NumPy2 support fix

pyproject.toml

@@ -44,3 +44,4 @@ exclude = '''
      )
 )
 '''
+

src/westpa/cli/tools/w_assign.py

@@ -474,17 +474,17 @@ def go(self):
 
             # Recursive mappers produce a generator rather than a list of labels
             # so consume the entire generator into a list
-            labels = [np.string_(label) for label in self.binning.mapper.labels]
+            labels = [np.bytes_(label) for label in self.binning.mapper.labels]
 
             self.output_file.create_dataset('bin_labels', data=labels, compression=9)
 
             if self.states:
                 nstates = len(self.states)
                 state_map[:] = nstates  # state_id == nstates => unknown state
-                state_labels = [np.string_(state['label']) for state in self.states]
+                state_labels = [np.bytes_(state['label']) for state in self.states]
 
                 for istate, sdict in enumerate(self.states):
-                    assert state_labels[istate] == np.string_(sdict['label'])  # sanity check
+                    assert state_labels[istate] == np.bytes_(sdict['label'])  # sanity check
                     state_assignments = assign(sdict['coords'])
                     for assignment in state_assignments:
                         state_map[assignment] = istate
@@ -558,7 +558,7 @@ def go(self):
                 shuffle=True,
                 chunks=h5io.calc_chunksize(pops_shape, weight_dtype),
             )
-            h5io.label_axes(pops_ds, [np.string_(i) for i in ['iteration', 'state', 'bin']])
+            h5io.label_axes(pops_ds, [np.bytes_(i) for i in ['iteration', 'state', 'bin']])
 
             pi.new_operation('Assigning to bins', iter_stop - iter_start)
             last_labels = None  # mapping of seg_id to last macrostate inhabited

src/westpa/core/data_manager.py

@@ -1545,7 +1545,7 @@
         #        dsopts['file'] = str(dsopts['file']).format(n_iter=n_iter)
         h5_auxfile = h5io.WESTPAH5File(dsopts['file'].format(n_iter=n_iter))
         h5group = group
-        if not ("iter_" + str(n_iter).zfill(8)) in h5_auxfile:
+        if ("iter_" + str(n_iter).zfill(8)) not in h5_auxfile:
             h5_auxfile.create_group("iter_" + str(n_iter).zfill(8))
         group = h5_auxfile[('/' + "iter_" + str(n_iter).zfill(8))]
 
@@ -1648,7 +1648,7 @@
     if 'file' in list(dsopts.keys()):
         import h5py
 
-        if not dsopts['h5path'] in h5group:
+        if dsopts['h5path'] not in h5group:
             h5group[dsopts['h5path']] = h5py.ExternalLink(
                 dsopts['file'].format(n_iter=n_iter), ("/" + "iter_" + str(n_iter).zfill(8) + "/" + dsopts['h5path'])
             )

src/westpa/core/h5io.py

@@ -342,10 +342,10 @@
     if len(units) and len(units) != len(labels):
         raise ValueError('number of units labels does not match number of axes')
 
-    h5object.attrs['axis_labels'] = np.array([np.string_(i) for i in labels])
+    h5object.attrs['axis_labels'] = np.array([np.bytes_(i) for i in labels])
 
     if len(units):
-        h5object.attrs['axis_units'] = np.array([np.string_(i) for i in units])
+        h5object.attrs['axis_units'] = np.array([np.bytes_(i) for i in units])
 
 
 NotGiven = object()

src/westpa/core/states.py

@@ -20,7 +20,7 @@ class BasisState:
     '''
 
     def __init__(self, label, probability, pcoord=None, auxref=None, state_id=None):
-        self.label = str(label, encoding="UTF-8") if type(label) is bytes else label
+        self.label = str(label, encoding="UTF-8") if isinstance(label, bytes) else label
         self.probability = probability
         self.pcoord = np.atleast_1d(pcoord)
         self.auxref = auxref

src/westpa/westext/stringmethod/string_method.py

@@ -176,7 +176,7 @@
                 ud[2:] = -self._kappan[ulen]
                 ld[:-2] = -self._kappan[ulen]
 
-                self._A[ulen] = np.mat([ud, d, ld])
+                self._A[ulen] = np.asmatrix([ud, d, ld])
 
             else:
                 self._A[ulen] = np.eye(ulen)

tests/test_tools/h5diff.py

@@ -33,11 +33,11 @@ def check_in_ref(self, name, obj):
             #   .dtype is referencing an attribute of a numpy array.
             if test_object[()].dtype.names is not None:
                 non_reference_test_elements = [
-                    x for i, x in enumerate(test_object[()][0]) if not test_object[()].dtype.names[i] in ref_names
+                    x for i, x in enumerate(test_object[()][0]) if test_object[()].dtype.names[i] not in ref_names
                 ]
 
                 non_reference_ref_elements = [
-                    x for i, x in enumerate(ref_object[()][0]) if not ref_object[()].dtype.names[i] in ref_names
+                    x for i, x in enumerate(ref_object[()][0]) if ref_object[()].dtype.names[i] not in ref_names
                 ]
 
             else: