From b5952d1479478d243270b75c30c7db886203447e Mon Sep 17 00:00:00 2001
From: "Jeremy M. G. Leung" <jml230@pitt.edu>
Date: Fri, 14 Feb 2025 14:58:29 -0500
Subject: [PATCH 1/9] remove extra export and classes

---
 src/westpa/core/_rc.py                    |  4 +-
 src/westpa/core/binning/_assign.pyx       |  1 -
 src/westpa/core/propagators/executable.py |  2 +-
 src/westpa/core/reweight/_reweight.pyx    | 32 ++++----
 src/westpa/core/sim_manager.py            |  2 +-
 src/westpa/core/yamlcfg.py                | 93 -----------------------
 6 files changed, 19 insertions(+), 115 deletions(-)

diff --git a/src/westpa/core/_rc.py b/src/westpa/core/_rc.py
index 50abbc30a..07efed852 100644
--- a/src/westpa/core/_rc.py
+++ b/src/westpa/core/_rc.py
@@ -16,7 +16,7 @@
 from westpa.core.binning.assign import BinMapper
 from westpa.core.binning import RectilinearBinMapper, RecursiveBinMapper, MABBinMapper, BinlessMapper
 from .yamlcfg import YAMLConfig
-from .yamlcfg import YAMLSystem
+from .systems import WESTSystem
 from . import extloader
 from ..work_managers import SerialWorkManager
 
@@ -548,7 +548,7 @@ def system_from_yaml(self, system_dict):
           the parsed settings from the config file.
         """
 
-        yamlSystem = YAMLSystem()
+        yamlSystem = WESTSystem()
         print("System building only off of the configuration file")
         # Now for the building of the system from YAML we need to use
         # require for these settings since they are musts.
diff --git a/src/westpa/core/binning/_assign.pyx b/src/westpa/core/binning/_assign.pyx
index 75a976c05..efcb71e23 100644
--- a/src/westpa/core/binning/_assign.pyx
+++ b/src/westpa/core/binning/_assign.pyx
@@ -71,7 +71,6 @@ cpdef rectilinear_assign(coord_t[:,:] coords,
 
             # backwards iteration needs signed values, so that the final != -1 works
             for idim in range(ndim-1,-1,-1):
-                found = 0
                 cval = coords[icoord,idim]
                 boundlen = boundlens[idim]
                 bvec = <coord_t*> boundvecs[idim]
diff --git a/src/westpa/core/propagators/executable.py b/src/westpa/core/propagators/executable.py
index e28734a90..16dd404a0 100644
--- a/src/westpa/core/propagators/executable.py
+++ b/src/westpa/core/propagators/executable.py
@@ -52,7 +52,7 @@ def pcoord_loader(fieldname, pcoord_return_filename, destobj, single_point):
             pcoord.shape = expected_shape
     if pcoord.shape != expected_shape:
         raise ValueError(
-            'progress coordinate data has incorrect shape {!r} [expected {!r}] Check pcoord.err or seg_logs for more information.'.format(
+            'progress coordinate data has incorrect shape {!r} [expected {!r}] Check get_pcoord stderr or seg_logs for more information.'.format(
                 pcoord.shape, expected_shape
             )
         )
diff --git a/src/westpa/core/reweight/_reweight.pyx b/src/westpa/core/reweight/_reweight.pyx
index a944a3cf9..3570a8719 100644
--- a/src/westpa/core/reweight/_reweight.pyx
+++ b/src/westpa/core/reweight/_reweight.pyx
@@ -4,40 +4,38 @@
 
 from __future__ import print_function,division
 import cython
-import numpy
 import numpy as np
 import h5py
 from scipy.sparse import csgraph
 import warnings
 from collections import Counter
-cimport numpy
 cimport numpy as np
 cimport scipy.linalg
 cimport scipy.linalg.cython_lapack as cl
 import scipy.linalg
 from libc.math cimport isnan
 
-ctypedef numpy.uint16_t index_t
-ctypedef numpy.float64_t weight_t
-ctypedef numpy.uint8_t bool_t
-ctypedef numpy.int64_t trans_t
-ctypedef numpy.uintp_t uint_t # 32 bits on 32-bit systems, 64 bits on 64-bit systems
+ctypedef np.uint16_t index_t
+ctypedef np.float64_t weight_t
+ctypedef np.uint8_t bool_t
+ctypedef np.int64_t trans_t
+ctypedef np.uintp_t uint_t # 32 bits on 32-bit systems, 64 bits on 64-bit systems
 ctypedef unsigned short Ushort
 ctypedef double complex Cdouble
 
-weight_dtype = numpy.float64
-index_dtype = numpy.uint16
-bool_dtype = numpy.bool_
-intc_dtype = numpy.intc
+weight_dtype = np.float64
+index_dtype = np.uint16
+bool_dtype = np.bool_
+intc_dtype = np.intc
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
-cpdef stats_process(numpy.ndarray[index_t, ndim=2] bin_assignments,
-                    numpy.ndarray[weight_t, ndim=1] weights,
-                    numpy.ndarray[weight_t, ndim=2] fluxes,
-                    numpy.ndarray[weight_t, ndim=1] populations,
-                    numpy.ndarray[trans_t, ndim=2] trans,
-                    numpy.ndarray[index_t, ndim=2] mask,
+cpdef stats_process(np.ndarray[index_t, ndim=2] bin_assignments,
+                    np.ndarray[weight_t, ndim=1] weights,
+                    np.ndarray[weight_t, ndim=2] fluxes,
+                    np.ndarray[weight_t, ndim=1] populations,
+                    np.ndarray[trans_t, ndim=2] trans,
+                    np.ndarray[index_t, ndim=2] mask,
                     str interval='timepoint'                        ):
     cdef:
         Py_ssize_t i,k
diff --git a/src/westpa/core/sim_manager.py b/src/westpa/core/sim_manager.py
index 163581ccc..e5acf0b04 100644
--- a/src/westpa/core/sim_manager.py
+++ b/src/westpa/core/sim_manager.py
@@ -306,7 +306,7 @@ def initialize_simulation(self, basis_states, target_states, start_states, segs_
 
         # Process start states
         # Unlike the above, does not create an ibstate group.
-        # TODO: Should it? I don't think so, if needed it can be traced back through basis_auxref
+        # Should it? I don't think so, if needed it can be traced back through basis_auxref
 
         # Here, we are trying to assign a state_id to the start state to be initialized, without actually
         # saving it to the ibstates records in any of the h5 files. It might actually be a problem
diff --git a/src/westpa/core/yamlcfg.py b/src/westpa/core/yamlcfg.py
index 812c9f183..6efa9b057 100644
--- a/src/westpa/core/yamlcfg.py
+++ b/src/westpa/core/yamlcfg.py
@@ -4,9 +4,7 @@
 
 import os
 import warnings
-
 import yaml
-import numpy as np
 
 try:
     from yaml import CLoader as YLoader
@@ -15,10 +13,6 @@
     from yaml import Loader as YLoader
 
 from . import extloader
-from .binning import NopMapper
-
-# Only needed for temporary class
-import westpa
 
 NotProvided = object()
 
@@ -302,90 +296,3 @@ def get_choice(self, key, choices, default=NotProvided, value_transform=None):
                 ),
             )
         return value
-
-
-# Temporary class here
-class YAMLSystem:
-    '''A description of the system being simulated, including the dimensionality and
-    data type of the progress coordinate, the number of progress coordinate entries
-    expected from each segment, and binning. To construct a simulation, the user must
-    subclass WESTSystem and set several instance variables.
-
-    At a minimum, the user must subclass ``WESTSystem`` and override
-    :method:`initialize` to set the data type and dimensionality of progress
-    coordinate data and define a bin mapper.
-
-    :ivar pcoord_ndim:    The number of dimensions in the progress coordinate.
-                          Defaults to 1 (i.e. a one-dimensional progress
-                          coordinate).
-    :ivar pcoord_dtype:   The data type of the progress coordinate, which must be
-                          callable (e.g. ``np.float32`` and ``long`` will work,
-                          but ``'<f4'`` and ``'<i8'`` will not).  Defaults to
-                          ``np.float64``.
-    :ivar pcoord_len:     The length of the progress coordinate time series
-                          generated by each segment, including *both* the initial
-                          and final values.  Defaults to 2 (i.e. only the initial
-                          and final progress coordinate values for a segment are
-                          returned from propagation).
-    :ivar bin_mapper:     A bin mapper describing the progress coordinate space.
-    :ivar bin_target_counts: A vector of target counts, one per bin.
-    '''
-
-    def __init__(self, rc=None):
-        self.rc = rc or westpa.rc
-
-        # Number of dimentions in progress coordinate data
-        self.pcoord_ndim = 1
-
-        # Length of progress coordinate data for each segment
-        self.pcoord_len = 2
-
-        # Data type of progress coordinate
-        self.pcoord_dtype = np.float32
-
-        # Mapper
-        self.bin_mapper = NopMapper()
-        # self.bin_mapper = None
-        self._bin_target_counts = None
-
-        self.bin_target_counts = [1]
-
-    @property
-    def bin_target_counts(self):
-        return self._bin_target_counts
-
-    @bin_target_counts.setter
-    def bin_target_counts(self, target_counts):
-        maxcount = max(target_counts)
-        self._bin_target_counts = np.array(target_counts, dtype=np.min_scalar_type(maxcount))
-
-    def initialize(self):
-        '''Prepare this system object for use in simulation or analysis,
-        creating a bin space, setting replicas per bin, and so on. This
-        function is called whenever a WEST tool creates an instance of the
-        system driver.
-        '''
-        pass
-
-    def prepare_run(self):
-        '''Prepare this system for use in a simulation run. Called by w_run in
-        all worker processes.'''
-        pass
-
-    def finalize_run(self):
-        '''A hook for system-specific processing for the end of a simulation run
-        (as defined by such things as maximum wallclock time, rather than perhaps
-        more scientifically-significant definitions of "the end of a simulation run")'''
-        pass
-
-    def new_pcoord_array(self, pcoord_len=None):
-        '''Return an appropriately-sized and -typed pcoord array for a timepoint, segment,
-        or number of segments. If ``pcoord_len`` is not specified (or None), then
-        a length appropriate for a segment is returned.'''
-
-        if pcoord_len is None:
-            pcoord_len = self.pcoord_len
-        return np.zeros((pcoord_len, self.pcoord_ndim), self.pcoord_dtype)
-
-    def new_region_set(self):
-        raise NotImplementedError('This method has been removed.')

From 9e1a6867adb9f6dd09398802f257121c6871a8c2 Mon Sep 17 00:00:00 2001
From: "Jeremy M. G. Leung" <jml230@pitt.edu>
Date: Fri, 14 Feb 2025 15:01:40 -0500
Subject: [PATCH 2/9] math.ceil and math.floor already returns int

---
 src/westpa/core/we_driver.py       | 5 ++---
 src/westpa/mclib/_mclib.pyx        | 8 ++++----
 src/westpa/oldtools/aframe/mcbs.py | 8 ++++----
 src/westpa/oldtools/stats/mcbs.py  | 4 ++--
 src/westpa/tools/binning.py        | 2 +-
 5 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/src/westpa/core/we_driver.py b/src/westpa/core/we_driver.py
index fa99a7610..67a1a0c60 100644
--- a/src/westpa/core/we_driver.py
+++ b/src/westpa/core/we_driver.py
@@ -281,7 +281,6 @@ def new_iteration(self, initial_states=None, target_states=None, new_weights=Non
 
         self.initial_binning = self.bin_mapper.construct_bins()
         self.final_binning = self.bin_mapper.construct_bins()
-        self.next_iter_binning = None
 
         flux_matrix = self.flux_matrix = np.zeros((nbins, nbins), dtype=np.float64)
         transition_matrix = self.transition_matrix = np.zeros((nbins, nbins), np.uint)
@@ -532,7 +531,7 @@ def _split_by_weight(self, bin, target_count, ideal_weight):
         to_split = segments[weights > self.weight_split_threshold * ideal_weight]
 
         for segment in to_split:
-            m = int(math.ceil(segment.weight / ideal_weight))
+            m = math.ceil(segment.weight / ideal_weight)
             bin.remove(segment)
             new_segments_list = self._split_walker(segment, m, bin)
             bin.update(new_segments_list)
@@ -625,7 +624,7 @@ def _split_by_threshold(self, bin, subgroup):
 
         to_split = segments[weights > self.largest_allowed_weight]
         for segment in to_split:
-            m = int(math.ceil(segment.weight / self.largest_allowed_weight))
+            m = math.ceil(segment.weight / self.largest_allowed_weight)
             bin.remove(segment)
             subgroup.remove(segment)
             new_segments_list = self._split_walker(segment, m, bin)
diff --git a/src/westpa/mclib/_mclib.pyx b/src/westpa/mclib/_mclib.pyx
index b57bf1777..94773eaae 100644
--- a/src/westpa/mclib/_mclib.pyx
+++ b/src/westpa/mclib/_mclib.pyx
@@ -151,8 +151,8 @@ cpdef mcbs_ci(dataset, estimator, alpha, dlen, n_sets=None, args=None, kwargs=No
         del indices
 
     f_synth_sorted = sort(f_synth)
-    lbi = int(math.floor(n_sets*alpha/2.0))
-    ubi = int(math.ceil(n_sets*(1-alpha/2.0)))
+    lbi = math.floor(n_sets*alpha/2.0)
+    ubi = math.ceil(n_sets*(1-alpha/2.0))
     lb = f_synth_sorted[lbi]
     ub = f_synth_sorted[ubi]
     sterr = numpy.std(f_synth_sorted)
@@ -200,8 +200,8 @@ cpdef mcbs_correltime_small(dataset, alpha, n_sets):
         raise ValueError('alpha ({}) > 0.5'.format(alpha))
 
     dlen = len(dataset)
-    lbi = int(math.floor(n_sets*alpha/2.0))
-    ubi = int(math.ceil(n_sets*(1-alpha/2.0)))
+    lbi = math.floor(n_sets*alpha/2.0)
+    ubi = math.ceil(n_sets*(1-alpha/2.0))
 
     synth_sets = numpy.empty((n_sets,)+dataset.shape, dtype=dataset.dtype)
     synth_acf_elems = numpy.empty((n_sets,), numpy.float64)
diff --git a/src/westpa/oldtools/aframe/mcbs.py b/src/westpa/oldtools/aframe/mcbs.py
index b7f3e1b04..f0d25abe4 100644
--- a/src/westpa/oldtools/aframe/mcbs.py
+++ b/src/westpa/oldtools/aframe/mcbs.py
@@ -55,7 +55,7 @@ def process_args(self, args, upcall=True):
         self.mcbs_alpha = 1 - args.mcbs_confidence
         self.mcbs_nsets = args.mcbs_size if args.mcbs_nsets else min(1000, calc_mcbs_nsets(self.mcbs_alpha))
         self.mcbs_display_confidence = '{:.{cp}f}'.format(
-            100 * args.mcbs_confidence, cp=-int(math.floor(math.log10(self.mcbs_alpha))) - 2
+            100 * args.mcbs_confidence, cp=-math.floor(math.log10(self.mcbs_alpha)) - 2
         )
         westpa.rc.pstatus(
             'Using bootstrap of {:d} sets to calculate {:s}% confidence interval (alpha={:g}).'.format(
@@ -90,7 +90,7 @@ def calc_mcbs_nsets(alpha):
 
 
 def calc_ci_bound_indices(n_sets, alpha):
-    return (int(math.floor(n_sets * alpha / 2)), int(math.ceil(n_sets * (1 - alpha / 2))))
+    return (math.floor(n_sets * alpha / 2), math.ceil(n_sets * (1 - alpha / 2)))
 
 
 def bootstrap_ci_ll(estimator, data, alpha, n_sets, storage, sort, eargs=(), ekwargs={}, fhat=None):
@@ -112,8 +112,8 @@ def bootstrap_ci_ll(estimator, data, alpha, n_sets, storage, sort, eargs=(), ekw
         storage[iset] = estimator(data[indices], *eargs, **ekwargs)
 
     synth_sorted = sort(storage)
-    lbi = int(math.floor(n_sets * alpha / 2))
-    ubi = int(math.ceil(n_sets * (1 - alpha / 2)))
+    lbi = math.floor(n_sets * alpha / 2)
+    ubi = math.ceil(n_sets * (1 - alpha / 2))
 
     lb = synth_sorted[lbi]
     ub = synth_sorted[ubi]
diff --git a/src/westpa/oldtools/stats/mcbs.py b/src/westpa/oldtools/stats/mcbs.py
index 89f3e61aa..f0b0ab9d8 100644
--- a/src/westpa/oldtools/stats/mcbs.py
+++ b/src/westpa/oldtools/stats/mcbs.py
@@ -81,8 +81,8 @@ def bootstrap_ci(estimator, data, alpha, n_sets=None, args=(), kwargs={}, sort=m
         f_synth[i] = estimator(data[indices], *args, **kwargs)
 
     f_synth_sorted = sort(f_synth)
-    lbi = int(math.floor(n_sets * alpha / 2))
-    ubi = int(math.ceil(n_sets * (1 - alpha / 2)))
+    lbi = math.floor(n_sets * alpha / 2)
+    ubi = math.ceil(n_sets * (1 - alpha / 2))
     lb = f_synth_sorted[lbi]
     ub = f_synth_sorted[ubi]
 
diff --git a/src/westpa/tools/binning.py b/src/westpa/tools/binning.py
index 668d18ef6..867a87446 100644
--- a/src/westpa/tools/binning.py
+++ b/src/westpa/tools/binning.py
@@ -144,7 +144,7 @@ def write_bin_info(mapper, assignments, weights, n_target_states, outfile=sys.st
     min_seg_weight = weights.min()
     max_seg_weight = weights.max()
 
-    ndec = int(math.ceil(-math.log10(1 / n_active)))
+    ndec = math.ceil(-math.log10(1 / n_active))
 
     outfile.write('{:d} segments\n'.format(len(weights)))
     outfile.write(

From fdbb70ae58c234eb112dd5fa9952f5fad54da89c Mon Sep 17 00:00:00 2001
From: "Jeremy M. G. Leung" <jml230@pitt.edu>
Date: Fri, 14 Feb 2025 15:04:20 -0500
Subject: [PATCH 3/9] change tests import

---
 tests/refs/odld/odld_system.py | 4 +---
 tests/test_yamlfe.py           | 5 +++--
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/tests/refs/odld/odld_system.py b/tests/refs/odld/odld_system.py
index e769b70b4..3c8ee0df2 100644
--- a/tests/refs/odld/odld_system.py
+++ b/tests/refs/odld/odld_system.py
@@ -1,11 +1,9 @@
 import numpy as np
 from numpy.random import Generator, MT19937
 
-from westpa.core.binning import RectilinearBinMapper
+from westpa.core.binning import RectilinearBinMapper, MABBinMapper, BinlessMapper
 from westpa.core.propagators import WESTPropagator
 from westpa.core.systems import WESTSystem
-from westpa.core.binning.mab import MABBinMapper
-from westpa.core.binning.binless import BinlessMapper
 
 PI = np.pi
 
diff --git a/tests/test_yamlfe.py b/tests/test_yamlfe.py
index c6eae389d..5ceb92fd5 100644
--- a/tests/test_yamlfe.py
+++ b/tests/test_yamlfe.py
@@ -1,11 +1,12 @@
 import numpy as np
 
 import westpa
-import westpa.core.yamlcfg as ycf
+from westpa.core.yamlcfg import ycf
+from westpa.core.systems import WESTSystem
 from westpa.core.binning import RectilinearBinMapper
 
 
-class TESTSystem(ycf.YAMLSystem):
+class TESTSystem(WESTSystem):
     def initialize(self):
         self.pcoord_ndim = 1
         self.pcoord_dtype = np.float32

From c6817c23e7d93c647960fefc52efe942405f8309 Mon Sep 17 00:00:00 2001
From: "Jeremy M. G. Leung" <jml230@pitt.edu>
Date: Fri, 14 Feb 2025 15:18:41 -0500
Subject: [PATCH 4/9] fix faulty import yamlcfg

---
 tests/test_yamlfe.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_yamlfe.py b/tests/test_yamlfe.py
index 5ceb92fd5..81d178ece 100644
--- a/tests/test_yamlfe.py
+++ b/tests/test_yamlfe.py
@@ -1,7 +1,7 @@
 import numpy as np
 
 import westpa
-from westpa.core.yamlcfg import ycf
+import westpa.core.yamlcfg as ycf
 from westpa.core.systems import WESTSystem
 from westpa.core.binning import RectilinearBinMapper
 

From ece683d7d47e986ff0db7750adae1cccce729dc8 Mon Sep 17 00:00:00 2001
From: "Jeremy M. G. Leung" <jml230@pitt.edu>
Date: Wed, 19 Feb 2025 15:16:55 -0500
Subject: [PATCH 5/9] first tests for westpa.tools.binning

---
 tests/test_binningfe.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 tests/test_binningfe.py

diff --git a/tests/test_binningfe.py b/tests/test_binningfe.py
new file mode 100644
index 000000000..92b0fe3de
--- /dev/null
+++ b/tests/test_binningfe.py
@@ -0,0 +1,13 @@
+import numpy as np
+
+from westpa.tools.binning import mapper_from_expr
+
+
+class TestBinParsing:
+    def testMapperFromExpr(self):
+        mapper = mapper_from_expr(r'[[-inf, 0, 15, np.inf]]')
+
+        assert mapper.ndim == 1
+        assert mapper.nbins == 3
+        assert np.array_equal(mapper._boundaries, [np.array([-float('inf'), 0, 15, float('inf')], dtype=np.float32)])
+        assert mapper.labels == ['[(-inf, 0.0)]', '[(0.0, 15.0)]', '[(15.0, inf)]']

From 99dbc8204b5eea7cf8b0bcad19878840e093788b Mon Sep 17 00:00:00 2001
From: "Jeremy M. G. Leung" <jml230@pitt.edu>
Date: Mon, 5 May 2025 12:04:14 -0400
Subject: [PATCH 6/9] add new YAMLSystem tests

---
 tests/test_yamlfe.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/tests/test_yamlfe.py b/tests/test_yamlfe.py
index 81d178ece..0dad31c25 100644
--- a/tests/test_yamlfe.py
+++ b/tests/test_yamlfe.py
@@ -1,4 +1,6 @@
+import pytest
 import numpy as np
+from numpy.testing import assert_array_equal
 
 import westpa
 import westpa.core.yamlcfg as ycf
@@ -112,3 +114,20 @@ def testYAMLFEConfig(self):
         rc.config['west', 'propagation', 'max_total_iteration'] = 1000
 
         assert rc.config['west', 'propagation', 'max_total_iteration'] == 1000
+
+    def testSystemDefaults(self):
+        # First the objects that will be used for testing
+        testSystem = WESTSystem()
+
+        with pytest.raises(NotImplementedError):
+            testSystem.new_region_set()
+
+        # Test that the new pcoord array is of the correct shape
+        test_zero = np.zeros((2, 1), np.float32)
+        pcoord_array = testSystem.new_pcoord_array()
+        assert testSystem.pcoord_len == 2
+        assert_array_equal(test_zero, pcoord_array)
+
+        testSystem.initialize()
+        testSystem.prepare_run()
+        testSystem.finalize_run()

From 641f4925e45c04d4c17aecada9a5b10f8676195f Mon Sep 17 00:00:00 2001
From: "Jeremy M. G. Leung" <jml230@pitt.edu>
Date: Mon, 5 May 2025 15:55:35 -0400
Subject: [PATCH 7/9] tests for split/merge by threshold

---
 tests/test_we_driver.py | 46 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/tests/test_we_driver.py b/tests/test_we_driver.py
index 7ba4aeaca..7d523c35f 100644
--- a/tests/test_we_driver.py
+++ b/tests/test_we_driver.py
@@ -251,5 +251,51 @@ def test_populate_initial(self):
             for tcount in range(30, 60):
                 yield self.check_populate_initial, prob, tcount
 
+    def test_merge_by_threshold(self):
+        # Create the segments
+        segments = [self.segment(0.0, 0.5, weight=0.25) for i in range(4)]
+        self.we_driver.smallest_allowed_weight = 0.5
+
+        # Create the bins
+        self.we_driver.new_iteration()
+        self.we_driver.assign(segments)
+        self.we_driver.construct_next()
+
+        for ibin, bin in enumerate(self.we_driver.next_iter_binning):
+            subgroup = self.we_driver.subgroup_function(self.we_driver, ibin, **self.we_driver.subgroup_function_kwargs)
+
+            if len(bin) > 0:
+                # Occupied bin
+                self.we_driver._merge_by_threshold(bin, subgroup[ibin])
+
+                assert len(self.we_driver.next_iter_binning[ibin]) == 1
+                assert np.allclose([seg.weight for seg in self.we_driver.next_iter_binning[0]], [1])
+            else:
+                # Unoccupied bins
+                assert len(self.we_driver.next_iter_binning[ibin]) == 0
+
+    def test_split_by_threshold(self):
+        # Create the segments
+        segments = [self.segment(0.0, 0.5, weight=1)]
+        self.we_driver.largest_allowed_weight = 0.125
+
+        # Create the bins
+        self.we_driver.new_iteration()
+        self.we_driver.assign(segments)
+        self.we_driver.construct_next()
+
+        for ibin, bin in enumerate(self.we_driver.next_iter_binning):
+            subgroup = self.we_driver.subgroup_function(self.we_driver, ibin, **self.we_driver.subgroup_function_kwargs)
+
+            if len(bin) > 0:
+                # Occupied bin
+                self.we_driver._split_by_threshold(bin, subgroup[ibin])
+
+                assert len(self.we_driver.next_iter_binning[ibin]) == 8
+                assert np.allclose([seg.weight for seg in self.we_driver.next_iter_binning[0]], [0.125 for _i in range(8)])
+            else:
+                # Unoccupied bins
+                assert len(self.we_driver.next_iter_binning[ibin]) == 0
+
     # TODO: add test for seeding the flux matrix based on recycling
     # TODO: add test for split after merge in adjust count

From 83dff7111989635d3ca16f145fe028a4ff700d26 Mon Sep 17 00:00:00 2001
From: "Jeremy M. G. Leung" <jml230@pitt.edu>
Date: Mon, 5 May 2025 17:07:12 -0400
Subject: [PATCH 8/9] some mundane value/type testing for yamlcfg

---
 tests/test_yamlfe.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/tests/test_yamlfe.py b/tests/test_yamlfe.py
index 0dad31c25..040c0dd8d 100644
--- a/tests/test_yamlfe.py
+++ b/tests/test_yamlfe.py
@@ -131,3 +131,16 @@ def testSystemDefaults(self):
         testSystem.initialize()
         testSystem.prepare_run()
         testSystem.finalize_run()
+
+
+class TestYAMLConfig:
+    def test_dubious_config_entry(self):
+        with pytest.warns(ycf.ConfigValueWarning):
+            ycf.warn_dubious_config_entry('1', 1, expected_type=str)
+            ycf.warn_dubious_config_entry('1', 1)
+
+    def test_check_bool(self):
+        with pytest.warns(ycf.ConfigValueWarning):
+            ycf.check_bool(100, action='warn')
+        with pytest.raises(ValueError):
+            ycf.check_bool(100, action='raise')

From d72a92878630f7a3f4396c0042b53d3879c0a2ab Mon Sep 17 00:00:00 2001
From: "Jeremy M. G. Leung" <jml230@pitt.edu>
Date: Tue, 6 May 2025 12:40:34 -0400
Subject: [PATCH 9/9] set next_iter_binning to None when creating new iteration

---
 src/westpa/core/we_driver.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/westpa/core/we_driver.py b/src/westpa/core/we_driver.py
index 67a1a0c60..d843c4d3b 100644
--- a/src/westpa/core/we_driver.py
+++ b/src/westpa/core/we_driver.py
@@ -281,6 +281,7 @@ def new_iteration(self, initial_states=None, target_states=None, new_weights=Non
 
         self.initial_binning = self.bin_mapper.construct_bins()
         self.final_binning = self.bin_mapper.construct_bins()
+        self.next_iter_binning = None
 
         flux_matrix = self.flux_matrix = np.zeros((nbins, nbins), dtype=np.float64)
         transition_matrix = self.transition_matrix = np.zeros((nbins, nbins), np.uint)