Fixes for w_ipa run_calculation and reading filenames from h5 file (#147

)

* added pull templates and issues templates

* removed westpa 2.0 workflows

* small fix to a potential bug in kinetics_tool

* Update README.rst

* Fixed a bug caused by bytestring when reading the basis state filename from west.h5

* Revert "Merge pull request #3 from westpa/main"

This reverts commit 7257846, reversing
changes made to b13b32a.

* documentation changes

* minor change`

* Update src/westpa/core/h5io.py

Changed based on review.

Co-authored-by: Jeremy Leung <63817169+jeremyleung521@users.noreply.github.com>

Co-authored-by: Jeremy Leung <jeremyleung521@gmail.com>
Co-authored-by: Jeremy Leung <63817169+jeremyleung521@users.noreply.github.com>
Co-authored-by: She Zhang <she.zhang@eyesopen.com>
Co-authored-by: Lillian Chong <ltchong@pitt.edu>

src/westpa/core/data_manager.py

@@ -534,7 +534,7 @@ def get_basis_states(self, n_iter=None):
                     state_id=i,
                     label=row['label'],
                     probability=row['probability'],
-                    auxref=str(row['auxref']) or None,
+                    auxref=h5io.tostr(row['auxref']) or None,
                     pcoord=pcoord.copy(),
                 )
                 for (i, (row, pcoord)) in enumerate(zip(bstate_index, bstate_pcoords))

src/westpa/core/h5io.py

@@ -77,6 +77,18 @@ def calc_chunksize(shape, dtype, max_chunksize=262144):
     return chunk_shape
 
 
+def tostr(b):
+    '''Convert a nonstandard string object ``b`` to str with the handling of the
+    case where ``b`` is bytes.'''
+
+    if b is None:
+        return None
+    elif isinstance(b, bytes):
+        return b.decode('utf-8')
+    else:
+        return str(b)
+
+
 #
 # Group and dataset manipulation functions
 #

src/westpa/tools/kinetics_tool.py

@@ -279,7 +279,7 @@ def run_calculation(
         # This is appropriate for bootstrapped quantities, I think.
         all_items = np.arange(1, len(start_pts) + 1)
         bootstrap_length = 0.5 * (len(start_pts) * (len(start_pts) + 1)) - np.delete(
-            all_items, np.arange(1, len(start_pts) + 1, step_iter)
+            all_items, np.arange(1, len(start_pts), step_iter)
         )
         if True:
             pi.new_operation('Calculating {}'.format(name), bootstrap_length[0])