First pass at fixes for numpy versiuon 2.0+

Author: gb119

Diff for: Stoner/Analysis.py

@@ -5,7 +5,10 @@
 import numpy as np
 import numpy.ma as ma
 
-from scipy.integrate import cumtrapz
+try:
+    from scipy.integrate import cumtrapz
+except ImportError:
+    from scipy.integrate import cumulative_trapezoid as cumtrapz
 from scipy.optimize import curve_fit
 
 from .tools import isiterable, isTuple

Diff for: Stoner/Core.py

@@ -26,7 +26,7 @@
 import csv
 
 import numpy as np
-from numpy import NaN  # NOQA pylint: disable=unused-import
+from numpy import nan  # NOQA pylint: disable=unused-import
 from numpy import ma
 
 from .compat import string_types, int_types, index_types, _pattern_type, path_types

Diff for: Stoner/Image/core.py

@@ -27,6 +27,7 @@
     transform,
 )
 
+from ..compat import np_version
 from ..core.base import typeHintedDict, metadataObject
 from ..core.exceptions import StonerLoadError, StonerUnrecognisedFormat
 from ..Core import DataFile
@@ -46,21 +47,37 @@
 
 IMAGE_FILES = [("Tiff File", "*.tif;*.tiff"), ("PNG files", "*.png", "Numpy Files", "*.npy")]
 
-dtype_range = {
-    np.bool_: (False, True),
-    np.bool8: (False, True),
-    np.uint8: (0, 255),
-    np.uint16: (0, 65535),
-    np.int8: (-128, 127),
-    np.int16: (-32768, 32767),
-    np.int64: (-(2**63), 2**63 - 1),
-    np.uint64: (0, 2**64 - 1),
-    np.int32: (-(2**31), 2**31 - 1),
-    np.uint32: (0, 2**32 - 1),
-    np.float16: (-1, 1),
-    np.float32: (-1, 1),
-    np.float64: (-1, 1),
-}
+if np_version.major == 1 and np_version.minor < 24:
+    dtype_range = {
+        np.bool_: (False, True),
+        np.bool8: (False, True),
+        np.uint8: (0, 255),
+        np.uint16: (0, 65535),
+        np.int8: (-128, 127),
+        np.int16: (-32768, 32767),
+        np.int64: (-(2**63), 2**63 - 1),
+        np.uint64: (0, 2**64 - 1),
+        np.int32: (-(2**31), 2**31 - 1),
+        np.uint32: (0, 2**32 - 1),
+        np.float16: (-1, 1),
+        np.float32: (-1, 1),
+        np.float64: (-1, 1),
+    }
+else:
+    dtype_range = {
+        np.bool_: (False, True),
+        np.uint8: (0, 255),
+        np.uint16: (0, 65535),
+        np.int8: (-128, 127),
+        np.int16: (-32768, 32767),
+        np.int64: (-(2**63), 2**63 - 1),
+        np.uint64: (0, 2**64 - 1),
+        np.int32: (-(2**31), 2**31 - 1),
+        np.uint32: (0, 2**32 - 1),
+        np.float16: (-1, 1),
+        np.float32: (-1, 1),
+        np.float64: (-1, 1),
+    }
 
 
 def _add_core_(result, other):

Diff for: Stoner/Image/util.py

@@ -9,6 +9,7 @@
 import numpy as np
 
 from ..tools.classes import Options
+from ..compat import np_version
 
 dtype_range = {
     np.bool_: (False, True),
@@ -24,7 +25,7 @@
     np.float64: (-1.0, 1.0),
 }
 
-if float(np.version.version.split(".")[1]) < 1.24:
+if np_version.major==1 and np_version.minon<24:
     dtype_range[np.bool8] = (False, True)
 
 integer_types = (np.uint8, np.uint16, np.int8, np.int16)

Diff for: Stoner/Util.py

@@ -79,7 +79,7 @@ def _h_sat_susceptibility(d, i, Ms_vals, Hsat_vals, h_sat_fraction):  # pylint:
     if hs.size > 1:
         Hsat_err[1 - i] = sem(hs)
     else:
-        Hsat_err[1 - i] = np.NaN
+        Hsat_err[1 - i] = np.nan
     return (Hsat, Hsat_err)
 
 
@@ -95,7 +95,7 @@ def _h_sat_delta_M(d, i, Ms_vals, Hsat_vals, h_sat_fraction):  # pylint: disable
     if hs.size > 1:
         hs = hs[np.argmin(np.abs(hs))]
     Hsat[1 - i] = hs  # Get the H_sat value
-    Hsat_err[1 - i] = np.NaN
+    Hsat_err[1 - i] = np.nan
     return (Hsat, Hsat_err)
 
 

Diff for: Stoner/compat.py

@@ -130,8 +130,9 @@ def get_filedialog(what="file", **opts):
         raise RuntimeError(f"Unable to recognise required file dialog type:{what}")
     return fileDialog.openDialog(mode=funcs[what], **opts)
 
-
-if np_version.minor >= 20:
+if np_version.major >= 2:
+    int_types += (int, np.int8, np.int16, np.int32, np.int64)
+elif np_version.minor >= 20:
     int_types += (int, np.int0, np.int8, np.int16, np.int32, np.int64)
 else:
     int_types += (np.int, np.int0, np.int8, np.int16, np.int32, np.int64)

Diff for: Stoner/core/base.py

@@ -24,7 +24,7 @@
 
 from dateutil import parser
 import numpy as np
-from numpy import NaN
+from numpy import nan
 import asteval
 
 try:
@@ -70,7 +70,7 @@ def literal_eval(string: str) -> Any:
     global _asteval_interp  # pylint: disable=W0603
     if _asteval_interp is None:
         _asteval_interp = asteval.Interpreter(
-            usersyms={"np": np, "re": re, "NaN": NaN, "nan": NaN, "None": None, "datetime": datetime}
+            usersyms={"np": np, "re": re, "NaN": nan, "nan": nan, "None": None, "datetime": datetime}
         )
     try:
         return _asteval_interp(string, show_errors=False)

Diff for: Stoner/core/utils.py

@@ -80,11 +80,11 @@ def add_core(other: Union["DataFile", np.ndarray, List[Numeric], MappingType], n
                     order[k] = newdata.find_col(k)
                 except (KeyError, re.error):
                     mask = newdata.mask
-                    newdata.add_column(np.ones(len(newdata)) * np.NaN, header=k)
+                    newdata.add_column(np.ones(len(newdata)) * np.nan, header=k)
                     newdata.mask[:, :-1] = mask
                     newdata.mask[:, -1] = np.ones(len(newdata), dtype=bool)
                     order[k] = newdata.shape[1] - 1
-            row = np.ones(newdata.shape[1]) * np.NaN
+            row = np.ones(newdata.shape[1]) * np.nan
             mask = np.ones_like(row, dtype=bool)
             for k in order:
                 row[order[k]] = other[k]

Diff for: Stoner/formats/data/instruments.py

@@ -193,7 +193,7 @@ def load_qdfile(new_data, filename=None, *args, **kargs):
         if data.shape[0] == 0:
             raise StonerLoadError("No data in file!")
         if data.shape[1] < len(column_headers):  # Trap for buggy QD software not giving ewnough columns of data
-            data = np.append(data, np.ones((data.shape[0], len(column_headers) - data.shape[1])) * np.NaN, axis=1)
+            data = np.append(data, np.ones((data.shape[0], len(column_headers) - data.shape[1])) * np.nan, axis=1)
         elif data.shape[1] > len(column_headers):  # too much data
             data = data[:, : len(column_headers) - data.shape[1]]
         new_data.data = data

Diff for: Stoner/formats/instruments.py

@@ -223,7 +223,7 @@ def _load(self, filename=None, *args, **kargs):
             if data.shape[0] == 0:
                 raise Core.StonerLoadError("No data in file!")
             if data.shape[1] < len(column_headers):  # Trap for buggy QD software not giving ewnough columns of data
-                data = np.append(data, np.ones((data.shape[0], len(column_headers) - data.shape[1])) * np.NaN, axis=1)
+                data = np.append(data, np.ones((data.shape[0], len(column_headers) - data.shape[1])) * np.nan, axis=1)
             elif data.shape[1] > len(column_headers):  # too much data
                 data = data[:, : len(column_headers) - data.shape[1]]
             self.data = data

Diff for: recipe/meta.yaml

@@ -17,13 +17,13 @@ build:
 
 requirements:
   build:
-    - python >=3.7
+    - python >=3.9
     - pytest
     - pytest-runner
 
   run:
-    - python >=3.7
-    - scipy>1.7
+    - python >=3.9
+    - scipy >1.7
     - numpy >=1.18
     - matplotlib >=3.0
     - scikit-image >=0.17
@@ -33,7 +33,7 @@ requirements:
     - image-registration >=0.2.1
     - lmfit >=0.9.7
     - memoization >=0.1.4
-    - npTDMS >=0.11
+    - npTDMS >=1.9.0
     - python-dateutil >=2.7.0
     - statsmodels
     - tabulate >=0.8

Diff for: requirements.txt

@@ -8,7 +8,7 @@ filemagic>=1.6
 image-registration>=0.2.1
 lmfit>=0.9.7
 memoization>=0.1.4
-npTDMS>=0.11
+npTDMS>=1.9.0
 python-dateutil>=2.7.0
 statsmodels
 tabulate>=0.8