westpa 2022.7__tar.gz → 2022.9__tar.gz

{westpa-2022.7/src/westpa.egg-info → westpa-2022.9}/PKG-INFO

@@ -1,6 +1,7 @@
 Metadata-Version: 2.1
 Name: westpa
-Version: 2022.7
+Version: 2022.9
+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
@@ -120,8 +121,8 @@ WESTPA is developed and tested on Unix-like operating systems, including Linux a
 
 Regardless of the chosen method of installation, before installing WESTPA, we recommend you to first install the Python 3 version provided by the latest free `Anaconda Python distribution`_. After installing Anaconda, create a new python environment for the WESTPA install with the following::
 
-    conda create -n westpa-2.0 python=3.9
-    conda activate westpa-2.0
+    conda create -n westpa python=3.11
+    conda activate westpa
 
 Then, we recommend installing WESTPA through conda or pip. Execute either of the following::
 
@@ -136,12 +137,12 @@ 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-main.tar.gz
+    tar xvzf westpa-2022.09.tar.gz
     cd westpa
     python -m pip install -e .
 
 .. _`releases page`: https://github.com/westpa/westpa/releases
-.. _`Anaconda Python distribution`: https://www.anaconda.com/products/individual
+.. _`Anaconda Python distribution`: https://www.anaconda.com/download
 .. _`wiki`: https://github.com/westpa/westpa/wiki/Installing-WESTPA
 
 ---------------

{westpa-2022.7 → westpa-2022.9}/README.rst

@@ -78,8 +78,8 @@ WESTPA is developed and tested on Unix-like operating systems, including Linux a
 
 Regardless of the chosen method of installation, before installing WESTPA, we recommend you to first install the Python 3 version provided by the latest free `Anaconda Python distribution`_. After installing Anaconda, create a new python environment for the WESTPA install with the following::
 
-    conda create -n westpa-2.0 python=3.9
-    conda activate westpa-2.0
+    conda create -n westpa python=3.11
+    conda activate westpa
 
 Then, we recommend installing WESTPA through conda or pip. Execute either of the following::
 
@@ -94,12 +94,12 @@ 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-main.tar.gz
+    tar xvzf westpa-2022.09.tar.gz
     cd westpa
     python -m pip install -e .
 
 .. _`releases page`: https://github.com/westpa/westpa/releases
-.. _`Anaconda Python distribution`: https://www.anaconda.com/products/individual
+.. _`Anaconda Python distribution`: https://www.anaconda.com/download
 .. _`wiki`: https://github.com/westpa/westpa/wiki/Installing-WESTPA
 
 ---------------

{westpa-2022.7 → westpa-2022.9}/setup.py

@@ -148,6 +148,7 @@ metadata = dict(
     package_data={},
     packages=find_packages(where='src'),
     package_dir={"": "src"},
+    description='WESTPA is a package for constructing and running stochastic simulations using the "weighted ensemble" approach of Huber and Kim (1996).',
 )
 
 

{westpa-2022.7 → westpa-2022.9}/src/westpa/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-04-02T11:29:16-0400",
+ "date": "2024-05-22T14:48:11-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "d48640fc3fff59f2f8470d6e7170a73f72fff5c6",
- "version": "2022.07"
+ "full-revisionid": "ce236bb304b11302a982af2ecb1f8cbb403d09f4",
+ "version": "2022.09"
 }
 '''  # END VERSION_JSON
 

{westpa-2022.7 → westpa-2022.9}/src/westpa/analysis/core.py

@@ -298,8 +298,8 @@ class Iteration:
     def basis_state_summaries(self):
         """pd.DataFrame: Basis state summary data."""
         df = pd.DataFrame(self.h5group['ibstates']['bstate_index'][:])
-        df['label'] = tostr(df['label'].str)
-        df['auxref'] = tostr(df['auxref'].str)
+        df['label'] = df['label'].str.decode('UTF-8')
+        df['auxref'] = df['auxref'].str.decode('UTF-8')
         return df
 
     @property
@@ -325,7 +325,7 @@ class Iteration:
         """pd.DataFrame or None: Target state summary data."""
         if self.has_target_states:
             df = pd.DataFrame(self.h5group['tstates']['index'][:])
-            df['label'] = tostr(df['label'].str)
+            df['label'] = df['label'].str.decode('UTF-8')
 
             return df
         else:

{westpa-2022.7 → westpa-2022.9}/src/westpa/cli/core/w_states.py

@@ -157,7 +157,7 @@ def initialize(mode, bstates, _bstate_file, tstates, _tstate_file):
                             bstate.probability *= pscale
 
                     # Assign progress coordinates to basis states
-                    sim_manager.get_bstate_pcoords(basis_states, n_iter)
+                    sim_manager.get_bstate_pcoords(basis_states)
                     data_manager.create_ibstate_group(basis_states, n_iter)
                     sim_manager.report_basis_states(basis_states)
 

{westpa-2022.7 → westpa-2022.9}/src/westpa/cli/tools/w_ipa.py

@@ -157,11 +157,11 @@ class WIPI(WESTParallelTool):
         # print(str(to_hash).encode('base64'))
         if self.debug_mode:
             for iarg, arg in enumerate(to_hash):
-                if not isinstance(arg, list):
-                    print('arg {num:02d} -- {arg:<20}'.format(num=iarg, arg=arg))
-                else:
+                if isinstance(arg, list):
                     for il, l in enumerate(arg):
-                        print('arg {num:02d} -- {arg:<20}'.format(num=il + iarg, arg=l))
+                        print('arg {num:02d} -- {arg:<20}'.format(num=il + iarg, arg=h5io.tostr(l)))
+                else:
+                    print('arg {num:02d} -- {arg:<20}'.format(num=iarg, arg=h5io.tostr(arg)))
             # print('args: {}'.format(to_hash))
         # This SHOULD produce the same output, maybe?  That would be nice, anyway.
         # But we'll need to test it more.

{westpa-2022.7 → westpa-2022.9}/src/westpa/cli/tools/w_pdist.py

@@ -423,7 +423,10 @@ Command-line options
             lb, ub = self.data_range[idim]
             # Advance just beyond the upper bound of the range, so that we catch
             # the maximum in the histogram
-            ub *= 1.01
+            if ub > 0:
+                ub *= 1.01
+            else:
+                ub /= 1.01
 
             boundset = np.linspace(lb, ub, bins + 1)
             midpoints = (boundset[:-1] + boundset[1:]) / 2.0
@@ -440,7 +443,10 @@ Command-line options
             lb, ub = self.data_range[idim]
             # Advance just beyond the upper bound of the range, so that we catch
             # the maximum in the histogram
-            ub *= 1.01
+            if ub > 0:
+                ub *= 1.01
+            else:
+                ub /= 1.01
 
             boundset = np.linspace(lb, ub, bins[idim] + 1)
             midpoints = (boundset[:-1] + boundset[1:]) / 2.0

{westpa-2022.7 → westpa-2022.9}/src/westpa/core/_rc.py

@@ -1,12 +1,13 @@
 """WEST run control and configuration routines"""
 
-import errno
-import logging
 import math
 import os
 import sys
+import errno
+import logging
 import warnings
 from copy import deepcopy
+from datetime import timedelta
 
 import numpy as np
 
@@ -231,6 +232,21 @@ class WESTRC:
         self.config_logging()
         self.config['args'] = {k: v for k, v in args.__dict__.items() if not k.startswith('_')}
         self.process_config()
+        self.time_config()
+
+    def time_config(self):
+        '''Convert non-pyYAML accepted time formats into seconds'''
+        max_run_wallclock = self.config.get(['west', 'propagation', 'max_run_wallclock'], None)
+        if isinstance(max_run_wallclock, str):
+            time_formats = ['days', 'hours', 'minutes', 'seconds']
+            wallclock_str = max_run_wallclock.split(':')
+            kwargs = {key: int(val) for key, val in zip(time_formats[-len(wallclock_str) :], wallclock_str)}
+            try:
+                diff = int(timedelta(**kwargs).total_seconds())
+                self.config['west']['propagation']['max_run_wallclock'] = diff
+                log.debug(f'Automatically converted {max_run_wallclock=} to {diff}')
+            except ValueError:
+                log.debug(f'Failed to convert {max_run_wallclock=} to seconds.')
 
     def process_config(self):
         log.debug('config: {!r}'.format(self.config))