westpa 2022.5__tar.gz → 2022.7__tar.gz

{westpa-2022.5/src/westpa.egg-info → westpa-2022.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: westpa
-Version: 2022.5
+Version: 2022.7
 Home-page: http://github.com/westpa/westpa
 License: MIT
 Classifier: Development Status :: 5 - Production/Stable
@@ -12,11 +12,33 @@ 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<2,>=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
 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 
@@ -26,7 +48,7 @@ WESTPA 2.0
 
 |docs| |usersgroup| |develgroup| 
 
-.. |ghactions| image:: https://github.com/westpa/westpa/actions/workflows/test.yaml/badge.svg?branch=westpa-2.0-restruct
+.. |ghactions| image:: https://github.com/westpa/westpa/actions/workflows/test.yaml/badge.svg?branch=westpa2
               :target: https://github.com/westpa/westpa/actions/workflows/test.yaml
               :alt: GitHub Actions
 
@@ -120,7 +142,7 @@ To install from source (**not recommended**), start by downloading the correspon
 
 .. _`releases page`: https://github.com/westpa/westpa/releases
 .. _`Anaconda Python distribution`: https://www.anaconda.com/products/individual
-.. _`wiki`: https://github.com/westpa/westpa/wiki/WESTPA-Quick-Install
+.. _`wiki`: https://github.com/westpa/westpa/wiki/Installing-WESTPA
 
 ---------------
 Getting started

{westpa-2022.5 → westpa-2022.7}/README.rst

@@ -6,7 +6,7 @@ WESTPA 2.0
 
 |docs| |usersgroup| |develgroup| 
 
-.. |ghactions| image:: https://github.com/westpa/westpa/actions/workflows/test.yaml/badge.svg?branch=westpa-2.0-restruct
+.. |ghactions| image:: https://github.com/westpa/westpa/actions/workflows/test.yaml/badge.svg?branch=westpa2
               :target: https://github.com/westpa/westpa/actions/workflows/test.yaml
               :alt: GitHub Actions
 
@@ -100,7 +100,7 @@ To install from source (**not recommended**), start by downloading the correspon
 
 .. _`releases page`: https://github.com/westpa/westpa/releases
 .. _`Anaconda Python distribution`: https://www.anaconda.com/products/individual
-.. _`wiki`: https://github.com/westpa/westpa/wiki/WESTPA-Quick-Install
+.. _`wiki`: https://github.com/westpa/westpa/wiki/Installing-WESTPA
 
 ---------------
 Getting started

{westpa-2022.5 → westpa-2022.7}/pyproject.toml

@@ -3,11 +3,13 @@ build-backend = 'setuptools.build_meta:__legacy__'
 # Minimum requirements for the build system to execute.
 # See current numpy pinning in https://github.com/scipy/oldest-supported-numpy
 requires = [
-    "setuptools>=40.8.0",
+    "setuptools >=40.8.0",
     "wheel",
-    "Cython>=0.29.16",  # Note: sync with setup.py
-    "oldest-supported-numpy",
-    "scipy>=0.19.1",
+    "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; python_version <'3.9'",
+    "numpy >=1.25.0, <2; python_version >='3.9'",
+    "scipy >=0.19.1",
     "versioneer-518"
 ]
 # Uncommenting this requires adding the top level of the repo to sys.path in the setup.py

{westpa-2022.5 → westpa-2022.7}/setup.py

@@ -109,7 +109,7 @@ CLASSIFIERS = [
 ]
 
 INSTALL_REQUIRES = [
-    "numpy >= 1.16.0",
+    "numpy >= 1.16.0, <2",
     "scipy >= 0.19.1",
     "h5py >= 2.10",
     "mdtraj >= 1.9.5",
@@ -124,7 +124,7 @@ INSTALL_REQUIRES = [
 ]
 
 EXTRAS_REQUIRE = {
-    "tests": ["pytest", "pytest-cov", "pytest-rerunfailures"],
+    "tests": ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout"],
     "mpi": ["mpi4py"],
 }
 

{westpa-2022.5 → westpa-2022.7}/src/westpa/__init__.py

@@ -12,7 +12,3 @@ rc = _rc.WESTRC()
 __version__ = get_versions()["version"]
 
 del get_versions
-
-from . import _version
-
-__version__ = _version.get_versions()['version']

{westpa-2022.5 → westpa-2022.7}/src/westpa/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2023-07-26T13:13:47-0400",
+ "date": "2024-04-02T11:29:16-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "e022c31147cf74334878926977dfc28a6dbf3bfc",
- "version": "2022.05"
+ "full-revisionid": "d48640fc3fff59f2f8470d6e7170a73f72fff5c6",
+ "version": "2022.07"
 }
 '''  # END VERSION_JSON
 

{westpa-2022.5 → westpa-2022.7}/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-2022.7}/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-2022.7}/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-2022.7}/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-2022.7}/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-2022.7}/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-2022.7}/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-2022.7}/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-2022.7}/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-2022.7}/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-2022.7}/src/westpa/cli/tools/w_multi_west.py

@@ -156,16 +156,9 @@ 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:
-        def __init__(self, weight=0, iteration=0, simid=0, recycled_in=0):
-            self.weight = weight
-            self.iteration = iteration
-            self.simid = simid
-            self.recycled_in = recycled_in
-
     def go(self):
         pi = self.progress.indicator
         self.istates = True  # Assume serendipitously istates is same between runs...
@@ -174,7 +167,11 @@ Command-line options
             self.open_files()
             self.total_number_of_walkers()
             if self.auxall is True:
-                self.aux = list(self.westH5[1]['iterations/iter_00000001/auxdata'].keys())
+                try:
+                    self.aux = list(self.westH5[1]['iterations/iter_00000001/auxdata'].keys())
+                except KeyError:
+                    self.aux = None
+                    log.warning('No auxdata. Proceeding forward without merging auxdata.')
             # Create a giant WEST.h5 file, separating the individual walkers, and renormalizing the weights.
             # It should then be compatible with existing toolsets.
             # Isn't really going to start with auxdata, but we'll add it in.
@@ -240,7 +237,7 @@ Command-line options
                 self.futr_iter[i] = []
                 self.past_rm[i] = []
                 self.futr_rm[i] = []
-            print(pi.new_operation('Recreating...', self.niters))
+            pi.new_operation('Recreating...', self.niters)
             # tracker = SummaryTracker()
             # self.output_file.close()
 
@@ -262,12 +259,20 @@ Command-line options
                         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'][:])
+                        final_istate_pcoord = np.append(final_istate_pcoord, west['ibstates/0/istate_pcoord'][:], axis=0)
 
                 # Saving them into self.output_file
                 self.output_file['ibstates/0'].create_dataset('istate_index', data=final_istate_index, dtype=istate_dtype)
                 self.output_file['ibstates/0'].create_dataset('istate_pcoord', data=final_istate_pcoord)
 
+                # Remaking the ibstates index link
+                master_index_row = self.output_file['ibstates/index'][0]
+                master_index_row['iter_valid'] = 0
+                master_index_row['n_bstates'] = len(self.output_file['ibstates/0/bstate_index'])
+                master_index_row['group_ref'] = self.output_file['ibstates/0'].ref
+
+                self.output_file['ibstates/index'][0] = master_index_row
+
             for iter in range(self.niters):
                 # We have the following datasets in each iteration:
                 # ibstates, which can now be combined with --ibstates

{westpa-2022.5 → westpa-2022.7}/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-2022.7}/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-2022.7}/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