseractable
 
+    def save(self, filename=None, **kargs):
+        """Stub method for a save function."""
+        raise NotImplementedError(f"Save is not implemented in {self.__class__}")
+
 
 @class_modifier(kerrfuncs, adaptor=image_file_adaptor)
 class KerrImageFile(ImageFile):
@@ -99,7 +103,7 @@ def __init__(self, *args, **kargs):
         self._image = self.image.view(KerrArray)
 
     @ImageFile.image.getter
-    def image(self):
+    def image(self):  # pylint disable=invalid-overridden-method
         """Access the image data."""
         return self._image.view(KerrArray)
 

Stoner/analysis/fitting/mixins.py

@@ -172,7 +172,9 @@ def wrapper(beta, x, y, sigma, *args):
 
 class _curve_fit_result:
 
-    """Represent a result from fitting using :py:func:`scipy.optimize.curve_fit` as a class to make handling easier."""
+    """Represent a result from fitting using :py:func:`scipy.optimize.curve_fit`
+    as a class to make handling easier.
+    """
 
     def __init__(self, popt, pcov, infodict, mesg, ier):
         """Store the results of the curve fit full_output fit.
@@ -1140,7 +1142,7 @@ def _func(x, *beta):
             raise TypeError(
                 "".join(
                     [
-                        f"curve_fit parameter 1 must be either a Model class from",
+                        "curve_fit parameter 1 must be either a Model class from",
                         f" lmfit or scipy.odr, or a callable, not a {type(func)}",
                     ]
                 )

Stoner/compat.py

@@ -21,14 +21,15 @@
     "_dummy",
 ]
 
-from sys import version_info as __vi__
+from sys import version_info as __vi__, modules
 from os import walk, makedirs
 from os.path import join, commonpath
 import fnmatch
-from inspect import signature, getfullargspec
 from shutil import which
 from pathlib import PurePath
 from packaging.version import parse as version_parse
+from inspect import signature
+import re
 
 import numpy as np
 import scipy as sp
@@ -39,6 +40,11 @@
 sp_version = version_parse(sp.__version__)
 mpl_version = version_parse(matplotlib.__version__)
 
+modules["sre_parse"] = re._parser
+modules["sre_constants"] = re._constants
+modules["sre_compile"] = re._compiler
+
+
 try:
     import hyperspy as hs  # Workaround an issue in hs 1.5.2 conda packages
 

Stoner/folders/core.py

@@ -346,7 +346,8 @@ def depth(self):
     def each(self):
         """Return a :py:class:`Stoner.folders.each.item` proxy object.
 
-        This is for calling attributes of the member type of the folder."""
+        This is for calling attributes of the member type of the folder.
+        """
         return EachItem(self)
 
     @property
@@ -441,7 +442,8 @@ def lsgrp(self):
     def metadata(self):
         """Return a :py:class:`Stoner.folders.metadata.MetadataProxy` object.
 
-        This allows for operations on combined metadata."""
+        This allows for operations on combined metadata.
+        """
         return MetadataProxy(self)
 
     @property
@@ -948,15 +950,15 @@ def __repr__(self):
         cls = type(self).__name__
         pth = self.key
         pattern = getattr(self, "pattern", "")
-        s = f"{cls}({pth}) with pattern {pattern} has {len(self)} files and {len(self.groups)} groups\n"
+        string = f"{cls}({pth}) with pattern {pattern} has {len(self)} files and {len(self.groups)} groups\n"
         if not short:
-            for r in self.ls:
-                s += "\t" + r + "\n"
+            for row in self.ls:
+                string += "\t" + row + "\n"
         for g in self.groups:  # iterate over groups
             r = self.groups[g].__repr__()
-            for l in r.split("\n"):  # indent each line by one tab
-                s += "\t" + l + "\n"
-        return s.strip()
+            for line in r.split("\n"):  # indent each line by one tab
+                string += "\t" + line + "\n"
+        return string.strip()
 
     def __reversed__(self):
         """Create an iterator function that runs backwards through the stored objects."""
@@ -1348,8 +1350,8 @@ def group(self, key):
 
         Args:
             key (string or callable or list):
-                Either a simple string or callable function or a list. If a string then it is interpreted as an item of
-                metadata in each file. If a callable function then takes a single argument x which should be an
+                Either a simple string or callable function or a list. If a string then it is interpreted as an item
+                of metadata in each file. If a callable function then takes a single argument x which should be an
                 instance of a metadataObject and returns some vale. If key is a list then the grouping is
                 done recursely for each element in key.
 
@@ -1473,7 +1475,7 @@ def make_name(self, value=None):
             name = f"Untitled-{self._last_name}"
         return name
 
-    def pop(self, name=-1, default=None):  # pylint: disable=arguments-differ
+    def pop(self, name=-1, default=None):  # pylint: disable=arguments-differ,arguments-renamed
         """Return and remove either a subgroup or named object from this folder."""
         try:
             ret = self[name]

Stoner/folders/each.py

@@ -76,6 +76,7 @@ def __setitem__(self, index, value):
         """
         if len(value) < len(self._folder):
             value = value + value[-1] * (len(self._folder) - len(value))
+        v = "."
         for v, data in zip(value, self._folder):
             data.setas[index] = v
         setas = self._folder._object_attrs.get("setas", self.collapse())

Stoner/plot/core.py

@@ -21,7 +21,7 @@
 from matplotlib import figure as mplfig
 from matplotlib import cm, colors, colormaps
 
-from Stoner.compat import string_types, index_types, int_types, get_func_params
+from Stoner.compat import string_types, index_types, int_types
 from Stoner.tools import AttributeStore, isnone, isanynone, all_type, isiterable, typedList, get_option, fix_signature
 from .formats import DefaultPlotStyle
 from .utils import errorfill
@@ -230,7 +230,8 @@ def labels(self, value):
     def showfig(self):
         """Return either the current figure or self or None.
 
-        The return value depends on whether the attribute is True or False or None."""
+        The return value depends on whether the attribute is True or False or None.
+        """
         if self._showfig is None or get_option("no_figs"):
             return None
         if self._showfig:
@@ -324,11 +325,14 @@ def _surface_plotter(self, x_coord, y_coord, z_coord, **kargs):
         ReturnsL
             A matplotib Figure
 
-        This function attempts to work the same as the 2D surface plotter pcolor, but draws a 3D axes set"""
+        This function attempts to work the same as the 2D surface plotter pcolor, but draws a 3D axes set
+        """
         if not _3D:
             raise RuntimeError("3D plotting Not available. Install matplotlib toolkits")
-        if not isinstance(ax := self.__figure.gca(), Axes3D):
+        if not isinstance(self.__figure.gca(), Axes3D):
             ax = plt.axes(projection="3d")
+        else:
+            ax = self.__figure.gca()
         z_coord = np.nan_to_num(z_coord)
         surf = ax.plot_surface(x_coord, y_coord, z_coord, **kargs)
         self.fig.colorbar(surf, shrink=0.5, aspect=5, extend="both")
@@ -1531,7 +1535,7 @@ def plot_xy(self, xcol=None, ycol=None, fmt=None, xerr=None, yerr=None, **kargs)
             if ix > 0:  # Hooks for multiple subplots
                 if multiple == "panels":
                     loc, lab = plt.yticks()
-                    lab = [l.get_text() for l in lab]
+                    lab = [label.get_text() for label in lab]
                     plt.yticks(loc[:-1], lab[:-1])
         return self.showfig