westpa 2022.7__cp311-cp311-macosx_10_9_x86_64.whl → 2022.8__cp311-cp311-macosx_10_9_x86_64.whl

westpa/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-04-02T11:29:16-0400",
+ "date": "2024-04-15T22:37:00-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "d48640fc3fff59f2f8470d6e7170a73f72fff5c6",
- "version": "2022.07"
+ "full-revisionid": "587296bd42835960dc67dc3e91ead8f4dd2c6d97",
+ "version": "2022.08"
 }
 '''  # END VERSION_JSON
 

westpa/core/propagators/executable.py

@@ -16,7 +16,7 @@ import numpy as np
 import westpa
 from westpa.core.extloader import get_object
 from westpa.core.propagators import WESTPropagator
-from westpa.core.states import BasisState, InitialState
+from westpa.core.states import BasisState, InitialState, return_state_type
 from westpa.core.segment import Segment
 from westpa.core.yamlcfg import check_bool
 
@@ -148,6 +148,7 @@ def seglog_loader(fieldname, log_file, segment, single_point):
 
         segment.data['iterh5/log'] = d.getvalue() + b'\x01'  # add tail protection
     except Exception as e:
+
         log.warning('could not read any data for {}: {}'.format(fieldname, str(e)))
     finally:
         d.close()
@@ -289,7 +290,7 @@ class ExecutablePropagator(WESTPropagator):
                 # can never disable pcoord collection
                 dsinfo['enabled'] = True
 
-            loader_directive = dsinfo.get('loader')
+            loader_directive = dsinfo.get('loader', None)
             if callable(loader_directive):
                 loader = loader_directive
             elif loader_directive in data_loaders.keys():
@@ -299,8 +300,12 @@ class ExecutablePropagator(WESTPropagator):
                     loader = get_object(loader_directive)
             elif dsname not in ['pcoord', 'seglog', 'restart', 'trajectory']:
                 loader = aux_data_loader
+            else:
+                # YOLO. Or maybe it wasn't specified.
+                loader = loader_directive
 
-            dsinfo['loader'] = loader
+            if loader:
+                dsinfo['loader'] = loader
             self.data_info.setdefault(dsname, {}).update(dsinfo)
 
         log.debug('data_info: {!r}'.format(self.data_info))
@@ -564,13 +569,16 @@ class ExecutablePropagator(WESTPropagator):
 
         return addtl_env, return_files, del_return_files
 
-    def retrieve_dataset_return(self, segment, return_files, del_return_files, single_point):
+    def retrieve_dataset_return(self, state, return_files, del_return_files, single_point):
         '''Retrieve returned data from the temporary locations directed by the environment variables.
-        ``segment`` is the ``Segment`` object that the return data is associated with. ``return_files``
-        is a ``dict`` where the keys are the dataset names and the values are the paths to the temporarily
-        files that contain the returned data. ``del_return_files`` is a ``dict`` where the keys are the
-        names of datasets to be deleted (if the corresponding value is set to ``True``) once the data is
-        retrieved.'''
+        ``state`` is a ``Segment``, ``BasisState`` , or ``InitialState``object that the return data is
+        associated with. ``return_files`` is a ``dict`` where the keys are the dataset names and
+        the values are the paths to the temporarily files that contain the returned data.
+        ``del_return_files`` is a ``dict`` where the keys are the names of datasets to be deleted
+        (if the corresponding value is set to ``True``) once the data is retrieved.'''
+
+        state_name, state_id = return_state_type(state)
+
         for dataset in self.data_info:
             if dataset not in return_files:
                 continue
@@ -582,10 +590,11 @@ class ExecutablePropagator(WESTPropagator):
             filename = return_files[dataset]
             loader = self.data_info[dataset]['loader']
             try:
-                loader(dataset, filename, segment, single_point=single_point)
+                loader(dataset, filename, state, single_point=single_point)
             except Exception as e:
-                log.error('could not read {} for segment {} from {!r}: {!r}'.format(dataset, segment.seg_id, filename, e))
-                segment.status = Segment.SEG_STATUS_FAILED
+                log.error('could not read {} for {} {} from {!r}: {!r}'.format(dataset, state_name, state_id, filename, e))
+                if isinstance(state, Segment):
+                    state.status = state.SEG_STATUS_FAILED
                 break
             else:
                 if del_return_files.get(dataset, False):
@@ -596,10 +605,10 @@ class ExecutablePropagator(WESTPropagator):
                             shutil.rmtree(filename)
                     except Exception as e:
                         log.warning(
-                            'could not delete {} file {!r} for segment {}: {!r}'.format(dataset, filename, segment.seg_id, e)
+                            'could not delete {} file {!r} for {} {}: {!r}'.format(dataset, filename, state_name, state_id, e)
                         )
                     else:
-                        log.debug('deleted {} file {!r} for segment {}'.format(dataset, filename, segment.seg_id))
+                        log.debug('deleted {} file {!r} for {} {}'.format(dataset, filename, state_name, state_id))
 
     # Specific functions required by the WEST framework
     def get_pcoord(self, state):

westpa/core/states.py

@@ -344,3 +344,16 @@ def pare_basis_initial_states(basis_states, initial_states, segments=None):
     )
 
     return return_bstates, return_istates
+
+
+def return_state_type(state_obj):
+    '''Convinience function for returning the state ID and type of the state_obj pointer'''
+
+    if isinstance(state_obj, Segment):
+        return type(state_obj).__name__, state_obj.seg_id
+    elif isinstance(state_obj, InitialState):
+        return type(state_obj).__name__, state_obj.state_id
+    elif isinstance(state_obj, BasisState):
+        return type(state_obj).__name__, state_obj.state_id
+    else:
+        return 'Unknown', float('inf')

westpa/core/trajectory.py

@@ -294,6 +294,7 @@ def load_trajectory(folder):
     '''
     traj_file = top_file = None
     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):

westpa/oldtools/aframe/data_reader.py

@@ -61,7 +61,7 @@ class WESTDataReaderMixin(AnalysisMixin):
         westpa.rc.pstatus("Using WEST data from '{}'".format(self.west_h5name))
 
         self.data_manager = westpa.rc.get_data_manager()
-        self.data_manager.backing_file = self.west_h5name
+        self.data_manager.we_h5filename = self.west_h5name
         self.data_manager.open_backing(mode='r')
 
         if upcall:

{westpa-2022.7.dist-info → westpa-2022.8.dist-info}/METADATA

@@ -1,6 +1,7 @@
 Metadata-Version: 2.1
 Name: westpa
-Version: 2022.7
+Version: 2022.8
+Summary: WESTPA is a package for constructing and running stochastic simulations using the "weighted ensemble" approach of Huber and Kim (1996).
 Home-page: http://github.com/westpa/westpa
 License: MIT
 Classifier: Development Status :: 5 - Production/Stable

{westpa-2022.7.dist-info → westpa-2022.8.dist-info}/RECORD

@@ -1,6 +1,6 @@
-westpa/_version.py,sha256=kgY0Vo1HgLoDf0W0yQvrVcgI_xCDyPtdG-tQoSq-lKA,499
+westpa/_version.py,sha256=ynQYEhRU4LpCFtVDYsxdHaJVVMjwxfKjIU7OxbyGJwA,499
 westpa/__init__.py,sha256=xyNfYIcP2ncBLu_foO1NKmJrQh8-uYdwvMuM0HsOG1M,329
-westpa/fasthist/_fasthist.cpython-311-darwin.so,sha256=vMyYxEeYr7Bq4R-b8mM1MKr-KTcuZoi7zeWBD0AG02E,268808
+westpa/fasthist/_fasthist.cpython-311-darwin.so,sha256=4qtQZmsMgBNNwegcsVOy47X8sh6yVk4cFhrZD6-zacc,268808
 westpa/fasthist/__init__.py,sha256=oWj0gKEkKfHjGHwkzmpgAxDz55h2ze_sqQVzWSsOP6s,1071
 westpa/fasthist/__main__.py,sha256=7XCBZvrKbBG3KEuQMpZD0jXa3vVMEVfZJTG8MmdbsrM,3902
 westpa/westext/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -41,20 +41,20 @@ westpa/core/extloader.py,sha256=yxyJN-lHo3Zjd6jS6_uhC1fIl52H-h8sbV9zYJfEWGg,2239
 westpa/core/sim_manager.py,sha256=-dbsf74Q6eSA9SZKUtcPYAekl6OSYKMTpB45VhVMcE0,37906
 westpa/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 westpa/core/h5io.py,sha256=x-n0jgekFhIi1tD7Ob7u_WUmATsulnMXsOvHkdUTHVg,37011
-westpa/core/trajectory.py,sha256=pGvaXNTLIpf9RZSabnvF8Bljppgx1mio01PF7yyEjE4,10912
+westpa/core/trajectory.py,sha256=DL7rsowKxBc1jwT7FPZFlfCWKuwagttZxd3SPgxZKU0,10913
 westpa/core/segment.py,sha256=Gd_5htIZ6xKxxCms9XMtJncehGvMVxZeNdy4drxrnpc,4421
 westpa/core/progress.py,sha256=tEDDn-JPY6ZNzYqyrdgA7peo7pDu8kOMvqfyiHWUgps,6753
 westpa/core/data_manager.py,sha256=xeqt1MtjMGSRs7QN2zxRi0KrQ1cIV4L7JlOnBx-DEYE,71783
-westpa/core/states.py,sha256=x35kads1nbE1jwWn7EH5oJElDnlERGvAzH-I2fGM7yU,12833
+westpa/core/states.py,sha256=umsdgSrYjt2vjw-1kQeiILWmureOBmBaOgg0nQxUVmA,13318
 westpa/core/yamlcfg.py,sha256=B78OEr1n_sIkW6kDzl3FO63tiugaT-1VutAgLxU0i7A,12696
 westpa/core/kinetics/matrates.py,sha256=1sf7L6ojLE8yT2sFfgeB8eqgjMHdMK2O_Xgyz_RjCzc,5554
 westpa/core/kinetics/events.py,sha256=VqYBN5rVOf3hAYUA6xQ6UN7GP6tVgRFIoP69tfGhkTo,6511
 westpa/core/kinetics/__init__.py,sha256=djtiki7X5-IEzwjwswbdgrolwUIzVAHKxCiI5B3WH28,510
-westpa/core/kinetics/_kinetics.cpython-311-darwin.so,sha256=Qd2mVGeWS--Pc88M-9wGpODvrUOvLgfMyu1L5362zTo,431408
+westpa/core/kinetics/_kinetics.cpython-311-darwin.so,sha256=yYTqnN_kD4rQh9q2ltR5f37oHIvIC-VSzBES2SwEXH4,431408
 westpa/core/kinetics/rate_averaging.py,sha256=gIKDXBAOSDI6KythepoC4QipUPksTRBc9zbM7DRtwo4,10300
 westpa/core/binning/binless_driver.py,sha256=T5qWpLnjxCS9RdKeWf7eVCC_s6TQFDENL7X3VG6JIYo,2231
 westpa/core/binning/mab_driver.py,sha256=azSqc9pqHk_zc1ptGNjXARDbK-UAnPVmCiYwebi5mPY,2223
-westpa/core/binning/_assign.cpython-311-darwin.so,sha256=Lu4AG9Ro4BFz2UM7C2t4VmlKAOM0QdBjvVR7dOJJf7s,293056
+westpa/core/binning/_assign.cpython-311-darwin.so,sha256=FrtUK91d13RiOuUgwe-j83XO2WZA805wosT_29sUqME,293056
 westpa/core/binning/binless.py,sha256=Fb9TI5swQntzXjmlWFbYQ9yjzjLxDKNVVdmRxRqOnIY,4056
 westpa/core/binning/__init__.py,sha256=XmjBP6fg_id_vDELkcWW3u2GeuL5OPWblvX-kc7mINk,1297
 westpa/core/binning/mab_manager.py,sha256=PUSA9J-dzmQdWQ9h5DEB9Eed6GVETf1EE43r6AvZLwI,9617
@@ -64,16 +64,16 @@ westpa/core/binning/mab.py,sha256=YgNWCistmKPFbQp9TpFgnpgGWc-HZTvSwB6ZugPS0Oo,11
 westpa/core/binning/bins.py,sha256=WDj7DNX3MTVkRvkgAooa9G8VThxw32uIfMTuk9sS194,1460
 westpa/core/reweight/matrix.py,sha256=219sRxkML1V9niPIndSoRvJAC0fUmpG0PLDKpmfWW-g,5509
 westpa/core/reweight/__init__.py,sha256=8goYojsHMcJCZblBC2sc2fcj-NUNVEstbSLswKNlVfg,284
-westpa/core/reweight/_reweight.cpython-311-darwin.so,sha256=qQMJ6kAmBAv81oPGj145ktn1zz51CGUptP8RNuOWMcI,350032
+westpa/core/reweight/_reweight.cpython-311-darwin.so,sha256=xisaXsja3l_6VwN78wchnrxSoAUxkOLxF1NKj3PReyI,350032
 westpa/core/propagators/__init__.py,sha256=rx_kkeg3Tbb_rI0uhLGCD3OwSYj9QuhxF8QGN3mILrg,2373
-westpa/core/propagators/executable.py,sha256=gm1TD3z9mA6o41j1kCRWwhv9mO1gX1pqJVoxBkG0kkM,31767
+westpa/core/propagators/executable.py,sha256=B9jU6RKkApr5cqH56n49IQ1i_cUcJUMfx6fmBZoWgPk,32071
 westpa/analysis/__init__.py,sha256=CcmVPCB9OSEib0mJ4U-s9v3nrj4h-T_9AGApAbPnn8I,268
 westpa/analysis/core.py,sha256=P_m5-sU1RURAtWQVlV_Y2pgPvwUjyCqFS-E4O3fsD4E,22399
 westpa/analysis/statistics.py,sha256=M3Gj1bOiAu_SA4upR7gENYEOP2gnIEaSOZeGyoIxAc8,789
 westpa/analysis/trajectories.py,sha256=jyrbbKOVyZ3GjHQushDS_G8C4IRXlUmxa-WzmEEVGwc,12878
 westpa/mclib/__init__.py,sha256=NskP81wKw-tHTniyJ8QbgKAHah5JdpCrnPKJo1T-nLw,11513
 westpa/mclib/__main__.py,sha256=cKqfE9koMcrHkslEPpFISA4Eblwl0mllaxn7pFeyX1A,881
-westpa/mclib/_mclib.cpython-311-darwin.so,sha256=fySkbzcjN8vbee_0jwI_BlmFZdQKoyIr4KzIX0If2Bw,272456
+westpa/mclib/_mclib.cpython-311-darwin.so,sha256=3rmp7AmrHQkUA_Yv21z8_1RKoCoP0sFdAapr5Hvhpt8,272456
 westpa/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 westpa/cli/tools/w_direct.py,sha256=5Z9eQpvpKM-40XdiI0L3t0O3jpjMx7tk8ndYAaJxvrc,22361
 westpa/cli/tools/w_dumpsegs.py,sha256=uv0WxvKGauyW6VT3zGyALUXVqSXwDrhwbF3ZVSJV9Mo,3952
@@ -107,7 +107,7 @@ westpa/cli/core/w_init.py,sha256=V_CvlAuq8flg-zUO01sbMGYkLqrEDD4DU9sV90bYFus,879
 westpa/cli/core/w_succ.py,sha256=ZK1MHHu7t53VdBrRgJUe7b1R8DnhMKPjHOqbbOjC_As,3074
 westpa/trajtree/__init__.py,sha256=K64Ok5bUP-fXo1H2rigJqxCnm-U23tJlRngNOnzR3gs,96
 westpa/trajtree/trajtree.py,sha256=sLf4kTi0QyvFdbSR__YcPwOR2wcOxtlkC4IPUFcq-9M,4497
-westpa/trajtree/_trajtree.cpython-311-darwin.so,sha256=mcF5FJelb4Ayz1aHFAh1MiU0HHJ8fGBPvU4jjSPT4lg,154960
+westpa/trajtree/_trajtree.cpython-311-darwin.so,sha256=eGHeJoq0xw7StCmzP25YHoYpT8_rXrNhjbD9lPXG1w8,154960
 westpa/oldtools/files.py,sha256=JmLtZqxD88cybEHcOU6kodAeOJYxylpYFl4OQqU13Hs,944
 westpa/oldtools/miscfn.py,sha256=595W28JazmiU9ioDgOKU9ZxtXJue_q-8WcpOKTgkikQ,909
 westpa/oldtools/__init__.py,sha256=rxAxsQNQMADy5j8xrqW_7Vk3D9ajM7lfDjHaKQHRDTI,62
@@ -118,7 +118,7 @@ westpa/oldtools/aframe/atool.py,sha256=5_ZkivLChU1wMaEvI-F7i-huMRYg2Dy8AH36eivWI
 westpa/oldtools/aframe/plotting.py,sha256=nyAPzSGQPfjcA7d-nDAsi2ewr3aFenJDHeVkSElDixo,2421
 westpa/oldtools/aframe/trajwalker.py,sha256=mXkLMg3aIBo76fogCXZs3xNwpTc9Y6qfHNIEhYRIERg,5540
 westpa/oldtools/aframe/__init__.py,sha256=1MMuHYaL790Y1bh7NU3gweTYRIr2xgR1U9bmNrJVrSM,1047
-westpa/oldtools/aframe/data_reader.py,sha256=-Nk4Mo9evt_-YwZHZiIkqlhVT3IlQ2WTPGYrHf8zj8Q,20926
+westpa/oldtools/aframe/data_reader.py,sha256=nuIkR-vFRW_stcXwcjMSZI1RO73By-x-phfTrlD73Jc,20927
 westpa/oldtools/aframe/transitions.py,sha256=3cQan9ju2s5hW9KvYs38kuKvSh5RjAsvHlvaY2eOZ_M,18542
 westpa/oldtools/aframe/base_mixin.py,sha256=OAK5NfVfwdPxvFzhxxT_oEnFKR_5s0NRoqTVA6G1gXY,654
 westpa/oldtools/aframe/iter_range.py,sha256=HFODveMwtKAbHXpbt8bII7edVy8RqwC-QPlLXLX66dU,8465
@@ -141,10 +141,10 @@ westpa/work_managers/zeromq/__init__.py,sha256=rrl4YbEaZr2AiEBTMlhvEFH83dBlAwWR_
 westpa/work_managers/zeromq/core.py,sha256=K3Iyrz5u2Dy-GgZFL3ZXDN2iaaLm7qL-A3cm4PdBiF8,22907
 westpa/work_managers/zeromq/work_manager.py,sha256=UB_WvnejDRVi1ZU2QWpP9uzhnccOH7b3qHgU-wSstTY,22425
 westpa/work_managers/zeromq/node.py,sha256=CeoJhXVqrZxrV3lMnDtm3LNkGFxjS4dr3E6wd7ZQRTE,4877
-westpa-2022.7.dist-info/RECORD,,
-westpa-2022.7.dist-info/LICENSE,sha256=I2wUldIRJmflTYUxmSiITSZEKvlovlMPrE3JU5IslkY,1074
-westpa-2022.7.dist-info/AUTHORS,sha256=YMi91-Fs-vFgZKUaItfh20uXthT9oe2Kq6CQXmqMGqg,671
-westpa-2022.7.dist-info/WHEEL,sha256=3Ij8bI-sb8yCMxXItr4MLlNoRGZb2WoUxQe9xIFR_DQ,111
-westpa-2022.7.dist-info/entry_points.txt,sha256=0Ym8meKTdYbUEMtUHF_4zaZP__4ldfFnoYXyYlKRB6s,1428
-westpa-2022.7.dist-info/top_level.txt,sha256=otaLnQtwo9jKCJmja4iOOsOVDThUvPfjJaeLrgGEhlE,7
-westpa-2022.7.dist-info/METADATA,sha256=RgNgH_WTNDP0G-ZCbQQkjjASW2pOXIiGNdxGZ0vavcI,7432
+westpa-2022.8.dist-info/RECORD,,
+westpa-2022.8.dist-info/LICENSE,sha256=I2wUldIRJmflTYUxmSiITSZEKvlovlMPrE3JU5IslkY,1074
+westpa-2022.8.dist-info/AUTHORS,sha256=YMi91-Fs-vFgZKUaItfh20uXthT9oe2Kq6CQXmqMGqg,671
+westpa-2022.8.dist-info/WHEEL,sha256=3Ij8bI-sb8yCMxXItr4MLlNoRGZb2WoUxQe9xIFR_DQ,111
+westpa-2022.8.dist-info/entry_points.txt,sha256=0Ym8meKTdYbUEMtUHF_4zaZP__4ldfFnoYXyYlKRB6s,1428
+westpa-2022.8.dist-info/top_level.txt,sha256=otaLnQtwo9jKCJmja4iOOsOVDThUvPfjJaeLrgGEhlE,7
+westpa-2022.8.dist-info/METADATA,sha256=mr5Ug2g18LvcWV8tCqcsU9e4990CspZUnMexqT9O5bE,7577