westpa 2022.6__cp39-cp39-macosx_10_9_x86_64.whl → 2022.7__cp39-cp39-macosx_10_9_x86_64.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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- westpa/__init__.py +0 -4
- westpa/_version.py +3 -3
- westpa/cli/tools/w_multi_west.py +15 -10
- westpa/core/binning/_assign.cpython-39-darwin.so +0 -0
- westpa/core/binning/assign.py +3 -1
- westpa/core/kinetics/_kinetics.cpython-39-darwin.so +0 -0
- westpa/core/propagators/executable.py +9 -7
- westpa/core/reweight/_reweight.cpython-39-darwin.so +0 -0
- westpa/core/states.py +19 -3
- westpa/core/yamlcfg.py +1 -0
- westpa/fasthist/_fasthist.cpython-39-darwin.so +0 -0
- westpa/mclib/_mclib.cpython-39-darwin.so +0 -0
- westpa/tools/__init__.py +1 -0
- westpa/trajtree/_trajtree.cpython-39-darwin.so +0 -0
- westpa/work_managers/environment.py +0 -1
- westpa/work_managers/zeromq/node.py +0 -1
- {westpa-2022.6.dist-info → westpa-2022.7.dist-info}/METADATA +5 -6
- {westpa-2022.6.dist-info → westpa-2022.7.dist-info}/RECORD +23 -23
- {westpa-2022.6.dist-info → westpa-2022.7.dist-info}/WHEEL +1 -1
- {westpa-2022.6.dist-info → westpa-2022.7.dist-info}/AUTHORS +0 -0
- {westpa-2022.6.dist-info → westpa-2022.7.dist-info}/LICENSE +0 -0
- {westpa-2022.6.dist-info → westpa-2022.7.dist-info}/entry_points.txt +0 -0
- {westpa-2022.6.dist-info → westpa-2022.7.dist-info}/top_level.txt +0 -0
westpa/__init__.py
CHANGED
westpa/_version.py
CHANGED
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@@ -8,11 +8,11 @@ import json
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version_json = '''
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{
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-
"date": "
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+
"date": "2024-04-02T11:29:16-0400",
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"dirty": false,
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"error": null,
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"full-revisionid": "
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"version": "2022.
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"full-revisionid": "d48640fc3fff59f2f8470d6e7170a73f72fff5c6",
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"version": "2022.07"
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}
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''' # END VERSION_JSON
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westpa/cli/tools/w_multi_west.py
CHANGED
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@@ -159,13 +159,6 @@ Command-line options
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except ValueError:
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self.total_walkers[:] += west['summary'][:-1]['n_particles'][: len(self.total_walkers)]
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class Segment:
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def __init__(self, weight=0, iteration=0, simid=0, recycled_in=0):
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self.weight = weight
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self.iteration = iteration
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self.simid = simid
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self.recycled_in = recycled_in
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-
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def go(self):
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pi = self.progress.indicator
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self.istates = True # Assume serendipitously istates is same between runs...
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@@ -174,7 +167,11 @@ Command-line options
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self.open_files()
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self.total_number_of_walkers()
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if self.auxall is True:
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-
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try:
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self.aux = list(self.westH5[1]['iterations/iter_00000001/auxdata'].keys())
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except KeyError:
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self.aux = None
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log.warning('No auxdata. Proceeding forward without merging auxdata.')
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# Create a giant WEST.h5 file, separating the individual walkers, and renormalizing the weights.
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# It should then be compatible with existing toolsets.
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# Isn't really going to start with auxdata, but we'll add it in.
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@@ -240,7 +237,7 @@ Command-line options
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self.futr_iter[i] = []
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self.past_rm[i] = []
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self.futr_rm[i] = []
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-
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pi.new_operation('Recreating...', self.niters)
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# tracker = SummaryTracker()
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# self.output_file.close()
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@@ -262,12 +259,20 @@ Command-line options
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if addition.dtype != istate_dtype:
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addition = create_idtype_array(addition)
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final_istate_index = np.append(final_istate_index, addition)
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final_istate_pcoord = np.append(final_istate_pcoord, west['ibstates/0/istate_pcoord'][:])
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final_istate_pcoord = np.append(final_istate_pcoord, west['ibstates/0/istate_pcoord'][:], axis=0)
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# Saving them into self.output_file
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self.output_file['ibstates/0'].create_dataset('istate_index', data=final_istate_index, dtype=istate_dtype)
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self.output_file['ibstates/0'].create_dataset('istate_pcoord', data=final_istate_pcoord)
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# Remaking the ibstates index link
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master_index_row = self.output_file['ibstates/index'][0]
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master_index_row['iter_valid'] = 0
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master_index_row['n_bstates'] = len(self.output_file['ibstates/0/bstate_index'])
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master_index_row['group_ref'] = self.output_file['ibstates/0'].ref
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self.output_file['ibstates/index'][0] = master_index_row
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for iter in range(self.niters):
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# We have the following datasets in each iteration:
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# ibstates, which can now be combined with --ibstates
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Binary file
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westpa/core/binning/assign.py
CHANGED
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@@ -40,7 +40,6 @@ the total number of bins within the mapper.
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'''
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import hashlib
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import logging
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import pickle
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@@ -410,6 +409,9 @@ class RecursiveBinMapper(BinMapper):
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# we have updated our list of recursed bins, so set our own start index to trigger a recursive
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# reassignment of mappers' output values
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# Note that we're reordering the recursion targets based on outer bin numbers (dict keys) first,
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# so the order the mappers were added no longer matters...
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self._recursion_targets = {k: self._recursion_targets[k] for k in sorted(self._recursion_targets)}
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self.start_index = self.start_index
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def assign(self, coords, mask=None, output=None):
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Binary file
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data = load_trajectory(coord_folder)
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segment.data['iterh5/trajectory'] = data
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except Exception as e:
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log.warning('could not read any data for
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log.warning('could not read any {} data for HDF5 Framework: {}'.format(fieldname, str(e)))
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def restart_loader(fieldname, restart_folder, segment, single_point):
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segment.data['iterh5/restart'] = d.getvalue() + b'\x01' # add tail protection
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except Exception as e:
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log.warning('could not read any data for
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log.warning('could not read any {} data for HDF5 Framework: {}'.format(fieldname, str(e)))
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finally:
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d.close()
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safe_extract(t, path=path)
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except ValueError as e:
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log.warning('could not write restart data for {}: {}'.format(str(segment), str(e)))
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log.warning('could not write HDF5 Framework restart data for {}: {}'.format(str(segment), str(e)))
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d = BytesIO()
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if segment.n_iter == 1:
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log.warning(
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log.warning('could not write restart data for {}: {}'.format(str(segment), str(e)))
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log.warning('could not write HDF5 Framework restart data for {}: {}'.format(str(segment), str(e)))
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finally:
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d.close()
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try:
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loader(dataset, filename, segment, single_point=single_point)
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log.error('could not read {} from {!r}: {!r}'.format(dataset, filename, e))
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log.error('could not read {} for segment {} from {!r}: {!r}'.format(dataset, segment.seg_id, filename, e))
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segment.status = Segment.SEG_STATUS_FAILED
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break
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shutil.rmtree(filename)
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log.warning(
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log.warning(
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'could not delete {} file {!r} for segment {}: {!r}'.format(dataset, filename, segment.seg_id, e)
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)
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# Specific functions required by the WEST framework
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def get_pcoord(self, state):
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Binary file
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westpa/core/states.py
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@classmethod
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def states_from_file(cls,
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def states_from_file(cls, statefile):
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for line in open_statefile:
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pass
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def as_numpy_record(self):
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open_statefile = statefile
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continue
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fields = line.split()
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labels.append(fields[0])
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pcoord_values.append(np.array(list(map(dtype, fields[1:])), dtype=dtype))
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westpa/core/yamlcfg.py
CHANGED
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Binary file
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Binary file
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westpa/tools/__init__.py
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'''tools -- classes for implementing command-line tools for WESTPA'''
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from .core import WESTTool, WESTParallelTool, WESTToolComponent, WESTSubcommand, WESTMasterCommand, WESTMultiTool
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from .data_reader import WESTDataReader, WESTDSSynthesizer, WESTWDSSynthesizer
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from .iter_range import IterRangeSelection
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Binary file
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Metadata-Version: 2.1
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Name: westpa
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Version: 2022.
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Version: 2022.7
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Home-page: http://github.com/westpa/westpa
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License: MIT
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Classifier: Development Status :: 5 - Production/Stable
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Requires-Python: >=3.6
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License-File: LICENSE
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License-File: AUTHORS
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Requires-Dist: numpy
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Requires-Dist: numpy <2,>=1.16.0
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Requires-Dist: h5py >=2.10
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Requires-Dist: tables ; python_version >= "3.9"
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Provides-Extra: dev
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Requires-Dist: pytest-cov ; extra == 'dev'
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|docs| |usersgroup| |develgroup|
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.. |ghactions| image:: https://github.com/westpa/westpa/actions/workflows/test.yaml/badge.svg?branch=
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.. |ghactions| image:: https://github.com/westpa/westpa/actions/workflows/test.yaml/badge.svg?branch=westpa2
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:target: https://github.com/westpa/westpa/actions/workflows/test.yaml
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:alt: GitHub Actions
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.. _`releases page`: https://github.com/westpa/westpa/releases
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.. _`Anaconda Python distribution`: https://www.anaconda.com/products/individual
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.. _`wiki`: https://github.com/westpa/westpa/wiki/WESTPA
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.. _`wiki`: https://github.com/westpa/westpa/wiki/Installing-WESTPA
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---------------
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Getting started
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westpa/_version.py,sha256=
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westpa/__init__.py,sha256=
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westpa/fasthist/_fasthist.cpython-39-darwin.so,sha256=
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westpa/_version.py,sha256=kgY0Vo1HgLoDf0W0yQvrVcgI_xCDyPtdG-tQoSq-lKA,499
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westpa/__init__.py,sha256=xyNfYIcP2ncBLu_foO1NKmJrQh8-uYdwvMuM0HsOG1M,329
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westpa/fasthist/_fasthist.cpython-39-darwin.so,sha256=xCo_qui4KeD3pBBK1_xFtO_V6aAwoiod5eH6AD0RuHE,268296
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westpa/fasthist/__init__.py,sha256=oWj0gKEkKfHjGHwkzmpgAxDz55h2ze_sqQVzWSsOP6s,1071
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westpa/fasthist/__main__.py,sha256=7XCBZvrKbBG3KEuQMpZD0jXa3vVMEVfZJTG8MmdbsrM,3902
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westpa/westext/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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@@ -25,7 +25,7 @@ westpa/tools/binning.py,sha256=oFtc_ld8b9JJUYt-AEMe4Z1L8XJ48Lsr8Iw6nTYgGNs,20718
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westpa/tools/selected_segs.py,sha256=cC6YKvhxj6IPz9ybF9Te89nBEKtcaypTjzKPPDQC2uc,4943
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westpa/tools/wipi.py,sha256=ozNkR9d3oAUQn_TCyCk2bEKQWEmn6_NOtjXzAJPN1kM,29046
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westpa/tools/plot.py,sha256=JlNe5GenVYjnEPNC_6kesu5qv9H6HFOfrBUjGHfSMqY,12854
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westpa/tools/__init__.py,sha256
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westpa/tools/__init__.py,sha256=HZ4dvK0DV20RfuSzbABWz1qJMIEd1MinBa4tnSDgXa0,1032
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westpa/tools/core.py,sha256=y8kn8TN_R8h3iRE5oES-0BFHk3QLQMOmN66HrlXLons,12102
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westpa/tools/dtypes.py,sha256=5aEHhfqX6BJuTBUyirehZJ_G3al1q5GSWZSHyQmhynU,913
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westpa/tools/data_reader.py,sha256=i4Uv4OGwiPN-vLrCGOf1vtgMgnLqIg0fYVA0Jn4iXG4,6316
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@@ -45,9 +45,9 @@ westpa/core/trajectory.py,sha256=pGvaXNTLIpf9RZSabnvF8Bljppgx1mio01PF7yyEjE4,109
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westpa/core/segment.py,sha256=Gd_5htIZ6xKxxCms9XMtJncehGvMVxZeNdy4drxrnpc,4421
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westpa/core/progress.py,sha256=tEDDn-JPY6ZNzYqyrdgA7peo7pDu8kOMvqfyiHWUgps,6753
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westpa/core/data_manager.py,sha256=xeqt1MtjMGSRs7QN2zxRi0KrQ1cIV4L7JlOnBx-DEYE,71783
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westpa/core/states.py,sha256=
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westpa/core/yamlcfg.py,sha256=
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westpa/core/kinetics/_kinetics.cpython-39-darwin.so,sha256=
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westpa/core/states.py,sha256=x35kads1nbE1jwWn7EH5oJElDnlERGvAzH-I2fGM7yU,12833
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westpa/core/yamlcfg.py,sha256=B78OEr1n_sIkW6kDzl3FO63tiugaT-1VutAgLxU0i7A,12696
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westpa/core/kinetics/_kinetics.cpython-39-darwin.so,sha256=1NnV-Fh9Jz4QQw1oSk2JQJNb919KHHBxhbAwuVPvs4w,430768
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westpa/core/kinetics/matrates.py,sha256=1sf7L6ojLE8yT2sFfgeB8eqgjMHdMK2O_Xgyz_RjCzc,5554
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westpa/core/kinetics/events.py,sha256=VqYBN5rVOf3hAYUA6xQ6UN7GP6tVgRFIoP69tfGhkTo,6511
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westpa/core/kinetics/__init__.py,sha256=djtiki7X5-IEzwjwswbdgrolwUIzVAHKxCiI5B3WH28,510
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@@ -56,23 +56,23 @@ westpa/core/binning/binless_driver.py,sha256=T5qWpLnjxCS9RdKeWf7eVCC_s6TQFDENL7X
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westpa/core/binning/mab_driver.py,sha256=azSqc9pqHk_zc1ptGNjXARDbK-UAnPVmCiYwebi5mPY,2223
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westpa/core/binning/binless.py,sha256=Fb9TI5swQntzXjmlWFbYQ9yjzjLxDKNVVdmRxRqOnIY,4056
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westpa/core/binning/__init__.py,sha256=XmjBP6fg_id_vDELkcWW3u2GeuL5OPWblvX-kc7mINk,1297
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westpa/core/binning/_assign.cpython-39-darwin.so,sha256=
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westpa/core/binning/_assign.cpython-39-darwin.so,sha256=6CtqrCeiMAvH9v9O_7I5WMlKX2N0O1DKAqw8aXoSLww,292536
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westpa/core/binning/mab_manager.py,sha256=PUSA9J-dzmQdWQ9h5DEB9Eed6GVETf1EE43r6AvZLwI,9617
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westpa/core/binning/assign.py,sha256=
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westpa/core/binning/assign.py,sha256=e1YWyU3R12evLAoIWUrEvv3uvdKFo4u_mfKGDcK5AVU,18028
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westpa/core/binning/binless_manager.py,sha256=XgsLaYhknzWA9IHCqOvmnLXSgM303KnKOUjLe1NM0Zw,9414
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westpa/core/binning/mab.py,sha256=YgNWCistmKPFbQp9TpFgnpgGWc-HZTvSwB6ZugPS0Oo,11614
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westpa/core/binning/bins.py,sha256=WDj7DNX3MTVkRvkgAooa9G8VThxw32uIfMTuk9sS194,1460
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westpa/core/reweight/matrix.py,sha256=219sRxkML1V9niPIndSoRvJAC0fUmpG0PLDKpmfWW-g,5509
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westpa/core/reweight/_reweight.cpython-39-darwin.so,sha256=
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westpa/core/reweight/_reweight.cpython-39-darwin.so,sha256=tRU0-6CFgdm-ElboN5i9fDxc4zIja887a2bv--CtrQA,349520
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westpa/core/reweight/__init__.py,sha256=8goYojsHMcJCZblBC2sc2fcj-NUNVEstbSLswKNlVfg,284
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westpa/core/propagators/__init__.py,sha256=rx_kkeg3Tbb_rI0uhLGCD3OwSYj9QuhxF8QGN3mILrg,2373
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westpa/core/propagators/executable.py,sha256=
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westpa/core/propagators/executable.py,sha256=gm1TD3z9mA6o41j1kCRWwhv9mO1gX1pqJVoxBkG0kkM,31767
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westpa/analysis/__init__.py,sha256=CcmVPCB9OSEib0mJ4U-s9v3nrj4h-T_9AGApAbPnn8I,268
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westpa/analysis/core.py,sha256=P_m5-sU1RURAtWQVlV_Y2pgPvwUjyCqFS-E4O3fsD4E,22399
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westpa/analysis/statistics.py,sha256=M3Gj1bOiAu_SA4upR7gENYEOP2gnIEaSOZeGyoIxAc8,789
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westpa/analysis/trajectories.py,sha256=jyrbbKOVyZ3GjHQushDS_G8C4IRXlUmxa-WzmEEVGwc,12878
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westpa/mclib/__init__.py,sha256=NskP81wKw-tHTniyJ8QbgKAHah5JdpCrnPKJo1T-nLw,11513
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westpa/mclib/_mclib.cpython-39-darwin.so,sha256=
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westpa/mclib/_mclib.cpython-39-darwin.so,sha256=BbVTq4ixUsiHsCmTpDIY-M93v1YbTpidB7JoOfu3YJ4,271888
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westpa/mclib/__main__.py,sha256=cKqfE9koMcrHkslEPpFISA4Eblwl0mllaxn7pFeyX1A,881
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westpa/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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westpa/cli/tools/w_direct.py,sha256=5Z9eQpvpKM-40XdiI0L3t0O3jpjMx7tk8ndYAaJxvrc,22361
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@@ -80,7 +80,7 @@ westpa/cli/tools/w_dumpsegs.py,sha256=uv0WxvKGauyW6VT3zGyALUXVqSXwDrhwbF3ZVSJV9M
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westpa/cli/tools/w_postanalysis_matrix.py,sha256=owHtPNcD2RF33C-3oq4LhNWG6M-_nWCGenrNtV574Dc,3227
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westpa/cli/tools/w_select.py,sha256=cNtuIgv8-P7bPyHDJmbrVwSasMFth5ULVTpz2QjVdfU,9717
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westpa/cli/tools/ploterr.py,sha256=Fm4Yoexm2c1H5_H8t2GMsXncHcJAltWpp0c5XMnDpW0,18906
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westpa/cli/tools/w_multi_west.py,sha256=
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westpa/cli/tools/w_multi_west.py,sha256=Vye1OTiyFHaUkPKMxyOediE1_6hq-EMp7SeoaVO7rwk,20049
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westpa/cli/tools/w_ntop.py,sha256=6wiGWA5ZUy9RU4cOy6J0qSXbHO5uScF19w9N9AmiktQ,8204
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westpa/cli/tools/w_kinavg.py,sha256=MjmomiIWoBnjfm8Pq-93y6DoCq26DbCxdJ5bcP-25Ys,4324
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westpa/cli/tools/w_eddist.py,sha256=pAZVIOSgMiJxo7f6AXES_UhAwMaeK4S5Tl58O21hB-w,20056
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@@ -105,7 +105,7 @@ westpa/cli/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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westpa/cli/core/w_truncate.py,sha256=-CHFOBr4NAZwGQ8-O5F7B0dPowpnFpm-mF9Us1gBgfo,1654
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westpa/cli/core/w_init.py,sha256=V_CvlAuq8flg-zUO01sbMGYkLqrEDD4DU9sV90bYFus,8793
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westpa/cli/core/w_succ.py,sha256=ZK1MHHu7t53VdBrRgJUe7b1R8DnhMKPjHOqbbOjC_As,3074
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westpa/trajtree/_trajtree.cpython-39-darwin.so,sha256=
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westpa/trajtree/_trajtree.cpython-39-darwin.so,sha256=HhAqB0unKqLkJVOyw2vxQA-CHbITpPCcJaxmN3tSQh8,154568
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westpa/trajtree/__init__.py,sha256=K64Ok5bUP-fXo1H2rigJqxCnm-U23tJlRngNOnzR3gs,96
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westpa/trajtree/trajtree.py,sha256=sLf4kTi0QyvFdbSR__YcPwOR2wcOxtlkC4IPUFcq-9M,4497
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westpa/oldtools/files.py,sha256=JmLtZqxD88cybEHcOU6kodAeOJYxylpYFl4OQqU13Hs,944
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@@ -135,16 +135,16 @@ westpa/work_managers/processes.py,sha256=zcHKanvTYnCNuU46F4EpqaRdj1XjtCe6ltw3g3b
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westpa/work_managers/threads.py,sha256=-Xktf-LPqVRf7sMW7Yqdc_ayO_4x_f0zA9iZS_G-fuI,2335
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westpa/work_managers/mpi.py,sha256=ArxswC1CMgBc5rZ1nr4cQQvwHlCWAcN-BkZt8ilhSgk,9511
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westpa/work_managers/serial.py,sha256=fo5Sql5wO4PdFy2VbcssWy0G459MJwKjRWkklK6nDxo,694
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westpa/work_managers/environment.py,sha256=
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westpa/work_managers/environment.py,sha256=WexOkNB8ovvByB78kXB6uzm7nlE-fIB42IpfLIvZzoI,4948
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westpa/work_managers/zeromq/worker.py,sha256=YE-iU7_yOiVIu8Aal5j-qrq8sNsG4JSVtRJAiFjnBcw,12940
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westpa/work_managers/zeromq/__init__.py,sha256=rrl4YbEaZr2AiEBTMlhvEFH83dBlAwWR_1L8UkqoJVs,438
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westpa/work_managers/zeromq/core.py,sha256=K3Iyrz5u2Dy-GgZFL3ZXDN2iaaLm7qL-A3cm4PdBiF8,22907
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westpa/work_managers/zeromq/work_manager.py,sha256=UB_WvnejDRVi1ZU2QWpP9uzhnccOH7b3qHgU-wSstTY,22425
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westpa/work_managers/zeromq/node.py,sha256=
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westpa-2022.
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westpa-2022.
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westpa/work_managers/zeromq/node.py,sha256=CeoJhXVqrZxrV3lMnDtm3LNkGFxjS4dr3E6wd7ZQRTE,4877
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westpa-2022.7.dist-info/RECORD,,
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westpa-2022.7.dist-info/LICENSE,sha256=I2wUldIRJmflTYUxmSiITSZEKvlovlMPrE3JU5IslkY,1074
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westpa-2022.7.dist-info/AUTHORS,sha256=YMi91-Fs-vFgZKUaItfh20uXthT9oe2Kq6CQXmqMGqg,671
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westpa-2022.7.dist-info/WHEEL,sha256=wEvD9HODgqXG21zAA07x3Gh0qpNEHOQ7qzjMqXvopac,109
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westpa-2022.7.dist-info/entry_points.txt,sha256=0Ym8meKTdYbUEMtUHF_4zaZP__4ldfFnoYXyYlKRB6s,1428
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westpa-2022.7.dist-info/top_level.txt,sha256=otaLnQtwo9jKCJmja4iOOsOVDThUvPfjJaeLrgGEhlE,7
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westpa-2022.7.dist-info/METADATA,sha256=RgNgH_WTNDP0G-ZCbQQkjjASW2pOXIiGNdxGZ0vavcI,7432
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File without changes
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