westpa 2022.5__tar.gz → 2022.6__tar.gz

{westpa-2022.5/src/westpa.egg-info → westpa-2022.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: westpa
-Version: 2022.5
+Version: 2022.6
 Home-page: http://github.com/westpa/westpa
 License: MIT
 Classifier: Development Status :: 5 - Production/Stable
@@ -12,11 +12,34 @@ Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Cython
 Requires-Python: >=3.6
+License-File: LICENSE
+License-File: AUTHORS
+Requires-Dist: numpy>=1.16.0
+Requires-Dist: scipy>=0.19.1
+Requires-Dist: h5py>=2.10
+Requires-Dist: mdtraj>=1.9.5
+Requires-Dist: pyyaml
+Requires-Dist: pyzmq
+Requires-Dist: matplotlib
+Requires-Dist: blessings
+Requires-Dist: ipykernel
+Requires-Dist: tqdm
+Requires-Dist: pandas
+Requires-Dist: tables<3.9; python_version < "3.9"
+Requires-Dist: tables; python_version >= "3.9"
 Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Requires-Dist: pytest-rerunfailures; extra == "tests"
+Requires-Dist: pytest-timeout; extra == "tests"
 Provides-Extra: mpi
+Requires-Dist: mpi4py; extra == "mpi"
 Provides-Extra: dev
-License-File: LICENSE
-License-File: AUTHORS
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest-rerunfailures; extra == "dev"
+Requires-Dist: pytest-timeout; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
 
 ===============
 WESTPA 2.0 

{westpa-2022.5 → westpa-2022.6}/pyproject.toml

@@ -5,7 +5,8 @@ build-backend = 'setuptools.build_meta:__legacy__'
 requires = [
     "setuptools>=40.8.0",
     "wheel",
-    "Cython>=0.29.16",  # Note: sync with setup.py
+    "Cython>=0.29.16; python_version >='3.10'",  # Note: sync with setup.py
+    "Cython<3.0.3, >=0.29.16; python_version < '3.10'",
     "oldest-supported-numpy",
     "scipy>=0.19.1",
     "versioneer-518"

{westpa-2022.5 → westpa-2022.6}/setup.py

@@ -120,11 +120,12 @@ INSTALL_REQUIRES = [
     "ipykernel",
     "tqdm",
     "pandas",
-    "tables",
+    "tables < 3.9; python_version < '3.9'",
+    "tables; python_version >= '3.9'",
 ]
 
 EXTRAS_REQUIRE = {
-    "tests": ["pytest", "pytest-cov", "pytest-rerunfailures"],
+    "tests": ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout"],
     "mpi": ["mpi4py"],
 }
 

{westpa-2022.5 → westpa-2022.6}/src/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-2022.5 → westpa-2022.6}/src/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-2022.5 → westpa-2022.6}/src/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-2022.5 → westpa-2022.6}/src/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-2022.5 → westpa-2022.6}/src/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-2022.5 → westpa-2022.6}/src/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-2022.5 → westpa-2022.6}/src/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-2022.5 → westpa-2022.6}/src/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-2022.5 → westpa-2022.6}/src/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-2022.5 → westpa-2022.6}/src/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-2022.5 → westpa-2022.6}/src/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-2022.5 → westpa-2022.6}/src/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-2022.5 → westpa-2022.6}/src/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-2022.5 → westpa-2022.6}/src/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-2022.5 → westpa-2022.6}/src/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