westpa 2022.4__tar.gz → 2022.6__tar.gz

{westpa-2022.4/src/westpa.egg-info → westpa-2022.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: westpa
-Version: 2022.4
+Version: 2022.6
 Home-page: http://github.com/westpa/westpa
 License: MIT
 Classifier: Development Status :: 5 - Production/Stable
@@ -12,17 +12,40 @@ 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 
 ===============
 
-|ghactions| |anaconda| |tutorial1| |tutorial2| 
+|ghactions| |anaconda| |tutorial| 
 
 |docs| |usersgroup| |develgroup| 
 
@@ -34,14 +57,10 @@ WESTPA 2.0
          :target: https://westpa.readthedocs.io/en/latest/?badge=latest
          :alt: Documentation Status
 
-.. |tutorial1| image:: https://img.shields.io/badge/WESTPA-tutorials-brightgreen.svg
-        :target: https://github.com/westpa/westpa_tutorials 
+.. |tutorial| image:: https://img.shields.io/badge/WESTPA-tutorials-blueviolet.svg
+        :target: https://github.com/westpa/tutorials
         :alt: WESTPA Tutorials GitHub
 
-.. |tutorial2| image:: https://img.shields.io/badge/WESTPA2-tutorials-blueviolet.svg
-        :target: https://github.com/westpa/westpa2_tutorials
-        :alt: WESTPA 2.0 Tutorials GitHub
-
 .. |usersgroup| image:: https://img.shields.io/badge/Google%20Group-Users-lightgrey.svg
         :target: http://groups.google.com/group/westpa-users 
         :alt: Users Google Group
@@ -80,7 +99,7 @@ WESTPA is free software, licensed under the terms of the MIT License. See the fi
 
 .. _survey: https://docs.google.com/forms/d/e/1FAIpQLSfWaB2aryInU06cXrCyAFmhD_gPibgOfFk-dspLEsXuS9-RGQ/viewform
 .. _page: https://westpa.github.io/westpa/overview.html
-.. _powerpoint: https://pitt.box.com/s/metui7tsfwh3bcv1xgbbj4g6fe0uokag
+.. _powerpoint: https://docs.google.com/presentation/d/1PKsklN5aYLlLSTDOLdNGti6pcGs4Rgxm/edit?usp=sharing&ouid=117278498028744119802&rtpof=true&sd=true
 
 ------------
 Requirements
@@ -88,7 +107,7 @@ Requirements
 
 WESTPA is written in Python and requires version 3.7 or later. WESTPA also requires a number of Python scientific software packages. 
 The simplest way to meet these requirements is to download the
-Anaconda Python distribution from www.continuum.io (free for all users).
+Anaconda Python distribution from www.anaconda.com (free for all users).
 
 WESTPA currently runs on Unix-like operating systems, including Linux and
 Mac OS X. It is developed and tested on x86_64 machines running Linux.
@@ -124,7 +143,7 @@ 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-Installation
+.. _`wiki`: https://github.com/westpa/westpa/wiki/WESTPA-Quick-Install
 
 ---------------
 Getting started
@@ -155,8 +174,8 @@ if a question one has was previously addressed). This is the preferred means
 for obtaining help and support. See http://groups.google.com/group/westpa-users
 to sign up or search archived messages.
 
-.. _FAQ: https://westpa.github.io/westpa/users_guide/faq.html
-
+.. _FAQ: https://github.com/westpa/westpa/wiki/Frequently-Asked-Questions
+ 
 ----------
 Developers
 ----------

{westpa-2022.4 → westpa-2022.6}/README.rst

@@ -2,7 +2,7 @@
 WESTPA 2.0 
 ===============
 
-|ghactions| |anaconda| |tutorial1| |tutorial2| 
+|ghactions| |anaconda| |tutorial| 
 
 |docs| |usersgroup| |develgroup| 
 
@@ -14,14 +14,10 @@ WESTPA 2.0
          :target: https://westpa.readthedocs.io/en/latest/?badge=latest
          :alt: Documentation Status
 
-.. |tutorial1| image:: https://img.shields.io/badge/WESTPA-tutorials-brightgreen.svg
-        :target: https://github.com/westpa/westpa_tutorials 
+.. |tutorial| image:: https://img.shields.io/badge/WESTPA-tutorials-blueviolet.svg
+        :target: https://github.com/westpa/tutorials
         :alt: WESTPA Tutorials GitHub
 
-.. |tutorial2| image:: https://img.shields.io/badge/WESTPA2-tutorials-blueviolet.svg
-        :target: https://github.com/westpa/westpa2_tutorials
-        :alt: WESTPA 2.0 Tutorials GitHub
-
 .. |usersgroup| image:: https://img.shields.io/badge/Google%20Group-Users-lightgrey.svg
         :target: http://groups.google.com/group/westpa-users 
         :alt: Users Google Group
@@ -60,7 +56,7 @@ WESTPA is free software, licensed under the terms of the MIT License. See the fi
 
 .. _survey: https://docs.google.com/forms/d/e/1FAIpQLSfWaB2aryInU06cXrCyAFmhD_gPibgOfFk-dspLEsXuS9-RGQ/viewform
 .. _page: https://westpa.github.io/westpa/overview.html
-.. _powerpoint: https://pitt.box.com/s/metui7tsfwh3bcv1xgbbj4g6fe0uokag
+.. _powerpoint: https://docs.google.com/presentation/d/1PKsklN5aYLlLSTDOLdNGti6pcGs4Rgxm/edit?usp=sharing&ouid=117278498028744119802&rtpof=true&sd=true
 
 ------------
 Requirements
@@ -68,7 +64,7 @@ Requirements
 
 WESTPA is written in Python and requires version 3.7 or later. WESTPA also requires a number of Python scientific software packages. 
 The simplest way to meet these requirements is to download the
-Anaconda Python distribution from www.continuum.io (free for all users).
+Anaconda Python distribution from www.anaconda.com (free for all users).
 
 WESTPA currently runs on Unix-like operating systems, including Linux and
 Mac OS X. It is developed and tested on x86_64 machines running Linux.
@@ -104,7 +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-Installation
+.. _`wiki`: https://github.com/westpa/westpa/wiki/WESTPA-Quick-Install
 
 ---------------
 Getting started
@@ -135,8 +131,8 @@ if a question one has was previously addressed). This is the preferred means
 for obtaining help and support. See http://groups.google.com/group/westpa-users
 to sign up or search archived messages.
 
-.. _FAQ: https://westpa.github.io/westpa/users_guide/faq.html
-
+.. _FAQ: https://github.com/westpa/westpa/wiki/Frequently-Asked-Questions
+ 
 ----------
 Developers
 ----------

{westpa-2022.4 → 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-2022.4 → 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", "nose"],
+    "tests": ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout"],
     "mpi": ["mpi4py"],
 }
 

{westpa-2022.4 → westpa-2022.6}/src/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-2022.4 → 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-2022.4 → 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-2022.4 → 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-2022.4 → 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-2022.4 → 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-2022.4 → westpa-2022.6}/src/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-2022.4 → 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-2022.4 → 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-2022.4 → 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-2022.4 → 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-2022.4 → 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-2022.4 → westpa-2022.6}/src/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-2022.4 → 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-2022.4 → 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-2022.4 → westpa-2022.6}/src/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