westpa 2022.10__cp311-cp311-macosx_10_9_x86_64.whl → 2022.12__cp311-cp311-macosx_10_9_x86_64.whl

westpa/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-05-30T14:33:52-0400",
+ "date": "2025-03-03T16:14:34-0500",
  "dirty": false,
  "error": null,
- "full-revisionid": "40fe71e4e393b47e0a231b178add25696e469405",
- "version": "2022.10"
+ "full-revisionid": "b3afe209fcffc6238c1d2ec700059c7e30f2adca",
+ "version": "2022.12"
 }
 '''  # END VERSION_JSON
 

westpa/cli/core/w_truncate.py

@@ -1,5 +1,5 @@
-import argparse
 import logging
+from argparse import ArgumentParser
 
 import westpa
 
@@ -14,7 +14,7 @@ traj_segs directory) is deleted or moved for the corresponding iterations.
 
 
 def entry_point():
-    parser = argparse.ArgumentParser(
+    parser = ArgumentParser(
         'w_truncate',
         description='''\
     Remove all iterations after a certain point in a WESTPA simulation.
@@ -30,7 +30,7 @@ def entry_point():
         metavar='WEST_H5FILE',
         help='''Take WEST data from WEST_H5FILE (default: read from the HDF5 file specified in west.cfg).''',
     )
-    parser.add_argument('-n', '--iter', dest='n_iter', type=int, help='Truncate this iteration and those following.')
+    parser.add_argument('-n', '--iter', dest='n_iter', type=int, default=0, help='Truncate this iteration and those following.')
 
     args = parser.parse_args()
     westpa.rc.process_args(args, config_required=False)
@@ -40,7 +40,15 @@ def entry_point():
 
     dm.open_backing()
     # max_iter = dm.current_iteration
-    n_iter = args.n_iter if args.n_iter > 0 else dm.current_iteration
+
+    if args.n_iter > dm.current_iteration:
+        parser.error(
+            'Provided iteration {} > current iteration {} of the {} HDF5 file. Exiting without doing anything.'.format(
+                args.n_iter, dm.current_iteration, dm.we_h5filename.split('/')[-1]
+            )
+        )
+    else:
+        n_iter = args.n_iter if args.n_iter > 0 else dm.current_iteration
 
     for i in range(n_iter, dm.current_iteration + 1):
         dm.del_iter_group(i)
@@ -48,8 +56,9 @@ def entry_point():
     dm.del_iter_summary(n_iter)
     dm.current_iteration = n_iter - 1
 
-    print('simulation data truncated after iteration {}'.format(dm.current_iteration))
-    print('\n' + warning_string)
+    westpa.rc.pstatus('simulation data truncated after iteration {}'.format(dm.current_iteration))
+    westpa.rc.pstatus('\n' + warning_string)
+    westpa.rc.pflush()
 
     dm.flush_backing()
     dm.close_backing()

westpa/cli/tools/w_assign.py

@@ -474,17 +474,17 @@ Command-line options
 
             # 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 @@ Command-line options
                 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

westpa/cli/tools/w_fluxanl.py

@@ -1,7 +1,6 @@
 import h5py
 import numpy as np
 from scipy.signal import fftconvolve
-from warnings import warn
 
 import westpa
 
@@ -12,7 +11,7 @@ from westpa.tools import WESTTool, WESTDataReader, IterRangeSelection
 from westpa.tools.dtypes import iter_block_ci_dtype as ci_dtype
 import westpa.mclib as mclib
 
-fluxentry_dtype = np.dtype([('n_iter', n_iter_dtype), ('flux', weight_dtype), ('count', np.uint)])
+fluxentry_dtype = np.dtype([('n_iter', n_iter_dtype), ('flux', weight_dtype), ('count', np.int32)])
 
 target_index_dtype = np.dtype(
     [
@@ -370,7 +369,6 @@ the true value of ``tau``.
 
 
 def entry_point():
-    warn('w_fluxanl is being deprecated.  Please use w_assign and w_direct instead.')
     WFluxanlTool().main()
 
 

westpa/cli/tools/w_ntop.py

@@ -190,9 +190,9 @@ Command-line arguments
                         weights = all_weights.take(segs)
 
                         if what == 'lowweight':
-                            indices = np.argsort(weights)[:count]
+                            indices = np.argsort(weights, kind='stable')[:count]
                         elif what == 'highweight':
-                            indices = np.argsort(weights)[::-1][:count]
+                            indices = np.argsort(weights, kind='stable')[::-1][:count]
                         else:
                             assert what == 'random'
                             indices = np.random.permutation(len(weights))

westpa/cli/tools/w_red.py

@@ -3,6 +3,11 @@ import numpy as np
 from westpa import rc
 from westpa.tools import WESTParallelTool
 
+try:
+    from numpy import trapezoid
+except ImportError:
+    from numpy import trapz as trapezoid
+
 
 class DurationCorrector(object):
     @staticmethod
@@ -128,9 +133,9 @@ class DurationCorrector(object):
 
         for i, tau in enumerate(taugrid):
             if i > 0 and tau < maxduration:
-                integral1[i] = np.trapz(f_tilde[: i + 1], taugrid[: i + 1])
+                integral1[i] = trapezoid(f_tilde[: i + 1], taugrid[: i + 1])
 
-        integral2 = np.trapz(integral1, taugrid)
+        integral2 = trapezoid(integral1, taugrid)
 
         if integral2 == 0:
             return 0.0

westpa/core/binning/assign.py

@@ -132,9 +132,9 @@ class RectilinearBinMapper(BinMapper):
     def boundaries(self, boundaries):
         del self._boundaries, self.labels
         self._boundaries = []
-        self.labels = labels = []
+        self.labels = []
         for boundset in boundaries:
-            boundarray = np.asarray(boundset, dtype=coord_dtype, order='C')
+            boundarray = np.ascontiguousarray(boundset, dtype=coord_dtype)
             db = np.diff(boundarray)
             if (db <= 0).any():
                 raise ValueError('boundary set must be strictly monotonically increasing')
@@ -146,8 +146,14 @@ class RectilinearBinMapper(BinMapper):
         _boundaries = self._boundaries
         binspace_shape = tuple(self._boundlens[:] - 1)
         for index in np.ndindex(binspace_shape):
-            bounds = [(_boundaries[idim][index[idim]], boundaries[idim][index[idim] + 1]) for idim in range(len(_boundaries))]
-            labels.append(repr(bounds))
+            label = (
+                '['
+                + ', '.join(
+                    f'({boundarray[index[idim]]!s}, {boundarray[index[idim] + 1]!s})' for idim, boundarray in enumerate(_boundaries)
+                )
+                + ']'
+            )
+            self.labels.append(label)
 
     def assign(self, coords, mask=None, output=None):
         try:
@@ -184,7 +190,7 @@ class PiecewiseBinMapper(BinMapper):
         self.functions = functions
         self.nbins = len(functions)
         self.index_dtype = np.min_scalar_type(self.nbins)
-        self.labels = [repr(func) for func in functions]
+        self.labels = [str(func) for func in functions]
 
     def assign(self, coords, mask=None, output=None):
         if output is None: