westpa 2022.9__cp311-cp311-macosx_10_9_x86_64.whl → 2022.11__cp311-cp311-macosx_10_9_x86_64.whl

westpa/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-05-22T14:48:11-0400",
+ "date": "2024-07-02T19:19:53-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "ce236bb304b11302a982af2ecb1f8cbb403d09f4",
- "version": "2022.09"
+ "full-revisionid": "a2d390ea5ff8681246351e21a0bdeaeedc00f366",
+ "version": "2022.11"
 }
 '''  # END VERSION_JSON
 

westpa/cli/core/w_truncate.py

@@ -1,5 +1,5 @@
-import argparse
 import logging
+from argparse import ArgumentParser
 
 import westpa
 
@@ -14,7 +14,7 @@ traj_segs directory) is deleted or moved for the corresponding iterations.
 
 
 def entry_point():
-    parser = argparse.ArgumentParser(
+    parser = ArgumentParser(
         'w_truncate',
         description='''\
     Remove all iterations after a certain point in a WESTPA simulation.
@@ -30,7 +30,7 @@ def entry_point():
         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.')
+    parser.add_argument('-n', '--iter', dest='n_iter', type=int, default=0, help='Truncate this iteration and those following.')
 
     args = parser.parse_args()
     westpa.rc.process_args(args, config_required=False)
@@ -40,7 +40,15 @@ def entry_point():
 
     dm.open_backing()
     # max_iter = dm.current_iteration
-    n_iter = args.n_iter if args.n_iter > 0 else dm.current_iteration
+
+    if args.n_iter > dm.current_iteration:
+        parser.error(
+            'Provided iteration {} > current iteration {} of the {} HDF5 file. Exiting without doing anything.'.format(
+                args.n_iter, dm.current_iteration, dm.we_h5filename.split('/')[-1]
+            )
+        )
+    else:
+        n_iter = args.n_iter if args.n_iter > 0 else dm.current_iteration
 
     for i in range(n_iter, dm.current_iteration + 1):
         dm.del_iter_group(i)
@@ -48,8 +56,9 @@ def entry_point():
     dm.del_iter_summary(n_iter)
     dm.current_iteration = n_iter - 1
 
-    print('simulation data truncated after iteration {}'.format(dm.current_iteration))
-    print('\n' + warning_string)
+    westpa.rc.pstatus('simulation data truncated after iteration {}'.format(dm.current_iteration))
+    westpa.rc.pstatus('\n' + warning_string)
+    westpa.rc.pflush()
 
     dm.flush_backing()
     dm.close_backing()

westpa/core/h5io.py

@@ -18,7 +18,6 @@ from tables import NaturalNameWarning
 
 from mdtraj import Trajectory, join as join_traj
 from mdtraj.utils import in_units_of, import_, ensure_type
-from mdtraj.utils.six import string_types
 from mdtraj.formats import HDF5TrajectoryFile
 from mdtraj.formats.hdf5 import _check_mode, Frames
 
@@ -554,7 +553,7 @@ class WESTIterationFile(HDF5TrajectoryFile):
                 node = self._get_node(where='/', name=name)
                 data = get_item(node, slice)
                 in_units = node.attrs.units
-                if not isinstance(in_units, string_types):
+                if not isinstance(in_units, str):
                     in_units = in_units.decode()
                 data = in_units_of(data, in_units, out_units)
                 return data

westpa/core/propagators/executable.py

@@ -278,7 +278,7 @@ class ExecutablePropagator(WESTPropagator):
         self.data_info['log'] = {'name': 'seglog', 'loader': seglog_loader, 'enabled': store_h5, 'filename': None, 'dir': False}
 
         # Grab config from west.executable.datasets, else fallback to west.data.datasets.
-        dataset_configs = config.get(["west", "executable", "datasets"], config.get(['west', 'data', 'datasets'], {}))
+        dataset_configs = config.get(["west", "executable", "datasets"]) or config.get(['west', 'data', 'datasets'], {})
         for dsinfo in dataset_configs:
             try:
                 dsname = dsinfo['name']

westpa/oldtools/aframe/plotting.py

@@ -66,10 +66,10 @@ else:
     cm_pdr = matplotlib.colors.LinearSegmentedColormap('pdr', _pdr_data, 2048)
     cm_pdr_r = cm_pdr.reversed()
 
-    matplotlib.cm.register_cmap('pdr', cm_pdr)
-    matplotlib.cm.register_cmap('pdr_r', cm_pdr_r)
-    matplotlib.cm.register_cmap('hovmol', cm_hovmol)
-    matplotlib.cm.register_cmap('hovmol_r', cm_hovmol_r)
+    matplotlib.colormaps.register(cmap=cm_pdr, name='pdr')
+    matplotlib.colormaps.register(cmap=cm_pdr_r, name='pdr_r')
+    matplotlib.colormaps.register(cmap=cm_hovmol, name='hovmol')
+    matplotlib.colormaps.register(cmap=cm_hovmol_r, name='hovmol_r')
 
     del cmap_data
 

{westpa-2022.9.dist-info → westpa-2022.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: westpa
-Version: 2022.9
+Version: 2022.11
 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

{westpa-2022.9.dist-info → westpa-2022.11.dist-info}/RECORD

@@ -1,6 +1,6 @@
-westpa/_version.py,sha256=LSHAM8jJ_erxibgj4h2_PXTivKwOfg1ZL92b--rsRXo,499
+westpa/_version.py,sha256=tWQgWvkf-J3h5mOX5Li8wSan3MM-AjT2sxSxH6w8Obk,499
 westpa/__init__.py,sha256=xyNfYIcP2ncBLu_foO1NKmJrQh8-uYdwvMuM0HsOG1M,329
-westpa/fasthist/_fasthist.cpython-311-darwin.so,sha256=G0wZno2Zw7MbxSQDZPBuAXRTWns9I8jUblfVWvFrIdo,246408
+westpa/fasthist/_fasthist.cpython-311-darwin.so,sha256=UjOx2l2AfI8sdTCSa1NEZDYfLp52HXdTzGK4xtjI9kI,246408
 westpa/fasthist/__init__.py,sha256=oWj0gKEkKfHjGHwkzmpgAxDz55h2ze_sqQVzWSsOP6s,1071
 westpa/fasthist/__main__.py,sha256=7XCBZvrKbBG3KEuQMpZD0jXa3vVMEVfZJTG8MmdbsrM,3902
 westpa/westext/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -40,7 +40,7 @@ westpa/core/textio.py,sha256=lqohyyyfMTkFvTdQ8V45yUpASiJsWTh42XAG15K63dA,2434
 westpa/core/extloader.py,sha256=yxyJN-lHo3Zjd6jS6_uhC1fIl52H-h8sbV9zYJfEWGg,2239
 westpa/core/sim_manager.py,sha256=eeCg5dALUyZ_Rm1eRRBSOpR_0UDBnyQlBvPkWY4IlzE,38653
 westpa/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-westpa/core/h5io.py,sha256=8oFrvNMFejgFGzxbcaHmdRqEd-PWjnOgyGjdI1Tdnb8,37128
+westpa/core/h5io.py,sha256=s3_Rt8ZjvCpumyDMKctQl406dmo8muRiHHd0L34Qtyk,37077
 westpa/core/trajectory.py,sha256=DL7rsowKxBc1jwT7FPZFlfCWKuwagttZxd3SPgxZKU0,10913
 westpa/core/segment.py,sha256=Gd_5htIZ6xKxxCms9XMtJncehGvMVxZeNdy4drxrnpc,4421
 westpa/core/progress.py,sha256=tEDDn-JPY6ZNzYqyrdgA7peo7pDu8kOMvqfyiHWUgps,6753
@@ -50,11 +50,11 @@ 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=bR5LamkSsDzWpBjVECzrPlc1ZBHrV_ML-VvnyX4FT6Q,387512
+westpa/core/kinetics/_kinetics.cpython-311-darwin.so,sha256=OzRNG2sC5j0PqlQdwYwCNcccg3-KW3cHauwIjwFYoKA,387512
 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=Yv7lYh6by5Fl0snIhrYtNirzP_OFeNzcfCvsjaFgY4c,264480
+westpa/core/binning/_assign.cpython-311-darwin.so,sha256=A-lyxVdQQ4JQA6cB8Qz3fqFlp3vlOXAwz_21BCehQqw,264480
 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=-bb9CdSXrx6XV8NWHa6Q1CTWVaGa4coAZn_lDlvHCkM,9815
@@ -64,16 +64,16 @@ westpa/core/binning/mab.py,sha256=X7L1jx--nNJTNA-PeJGDpwSa2PDMoMb4OtLpjffXQ4A,16
 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=Rc3ETz8Ja06s1O-4qVQ9nCairrv94xpyBYiPNYGuaaI,303264
+westpa/core/reweight/_reweight.cpython-311-darwin.so,sha256=7O7qCRpA-O2vXAaHOeAG0-hi7YR2ZaM2fJghw2GXO0o,303264
 westpa/core/propagators/__init__.py,sha256=rx_kkeg3Tbb_rI0uhLGCD3OwSYj9QuhxF8QGN3mILrg,2373
-westpa/core/propagators/executable.py,sha256=6YuNMZ7if4jGtZ2OV0k_7jmBvtHFfdaIX-LLQJ_KIc8,32201
+westpa/core/propagators/executable.py,sha256=yYextknWycTtyUTFMNyIt6EeLblMdWOJM7YJ4FsZ93E,32203
 westpa/analysis/__init__.py,sha256=CcmVPCB9OSEib0mJ4U-s9v3nrj4h-T_9AGApAbPnn8I,268
 westpa/analysis/core.py,sha256=rZ7xcrskpPwy2lrB27gXT4mSQRbqnPj9D8yA-Utve-M,22426
 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=i0EPM8vloPwBFYJxnREC2xVGo_O7Mo_HBDgWRorrqYc,246144
+westpa/mclib/_mclib.cpython-311-darwin.so,sha256=KmlWfftO7z1aSBwi3rPMyw7lS2DyvZoi6ADW8Q8kATU,246144
 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
@@ -102,12 +102,12 @@ westpa/cli/core/w_fork.py,sha256=UZVY6nUdMRRbKPfNFGAfEAu7tVhu7NewopPdQ0s8cz8,569
 westpa/cli/core/w_states.py,sha256=Fkr0WdUut59vPtj0_TZWAmY5_qf5H_WsoiusO7Slz50,9433
 westpa/cli/core/w_run.py,sha256=9fLOJjCYQadB28gdsKwGxwjJtSB5u0DRITzAWmL3rJg,2159
 westpa/cli/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-westpa/cli/core/w_truncate.py,sha256=-CHFOBr4NAZwGQ8-O5F7B0dPowpnFpm-mF9Us1gBgfo,1654
+westpa/cli/core/w_truncate.py,sha256=QdIwMespZD69t3tDkqC1bZRo4CICs18ShlVXYSeFPd8,2030
 westpa/cli/core/w_init.py,sha256=V_CvlAuq8flg-zUO01sbMGYkLqrEDD4DU9sV90bYFus,8793
 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=L3zfWXIZDjNu2bkKR2m8JeFkHzA1lxDAyOwxlnGP0H4,131000
+westpa/trajtree/_trajtree.cpython-311-darwin.so,sha256=RuP1OjinWsi43HK_pVCr7EaEapEvSy651s5cP7Ui9jY,131000
 westpa/oldtools/files.py,sha256=JmLtZqxD88cybEHcOU6kodAeOJYxylpYFl4OQqU13Hs,944
 westpa/oldtools/miscfn.py,sha256=595W28JazmiU9ioDgOKU9ZxtXJue_q-8WcpOKTgkikQ,909
 westpa/oldtools/__init__.py,sha256=rxAxsQNQMADy5j8xrqW_7Vk3D9ajM7lfDjHaKQHRDTI,62
@@ -115,7 +115,7 @@ westpa/oldtools/cmds/w_ttimes.py,sha256=Ny_l_N7k__4eE71h9ugpk_jr6VZbDH3p4lylFzzl
 westpa/oldtools/cmds/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 westpa/oldtools/aframe/binning.py,sha256=L259HcIn-1Qz1AKUWBXjZ3HFE0odry7OZf-aG070fSE,7565
 westpa/oldtools/aframe/atool.py,sha256=5_ZkivLChU1wMaEvI-F7i-huMRYg2Dy8AH36eivWI0Y,2185
-westpa/oldtools/aframe/plotting.py,sha256=nyAPzSGQPfjcA7d-nDAsi2ewr3aFenJDHeVkSElDixo,2421
+westpa/oldtools/aframe/plotting.py,sha256=2XZwZRzH_Fr-9xctoGy0txU7LUwF_BnCUF4MUsIh4UQ,2469
 westpa/oldtools/aframe/trajwalker.py,sha256=mXkLMg3aIBo76fogCXZs3xNwpTc9Y6qfHNIEhYRIERg,5540
 westpa/oldtools/aframe/__init__.py,sha256=1MMuHYaL790Y1bh7NU3gweTYRIr2xgR1U9bmNrJVrSM,1047
 westpa/oldtools/aframe/data_reader.py,sha256=nuIkR-vFRW_stcXwcjMSZI1RO73By-x-phfTrlD73Jc,20927
@@ -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-2022.9.dist-info/RECORD,,
-westpa-2022.9.dist-info/LICENSE,sha256=I2wUldIRJmflTYUxmSiITSZEKvlovlMPrE3JU5IslkY,1074
-westpa-2022.9.dist-info/AUTHORS,sha256=YMi91-Fs-vFgZKUaItfh20uXthT9oe2Kq6CQXmqMGqg,671
-westpa-2022.9.dist-info/WHEEL,sha256=3Ij8bI-sb8yCMxXItr4MLlNoRGZb2WoUxQe9xIFR_DQ,111
-westpa-2022.9.dist-info/entry_points.txt,sha256=0Ym8meKTdYbUEMtUHF_4zaZP__4ldfFnoYXyYlKRB6s,1428
-westpa-2022.9.dist-info/top_level.txt,sha256=otaLnQtwo9jKCJmja4iOOsOVDThUvPfjJaeLrgGEhlE,7
-westpa-2022.9.dist-info/METADATA,sha256=rqV52tmwSCbCr7PszXjXvfBm-by3neUyWB1QCZViw-4,7562
+westpa-2022.11.dist-info/RECORD,,
+westpa-2022.11.dist-info/LICENSE,sha256=I2wUldIRJmflTYUxmSiITSZEKvlovlMPrE3JU5IslkY,1074
+westpa-2022.11.dist-info/AUTHORS,sha256=YMi91-Fs-vFgZKUaItfh20uXthT9oe2Kq6CQXmqMGqg,671
+westpa-2022.11.dist-info/WHEEL,sha256=tiABefSBUedU9YCr1NdKrBy4Ki45oQg3rWot6FlXaMY,110
+westpa-2022.11.dist-info/entry_points.txt,sha256=0Ym8meKTdYbUEMtUHF_4zaZP__4ldfFnoYXyYlKRB6s,1428
+westpa-2022.11.dist-info/top_level.txt,sha256=otaLnQtwo9jKCJmja4iOOsOVDThUvPfjJaeLrgGEhlE,7
+westpa-2022.11.dist-info/METADATA,sha256=ZNUuNk0-tU-eHAT3nKAXC1KnqXbsj-P-vuEiaFXy2ZA,7563

{westpa-2022.9.dist-info → westpa-2022.11.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (70.2.0)
 Root-Is-Purelib: false
 Tag: cp311-cp311-macosx_10_9_x86_64