westpa 2022.5__cp310-cp310-macosx_10_9_x86_64.whl → 2022.6__cp310-cp310-macosx_10_9_x86_64.whl

westpa/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2023-07-26T13:13:47-0400",
+ "date": "2023-10-20T12:52:31-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "e022c31147cf74334878926977dfc28a6dbf3bfc",
- "version": "2022.05"
+ "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/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

@@ -156,7 +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:

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

@@ -644,7 +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__)
 
@@ -19,6 +21,7 @@ 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):
@@ -212,7 +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
@@ -244,6 +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
 
 
@@ -252,7 +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")
@@ -262,15 +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
@@ -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]

westpa/core/h5io.py

@@ -101,7 +101,6 @@ def tostr(b):
 
 
 def is_within_directory(directory, target):
-
     abs_directory = os.path.abspath(directory)
     abs_target = os.path.abspath(target)
 
@@ -111,7 +110,6 @@ def is_within_directory(directory, target):
 
 
 def safe_extract(tar, path=".", members=None, *, numeric_owner=False):
-
     for member in tar.getmembers():
         member_path = os.path.join(path, member.name)
         if not is_within_directory(path, member_path):
@@ -220,7 +218,7 @@ def load_west(filename):
 
             raw_pcoord = iter_group['pcoord'][:]
             if raw_pcoord.ndim != 3:
-                log.warn('pcoord is expected to be a 3-d ndarray instead of {}-d'.format(raw_pcoord.ndim))
+                log.warning('pcoord is expected to be a 3-d ndarray instead of {}-d'.format(raw_pcoord.ndim))
                 continue
             # ignore the first frame of each segment
             if raw_pcoord.shape[1] == traj.n_frames + 1:
@@ -374,7 +372,6 @@ class WESTPAH5File(h5py.File):
     _this_fileformat_version = 8
 
     def __init__(self, *args, **kwargs):
-
         # These values are used for creating files or reading files where this
         # data is not stored. Otherwise, values stored as attributes on the root
         # group are used instead.
@@ -919,7 +916,6 @@ class MultiDSSpec(DSSpec):
 class IterBlockedDataset:
     @classmethod
     def empty_like(cls, blocked_dataset):
-
         source = blocked_dataset.data if blocked_dataset.data is not None else blocked_dataset.dataset
 
         newbds = cls(

westpa/core/propagators/__init__.py

@@ -10,7 +10,6 @@ def blocked_iter(blocksize, iterable, fillvalue=None):
 
 class WESTPropagator:
     def __init__(self, rc=None):
-
         # For maximum flexibility, the basis states and initial states valid
         # at the point in the simulation when the propgator is used must be
         # available in several routines, and it is inconvenient to pass them

westpa/core/propagators/executable.py

@@ -372,7 +372,7 @@ class ExecutablePropagator(WESTPropagator):
         return (rc, rusage)
 
     def exec_child_from_child_info(self, child_info, template_args, environ):
-        for (key, value) in child_info.get('environ', {}).items():
+        for key, value in child_info.get('environ', {}).items():
             environ[key] = self.makepath(value)
         return self.exec_child(
             executable=self.makepath(child_info['executable'], template_args),
@@ -443,7 +443,6 @@ class ExecutablePropagator(WESTPropagator):
             initial_state = self.initial_states[segment.initial_state_id]
 
             if initial_state.istate_type == InitialState.ISTATE_TYPE_START:
-
                 basis_state = BasisState(
                     label=f"sstate_{initial_state.state_id}", pcoord=initial_state.pcoord, probability=0.0, auxref=""
                 )
@@ -465,7 +464,6 @@ class ExecutablePropagator(WESTPropagator):
                 environ[self.ENV_PARENT_DATA_REF] = environ[self.ENV_BSTATE_DATA_REF]
 
             elif initial_state.istate_type == InitialState.ISTATE_TYPE_START:
-
                 # This points to the start-state PDB
                 environ[self.ENV_PARENT_DATA_REF] = environ[self.ENV_BSTATE_DATA_REF] + '/' + initial_state.basis_auxref
             else:  # initial_state.type == InitialState.ISTATE_TYPE_GENERATED

westpa/core/sim_manager.py

@@ -37,7 +37,7 @@ class PropagationError(RuntimeError):
 class WESimManager:
     def process_config(self):
         config = self.rc.config
-        for (entry, type_) in [('gen_istates', bool), ('block_size', int), ('save_transition_matrices', bool)]:
+        for entry, type_ in [('gen_istates', bool), ('block_size', int), ('save_transition_matrices', bool)]:
             config.require_type_if_present(['west', 'propagation', entry], type_)
 
         self.do_gen_istates = config.get(['west', 'propagation', 'gen_istates'], False)
@@ -136,7 +136,7 @@ class WESimManager:
     def invoke_callbacks(self, hook, *args, **kwargs):
         callbacks = self._callback_table.get(hook, [])
         sorted_callbacks = sorted(callbacks)
-        for (priority, name, fn) in sorted_callbacks:
+        for priority, name, fn in sorted_callbacks:
             log.debug('invoking callback {!r} for hook {!r}'.format(fn, hook))
             fn(*args, **kwargs)
 
@@ -478,7 +478,7 @@ class 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
@@ -733,7 +733,6 @@ class WESimManager:
 
         iter_elapsed = 0
         while self.n_iter <= max_iter:
-
             if max_walltime and time.time() + 1.1 * iter_elapsed >= run_killtime:
                 self.rc.pstatus('Iteration {:d} would require more than the allotted time. Ending run.'.format(self.n_iter))
                 return

westpa/core/trajectory.py

@@ -293,12 +293,20 @@ def load_trajectory(folder):
     trajectory file contains topology data (e.g., HDF5 format).
     '''
     traj_file = top_file = None
-    for filename in os.listdir(folder):
+    file_list = [f_name for f_name in os.listdir(folder) if not f_name.startswith('.')]
+    for filename in file_list:
         filepath = os.path.join(folder, filename)
         if not os.path.isfile(filepath):
             continue
 
         ext = get_extension(filename).lower()
+        # Catching trajectory formats that can be topology and trajectories at the same time.
+        # Only activates when there is a single file.
+        if len(file_list) < 2 and ext in TOPOLOGY_EXTS and ext in TRAJECTORY_EXTS:
+            top_file = filename
+            traj_file = filename
+
+        # Assuming topology file is copied first.
         if ext in TOPOLOGY_EXTS and top_file is None:
             top_file = filename
         elif ext in TRAJECTORY_EXTS and traj_file is None:

westpa/core/we_driver.py

@@ -189,7 +189,7 @@ class WEDriver:
     def recycling_segments(self):
         '''Segments designated for recycling'''
         if len(self.target_states):
-            for (ibin, tstate) in self.target_states.items():
+            for ibin, tstate in self.target_states.items():
                 for segment in self.final_binning[ibin]:
                     yield segment
         else:
@@ -298,14 +298,14 @@ class WEDriver:
             init_pcoords = np.empty((len(new_weights), self.system.pcoord_ndim), dtype=self.system.pcoord_dtype)
             prev_init_pcoords = np.empty((len(new_weights), self.system.pcoord_ndim), dtype=self.system.pcoord_dtype)
 
-            for (ientry, entry) in enumerate(new_weights):
+            for ientry, entry in enumerate(new_weights):
                 init_pcoords[ientry] = entry.new_init_pcoord
                 prev_init_pcoords[ientry] = entry.prev_init_pcoord
 
             init_assignments = self.bin_mapper.assign(init_pcoords)
             prev_init_assignments = self.bin_mapper.assign(prev_init_pcoords)
 
-            for (entry, i, j) in zip(new_weights, prev_init_assignments, init_assignments):
+            for entry, i, j in zip(new_weights, prev_init_assignments, init_assignments):
                 flux_matrix[i, j] += entry.weight
                 transition_matrix[i, j] += 1
 
@@ -351,7 +351,7 @@ class 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
@@ -391,7 +391,7 @@ class WEDriver:
 
         used_istate_ids = set()
         istateiter = iter(self.avail_initial_states.values())
-        for (ibin, target_state) in self.target_states.items():
+        for ibin, target_state in self.target_states.items():
             target_bin = self.next_iter_binning[ibin]
             for segment in set(target_bin):
                 initial_state = next(istateiter)
@@ -657,7 +657,7 @@ class WEDriver:
         # Then and only then adjust for correct particle count
         total_number_of_subgroups = 0
         total_number_of_particles = 0
-        for (ibin, bin) in enumerate(self.next_iter_binning):
+        for ibin, bin in enumerate(self.next_iter_binning):
             if len(bin) == 0:
                 continue
 
@@ -740,7 +740,7 @@ class WEDriver:
 
         # Create dummy segments
         segments = []
-        for (seg_id, (initial_state, weight)) in enumerate(zip(initial_states, weights)):
+        for seg_id, (initial_state, weight) in enumerate(zip(initial_states, weights)):
             dummy_segment = Segment(
                 n_iter=0,
                 seg_id=seg_id,