westpa 2022.4__cp38-cp38-macosx_10_9_x86_64.whl → 2022.6__cp38-cp38-macosx_10_9_x86_64.whl

westpa/_version.py

@@ -1,5 +1,5 @@
 
-# This file was generated by 'versioneer.py' (0.28) from
+# This file was generated by 'versioneer.py' (0.29) from
 # revision-control system data, or from the parent directory name of an
 # unpacked source archive. Distribution tarballs contain a pre-generated copy
 # of this file.
@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2023-02-01T14:01:18-0500",
+ "date": "2023-10-20T12:52:31-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "c5ee2fcdb8b82ee3cbfd2894065a375157a6ba75",
- "version": "2022.04"
+ "full-revisionid": "ef5fbd3e0aeb4d08160fc56ee39cca6ba75e3217",
+ "version": "2022.06"
 }
 '''  # END VERSION_JSON
 

westpa/cli/core/w_fork.py

@@ -101,7 +101,7 @@ def entry_point():
     state_map = np.empty((n_segments,), dtype=state_map_dtype)
     state_map['old_n_iter'] = n_iter
 
-    for (iseg, (index_row, pcoord)) in enumerate(zip(old_index, old_final_pcoords)):
+    for iseg, (index_row, pcoord) in enumerate(zip(old_index, old_final_pcoords)):
         istate = istates[iseg]
         istate.iter_created = 0
         istate.iter_used = 1

westpa/cli/core/w_init.py

@@ -18,7 +18,6 @@ EPS = np.finfo(np.float64).eps
 
 
 def entry_point():
-
     parser = argparse.ArgumentParser(
         'w_init',
         description='''\

westpa/cli/core/w_run.py

@@ -30,7 +30,6 @@ def entry_point():
 
 
 def run_simulation():
-
     work_manager = westpa.rc.work_manager = make_work_manager()
 
     # Load the sim manager and other drivers

westpa/cli/core/w_states.py

@@ -102,7 +102,6 @@ def entry_point():
 
 # TODO: This would benefit from a refactor to set default args to None, and replace some of those "if <argument>" clauses
 def initialize(mode, bstates, _bstate_file, tstates, _tstate_file):
-
     work_manager = make_work_manager()
 
     system = westpa.rc.get_system_driver()
@@ -116,7 +115,6 @@ def initialize(mode, bstates, _bstate_file, tstates, _tstate_file):
 
             assert mode in ('show', 'replace', 'append')
             if mode == 'show':
-
                 basis_states = data_manager.get_basis_states(n_iter)
                 if basis_states:
                     bstate_file = sys.stdout if not _bstate_file else open(_bstate_file, 'wt')

westpa/cli/core/w_succ.py

@@ -57,7 +57,7 @@ class WSucc(CommonOutputMixin, WESTDataReaderMixin, WESTAnalysisTool):
             # The above HDF5 selection always returns a vector; we want a 2-d array
             final_pcoords.shape = (len(recycled_seg_ids), pcoord_ndim)
 
-            for (ipc, seg_id) in enumerate(recycled_seg_ids):
+            for ipc, seg_id in enumerate(recycled_seg_ids):
                 self.output_file.write('%8d    %8d    %20.14g' % (n_iter, seg_id, seg_index[seg_id]['weight']))
                 fields = ['']
                 for field in final_pcoords[ipc]:

westpa/cli/core/w_truncate.py

@@ -23,10 +23,21 @@ def entry_point():
     )
 
     westpa.rc.add_args(parser)
+    parser.add_argument(
+        '-W',
+        '--west-data',
+        dest='we_h5filename',
+        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.')
+
     args = parser.parse_args()
     westpa.rc.process_args(args, config_required=False)
     dm = westpa.rc.get_data_manager()
+    if args.we_h5filename:
+        dm.we_h5filename = args.we_h5filename
+
     dm.open_backing()
     # max_iter = dm.current_iteration
     n_iter = args.n_iter if args.n_iter > 0 else dm.current_iteration

westpa/cli/tools/w_assign.py

@@ -33,7 +33,6 @@ def parse_pcoord_value(pc_str):
 def _assign_label_pop(
     n_iter, lb, ub, mapper, nstates, state_map, last_labels, parent_id_dsspec, weight_dsspec, pcoord_dsspec, subsample
 ):
-
     nbins = len(state_map) - 1
     parent_ids = parent_id_dsspec.get_iter_data(n_iter, index_exp[lb:ub])
     weights = weight_dsspec.get_iter_data(n_iter, index_exp[lb:ub])

westpa/cli/tools/w_bins.py

@@ -68,7 +68,6 @@ modify the binning for the current iteration of a WEST simulation.
         rebin_parser.set_defaults(func=self.cmd_rebin)
 
     def process_args(self, args):
-
         self.data_reader.process_args(args)
         self.data_reader.open(mode='r+')
         self.n_iter = getattr(args, 'n_iter', None) or self.data_reader.current_iteration

westpa/cli/tools/w_dumpsegs.py

@@ -64,7 +64,7 @@ significant analysis tasks).
             + '\n'
         )
         pcoord_lines = '  pcoord[0]  = {init_pcoord}\n  pcoord[-1] = {final_pcoord}' + '\n'
-        for (_seg_id, segment) in enumerate(segments):
+        for _seg_id, segment in enumerate(segments):
             parents_str = '[' + ', '.join(map(str, sorted(segment.wtg_parent_ids))) + ']'
             init_pcoord_str = '[' + ', '.join('{pcval:<12.6g}'.format(pcval=float(pce)) for pce in segment.pcoord[0]) + ']'
             final_pcoord_str = '[' + ', '.join('{pcval:<12.6g}'.format(pcval=float(pce)) for pce in segment.pcoord[-1]) + ']'

westpa/cli/tools/w_eddist.py

@@ -68,7 +68,6 @@ def _remote_min_max(ndim, dset_dtype, n_iter, dsspec):
 
 
 def _remote_bin_iter(iiter, n_iter, dsspec, wt_dsspec, initpoint, binbounds, ignore_out_of_range):
-
     iter_hist_shape = tuple(len(bounds) - 1 for bounds in binbounds)
     iter_hist = np.zeros(iter_hist_shape, dtype=np.float64)
 
@@ -220,7 +219,6 @@ Command-line options
         self.compress_output = False
 
     def add_args(self, parser):
-
         parser.add_argument(
             '-b',
             '--bins',
@@ -300,7 +298,6 @@ Command-line options
         self.compress_output = args.compress or False
 
     def go(self):
-
         pi = self.progress.indicator
         pi.operation = 'Initializing'
         with pi:
@@ -334,7 +331,6 @@ Command-line options
 
     @staticmethod
     def parse_binspec(binspec):
-
         namespace = {'numpy': np, 'np': np, 'inf': float('inf')}
 
         try:

westpa/cli/tools/w_ipa.py

@@ -641,7 +641,6 @@ class WIPI(WESTParallelTool):
         return self._future
 
     class Future(WIPIDataset):
-
         # This isn't a real fancy one.
         def __getitem__(self, value):
             if isinstance(value, str):

westpa/cli/tools/w_multi_west.py

@@ -74,11 +74,23 @@ def get_bin_mapper(we_h5file, hashval):
         raise KeyError('hash {} not found'.format(hashval))
 
 
+def create_idtype_array(input_array):
+    '''Return a new array with the new istate_dtype while preserving old data.'''
+    new_array = np.zeros(input_array.shape, dtype=istate_dtype)
+    for j in input_array.dtype.names:
+        new_array[j] = input_array[j].copy()
+
+    # Need to turn 'basis_auxref' to empty bytestrings...
+    new_array['basis_auxref'] = b''
+
+    return new_array
+
+
 class WMultiWest(WESTMultiTool):
     prog = 'w_multi_west'
     description = '''\
 Tool designed to combine multiple WESTPA simulations while accounting for
-reweighting.  Test code thus far.
+reweighting.
 -----------------------------------------------------------------------------
 Command-line options
 -----------------------------------------------------------------------------
@@ -144,7 +156,7 @@ Command-line options
             # Sometimes, we're smaller or larger by one.  Hm.
             try:
                 self.total_walkers[:] += west['summary'][:-1]['n_particles']
-            except (ValueError):
+            except ValueError:
                 self.total_walkers[:] += west['summary'][:-1]['n_particles'][: len(self.total_walkers)]
 
     class Segment:
@@ -243,8 +255,13 @@ Command-line options
                     if ifile == 0:
                         final_istate_index = west['ibstates/0/istate_index']
                         final_istate_pcoord = west['ibstates/0/istate_pcoord']
+                        if final_istate_index.dtype != istate_dtype:
+                            final_istate_index = create_idtype_array(final_istate_index)
                     else:
-                        final_istate_index = np.append(final_istate_index, west['ibstates/0/istate_index'][:])
+                        addition = west['ibstates/0/istate_index'][:]
+                        if addition.dtype != istate_dtype:
+                            addition = create_idtype_array(addition)
+                        final_istate_index = np.append(final_istate_index, addition)
                         final_istate_pcoord = np.append(final_istate_pcoord, west['ibstates/0/istate_pcoord'][:])
 
                 # Saving them into self.output_file

westpa/cli/tools/w_pdist.py

@@ -51,7 +51,6 @@ def _remote_min_max(ndim, dset_dtype, n_iter, dsspec):
 
 
 def _remote_bin_iter(iiter, n_iter, dsspec, wt_dsspec, initpoint, binbounds, ignore_out_of_range):
-
     iter_hist_shape = tuple(len(bounds) - 1 for bounds in binbounds)
     iter_hist = np.zeros(iter_hist_shape, dtype=np.float64)
 

westpa/cli/tools/w_red.py

@@ -333,7 +333,6 @@ class RateCalculator:
         return self._dc
 
     def calc_rate(self, i_iter=None, red=False, **kwargs):
-
         if i_iter is None:
             i_iter = self.n_iters
 

westpa/core/_rc.py

@@ -14,7 +14,6 @@ import westpa
 import westpa.core.data_manager
 from westpa.core.binning.assign import BinMapper
 from westpa.core.binning import RectilinearBinMapper, RecursiveBinMapper, MABBinMapper, BinlessMapper
-from westpa.core.extloader import get_object
 from .yamlcfg import YAMLConfig
 from .yamlcfg import YAMLSystem
 from . import extloader
@@ -31,7 +30,7 @@ def bins_from_yaml_dict(bin_dict):
         mapper_type = getattr(sys.modules['westpa.core.binning'], typename)
     except AttributeError:
         try:
-            mapper_type = get_object(typename)
+            mapper_type = extloader.get_object(typename)
         except AttributeError:
             raise KeyError('unknown bin mapper type {!r}'.format(typename))
 
@@ -161,7 +160,10 @@ class WESTRC:
         self.rcfile = os.environ.get(self.ENV_RUNTIME_CONFIG) or self.RC_DEFAULT_FILENAME
 
         self.config = YAMLConfig()
-        self.process_name = os.path.splitext(os.path.basename(sys.argv[0]))[0]
+        try:
+            self.process_name = os.path.splitext(os.path.basename(sys.argv[0]))[0]
+        except (TypeError, IndexError):
+            self.process_name = "unknown"
 
         # Crucial simulation and analysis drivers
         self._system = None
@@ -340,21 +342,23 @@ class WESTRC:
 
     def new_sim_manager(self):
         drivername = self.config.get(['west', 'drivers', 'sim_manager'], 'default')
-        use_mab = self.detect_mab_mapper()
-        use_binless = self.detect_binless_mapper()
 
-        if use_mab:
-            from .binning.mab_manager import MABSimManager
+        if drivername.lower() == 'default':
+            use_mab = self.detect_mab_mapper()
+            use_binless = self.detect_binless_mapper()
+
+            if use_mab:
+                from .binning.mab_manager import MABSimManager
 
-            sim_manager = MABSimManager(rc=self)
-        elif use_binless:
-            from .binning.binless_manager import BinlessSimManager
+                sim_manager = MABSimManager(rc=self)
+            elif use_binless:
+                from .binning.binless_manager import BinlessSimManager
 
-            sim_manager = BinlessSimManager(rc=self)
-        elif drivername.lower() == 'default':
-            from .sim_manager import WESimManager
+                sim_manager = BinlessSimManager(rc=self)
+            else:
+                from .sim_manager import WESimManager
 
-            sim_manager = WESimManager(rc=self)
+                sim_manager = WESimManager(rc=self)
         else:
             sim_manager = extloader.get_object(drivername)(rc=self)
 
@@ -386,23 +390,25 @@ class WESTRC:
         import westpa
 
         drivername = self.config.get(['west', 'drivers', 'we_driver'], 'default')
-        use_mab = self.detect_mab_mapper()
-        use_binless = self.detect_binless_mapper()
 
-        if use_mab:
-            from .binning.mab_driver import MABDriver
+        if drivername.lower() == 'default':
+            use_mab = self.detect_mab_mapper()
+            use_binless = self.detect_binless_mapper()
+            if use_mab:
+                from .binning.mab_driver import MABDriver
 
-            we_driver = MABDriver()
-        elif use_binless:
-            from .binning.binless_driver import BinlessDriver
+                we_driver = MABDriver()
+            elif use_binless:
+                from .binning.binless_driver import BinlessDriver
 
-            we_driver = BinlessDriver()
-        elif drivername.lower() == 'default':
-            from .we_driver import WEDriver
+                we_driver = BinlessDriver()
+            else:
+                from .we_driver import WEDriver
 
-            we_driver = WEDriver()
+                we_driver = WEDriver()
         else:
             we_driver = extloader.get_object(drivername)(rc=self)
+
         log.debug('loaded WE algorithm driver: {!r}'.format(we_driver))
 
         subgroup_function = self.config.get(['west', 'drivers', 'subgroup_function'], 'default')
@@ -638,7 +644,6 @@ class WESTRC:
         return self.work_manager
 
     def clear_state(self):
-
         self._sim_manager = None
         self._system = None
         self._data_manager = None

westpa/core/binning/assign.py

@@ -429,7 +429,7 @@ class RecursiveBinMapper(BinMapper):
         # Which coordinates do we need to reassign, because they landed in
         # bins with embedded mappers?
         rmasks = {}
-        for (rindex, mapper) in self._recursion_targets.items():
+        for rindex, mapper in self._recursion_targets.items():
             omask = output == rindex
             mmask |= omask
             rmasks[rindex] = omask
@@ -441,7 +441,7 @@ class RecursiveBinMapper(BinMapper):
             output_map(output, omap, mask & ~mmask)
 
         # do any recursive assignments necessary
-        for (rindex, mapper) in self._recursion_targets.items():
+        for rindex, mapper in self._recursion_targets.items():
             mapper.assign(coords, mask & rmasks[rindex], output)
 
         return output

westpa/core/binning/binless_driver.py

@@ -33,7 +33,7 @@ class BinlessDriver(WEDriver):
         final_binning = self.final_binning
         flux_matrix = self.flux_matrix
         transition_matrix = self.transition_matrix
-        for (segment, iidx, fidx) in zip(segments, initial_assignments, final_assignments):
+        for segment, iidx, fidx in zip(segments, initial_assignments, final_assignments):
             initial_binning[iidx].add(segment)
             final_binning[fidx].add(segment)
             flux_matrix[iidx, fidx] += segment.weight

westpa/core/binning/binless_manager.py

@@ -75,8 +75,31 @@ class BinlessSimManager(WESimManager):
                 log.error('unknown future {!r} received from work manager'.format(future))
                 raise AssertionError('untracked future {!r}'.format(future))
 
+        # Collectively assign all segments to their bins...
         self.we_driver.assign(self.segments.values())
-        self.get_istate_futures()
+
+        # For cases where we need even more istates for recycled trajectories
+        # futures should be empty at this point.
+        istate_gen_futures = self.get_istate_futures()
+        futures.update(istate_gen_futures)
+
+        # Wait for istate_gen_futures and catch untracked futures.
+        while futures:
+            future = self.work_manager.wait_any(futures)
+            futures.remove(future)
+
+            if future in istate_gen_futures:
+                istate_gen_futures.remove(future)
+                _basis_state, initial_state = future.get_result()
+                log.debug('received newly-prepared initial state {!r}'.format(initial_state))
+                initial_state.istate_status = InitialState.ISTATE_STATUS_PREPARED
+                with self.data_manager.expiring_flushing_lock():
+                    self.data_manager.update_initial_states([initial_state], n_iter=self.n_iter + 1)
+                self.we_driver.avail_initial_states[initial_state.state_id] = initial_state
+            else:
+                log.error('unknown future {!r} received from work manager'.format(future))
+                raise AssertionError('untracked future {!r}'.format(future))
+
         log.debug('done with propagation')
         self.save_bin_data()
         self.data_manager.flush_backing()
@@ -132,7 +155,7 @@ class BinlessSimManager(WESimManager):
         for iseg, segment in enumerate(segments.values()):
             initial_pcoords[iseg] = segment.pcoord[0]
         initial_assignments = self.system.bin_mapper.assign(initial_pcoords)
-        for (segment, assignment) in zip(iter(segments.values()), initial_assignments):
+        for segment, assignment in zip(iter(segments.values()), initial_assignments):
             initial_binning[assignment].add(segment)
         self.report_bin_statistics(initial_binning, [], save_summary=True)
         del initial_pcoords, initial_binning

westpa/core/binning/mab.py

@@ -1,7 +1,9 @@
-import numpy as np
-from westpa.core.binning import FuncBinMapper
 import logging
+import numpy as np
 import westpa
+from westpa.core.binning import FuncBinMapper
+from os.path import expandvars
+
 
 log = logging.getLogger(__name__)
 
@@ -19,11 +21,15 @@ def map_mab(coords, mask, output, *args, **kwargs):
     skip = kwargs.get("skip")
     nbins_per_dim = kwargs.get("nbins_per_dim")
     mab_log = kwargs.get("mab_log")
+    bin_log = kwargs.get("bin_log")
     ndim = len(nbins_per_dim)
 
     if not np.any(mask):
         return output
 
+    if skip is None:
+        skip = [0] * ndim
+
     allcoords = np.copy(coords)
     allmask = np.copy(mask)
 
@@ -209,7 +215,6 @@ def map_mab(coords, mask, output, *args, **kwargs):
         # the following are for the "linear" portion
         if not special:
             for n in range(ndim):
-
                 # if skipped, it's added to the same bin as the special walkers above
                 if skip[n] != 0:
                     holder = boundary_base + n
@@ -241,6 +246,18 @@ def map_mab(coords, mask, output, *args, **kwargs):
         # output is the main list that, for each segment, holds the bin assignment
         output[i] = holder
 
+    if bin_log and report:
+        if westpa.rc.sim_manager.n_iter:
+            with open(expandvars("$WEST_SIM_ROOT/binbounds.log"), 'a') as bb_file:
+                bb_file.write(f'{westpa.rc.sim_manager.n_iter}\n')  # Iteration Number
+                for n in range(ndim):
+                    bb_file.write(f'{np.linspace(minlist[n], maxlist[n], nbins_per_dim[n] + 1)}\t')  # Write binbounds per dim
+                bb_file.write(f'\n{minlist} {maxlist}\n')  # Min/Max pcoord
+                if bottleneck_base > boundary_base:
+                    bb_file.write(f'{flipdifflist} {difflist}\n\n')  # Bottlenecks
+                else:
+                    bb_file.write('\n')
+
     return output
 
 
@@ -249,7 +266,7 @@ class MABBinMapper(FuncBinMapper):
     the progress coordinte. Extrema and bottleneck segments are assigned
     to their own bins.'''
 
-    def __init__(self, nbins, direction=None, skip=None, bottleneck=True, pca=False, mab_log=False):
+    def __init__(self, nbins, direction=None, skip=None, bottleneck=True, pca=False, mab_log=False, bin_log=False):
         # Verifying parameters
         if nbins is None:
             raise ValueError("nbins_per_dim is missing")
@@ -259,15 +276,17 @@ class MABBinMapper(FuncBinMapper):
             direction = [0] * ndim
         elif len(direction) != ndim:
             direction = [0] * ndim
-            log.warn("Direction list is not the correct dimensions, setting to defaults.")
+            log.warning("Direction list is not the correct dimensions, setting to defaults.")
 
         if skip is None:
             skip = [0] * ndim
         elif len(skip) != ndim:
             skip = [0] * ndim
-            log.warn("Skip list is not the correct dimensions, setting to defaults.")
+            log.warning("Skip list is not the correct dimensions, setting to defaults.")
 
-        kwargs = dict(nbins_per_dim=nbins, direction=direction, skip=skip, bottleneck=bottleneck, pca=pca, mab_log=mab_log)
+        kwargs = dict(
+            nbins_per_dim=nbins, direction=direction, skip=skip, bottleneck=bottleneck, pca=pca, mab_log=mab_log, bin_log=bin_log
+        )
         # the following is neccessary because functional bin mappers need to "reserve"
         # bins and tell the sim manager how many bins they will need to use, this is
         # determined by taking all direction/skipping info into account

westpa/core/binning/mab_driver.py

@@ -33,7 +33,7 @@ class MABDriver(WEDriver):
         final_binning = self.final_binning
         flux_matrix = self.flux_matrix
         transition_matrix = self.transition_matrix
-        for (segment, iidx, fidx) in zip(segments, initial_assignments, final_assignments):
+        for segment, iidx, fidx in zip(segments, initial_assignments, final_assignments):
             initial_binning[iidx].add(segment)
             final_binning[fidx].add(segment)
             flux_matrix[iidx, fidx] += segment.weight

westpa/core/binning/mab_manager.py

@@ -75,8 +75,31 @@ class MABSimManager(WESimManager):
                 log.error('unknown future {!r} received from work manager'.format(future))
                 raise AssertionError('untracked future {!r}'.format(future))
 
+        # Collectively assign all segments to their bins...
         self.we_driver.assign(self.segments.values())
-        self.get_istate_futures()
+
+        # For cases where we need even more istates for recycled trajectories
+        # futures should be empty at this point.
+        istate_gen_futures = self.get_istate_futures()
+        futures.update(istate_gen_futures)
+
+        # Wait for istate_gen_futures and catch untracked futures.
+        while futures:
+            future = self.work_manager.wait_any(futures)
+            futures.remove(future)
+
+            if future in istate_gen_futures:
+                istate_gen_futures.remove(future)
+                _basis_state, initial_state = future.get_result()
+                log.debug('received newly-prepared initial state {!r}'.format(initial_state))
+                initial_state.istate_status = InitialState.ISTATE_STATUS_PREPARED
+                with self.data_manager.expiring_flushing_lock():
+                    self.data_manager.update_initial_states([initial_state], n_iter=self.n_iter + 1)
+                self.we_driver.avail_initial_states[initial_state.state_id] = initial_state
+            else:
+                log.error('unknown future {!r} received from work manager'.format(future))
+                raise AssertionError('untracked future {!r}'.format(future))
+
         log.debug('done with propagation')
         self.save_bin_data()
         self.data_manager.flush_backing()
@@ -135,7 +158,7 @@ class MABSimManager(WESimManager):
         # Assign this iteration's segments' initial points to bins and report on bin population
         initial_binning = self.system.bin_mapper.construct_bins()
         initial_assignments = self.system.bin_mapper.assign(pcoords_with_weights)
-        for (segment, assignment) in zip(iter(segments.values()), initial_assignments):
+        for segment, assignment in zip(iter(segments.values()), initial_assignments):
             initial_binning[assignment].add(segment)
         self.report_bin_statistics(initial_binning, [], save_summary=True)
         del pcoords_with_weights, initial_binning

westpa/core/data_manager.py

@@ -231,7 +231,7 @@ class WESTDataManager:
     def process_config(self):
         config = self.rc.config
 
-        for (entry, type_) in [('iter_prec', int)]:
+        for entry, type_ in [('iter_prec', int)]:
             config.require_type_if_present(['west', 'data', entry], type_)
 
         self.we_h5filename = config.get_path(['west', 'data', 'west_data_file'], default=self.default_we_h5filename)
@@ -263,7 +263,6 @@ class WESTDataManager:
                 raise ValueError('cannot override pcoord storage location')
 
     def __init__(self, rc=None):
-
         self.rc = rc or westpa.rc
 
         self.we_h5filename = self.default_we_h5filename
@@ -401,7 +400,7 @@ class WESTDataManager:
         be propagated.  A complete set is required, even if nominally appending to an existing set,
         which simplifies the mapping of IDs to the table.'''
 
-        system = westpa.rc.get_system_driver()
+        system = self.system
 
         n_iter = n_iter or self.current_iteration
 
@@ -519,7 +518,7 @@ class WESTDataManager:
             master_index_row['group_ref'] = state_group.ref
 
             if basis_states:
-                system = westpa.rc.get_system_driver()
+                system = self.system
                 state_table = np.empty((len(basis_states),), dtype=bstate_dtype)
                 state_pcoords = np.empty((len(basis_states), system.pcoord_ndim), dtype=system.pcoord_dtype)
                 for i, state in enumerate(basis_states):
@@ -616,7 +615,7 @@ class WESTDataManager:
         '''Create storage for ``n_states`` initial states associated with iteration ``n_iter``, and
         return bare InitialState objects with only state_id set.'''
 
-        system = westpa.rc.get_system_driver()
+        system = self.system
         with self.lock:
             n_iter = n_iter or self.current_iteration
             ibstate_group = self.find_ibstate_group(n_iter)
@@ -659,7 +658,7 @@ class WESTDataManager:
     def update_initial_states(self, initial_states, n_iter=None):
         '''Save the given initial states in the HDF5 file'''
 
-        system = westpa.rc.get_system_driver()
+        system = self.system
         initial_states = sorted(initial_states, key=attrgetter('state_id'))
         if not initial_states:
             return
@@ -854,7 +853,7 @@ class WESTDataManager:
             pcoord = np.empty((n_particles, pcoord_len, pcoord_ndim), pcoord_dtype)
 
             total_parents = 0
-            for (seg_id, segment) in enumerate(segments):
+            for seg_id, segment in enumerate(segments):
                 if segment.seg_id is not None:
                     assert segment.seg_id == seg_id
                 else:
@@ -895,7 +894,7 @@ class WESTDataManager:
                 wtgraph_ds = iter_group.create_dataset('wtgraph', (total_parents,), seg_id_dtype, compression='gzip', shuffle=True)
                 parents = np.empty((total_parents,), seg_id_dtype)
 
-                for (seg_id, segment) in enumerate(segments):
+                for seg_id, segment in enumerate(segments):
                     offset = seg_index_table[seg_id]['wtg_offset']
                     extent = seg_index_table[seg_id]['wtg_n_parents']
                     parent_list = list(segment.wtg_parent_ids)
@@ -986,7 +985,7 @@ class WESTDataManager:
             # read summary data so that we have valud parent and weight transfer information
             si_dsid.read(si_msel, si_fsel, seg_index_entries)
 
-            for (iseg, (segment, ientry)) in enumerate(zip(segments, seg_index_entries)):
+            for iseg, (segment, ientry) in enumerate(zip(segments, seg_index_entries)):
                 ientry['status'] = segment.status
                 ientry['endpoint_type'] = segment.endpoint_type or Segment.SEG_ENDPOINT_UNSET
                 ientry['cputime'] = segment.cputime
@@ -1021,7 +1020,7 @@ class WESTDataManager:
 
             # Then we iterate over data sets and store data
             if dsets:
-                for (dsname, (shape, dtype)) in dsets.items():
+                for dsname, (shape, dtype) in dsets.items():
                     # dset = self._require_aux_dataset(iter_group, dsname, n_total_segments, shape, dtype)
                     try:
                         dsopts = self.dataset_options[dsname]
@@ -1128,7 +1127,8 @@ class WESTDataManager:
                         ds = None
 
                     if ds is not None:
-                        for (seg_id, segment) in enumerate(segments):
+                        for segment in segments:
+                            seg_id = segment.seg_id
                             segment.data[dsname] = ds[seg_id]
 
         return segments
@@ -1286,7 +1286,7 @@ class WESTDataManager:
         if not new_weights:
             return
 
-        system = westpa.rc.get_system_driver()
+        system = self.system
 
         index = np.empty(len(new_weights), dtype=nw_index_dtype)
         prev_init_pcoords = system.new_pcoord_array(len(new_weights))