westpa 2022.6__tar.gz → 2022.8__tar.gz

{westpa-2022.6/src/westpa.egg-info → westpa-2022.8}/PKG-INFO

@@ -1,6 +1,7 @@
 Metadata-Version: 2.1
 Name: westpa
-Version: 2022.6
+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
@@ -14,7 +15,7 @@ Classifier: Programming Language :: Cython
 Requires-Python: >=3.6
 License-File: LICENSE
 License-File: AUTHORS
-Requires-Dist: numpy>=1.16.0
+Requires-Dist: numpy<2,>=1.16.0
 Requires-Dist: scipy>=0.19.1
 Requires-Dist: h5py>=2.10
 Requires-Dist: mdtraj>=1.9.5
@@ -25,8 +26,7 @@ Requires-Dist: blessings
 Requires-Dist: ipykernel
 Requires-Dist: tqdm
 Requires-Dist: pandas
-Requires-Dist: tables<3.9; python_version < "3.9"
-Requires-Dist: tables; python_version >= "3.9"
+Requires-Dist: tables
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
@@ -49,7 +49,7 @@ WESTPA 2.0
 
 |docs| |usersgroup| |develgroup| 
 
-.. |ghactions| image:: https://github.com/westpa/westpa/actions/workflows/test.yaml/badge.svg?branch=westpa-2.0-restruct
+.. |ghactions| image:: https://github.com/westpa/westpa/actions/workflows/test.yaml/badge.svg?branch=westpa2
               :target: https://github.com/westpa/westpa/actions/workflows/test.yaml
               :alt: GitHub Actions
 
@@ -143,7 +143,7 @@ To install from source (**not recommended**), start by downloading the correspon
 
 .. _`releases page`: https://github.com/westpa/westpa/releases
 .. _`Anaconda Python distribution`: https://www.anaconda.com/products/individual
-.. _`wiki`: https://github.com/westpa/westpa/wiki/WESTPA-Quick-Install
+.. _`wiki`: https://github.com/westpa/westpa/wiki/Installing-WESTPA
 
 ---------------
 Getting started

{westpa-2022.6 → westpa-2022.8}/README.rst

@@ -6,7 +6,7 @@ WESTPA 2.0
 
 |docs| |usersgroup| |develgroup| 
 
-.. |ghactions| image:: https://github.com/westpa/westpa/actions/workflows/test.yaml/badge.svg?branch=westpa-2.0-restruct
+.. |ghactions| image:: https://github.com/westpa/westpa/actions/workflows/test.yaml/badge.svg?branch=westpa2
               :target: https://github.com/westpa/westpa/actions/workflows/test.yaml
               :alt: GitHub Actions
 
@@ -100,7 +100,7 @@ To install from source (**not recommended**), start by downloading the correspon
 
 .. _`releases page`: https://github.com/westpa/westpa/releases
 .. _`Anaconda Python distribution`: https://www.anaconda.com/products/individual
-.. _`wiki`: https://github.com/westpa/westpa/wiki/WESTPA-Quick-Install
+.. _`wiki`: https://github.com/westpa/westpa/wiki/Installing-WESTPA
 
 ---------------
 Getting started

{westpa-2022.6 → westpa-2022.8}/pyproject.toml

@@ -3,12 +3,13 @@ build-backend = 'setuptools.build_meta:__legacy__'
 # Minimum requirements for the build system to execute.
 # See current numpy pinning in https://github.com/scipy/oldest-supported-numpy
 requires = [
-    "setuptools>=40.8.0",
+    "setuptools >=40.8.0",
     "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",
-    "scipy>=0.19.1",
+    "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'",
+    "scipy >=0.19.1",
     "versioneer-518"
 ]
 # Uncommenting this requires adding the top level of the repo to sys.path in the setup.py

{westpa-2022.6 → westpa-2022.8}/setup.py

@@ -109,7 +109,7 @@ CLASSIFIERS = [
 ]
 
 INSTALL_REQUIRES = [
-    "numpy >= 1.16.0",
+    "numpy >= 1.16.0, <2",
     "scipy >= 0.19.1",
     "h5py >= 2.10",
     "mdtraj >= 1.9.5",
@@ -120,8 +120,7 @@ INSTALL_REQUIRES = [
     "ipykernel",
     "tqdm",
     "pandas",
-    "tables < 3.9; python_version < '3.9'",
-    "tables; python_version >= '3.9'",
+    "tables",
 ]
 
 EXTRAS_REQUIRE = {
@@ -149,6 +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-2022.6 → westpa-2022.8}/src/westpa/__init__.py

@@ -12,7 +12,3 @@ rc = _rc.WESTRC()
 __version__ = get_versions()["version"]
 
 del get_versions
-
-from . import _version
-
-__version__ = _version.get_versions()['version']

{westpa-2022.6 → westpa-2022.8}/src/westpa/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2023-10-20T12:52:31-0400",
+ "date": "2024-04-15T22:37:00-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "ef5fbd3e0aeb4d08160fc56ee39cca6ba75e3217",
- "version": "2022.06"
+ "full-revisionid": "587296bd42835960dc67dc3e91ead8f4dd2c6d97",
+ "version": "2022.08"
 }
 '''  # END VERSION_JSON
 

{westpa-2022.6 → westpa-2022.8}/src/westpa/cli/tools/w_multi_west.py

@@ -159,13 +159,6 @@ Command-line options
             except ValueError:
                 self.total_walkers[:] += west['summary'][:-1]['n_particles'][: len(self.total_walkers)]
 
-    class Segment:
-        def __init__(self, weight=0, iteration=0, simid=0, recycled_in=0):
-            self.weight = weight
-            self.iteration = iteration
-            self.simid = simid
-            self.recycled_in = recycled_in
-
     def go(self):
         pi = self.progress.indicator
         self.istates = True  # Assume serendipitously istates is same between runs...
@@ -174,7 +167,11 @@ Command-line options
             self.open_files()
             self.total_number_of_walkers()
             if self.auxall is True:
-                self.aux = list(self.westH5[1]['iterations/iter_00000001/auxdata'].keys())
+                try:
+                    self.aux = list(self.westH5[1]['iterations/iter_00000001/auxdata'].keys())
+                except KeyError:
+                    self.aux = None
+                    log.warning('No auxdata. Proceeding forward without merging auxdata.')
             # Create a giant WEST.h5 file, separating the individual walkers, and renormalizing the weights.
             # It should then be compatible with existing toolsets.
             # Isn't really going to start with auxdata, but we'll add it in.
@@ -240,7 +237,7 @@ Command-line options
                 self.futr_iter[i] = []
                 self.past_rm[i] = []
                 self.futr_rm[i] = []
-            print(pi.new_operation('Recreating...', self.niters))
+            pi.new_operation('Recreating...', self.niters)
             # tracker = SummaryTracker()
             # self.output_file.close()
 
@@ -262,12 +259,20 @@ Command-line options
                         if addition.dtype != istate_dtype:
                             addition = create_idtype_array(addition)
                         final_istate_index = np.append(final_istate_index, addition)
-                        final_istate_pcoord = np.append(final_istate_pcoord, west['ibstates/0/istate_pcoord'][:])
+                        final_istate_pcoord = np.append(final_istate_pcoord, west['ibstates/0/istate_pcoord'][:], axis=0)
 
                 # Saving them into self.output_file
                 self.output_file['ibstates/0'].create_dataset('istate_index', data=final_istate_index, dtype=istate_dtype)
                 self.output_file['ibstates/0'].create_dataset('istate_pcoord', data=final_istate_pcoord)
 
+                # Remaking the ibstates index link
+                master_index_row = self.output_file['ibstates/index'][0]
+                master_index_row['iter_valid'] = 0
+                master_index_row['n_bstates'] = len(self.output_file['ibstates/0/bstate_index'])
+                master_index_row['group_ref'] = self.output_file['ibstates/0'].ref
+
+                self.output_file['ibstates/index'][0] = master_index_row
+
             for iter in range(self.niters):
                 # We have the following datasets in each iteration:
                 # ibstates, which can now be combined with --ibstates