westpa 2022.10__tar.gz → 2022.12__tar.gz

{westpa-2022.10 → westpa-2022.12}/AUTHORS

@@ -4,18 +4,18 @@ in collaboration with Daniel Zuckerman (zuckermd@ohsu.edu)
 The original version of WESTPA was written by Matthew Zwier (matthew.zwier@drake.edu) 
 as part of his Ph.D. dissertation with Lillian Chong.
 
-Other contributors are the following (In alphabetical order)
+Other core contributors are the following (in alphabetical order)
 
 Joshua Adelman
-Alex DeGrave
-Page Harrison
-Joseph Kaus
-Patrick Pisciuneri
-A. J. Pratt
-Nicholas Rego
+Anthony Bogetti
+Jeremy Leung
+AJ Pratt
+John Russo
 Ali Saglam
-David Wang
+Jeff Thompson
 Kim Wong
+Darian Yang
+She Zhang
 
 The work manager interface is derived from the ``concurrent.futures`` module
 of Python 3.2 by Brian Quinlan, (C) 2011 the Python Software Foundation.

{westpa-2022.10/src/westpa.egg-info → westpa-2022.12}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: westpa
-Version: 2022.10
+Version: 2022.12
 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
@@ -12,10 +12,11 @@ Classifier: Operating System :: POSIX
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Cython
-Requires-Python: >=3.6
+Requires-Python: >=3.9
 License-File: LICENSE
 License-File: AUTHORS
-Requires-Dist: numpy<2,>=1.16.0
+Requires-Dist: numpy<3,>=1.25.0; python_version >= "3.10"
+Requires-Dist: numpy<2,>=1.25.0; python_version < "3.10"
 Requires-Dist: scipy>=0.19.1
 Requires-Dist: h5py>=2.10
 Requires-Dist: mdtraj>=1.9.5
@@ -40,6 +41,15 @@ Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: pytest-rerunfailures; extra == "dev"
 Requires-Dist: pytest-timeout; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 ===============
 WESTPA 2.0 
@@ -105,7 +115,7 @@ WESTPA is free software, licensed under the terms of the MIT License. See the fi
 Requirements
 ------------
 
-WESTPA is written in Python and requires version 3.7 or later. WESTPA also requires a number of Python scientific software packages. 
+WESTPA is written in Python and requires version 3.9 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.anaconda.com (free for all users).
 
@@ -137,7 +147,7 @@ See the install instructions on our `wiki`_ for more detailed information.
 
 To install from source (**not recommended**), start by downloading the corresponding tar.gz file from the `releases page`_. After downloading the file, unpack the file and install WESTPA by executing the following::
 
-    tar xvzf westpa-2022.09.tar.gz
+    tar xvzf westpa-2022.11.tar.gz
     cd westpa
     python -m pip install -e .
 

{westpa-2022.10 → westpa-2022.12}/README.rst

@@ -62,7 +62,7 @@ WESTPA is free software, licensed under the terms of the MIT License. See the fi
 Requirements
 ------------
 
-WESTPA is written in Python and requires version 3.7 or later. WESTPA also requires a number of Python scientific software packages. 
+WESTPA is written in Python and requires version 3.9 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.anaconda.com (free for all users).
 
@@ -94,7 +94,7 @@ See the install instructions on our `wiki`_ for more detailed information.
 
 To install from source (**not recommended**), start by downloading the corresponding tar.gz file from the `releases page`_. After downloading the file, unpack the file and install WESTPA by executing the following::
 
-    tar xvzf westpa-2022.09.tar.gz
+    tar xvzf westpa-2022.11.tar.gz
     cd westpa
     python -m pip install -e .
 

{westpa-2022.10 → westpa-2022.12}/pyproject.toml

@@ -7,8 +7,8 @@ requires = [
     "wheel",
     "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'",
+    "numpy >=2.0.0, <3; python_version >='3.10'",  # Force numpy>=2 during build time so it works on both 1.XX and 2.XX
+    "numpy < 2.0.0; python_version <'3.10'", # Numpy 2 builds break PyTables on python 3.9
     "scipy >=0.19.1",
     "versioneer-518"
 ]
@@ -45,3 +45,16 @@ exclude = '''
      )
 )
 '''
+
+# See the docstring in versioneer.py for instructions. Note that you must
+# re-run 'versioneer.py setup' after changing this section, and commit the
+# resulting files.
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440"
+versionfile_source = "src/westpa/_version.py"
+versionfile_build = "westpa/_version.py"
+tag_prefix = "v"
+parentdir_prefix = "westpa-"
+

westpa-2022.12/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

{westpa-2022.10 → westpa-2022.12}/setup.py

@@ -109,7 +109,8 @@ CLASSIFIERS = [
 ]
 
 INSTALL_REQUIRES = [
-    "numpy >= 1.16.0, <2",
+    "numpy >= 1.25.0, <3; python_version >='3.10'",
+    "numpy >= 1.25.0, <2; python_version <'3.10'",  # pytables is broken for numpy2/py3.9
     "scipy >= 0.19.1",
     "h5py >= 2.10",
     "mdtraj >= 1.9.5",
@@ -139,7 +140,7 @@ metadata = dict(
     version=versioneer.get_version(),
     keywords='',
     cmdclass=versioneer.get_cmdclass(),
-    python_requires=">=3.6",
+    python_requires=">=3.9",
     zip_safe=False,
     classifiers=CLASSIFIERS,
     entry_points={'console_scripts': console_scripts},

{westpa-2022.10 → westpa-2022.12}/src/westpa/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-05-30T14:33:52-0400",
+ "date": "2025-03-03T16:14:34-0500",
  "dirty": false,
  "error": null,
- "full-revisionid": "40fe71e4e393b47e0a231b178add25696e469405",
- "version": "2022.10"
+ "full-revisionid": "b3afe209fcffc6238c1d2ec700059c7e30f2adca",
+ "version": "2022.12"
 }
 '''  # END VERSION_JSON
 

{westpa-2022.10 → westpa-2022.12}/src/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-2022.10 → westpa-2022.12}/src/westpa/cli/tools/w_assign.py

@@ -474,17 +474,17 @@ Command-line options
 
             # Recursive mappers produce a generator rather than a list of labels
             # so consume the entire generator into a list
-            labels = [np.string_(label) for label in self.binning.mapper.labels]
+            labels = [np.bytes_(label) for label in self.binning.mapper.labels]
 
             self.output_file.create_dataset('bin_labels', data=labels, compression=9)
 
             if self.states:
                 nstates = len(self.states)
                 state_map[:] = nstates  # state_id == nstates => unknown state
-                state_labels = [np.string_(state['label']) for state in self.states]
+                state_labels = [np.bytes_(state['label']) for state in self.states]
 
                 for istate, sdict in enumerate(self.states):
-                    assert state_labels[istate] == np.string_(sdict['label'])  # sanity check
+                    assert state_labels[istate] == np.bytes_(sdict['label'])  # sanity check
                     state_assignments = assign(sdict['coords'])
                     for assignment in state_assignments:
                         state_map[assignment] = istate
@@ -558,7 +558,7 @@ Command-line options
                 shuffle=True,
                 chunks=h5io.calc_chunksize(pops_shape, weight_dtype),
             )
-            h5io.label_axes(pops_ds, [np.string_(i) for i in ['iteration', 'state', 'bin']])
+            h5io.label_axes(pops_ds, [np.bytes_(i) for i in ['iteration', 'state', 'bin']])
 
             pi.new_operation('Assigning to bins', iter_stop - iter_start)
             last_labels = None  # mapping of seg_id to last macrostate inhabited

{westpa-2022.10 → westpa-2022.12}/src/westpa/cli/tools/w_fluxanl.py

@@ -1,7 +1,6 @@
 import h5py
 import numpy as np
 from scipy.signal import fftconvolve
-from warnings import warn
 
 import westpa
 
@@ -12,7 +11,7 @@ from westpa.tools import WESTTool, WESTDataReader, IterRangeSelection
 from westpa.tools.dtypes import iter_block_ci_dtype as ci_dtype
 import westpa.mclib as mclib
 
-fluxentry_dtype = np.dtype([('n_iter', n_iter_dtype), ('flux', weight_dtype), ('count', np.uint)])
+fluxentry_dtype = np.dtype([('n_iter', n_iter_dtype), ('flux', weight_dtype), ('count', np.int32)])
 
 target_index_dtype = np.dtype(
     [
@@ -370,7 +369,6 @@ the true value of ``tau``.
 
 
 def entry_point():
-    warn('w_fluxanl is being deprecated.  Please use w_assign and w_direct instead.')
     WFluxanlTool().main()
 
 

{westpa-2022.10 → westpa-2022.12}/src/westpa/cli/tools/w_ntop.py

@@ -190,9 +190,9 @@ Command-line arguments
                         weights = all_weights.take(segs)
 
                         if what == 'lowweight':
-                            indices = np.argsort(weights)[:count]
+                            indices = np.argsort(weights, kind='stable')[:count]
                         elif what == 'highweight':
-                            indices = np.argsort(weights)[::-1][:count]
+                            indices = np.argsort(weights, kind='stable')[::-1][:count]
                         else:
                             assert what == 'random'
                             indices = np.random.permutation(len(weights))

{westpa-2022.10 → westpa-2022.12}/src/westpa/cli/tools/w_red.py

@@ -3,6 +3,11 @@ import numpy as np
 from westpa import rc
 from westpa.tools import WESTParallelTool
 
+try:
+    from numpy import trapezoid
+except ImportError:
+    from numpy import trapz as trapezoid
+
 
 class DurationCorrector(object):
     @staticmethod
@@ -128,9 +133,9 @@ class DurationCorrector(object):
 
         for i, tau in enumerate(taugrid):
             if i > 0 and tau < maxduration:
-                integral1[i] = np.trapz(f_tilde[: i + 1], taugrid[: i + 1])
+                integral1[i] = trapezoid(f_tilde[: i + 1], taugrid[: i + 1])
 
-        integral2 = np.trapz(integral1, taugrid)
+        integral2 = trapezoid(integral1, taugrid)
 
         if integral2 == 0:
             return 0.0