More NumPy 2.0 compatibility fixes

pyteomics/auxiliary/math.py

@@ -27,9 +27,9 @@ def linear_regression_vertical(x, y=None, a=None, b=None):
     """
 
     import numpy as np
-    x = np.array(x, copy=False)
+    x = np.asarray(x)
     if y is not None:
-        y = np.array(y, copy=False)
+        y = np.asarray(y)
     else:
         if len(x.shape) != 2 or x.shape[-1] != 2:
             raise PyteomicsError(
@@ -76,9 +76,9 @@ def linear_regression_perpendicular(x, y=None):
     """
 
     import numpy as np
-    x = np.array(x, copy=False)
+    x = np.asarray(x)
     if y is not None:
-        y = np.array(y, copy=False)
+        y = np.asarray(y)
         data = np.hstack((x.reshape((-1, 1)), y.reshape((-1, 1))))
     else:
         if len(x.shape) != 2 or x.shape[-1] != 2:

pyteomics/parser.py

@@ -1143,7 +1143,7 @@ def coverage(protein, peptides):
             '(?={})'.format(re.sub(r'[^A-Z]', '', peptide)), protein)]
         for i in indices:
             mask[i:i + len(peptide)] = 1
-    return mask.sum(dtype=float) / mask.size
+    return float(mask.sum(dtype=float) / mask.size)
 
 
 if __name__ == "__main__":

pyteomics/version.py

@@ -19,7 +19,7 @@
 
 """
 
-__version__ = '4.7.2'
+__version__ = '4.7.3a1'
 
 from collections import namedtuple
 import re

tests/data.py

@@ -3,7 +3,7 @@
 """
 
 import numpy as np
-from copy import deepcopy
+from copy import copy
 import sys
 from pyteomics.auxiliary import basestring
 
@@ -1415,14 +1415,14 @@ def makeCA(arr):
                                  'scans': '3',
                                  'title': 'Spectrum 2'}}]
 
-mgf_spectra_short_no_charges = deepcopy(mgf_spectra_short)
+mgf_spectra_short_no_charges = list(map(copy, mgf_spectra_short))
 for s in mgf_spectra_short_no_charges:
     del s['charge array']
-mgf_spectra_long_no_charges = deepcopy(mgf_spectra_long)
+mgf_spectra_long_no_charges = list(map(copy, mgf_spectra_long))
 for s in mgf_spectra_long_no_charges:
     del s['charge array']
 
-mgf_spectra_lists = deepcopy(mgf_spectra_long)
+mgf_spectra_lists = list(map(copy, mgf_spectra_long))
 for s in mgf_spectra_lists:
     for key in ['m/z array', 'intensity array', 'charge array']:
         s[key] = list(s[key])

tests/test_mgf.py

@@ -71,14 +71,14 @@ def test_read_no_charges(self):
             self.assertEqual(data.mgf_spectra_short_no_charges, list(reader))
 
     def test_read_with_ions(self):
-        for spec_data, spec_read in zip(data.mgf_spectra_annotated_long, list(self.spectra_annotated)):
+        for spec_data, spec_read in zip(data.mgf_spectra_annotated_long, self.spectra_annotated):
             # Check that the spectra have the same dict keys
             self.assertEqual(spec_data.keys(), spec_read.keys())
-            for key in spec_data.keys():
-                if type(spec_data[key]) == dict:
-                    self.assertDictEqual(spec_data[key], spec_read[key])
-                else:
+            for key in spec_data:
+                if key == 'ion array':
                     np.testing.assert_array_equal(spec_data[key], spec_read[key])
+                else:
+                    self.assertEqual(spec_data[key], spec_read[key])
 
     def test_read_write_with_ions(self):
         formats = ['{:.6f} {:.6f} {}', '%.6f %.6f %s']
@@ -91,11 +91,11 @@ def test_read_write_with_ions(self):
             for spec_data, spec_read in zip(data.mgf_spectra_annotated_long, spectra):
                 # Check that the spectra have the same dict keys
                 self.assertEqual(spec_data.keys(), spec_read.keys())
-                for key in spec_data.keys():
-                    if type(spec_data[key]) == dict:
-                        self.assertDictEqual(spec_data[key], spec_read[key])
-                    else:
+                for key in spec_data:
+                    if key == 'ion array':
                         np.testing.assert_array_equal(spec_data[key], spec_read[key])
+                    else:
+                        self.assertEqual(spec_data[key], spec_read[key])
 
     def test_read_array_conversion(self):
         with mgf.read(self.path, convert_arrays=0) as reader:

tests/test_ms2.py

@@ -25,26 +25,26 @@ def test_read(self):
 
     def test_read_no_charges(self):
         with read(self.path, convert_arrays=False, read_charges=False) as reader:
-            lhs = copy.deepcopy(data.ms2_spectra_lists)
+            lhs = list(map(copy.copy, data.ms2_spectra_lists))
             for spec in lhs:
                 del spec['charge array']
             self.assertEqual(lhs, list(reader))
 
         with read(self.path, convert_arrays=1, read_charges=False) as reader:
-            lhs = copy.deepcopy(data.ms2_spectra)
+            lhs = list(map(copy.copy, data.ms2_spectra))
             for spec in lhs:
                 del spec['charge array']
             self.assertEqual(lhs, list(reader))
 
     def test_read_no_resolution(self):
         with read(self.path, convert_arrays=False, read_resolutions=False) as reader:
-            lhs = copy.deepcopy(data.ms2_spectra_lists)
+            lhs = list(map(copy.copy, data.ms2_spectra_lists))
             for spec in lhs:
                 del spec['resolution array']
             self.assertEqual(lhs, list(reader))
 
         with read(self.path, convert_arrays=1, read_resolutions=False) as reader:
-            lhs = copy.deepcopy(data.ms2_spectra)
+            lhs = list(map(copy.copy, data.ms2_spectra))
             for spec in lhs:
                 del spec['resolution array']
             self.assertEqual(lhs, list(reader))
@@ -77,7 +77,7 @@ def test_indexedms2_picklable(self):
             self.assertEqual(reader.block_size, 12345)
             self.assertEqual(reader._read_charges, False)
             self.assertEqual(reader._read_resolutions, False)
-            lhs = copy.deepcopy(data.ms2_spectra)
+            lhs = list(map(copy.copy, data.ms2_spectra))
             for spec in lhs:
                 del spec['resolution array']
                 del spec['charge array']
@@ -94,7 +94,7 @@ def test_ms2_picklable(self):
         with pickle.loads(spec) as reader:
             self.assertEqual(reader._read_charges, False)
             self.assertEqual(reader._read_resolutions, False)
-            lhs = copy.deepcopy(data.ms2_spectra)
+            lhs = list(map(copy.copy, data.ms2_spectra))
             for spec in lhs:
                 del spec['resolution array']
                 del spec['charge array']