Adjust for testing against Python 3.11 and scipy 1.10 and current sci…

…kit-image

.github/workflows/run-tests-action.yaml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7","3.8","3.9", "3.10", 3.11]
+        python-version: ["3.7","3.8","3.9", "3.10", "3.11"]
         os: ["ubuntu-latest"]
     steps:
       - name: Check out repository code

Makefile

@@ -14,7 +14,7 @@ clean:
 	- find -name '__pycache__' -exec rm -rf {} \;
 
 test:
-	pytest -n `python -c 'import os;print(min(12,os.cpu_count()))'`
+	pytest -n `python -c 'import os;print(min(8,os.cpu_count()))'`
 
 test-single:
 	pytest --pdb

Stoner/Core.py

@@ -789,7 +789,6 @@ def _repr_table_(self, fmt="rst"):
         for ic, c in enumerate(interesting):
             if c >= 0:
                 if shorten[0]:
-
                     col_out = np.where(self.mask[: r // 2 - 1, c], "#####", self.data[: r // 2 - 1, c].astype(str))
                     outp[1 : r // 2, ic + 1] = col_out
                     col_out = np.where(self.mask[-r // 2 :, c], "#####", self.data[-r // 2 :, c].astype(str))

Stoner/Image/core.py

@@ -25,7 +25,6 @@
     morphology,
     segmentation,
     transform,
-    viewer,
 )
 
 from ..core.base import typeHintedDict, metadataObject
@@ -146,7 +145,6 @@ def copy_into(source: "ImageFile", dest: "ImageFile") -> "ImageFile":
         morphology,
         segmentation,
         transform,
-        viewer,
     ]
 )
 @class_modifier([ndi], transpose=True)
@@ -688,7 +686,6 @@ def __delitem__(self, index):
         morphology,
         segmentation,
         transform,
-        viewer,
     ],
     adaptor=image_file_adaptor,
 )

Stoner/Image/folders.py

@@ -7,7 +7,6 @@
 from json import loads, dumps
 from copy import deepcopy, copy
 
-from skimage.viewer import CollectionViewer
 import numpy as np
 from matplotlib.pyplot import figure, Figure, subplot, tight_layout
 from PIL.TiffImagePlugin import ImageFileDirectory_v2
@@ -234,7 +233,6 @@ def from_tiff(cls, filename, **kargs):
         with Image.open(filename, "r") as img:
             tags = img.tag_v2
             if 270 in tags:
-
                 try:
                     userdata = loads(tags[270])
                     typ = userdata.get("type", cls.__name__)
@@ -481,12 +479,6 @@ def to_tiff(self, filename):
         imlist[0].save(tiffname, save_all=True, append_images=imlist[1:], tiffinfo=ifd)
         return self
 
-    def view(self):
-        """Create a matplotlib animated view of the contents."""
-        cv = CollectionViewer(list(self.images))
-        cv.show()
-        return cv
-
 
 class ImageFolder(ImageFolderMixin, DiskBasedFolderMixin, baseFolder):
 

Stoner/__init__.py

@@ -35,7 +35,7 @@
 Options = _Options()
 
 
-__version_info__ = ("0", "10", "6")
+__version_info__ = ("0", "10", "7")
 __version__ = ".".join(__version_info__)
 
 __homepath__ = pathlib.Path(__file__).parent.resolve()

Stoner/analysis/fitting/mixins.py

@@ -528,7 +528,6 @@ def annotate_fit(self, model, x=None, y=None, z=None, text_only=False, **kargs):
             raise RuntimeError(f"model should be either an lmfit.Model or a callable function, not a {type(model)}")
 
         if prefix is not None:
-
             if isinstance(prefix, (list, tuple)):
                 prefix = prefix[0]
 
@@ -605,7 +604,6 @@ def _get_curve_fit_data(self, xcol, ycol, bounds, sigma):
             xdat = working[:, self.find_col(xcol)]
 
         for i, yc in enumerate(ycol):
-
             if isinstance(yc, index_types):
                 ydat = working[:, self.find_col(yc)]
             elif isinstance(yc, np.ndarray) and yc.ndim == 1 and len(yc) == len(self):
@@ -1172,7 +1170,6 @@ def _func(x, *beta):
         retvals = []
         i = None
         for i, ydat in enumerate(ydata):
-
             if isinstance(sigma, np.ndarray) and sigma.shape[0] > 1:
                 if sigma.shape[0] == len(ycol):
                     s = sigma[i]

Stoner/analysis/fitting/models/__init__.py

@@ -95,7 +95,6 @@ def hinter(**kwargs):
     """
 
     class _ModelDecorator(Model):
-
         __doc__ = model_func.__doc__
 
         def __init__(self, *args, **kargs):

Stoner/analysis/fitting/models/generic.py

@@ -117,7 +117,6 @@ class Linear(_Linear):
 
 
 class Quadratic(_Quadratic):
-
     r"""A Simple quadratic fitting function.
 
     Args:
@@ -139,7 +138,6 @@ class Quadratic(_Quadratic):
 
 
 class PowerLaw(_PowerLaw):
-
     r"""Power Law Fitting Equation.
 
     Args:
@@ -160,7 +158,6 @@ class PowerLaw(_PowerLaw):
 
 
 class StretchedExp(Model):
-
     r"""A stretched exponential fuinction.
 
     Args:
@@ -199,7 +196,6 @@ def guess(self, data, x=None, **kwargs):
 
 
 class Lorentzian_diff(Model):
-
     r"""Provides a lmfit Model rerprenting the differential form of a Lorentzian Peak.
 
     Args:

Stoner/analysis/fitting/models/magnetism.py

@@ -155,7 +155,6 @@ def fmr_power(H, H_res, Delta_H, K_1, K_2):
 
 
 class BlochLaw(Model):
-
     r"""Bloch's law for spontaneous magnetism at low temperatures.
 
     Args:
@@ -242,7 +241,6 @@ def guess(self, data, x=None, **kwargs):
 
 
 class BlochLawThin(Model):
-
     r"""Bloch's law for spontaneous magnetism at low temperatures - thin film version.
 
     Args:
@@ -320,7 +318,6 @@ def blochs_law_thinfilm(self, T, D, Bz, S, v_ws, a, nz):
 
 
 class Langevin(Model):
-
     r"""The Langevin function for paramagnetic M-H loops.
 
     Args:
@@ -367,7 +364,6 @@ def guess(self, data, x=None, **kwargs):
 
 
 class KittelEquation(Model):
-
     r"""Kittel Equation for finding ferromagnetic resonance peak in frequency with field.
 
     Args:
@@ -412,7 +408,6 @@ def guess(self, data, x=None, **kwargs):
 
 
 class Inverse_Kittel(Model):
-
     r"""Kittel Equation for finding ferromagnetic resonance peak in frequency with field.
 
     Args:
@@ -453,7 +448,6 @@ def guess(self, data, x=None, **kwargs):
 
 
 class FMR_Power(Model):
-
     r"""Combine a Lorentzian and differential Lorenztion peak as measured in an FMR experiment.
 
     Args:

Stoner/analysis/fitting/models/superconductivity.py

@@ -138,7 +138,15 @@ def strijkers(V, omega, delta, P, Z):
             :include-source:
             :outname: strijkers_func
     """
-    return _strijkers_core(V, omega, delta, P, Z)
+    if isinstance(V, np.ma.MaskedArray):
+        mask = V.mask
+        V = np.array(V)
+    else:
+        mask = False
+    ret = _strijkers_core(V, omega, delta, P, Z)
+    ret = np.ma.MaskedArray(ret)
+    ret.mask = mask
+    return ret
 
 
 def rsj_noiseless(I, Ic_p, Ic_n, Rn, V_offset):
@@ -349,7 +357,6 @@ def guess(self, data, **kwargs):  # pylint: disable=unused-argument
 
 
 class RSJ_Noiseless(Model):
-
     r"""Implement a simple noiseless RSJ model.
 
     Args:
@@ -403,7 +410,6 @@ def guess(self, data, **kwargs):
 
 
 class RSJ_Simple(Model):
-
     r"""Implements a simple noiseless symmetric RSJ model.
 
     Args:
@@ -456,7 +462,6 @@ def guess(self, data, **kwargs):
 
 
 class Ic_B_Airy(Model):
-
     r"""Critical Current for a round Josepshon Junction wrt to Field.
 
     Args:

Stoner/analysis/fitting/models/thermal.py

@@ -122,7 +122,6 @@ def vftEquation(x, A, DE, x_0):
 
 
 class Arrhenius(Model):
-
     r"""Arrhenius Equation without T dependendent prefactor.
 
     Args:
@@ -160,7 +159,6 @@ def guess(self, data, x=None, **kwargs):
 
 
 class NDimArrhenius(Model):
-
     r"""Arrhenius Equation without T dependendent prefactor for various dimensions.
 
     Args:
@@ -199,7 +197,6 @@ def guess(self, data, x=None, **kwargs):
 
 
 class ModArrhenius(Model):
-
     r"""Arrhenius Equation with a variable T power dependent prefactor.
 
     Args:
@@ -238,7 +235,6 @@ def guess(self, data, x=None, **kwargs):
 
 
 class VFTEquation(Model):
-
     r"""Vogel-Flucher-Tammann (VFT) Equation without T dependendent prefactor.
 
     Args:

Stoner/compat.py

@@ -88,6 +88,16 @@ def get_func_params(func):
 int_types = (int,)
 path_types = (str, PurePath)
 
+##### Monkey patch numpy for removed attributes as a compatibiliyu hack
+if not hasattr(np, "float"):
+    np.float = float
+
+if not hasattr(np, "bool"):
+    np.bool = bool
+
+if not hasattr(np, "str"):
+    np.str = str
+
 
 def str2bytes(data):
     """Encode a unicode string into UTF-8."""

Stoner/core/array.py

@@ -19,7 +19,6 @@
 
 
 class DataArray(ma.MaskedArray):
-
     r"""A sub class of :py:class:`numpy.ma.MaskedArray` with a copy of the setas attribute to allow indexing by name.
 
     Attributes:

Stoner/core/base.py

@@ -432,7 +432,7 @@ def __mungevalue(self, typ: str, value: Any) -> Any:
         ret = None
         if typ == "Invalid Type":  # Short circuit here
             return repr(value)
-        for (regexp, valuetype) in self.__tests:
+        for regexp, valuetype in self.__tests:
             matched = regexp.search(typ)
             if matched is not None:
                 if isinstance(valuetype, _evaluatable):
@@ -450,18 +450,12 @@ def __mungevalue(self, typ: str, value: Any) -> Any:
                     if isinstance(ret, datetime.datetime):
                         break  # Alreadu a datetime object
                     try:
-                        ret = literal_eval(value)
+                        ret = parser.parse(value)
                     except ValueError:
-                        ret = str(ret)
-                    if isinstance(ret, datetime.datetime):
-                        break  # Got us a datetime object now
-                    elif isinstance(ret, string_types):  # try parsing as a string now
                         try:
-                            ret = _parse_date(ret)
-                            break
-                        except (ValueError, OverflowError):
-                            pass  # fall back
-                    ret = datetime.datetime(1970, 1, 1)  # unparsable time
+                            ret = literal_eval(value)
+                        except ValueError:
+                            ret = str(value)
                     break
                 else:
                     ret = valuetype(value)

Stoner/core/setas.py

@@ -745,7 +745,7 @@ def to_dict(self):
         If multiple columns are assigned to the same type, then the column names are
         returned as a list. If column headers are duplicated"""
         ret = dict()
-        for (k, ch) in zip(self._setas, self._unique_headers):
+        for k, ch in zip(self._setas, self._unique_headers):
             if k != ".":
                 if k in ret:
                     ret[k].append(ch)

Stoner/folders/mixins.py

@@ -328,7 +328,7 @@ def fetch(self):
         With multiprocess enabled this will parallel load the contents of the folder into memory.
         """
         p, imap = get_pool()
-        for (f, name) in imap(
+        for f, name in imap(
             partial(_loader, loader=self.loader, typ=self._type, directory=self.directory), self.not_loaded
         ):
             self.__setter__(
@@ -527,7 +527,6 @@ def extract(self, *metadata, **kargs):
         metadata = args
 
         def _extractor(group, _, metadata):
-
             results = group.type()
             results.metadata = group[0].metadata
             headers = []
@@ -752,7 +751,6 @@ class DataFolder(DataMethodsMixin, DiskBasedFolderMixin, baseFolder):
     """
 
     def __init__(self, *args, **kargs):
-
         self.type = kargs.pop("type", make_Data(None))
         super().__init__(*args, **kargs)
 

Stoner/formats/attocube.py

@@ -371,7 +371,6 @@ def to_hdf5(self, filename=None):
             mode = "r+" if path.exists(filename) else "w"
         self.filename = filename
         with HDFFileManager(self.filename, mode=mode) as f:
-
             f.attrs["type"] = type(self).__name__
             f.attrs["module"] = type(self).__module__
             f.attrs["scan_no"] = self.scan_no

Stoner/formats/instruments.py

@@ -67,7 +67,7 @@ def _load(self, filename=None, *args, **kargs):
                 "Number of Breakpoints",
             ]:
                 raise Core.StonerLoadError("Header did not contain recognised keys.")
-            for (k, v) in zip(keys, vals):
+            for k, v in zip(keys, vals):
                 v = v.split()[0]
                 self.metadata[k] = string_to_type(v)
             headers = bytes2str(next(data)).strip().split()

Stoner/formats/maximus.py

@@ -518,7 +518,6 @@ def _read_pointscan(files, header):
 
 
 if __name__ == "__main__":
-
     # Test by reading all files
     for infile in Path(".").glob("*.hdr"):
         hdr, data, dims = read_scan(infile.stem)

Stoner/plot/core.py

@@ -73,7 +73,6 @@ def __mpl3DQuiver(x_coord, y_coord, z_coord, u_comp, v_comp, w_comp, **kargs):
 
 
 class PlotMixin:
-
     r"""A mixin class that works with :py:class:`Stoner.Core.DataFile` to add additional plotting functionality.
 
     Args: