From 2a4f1b49fe3cf2f31fe6095e0993e2c3299bdd0e Mon Sep 17 00:00:00 2001
From: "Jeremy M. G. Leung" <63817169+jeremyleung521@users.noreply.github.com>
Date: Wed, 9 Aug 2023 14:52:28 -0400
Subject: [PATCH 1/2] Fix for istate_futures race condition (#334)

* added a while block for mab_manager and binless_manager to wait for istates_futures

* add in extra checks for futures

* forgot the most obvious part of waiting and fetching the future

* add in barebone tests for mab and binless sim_managers

* replace logging.warn with logging.warning
---
 src/westpa/core/binning/binless_manager.py | 25 +++++-
 src/westpa/core/binning/mab.py             |  4 +-
 src/westpa/core/binning/mab_manager.py     | 25 +++++-
 src/westpa/core/h5io.py                    |  2 +-
 src/westpa/work_managers/zeromq/core.py    |  2 +-
 tests/fixtures/odld/odld_system.py         | 26 ++++++
 tests/fixtures/odld/west_binless.cfg       | 36 +++++++++
 tests/fixtures/odld/west_mab.cfg           | 36 +++++++++
 tests/test_sim_manager.py                  | 94 ++++++++++++++++++++++
 9 files changed, 244 insertions(+), 6 deletions(-)
 create mode 100644 tests/fixtures/odld/west_binless.cfg
 create mode 100644 tests/fixtures/odld/west_mab.cfg

diff --git a/src/westpa/core/binning/binless_manager.py b/src/westpa/core/binning/binless_manager.py
index c3ace0c5a..d038c0630 100644
--- a/src/westpa/core/binning/binless_manager.py
+++ b/src/westpa/core/binning/binless_manager.py
@@ -75,8 +75,31 @@ def propagate(self):
                 log.error('unknown future {!r} received from work manager'.format(future))
                 raise AssertionError('untracked future {!r}'.format(future))
 
+        # Collectively assign all segments to their bins...
         self.we_driver.assign(self.segments.values())
-        self.get_istate_futures()
+
+        # For cases where we need even more istates for recycled trajectories
+        # futures should be empty at this point.
+        istate_gen_futures = self.get_istate_futures()
+        futures.update(istate_gen_futures)
+
+        # Wait for istate_gen_futures and catch untracked futures.
+        while futures:
+            future = self.work_manager.wait_any(futures)
+            futures.remove(future)
+
+            if future in istate_gen_futures:
+                istate_gen_futures.remove(future)
+                _basis_state, initial_state = future.get_result()
+                log.debug('received newly-prepared initial state {!r}'.format(initial_state))
+                initial_state.istate_status = InitialState.ISTATE_STATUS_PREPARED
+                with self.data_manager.expiring_flushing_lock():
+                    self.data_manager.update_initial_states([initial_state], n_iter=self.n_iter + 1)
+                self.we_driver.avail_initial_states[initial_state.state_id] = initial_state
+            else:
+                log.error('unknown future {!r} received from work manager'.format(future))
+                raise AssertionError('untracked future {!r}'.format(future))
+
         log.debug('done with propagation')
         self.save_bin_data()
         self.data_manager.flush_backing()
diff --git a/src/westpa/core/binning/mab.py b/src/westpa/core/binning/mab.py
index 0fe67299c..f491cfbe8 100644
--- a/src/westpa/core/binning/mab.py
+++ b/src/westpa/core/binning/mab.py
@@ -262,13 +262,13 @@ def __init__(self, nbins, direction=None, skip=None, bottleneck=True, pca=False,
             direction = [0] * ndim
         elif len(direction) != ndim:
             direction = [0] * ndim
-            log.warn("Direction list is not the correct dimensions, setting to defaults.")
+            log.warning("Direction list is not the correct dimensions, setting to defaults.")
 
         if skip is None:
             skip = [0] * ndim
         elif len(skip) != ndim:
             skip = [0] * ndim
-            log.warn("Skip list is not the correct dimensions, setting to defaults.")
+            log.warning("Skip list is not the correct dimensions, setting to defaults.")
 
         kwargs = dict(nbins_per_dim=nbins, direction=direction, skip=skip, bottleneck=bottleneck, pca=pca, mab_log=mab_log)
         # the following is neccessary because functional bin mappers need to "reserve"
diff --git a/src/westpa/core/binning/mab_manager.py b/src/westpa/core/binning/mab_manager.py
index 79e5c7984..fcb570520 100644
--- a/src/westpa/core/binning/mab_manager.py
+++ b/src/westpa/core/binning/mab_manager.py
@@ -75,8 +75,31 @@ def propagate(self):
                 log.error('unknown future {!r} received from work manager'.format(future))
                 raise AssertionError('untracked future {!r}'.format(future))
 
+        # Collectively assign all segments to their bins...
         self.we_driver.assign(self.segments.values())
-        self.get_istate_futures()
+
+        # For cases where we need even more istates for recycled trajectories
+        # futures should be empty at this point.
+        istate_gen_futures = self.get_istate_futures()
+        futures.update(istate_gen_futures)
+
+        # Wait for istate_gen_futures and catch untracked futures.
+        while futures:
+            future = self.work_manager.wait_any(futures)
+            futures.remove(future)
+
+            if future in istate_gen_futures:
+                istate_gen_futures.remove(future)
+                _basis_state, initial_state = future.get_result()
+                log.debug('received newly-prepared initial state {!r}'.format(initial_state))
+                initial_state.istate_status = InitialState.ISTATE_STATUS_PREPARED
+                with self.data_manager.expiring_flushing_lock():
+                    self.data_manager.update_initial_states([initial_state], n_iter=self.n_iter + 1)
+                self.we_driver.avail_initial_states[initial_state.state_id] = initial_state
+            else:
+                log.error('unknown future {!r} received from work manager'.format(future))
+                raise AssertionError('untracked future {!r}'.format(future))
+
         log.debug('done with propagation')
         self.save_bin_data()
         self.data_manager.flush_backing()
diff --git a/src/westpa/core/h5io.py b/src/westpa/core/h5io.py
index ed2941c2a..37cc532a2 100644
--- a/src/westpa/core/h5io.py
+++ b/src/westpa/core/h5io.py
@@ -220,7 +220,7 @@ def load_west(filename):
 
             raw_pcoord = iter_group['pcoord'][:]
             if raw_pcoord.ndim != 3:
-                log.warn('pcoord is expected to be a 3-d ndarray instead of {}-d'.format(raw_pcoord.ndim))
+                log.warning('pcoord is expected to be a 3-d ndarray instead of {}-d'.format(raw_pcoord.ndim))
                 continue
             # ignore the first frame of each segment
             if raw_pcoord.shape[1] == traj.n_frames + 1:
diff --git a/src/westpa/work_managers/zeromq/core.py b/src/westpa/work_managers/zeromq/core.py
index 8c217d5a2..d93450ede 100644
--- a/src/westpa/work_managers/zeromq/core.py
+++ b/src/westpa/work_managers/zeromq/core.py
@@ -439,7 +439,7 @@ def message_validation(self, msg):
                 self.log.error('message validation falied: {!s}'.format(e))
                 sys.exit(1)
             elif self.validation_fail_action == 'warn':
-                self.log.warn('message validation falied: {!s}'.format(e))
+                self.log.warning('message validation falied: {!s}'.format(e))
 
     def recv_message(self, socket, flags=0, validate=True, timeout=None):
         '''Receive a message object from the given socket, using the given flags.
diff --git a/tests/fixtures/odld/odld_system.py b/tests/fixtures/odld/odld_system.py
index 0d17b92b0..4e3d23010 100644
--- a/tests/fixtures/odld/odld_system.py
+++ b/tests/fixtures/odld/odld_system.py
@@ -4,6 +4,8 @@
 from westpa.core.binning import RectilinearBinMapper
 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
 
@@ -103,3 +105,27 @@ def initialize(self):
         self.bin_mapper = RectilinearBinMapper([list(np.arange(0.0, 10.1, 0.1))])
         self.bin_target_counts = np.empty((self.bin_mapper.nbins,), np.int_)
         self.bin_target_counts[...] = 10
+
+
+class MABODLDSystem(WESTSystem):
+    def initialize(self):
+        self.pcoord_ndim = 1
+        self.pcoord_dtype = pcoord_dtype
+        self.pcoord_len = pcoord_len
+
+        # self.bin_mapper = RectilinearBinMapper([[0,1.3] + list(np.arange(1.4, 10.1, 0.1)) + [float('inf')]])
+        self.bin_mapper = MABBinMapper([10])
+        self.bin_target_counts = np.empty((self.bin_mapper.nbins,), np.int_)
+        self.bin_target_counts[...] = 10
+
+
+class BinlessODLDSystem(WESTSystem):
+    def initialize(self):
+        self.pcoord_ndim = 1
+        self.pcoord_dtype = pcoord_dtype
+        self.pcoord_len = pcoord_len
+
+        # self.bin_mapper = RectilinearBinMapper([[0,1.3] + list(np.arange(1.4, 10.1, 0.1)) + [float('inf')]])
+        self.bin_mapper = BinlessMapper(ngroups=10, ndims=1, group_function='westpa.core.we_driver._group_walkers_identity')
+        self.bin_target_counts = np.empty((self.bin_mapper.nbins,), np.int_)
+        self.bin_target_counts[...] = 10
diff --git a/tests/fixtures/odld/west_binless.cfg b/tests/fixtures/odld/west_binless.cfg
new file mode 100644
index 000000000..577b90c71
--- /dev/null
+++ b/tests/fixtures/odld/west_binless.cfg
@@ -0,0 +1,36 @@
+# The master WEST configuration file for a simulation.
+# vi: set filetype=yaml :
+---
+west: 
+  system:
+    driver: odld_system.BinlessODLDSystem
+    module_path: $WEST_SIM_ROOT
+  propagation:
+    max_total_iterations: 100
+    max_run_wallclock: 3:00:00
+    propagator: odld_system.ODLDPropagator
+    gen_istates: true
+    block_size: 10000
+  data:
+    west_data_file: west.h5
+    aux_compression_threshold: 16384 # data sets bigger than this are compressed
+                                     # unless overridden by an entry in ``datasets`` below
+    datasets: # dataset storage options
+      - name: displacement            # name used to refer to this in segment.data/env vars
+        #h5path: auxdata/displacement # HDF5 storage path, overrides default
+        #store: true                  # store when writing segment data (defaults to true)
+        #load:  true                  # load when reading segment data (defaults to false)
+        store: false
+        load: false
+        dtype: float32                # numpy dtype
+        compression: false            # whether to store compressed
+        scaleoffset: 4                # whether to store with scale/offset filter
+        chunks: null                  # custom chunking, or null for auto/no chunking
+                                      #  - ignored if necessary for other options
+      - name: pcoord                  # you can mess CAREFULLY with pcoord as well
+        scaleoffset: 4
+        
+    data_refs: # how to convert segments and states to paths, etc
+      segment:       $WEST_SIM_ROOT/traj_segs/{segment.n_iter:06d}/{segment.seg_id:06d}
+      basis_state:   $WEST_SIM_ROOT/bstates/{basis_state.auxref}
+      initial_state: $WEST_SIM_ROOT/istates/{initial_state.iter_created}/{initial_state.state_id}.gro
diff --git a/tests/fixtures/odld/west_mab.cfg b/tests/fixtures/odld/west_mab.cfg
new file mode 100644
index 000000000..e79ee7a12
--- /dev/null
+++ b/tests/fixtures/odld/west_mab.cfg
@@ -0,0 +1,36 @@
+# The master WEST configuration file for a simulation.
+# vi: set filetype=yaml :
+---
+west: 
+  system:
+    driver: odld_system.MABODLDSystem
+    module_path: $WEST_SIM_ROOT
+  propagation:
+    max_total_iterations: 100
+    max_run_wallclock: 3:00:00
+    propagator: odld_system.ODLDPropagator
+    gen_istates: true
+    block_size: 10000
+  data:
+    west_data_file: west.h5
+    aux_compression_threshold: 16384 # data sets bigger than this are compressed
+                                     # unless overridden by an entry in ``datasets`` below
+    datasets: # dataset storage options
+      - name: displacement            # name used to refer to this in segment.data/env vars
+        #h5path: auxdata/displacement # HDF5 storage path, overrides default
+        #store: true                  # store when writing segment data (defaults to true)
+        #load:  true                  # load when reading segment data (defaults to false)
+        store: false
+        load: false
+        dtype: float32                # numpy dtype
+        compression: false            # whether to store compressed
+        scaleoffset: 4                # whether to store with scale/offset filter
+        chunks: null                  # custom chunking, or null for auto/no chunking
+                                      #  - ignored if necessary for other options
+      - name: pcoord                  # you can mess CAREFULLY with pcoord as well
+        scaleoffset: 4
+        
+    data_refs: # how to convert segments and states to paths, etc
+      segment:       $WEST_SIM_ROOT/traj_segs/{segment.n_iter:06d}/{segment.seg_id:06d}
+      basis_state:   $WEST_SIM_ROOT/bstates/{basis_state.auxref}
+      initial_state: $WEST_SIM_ROOT/istates/{initial_state.iter_created}/{initial_state.state_id}.gro
diff --git a/tests/test_sim_manager.py b/tests/test_sim_manager.py
index 6b143eb8b..b3fdc2b17 100755
--- a/tests/test_sim_manager.py
+++ b/tests/test_sim_manager.py
@@ -178,3 +178,97 @@ def test_pre_we(self):
 
     def test_post_we(self):
         self.sim_manager.post_we()
+
+
+class TestMABSimManager(TestSimManager):
+    def setUp(self):
+        parser = argparse.ArgumentParser()
+        westpa.rc.add_args(parser)
+
+        here = os.path.dirname(__file__)
+        os.environ['WEST_SIM_ROOT'] = os.path.join(here, 'fixtures', 'odld')
+
+        config_file_name = os.path.join(here, 'fixtures', 'odld', 'west_mab.cfg')
+        args = parser.parse_args(['-r={}'.format(config_file_name)])
+        westpa.rc.process_args(args)
+        self.sim_manager = westpa.rc.get_sim_manager()
+        self.test_dir = tempfile.mkdtemp()
+        self.hdf5 = os.path.join(self.test_dir, "west.h5")
+        self.basis_states = [BasisState(label="label", probability=1.0)]
+        self.segments = [self.segment(0.0, 1.5, weight=0.125) for _i in range(4)] + [
+            self.segment(1.5, 0.5, weight=0.125) for _i in range(4)
+        ]
+        self.sim_manager.we_driver.new_iteration()
+        self.sim_manager.we_driver.assign(self.segments)
+        self.sim_manager.we_driver.construct_next()
+        self.sim_manager.segments = {segment.seg_id: segment for segment in self.segments}
+        self.sim_manager.incomplete_segments = self.sim_manager.segments
+        self.sim_manager.current_iter_istates = self.sim_manager.segments
+        self.sim_manager.completed_segments = self.sim_manager.segments
+        self.sim_manager.report_bin_statistics = MagicMock(return_value=True)
+
+        data = self.sim_manager.we_driver.rc.get_data_manager()
+        data.we_h5filename = self.hdf5
+        data.prepare_backing()
+        data.create_ibstate_group([])
+        data.create_initial_states(1)
+        data.save_target_states([])
+        data.update_segments = MagicMock(return_value=None)
+
+        n_iter = 0
+        it_name = data.iter_group_name(n_iter)
+        for group in ["seg_index", "parents", "ibstates", "pcoord"]:
+            data.we_h5file.create_group(it_name + "/" + group)
+        data.get_new_weight_data = MagicMock(return_value=None)
+        data.get_segments = MagicMock(return_value=self.segments)
+        self.sim_manager.we_driver.rc.get_data_manager = MagicMock(return_value=data)
+        self.sim_manager.n_iter = n_iter
+
+
+class TestBinlessSimManager(TestSimManager):
+    def setUp(self):
+        parser = argparse.ArgumentParser()
+        westpa.rc.add_args(parser)
+
+        here = os.path.dirname(__file__)
+        os.environ['WEST_SIM_ROOT'] = os.path.join(here, 'fixtures', 'odld')
+
+        config_file_name = os.path.join(here, 'fixtures', 'odld', 'west_binless.cfg')
+        args = parser.parse_args(['-r={}'.format(config_file_name)])
+        westpa.rc.process_args(args)
+        self.sim_manager = westpa.rc.get_sim_manager()
+        self.test_dir = tempfile.mkdtemp()
+        self.hdf5 = os.path.join(self.test_dir, "west.h5")
+        self.basis_states = [BasisState(label="label", probability=1.0)]
+        self.segments = [self.segment(0.0, 1.5, weight=0.125) for _i in range(4)] + [
+            self.segment(1.5, 0.5, weight=0.125) for _i in range(4)
+        ]
+        self.sim_manager.we_driver.new_iteration()
+        self.sim_manager.we_driver.assign(self.segments)
+        self.sim_manager.we_driver.construct_next()
+        self.sim_manager.segments = {segment.seg_id: segment for segment in self.segments}
+        self.sim_manager.incomplete_segments = self.sim_manager.segments
+        self.sim_manager.current_iter_istates = self.sim_manager.segments
+        self.sim_manager.completed_segments = self.sim_manager.segments
+        self.sim_manager.report_bin_statistics = MagicMock(return_value=True)
+
+        data = self.sim_manager.we_driver.rc.get_data_manager()
+        data.we_h5filename = self.hdf5
+        data.prepare_backing()
+        data.create_ibstate_group([])
+        data.create_initial_states(1)
+        data.save_target_states([])
+        data.update_segments = MagicMock(return_value=None)
+
+        n_iter = 0
+        it_name = data.iter_group_name(n_iter)
+        for group in ["seg_index", "parents", "ibstates", "pcoord"]:
+            data.we_h5file.create_group(it_name + "/" + group)
+        data.get_new_weight_data = MagicMock(return_value=None)
+        data.get_segments = MagicMock(return_value=self.segments)
+        self.sim_manager.we_driver.rc.get_data_manager = MagicMock(return_value=data)
+        self.sim_manager.n_iter = n_iter
+
+    @pytest.mark.skip('Not configured')
+    def test_run(self):
+        self.sim_manager.run()

From 661ee1aae1429434f26a0fc8e4d27a9acf50432c Mon Sep 17 00:00:00 2001
From: "Jeremy M. G. Leung" <63817169+jeremyleung521@users.noreply.github.com>
Date: Fri, 11 Aug 2023 14:47:03 -0400
Subject: [PATCH 2/2] Pre commit version autoupdate (#338)

* pre-commit autoupdate

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* flake8 update

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .flake8                                       | 21 ++++++++++++-------
 .pre-commit-config.yaml                       |  9 +++++---
 examples/ex_graphtest.py                      |  6 +++---
 src/westpa/cli/core/w_fork.py                 |  2 +-
 src/westpa/cli/core/w_init.py                 |  1 -
 src/westpa/cli/core/w_run.py                  |  1 -
 src/westpa/cli/core/w_states.py               |  2 --
 src/westpa/cli/core/w_succ.py                 |  2 +-
 src/westpa/cli/tools/w_assign.py              |  1 -
 src/westpa/cli/tools/w_bins.py                |  1 -
 src/westpa/cli/tools/w_dumpsegs.py            |  2 +-
 src/westpa/cli/tools/w_eddist.py              |  4 ----
 src/westpa/cli/tools/w_ipa.py                 |  1 -
 src/westpa/cli/tools/w_multi_west.py          |  2 +-
 src/westpa/cli/tools/w_pdist.py               |  1 -
 src/westpa/cli/tools/w_red.py                 |  1 -
 src/westpa/core/_rc.py                        |  1 -
 src/westpa/core/binning/assign.py             |  4 ++--
 src/westpa/core/binning/binless_driver.py     |  2 +-
 src/westpa/core/binning/binless_manager.py    |  2 +-
 src/westpa/core/binning/mab.py                |  1 -
 src/westpa/core/binning/mab_driver.py         |  2 +-
 src/westpa/core/binning/mab_manager.py        |  2 +-
 src/westpa/core/data_manager.py               | 11 +++++-----
 src/westpa/core/h5io.py                       |  4 ----
 src/westpa/core/propagators/__init__.py       |  1 -
 src/westpa/core/propagators/executable.py     |  4 +---
 src/westpa/core/sim_manager.py                |  7 +++----
 src/westpa/core/we_driver.py                  | 14 ++++++-------
 src/westpa/oldtools/aframe/binning.py         |  4 ++--
 src/westpa/oldtools/aframe/data_reader.py     |  7 +++----
 src/westpa/oldtools/aframe/kinetics.py        |  1 -
 src/westpa/oldtools/aframe/trajwalker.py      |  2 +-
 src/westpa/oldtools/aframe/transitions.py     |  4 +---
 src/westpa/oldtools/cmds/w_ttimes.py          |  6 ++----
 src/westpa/tools/binning.py                   |  5 +----
 src/westpa/tools/kinetics_tool.py             |  3 ---
 src/westpa/tools/selected_segs.py             |  1 -
 src/westpa/trajtree/trajtree.py               |  2 --
 .../westext/adaptvoronoi/adaptVor_driver.py   |  2 --
 .../hamsm_restarting/example_overrides.py     |  1 -
 .../hamsm_restarting/restart_driver.py        | 19 +----------------
 .../westext/stringmethod/string_driver.py     |  1 -
 .../westext/stringmethod/string_method.py     |  2 --
 src/westpa/westext/weed/weed_driver.py        |  4 ++--
 src/westpa/westext/wess/ProbAdjust.py         |  1 -
 src/westpa/westext/wess/wess_driver.py        |  4 ++--
 src/westpa/work_managers/environment.py       |  1 -
 src/westpa/work_managers/mpi.py               |  7 -------
 src/westpa/work_managers/zeromq/core.py       |  4 ----
 .../work_managers/zeromq/work_manager.py      |  3 +--
 src/westpa/work_managers/zeromq/worker.py     |  1 -
 tests/fixtures/odld/odld_system.py            |  1 -
 tests/refs/odld_system.py                     |  1 -
 tests/test_binning.py                         |  1 -
 tests/test_tools/common.py                    |  1 -
 tests/test_tools/h5diff.py                    | 12 +++--------
 tests/test_tools/test_w_assign.py             |  1 -
 tests/test_tools/test_w_direct.py             |  2 --
 tests/test_tools/test_w_ipa.py                |  1 -
 tests/test_tools/test_w_trace.py              |  2 --
 tests/test_we_driver.py                       |  1 -
 .../test_zeromq/test_worker.py                |  1 -
 tests/test_yamlfe.py                          |  1 +
 64 files changed, 69 insertions(+), 153 deletions(-)

diff --git a/.flake8 b/.flake8
index ed940a1da..f9c4b8960 100644
--- a/.flake8
+++ b/.flake8
@@ -1,10 +1,17 @@
 [flake8]
 max-line-length = 132
 ignore =
-    E203,  # space before : (needed for how black formats slicing)
-    E266,  # too many leading '#' for block comment 
-    E501,  # line lengths too long
-    W503,  # line break before binary operator
-    W504,  # line break after binary operator
-    E402,  # module level import not at top of file
-    E731,  # do not assign a lambda expression, use a def
+    # space before : (needed for how black formats slicing)
+    E203,
+    # too many leading '#' for block comment 
+    E266,
+    # line lengths too long
+    E501,
+    # line break before binary operator
+    W503,
+    # line break after binary operator
+    W504,
+    # module level import not at top of file
+    E402,
+    # do not assign a lambda expression, use a def
+    E731,
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 144ee823f..4383f767f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.4.0
     hooks:
     -   id: end-of-file-fixer
         types: [python]
@@ -8,7 +8,7 @@ repos:
         types: [python]
 
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.7.0
     hooks:
       - id: black
         language_version: python3
@@ -19,7 +19,7 @@ repos:
               | doc
           )
   - repo: https://github.com/pycqa/flake8
-    rev: 4.0.1
+    rev: 6.1.0
     hooks:
     -   id: flake8
         exclude: > 
@@ -28,3 +28,6 @@ repos:
               | _version.py
               | doc
           )
+
+ci:
+  autoupdate_branch: 'develop'
diff --git a/examples/ex_graphtest.py b/examples/ex_graphtest.py
index 0e35e66a2..0bfd2c933 100644
--- a/examples/ex_graphtest.py
+++ b/examples/ex_graphtest.py
@@ -56,9 +56,9 @@ def get_all_leaves(n_iter, iter_group):
 # print(leaves_by_branchpoint)
 print('there are {:d} branch points leading to approximately independent trajectory bundles'.format(len(leaves_by_branchpoint)))
 # for ((branch,node),leaves) in leaves_by_branchpoint.iteritems():
-for (branchnode, subtrees) in leaves_by_branchpoint.items():
+for branchnode, subtrees in leaves_by_branchpoint.items():
     print('  branch point {}:{} has {} independent subtree(s)'.format(branchnode.n_iter, branchnode.seg_id, len(subtrees)))
-    for (subtree, leaves) in subtrees.items():
+    for subtree, leaves in subtrees.items():
         leaves = list(leaves)
         weights = np.fromiter((leaf.weight for leaf in leaves), dtype=np.float64)
         max_weight_node = leaves[np.argmax(weights)]
@@ -71,7 +71,7 @@ def get_all_leaves(n_iter, iter_group):
         # print('subtree rooted at point ({},{}) contains {:d} leaves'.format(node.n_iter, node.seg_id,len(leaves)))
         # print('  of which ({},{}) has the highest weight ({!r})'.format(max_weight_node.n_iter, max_weight_node.seg_id,
         #                                                                max_weight_node.weight))
-for (root, leaves) in leftovers_by_root.items():
+for root, leaves in leftovers_by_root.items():
     print('{} trajectories from root {}:{} pruned due to shared history'.format(len(leaves), root.n_iter, root.seg_id))
 
 
diff --git a/src/westpa/cli/core/w_fork.py b/src/westpa/cli/core/w_fork.py
index 515395317..4c56b14cb 100644
--- a/src/westpa/cli/core/w_fork.py
+++ b/src/westpa/cli/core/w_fork.py
@@ -101,7 +101,7 @@ def entry_point():
     state_map = np.empty((n_segments,), dtype=state_map_dtype)
     state_map['old_n_iter'] = n_iter
 
-    for (iseg, (index_row, pcoord)) in enumerate(zip(old_index, old_final_pcoords)):
+    for iseg, (index_row, pcoord) in enumerate(zip(old_index, old_final_pcoords)):
         istate = istates[iseg]
         istate.iter_created = 0
         istate.iter_used = 1
diff --git a/src/westpa/cli/core/w_init.py b/src/westpa/cli/core/w_init.py
index 71c85951e..4ff212697 100644
--- a/src/westpa/cli/core/w_init.py
+++ b/src/westpa/cli/core/w_init.py
@@ -18,7 +18,6 @@
 
 
 def entry_point():
-
     parser = argparse.ArgumentParser(
         'w_init',
         description='''\
diff --git a/src/westpa/cli/core/w_run.py b/src/westpa/cli/core/w_run.py
index 8ec4da571..232ceddfb 100644
--- a/src/westpa/cli/core/w_run.py
+++ b/src/westpa/cli/core/w_run.py
@@ -30,7 +30,6 @@ def entry_point():
 
 
 def run_simulation():
-
     work_manager = westpa.rc.work_manager = make_work_manager()
 
     # Load the sim manager and other drivers
diff --git a/src/westpa/cli/core/w_states.py b/src/westpa/cli/core/w_states.py
index a758f7c4c..b7033fe2a 100644
--- a/src/westpa/cli/core/w_states.py
+++ b/src/westpa/cli/core/w_states.py
@@ -102,7 +102,6 @@ def entry_point():
 
 # TODO: This would benefit from a refactor to set default args to None, and replace some of those "if <argument>" clauses
 def initialize(mode, bstates, _bstate_file, tstates, _tstate_file):
-
     work_manager = make_work_manager()
 
     system = westpa.rc.get_system_driver()
@@ -116,7 +115,6 @@ def initialize(mode, bstates, _bstate_file, tstates, _tstate_file):
 
             assert mode in ('show', 'replace', 'append')
             if mode == 'show':
-
                 basis_states = data_manager.get_basis_states(n_iter)
                 if basis_states:
                     bstate_file = sys.stdout if not _bstate_file else open(_bstate_file, 'wt')
diff --git a/src/westpa/cli/core/w_succ.py b/src/westpa/cli/core/w_succ.py
index 7323e1a4a..aba2c17e8 100644
--- a/src/westpa/cli/core/w_succ.py
+++ b/src/westpa/cli/core/w_succ.py
@@ -57,7 +57,7 @@ def find_successful_trajs(self):
             # The above HDF5 selection always returns a vector; we want a 2-d array
             final_pcoords.shape = (len(recycled_seg_ids), pcoord_ndim)
 
-            for (ipc, seg_id) in enumerate(recycled_seg_ids):
+            for ipc, seg_id in enumerate(recycled_seg_ids):
                 self.output_file.write('%8d    %8d    %20.14g' % (n_iter, seg_id, seg_index[seg_id]['weight']))
                 fields = ['']
                 for field in final_pcoords[ipc]:
diff --git a/src/westpa/cli/tools/w_assign.py b/src/westpa/cli/tools/w_assign.py
index 877baf9e6..834c4862a 100644
--- a/src/westpa/cli/tools/w_assign.py
+++ b/src/westpa/cli/tools/w_assign.py
@@ -33,7 +33,6 @@ def parse_pcoord_value(pc_str):
 def _assign_label_pop(
     n_iter, lb, ub, mapper, nstates, state_map, last_labels, parent_id_dsspec, weight_dsspec, pcoord_dsspec, subsample
 ):
-
     nbins = len(state_map) - 1
     parent_ids = parent_id_dsspec.get_iter_data(n_iter, index_exp[lb:ub])
     weights = weight_dsspec.get_iter_data(n_iter, index_exp[lb:ub])
diff --git a/src/westpa/cli/tools/w_bins.py b/src/westpa/cli/tools/w_bins.py
index 99347bf86..0318e127b 100644
--- a/src/westpa/cli/tools/w_bins.py
+++ b/src/westpa/cli/tools/w_bins.py
@@ -68,7 +68,6 @@ def add_args(self, parser):
         rebin_parser.set_defaults(func=self.cmd_rebin)
 
     def process_args(self, args):
-
         self.data_reader.process_args(args)
         self.data_reader.open(mode='r+')
         self.n_iter = getattr(args, 'n_iter', None) or self.data_reader.current_iteration
diff --git a/src/westpa/cli/tools/w_dumpsegs.py b/src/westpa/cli/tools/w_dumpsegs.py
index d67febd8b..23ad57668 100644
--- a/src/westpa/cli/tools/w_dumpsegs.py
+++ b/src/westpa/cli/tools/w_dumpsegs.py
@@ -64,7 +64,7 @@ def go(self):
             + '\n'
         )
         pcoord_lines = '  pcoord[0]  = {init_pcoord}\n  pcoord[-1] = {final_pcoord}' + '\n'
-        for (_seg_id, segment) in enumerate(segments):
+        for _seg_id, segment in enumerate(segments):
             parents_str = '[' + ', '.join(map(str, sorted(segment.wtg_parent_ids))) + ']'
             init_pcoord_str = '[' + ', '.join('{pcval:<12.6g}'.format(pcval=float(pce)) for pce in segment.pcoord[0]) + ']'
             final_pcoord_str = '[' + ', '.join('{pcval:<12.6g}'.format(pcval=float(pce)) for pce in segment.pcoord[-1]) + ']'
diff --git a/src/westpa/cli/tools/w_eddist.py b/src/westpa/cli/tools/w_eddist.py
index e731e44c4..2325ef7de 100644
--- a/src/westpa/cli/tools/w_eddist.py
+++ b/src/westpa/cli/tools/w_eddist.py
@@ -68,7 +68,6 @@ def _remote_min_max(ndim, dset_dtype, n_iter, dsspec):
 
 
 def _remote_bin_iter(iiter, n_iter, dsspec, wt_dsspec, initpoint, binbounds, ignore_out_of_range):
-
     iter_hist_shape = tuple(len(bounds) - 1 for bounds in binbounds)
     iter_hist = np.zeros(iter_hist_shape, dtype=np.float64)
 
@@ -220,7 +219,6 @@ def __init__(self):
         self.compress_output = False
 
     def add_args(self, parser):
-
         parser.add_argument(
             '-b',
             '--bins',
@@ -300,7 +298,6 @@ def process_args(self, args):
         self.compress_output = args.compress or False
 
     def go(self):
-
         pi = self.progress.indicator
         pi.operation = 'Initializing'
         with pi:
@@ -334,7 +331,6 @@ def go(self):
 
     @staticmethod
     def parse_binspec(binspec):
-
         namespace = {'numpy': np, 'np': np, 'inf': float('inf')}
 
         try:
diff --git a/src/westpa/cli/tools/w_ipa.py b/src/westpa/cli/tools/w_ipa.py
index 1ae218678..adb433fea 100644
--- a/src/westpa/cli/tools/w_ipa.py
+++ b/src/westpa/cli/tools/w_ipa.py
@@ -641,7 +641,6 @@ def future(self, value=None):
         return self._future
 
     class Future(WIPIDataset):
-
         # This isn't a real fancy one.
         def __getitem__(self, value):
             if isinstance(value, str):
diff --git a/src/westpa/cli/tools/w_multi_west.py b/src/westpa/cli/tools/w_multi_west.py
index 30fe75f48..0ab01f00e 100644
--- a/src/westpa/cli/tools/w_multi_west.py
+++ b/src/westpa/cli/tools/w_multi_west.py
@@ -156,7 +156,7 @@ def total_number_of_walkers(self):
             # Sometimes, we're smaller or larger by one.  Hm.
             try:
                 self.total_walkers[:] += west['summary'][:-1]['n_particles']
-            except (ValueError):
+            except ValueError:
                 self.total_walkers[:] += west['summary'][:-1]['n_particles'][: len(self.total_walkers)]
 
     class Segment:
diff --git a/src/westpa/cli/tools/w_pdist.py b/src/westpa/cli/tools/w_pdist.py
index b46e147e2..6bfd078da 100644
--- a/src/westpa/cli/tools/w_pdist.py
+++ b/src/westpa/cli/tools/w_pdist.py
@@ -51,7 +51,6 @@ def _remote_min_max(ndim, dset_dtype, n_iter, dsspec):
 
 
 def _remote_bin_iter(iiter, n_iter, dsspec, wt_dsspec, initpoint, binbounds, ignore_out_of_range):
-
     iter_hist_shape = tuple(len(bounds) - 1 for bounds in binbounds)
     iter_hist = np.zeros(iter_hist_shape, dtype=np.float64)
 
diff --git a/src/westpa/cli/tools/w_red.py b/src/westpa/cli/tools/w_red.py
index 3c01ca0fa..f3280c2ef 100644
--- a/src/westpa/cli/tools/w_red.py
+++ b/src/westpa/cli/tools/w_red.py
@@ -333,7 +333,6 @@ def _get_corrector(self):
         return self._dc
 
     def calc_rate(self, i_iter=None, red=False, **kwargs):
-
         if i_iter is None:
             i_iter = self.n_iters
 
diff --git a/src/westpa/core/_rc.py b/src/westpa/core/_rc.py
index 214e45cd6..5f35cd51c 100644
--- a/src/westpa/core/_rc.py
+++ b/src/westpa/core/_rc.py
@@ -644,7 +644,6 @@ def get_work_manager(self):
         return self.work_manager
 
     def clear_state(self):
-
         self._sim_manager = None
         self._system = None
         self._data_manager = None
diff --git a/src/westpa/core/binning/assign.py b/src/westpa/core/binning/assign.py
index fc8ec4d24..0c2683a94 100644
--- a/src/westpa/core/binning/assign.py
+++ b/src/westpa/core/binning/assign.py
@@ -429,7 +429,7 @@ def assign(self, coords, mask=None, output=None):
         # Which coordinates do we need to reassign, because they landed in
         # bins with embedded mappers?
         rmasks = {}
-        for (rindex, mapper) in self._recursion_targets.items():
+        for rindex, mapper in self._recursion_targets.items():
             omask = output == rindex
             mmask |= omask
             rmasks[rindex] = omask
@@ -441,7 +441,7 @@ def assign(self, coords, mask=None, output=None):
             output_map(output, omap, mask & ~mmask)
 
         # do any recursive assignments necessary
-        for (rindex, mapper) in self._recursion_targets.items():
+        for rindex, mapper in self._recursion_targets.items():
             mapper.assign(coords, mask & rmasks[rindex], output)
 
         return output
diff --git a/src/westpa/core/binning/binless_driver.py b/src/westpa/core/binning/binless_driver.py
index 5bc4b6065..c3ef5f2e8 100644
--- a/src/westpa/core/binning/binless_driver.py
+++ b/src/westpa/core/binning/binless_driver.py
@@ -33,7 +33,7 @@ def assign(self, segments, initializing=False):
         final_binning = self.final_binning
         flux_matrix = self.flux_matrix
         transition_matrix = self.transition_matrix
-        for (segment, iidx, fidx) in zip(segments, initial_assignments, final_assignments):
+        for segment, iidx, fidx in zip(segments, initial_assignments, final_assignments):
             initial_binning[iidx].add(segment)
             final_binning[fidx].add(segment)
             flux_matrix[iidx, fidx] += segment.weight
diff --git a/src/westpa/core/binning/binless_manager.py b/src/westpa/core/binning/binless_manager.py
index d038c0630..78aa3a47d 100644
--- a/src/westpa/core/binning/binless_manager.py
+++ b/src/westpa/core/binning/binless_manager.py
@@ -155,7 +155,7 @@ def prepare_iteration(self):
         for iseg, segment in enumerate(segments.values()):
             initial_pcoords[iseg] = segment.pcoord[0]
         initial_assignments = self.system.bin_mapper.assign(initial_pcoords)
-        for (segment, assignment) in zip(iter(segments.values()), initial_assignments):
+        for segment, assignment in zip(iter(segments.values()), initial_assignments):
             initial_binning[assignment].add(segment)
         self.report_bin_statistics(initial_binning, [], save_summary=True)
         del initial_pcoords, initial_binning
diff --git a/src/westpa/core/binning/mab.py b/src/westpa/core/binning/mab.py
index f491cfbe8..a2e0e889f 100644
--- a/src/westpa/core/binning/mab.py
+++ b/src/westpa/core/binning/mab.py
@@ -212,7 +212,6 @@ def map_mab(coords, mask, output, *args, **kwargs):
         # the following are for the "linear" portion
         if not special:
             for n in range(ndim):
-
                 # if skipped, it's added to the same bin as the special walkers above
                 if skip[n] != 0:
                     holder = boundary_base + n
diff --git a/src/westpa/core/binning/mab_driver.py b/src/westpa/core/binning/mab_driver.py
index 96b4a6877..bc8fd704e 100644
--- a/src/westpa/core/binning/mab_driver.py
+++ b/src/westpa/core/binning/mab_driver.py
@@ -33,7 +33,7 @@ def assign(self, segments, initializing=False):
         final_binning = self.final_binning
         flux_matrix = self.flux_matrix
         transition_matrix = self.transition_matrix
-        for (segment, iidx, fidx) in zip(segments, initial_assignments, final_assignments):
+        for segment, iidx, fidx in zip(segments, initial_assignments, final_assignments):
             initial_binning[iidx].add(segment)
             final_binning[fidx].add(segment)
             flux_matrix[iidx, fidx] += segment.weight
diff --git a/src/westpa/core/binning/mab_manager.py b/src/westpa/core/binning/mab_manager.py
index fcb570520..f09167d03 100644
--- a/src/westpa/core/binning/mab_manager.py
+++ b/src/westpa/core/binning/mab_manager.py
@@ -158,7 +158,7 @@ def prepare_iteration(self):
         # Assign this iteration's segments' initial points to bins and report on bin population
         initial_binning = self.system.bin_mapper.construct_bins()
         initial_assignments = self.system.bin_mapper.assign(pcoords_with_weights)
-        for (segment, assignment) in zip(iter(segments.values()), initial_assignments):
+        for segment, assignment in zip(iter(segments.values()), initial_assignments):
             initial_binning[assignment].add(segment)
         self.report_bin_statistics(initial_binning, [], save_summary=True)
         del pcoords_with_weights, initial_binning
diff --git a/src/westpa/core/data_manager.py b/src/westpa/core/data_manager.py
index 78e256a69..56c416495 100644
--- a/src/westpa/core/data_manager.py
+++ b/src/westpa/core/data_manager.py
@@ -231,7 +231,7 @@ def expiring_flushing_lock(self):
     def process_config(self):
         config = self.rc.config
 
-        for (entry, type_) in [('iter_prec', int)]:
+        for entry, type_ in [('iter_prec', int)]:
             config.require_type_if_present(['west', 'data', entry], type_)
 
         self.we_h5filename = config.get_path(['west', 'data', 'west_data_file'], default=self.default_we_h5filename)
@@ -263,7 +263,6 @@ def process_config(self):
                 raise ValueError('cannot override pcoord storage location')
 
     def __init__(self, rc=None):
-
         self.rc = rc or westpa.rc
 
         self.we_h5filename = self.default_we_h5filename
@@ -854,7 +853,7 @@ def prepare_iteration(self, n_iter, segments):
             pcoord = np.empty((n_particles, pcoord_len, pcoord_ndim), pcoord_dtype)
 
             total_parents = 0
-            for (seg_id, segment) in enumerate(segments):
+            for seg_id, segment in enumerate(segments):
                 if segment.seg_id is not None:
                     assert segment.seg_id == seg_id
                 else:
@@ -895,7 +894,7 @@ def prepare_iteration(self, n_iter, segments):
                 wtgraph_ds = iter_group.create_dataset('wtgraph', (total_parents,), seg_id_dtype, compression='gzip', shuffle=True)
                 parents = np.empty((total_parents,), seg_id_dtype)
 
-                for (seg_id, segment) in enumerate(segments):
+                for seg_id, segment in enumerate(segments):
                     offset = seg_index_table[seg_id]['wtg_offset']
                     extent = seg_index_table[seg_id]['wtg_n_parents']
                     parent_list = list(segment.wtg_parent_ids)
@@ -986,7 +985,7 @@ def update_segments(self, n_iter, segments):
             # read summary data so that we have valud parent and weight transfer information
             si_dsid.read(si_msel, si_fsel, seg_index_entries)
 
-            for (iseg, (segment, ientry)) in enumerate(zip(segments, seg_index_entries)):
+            for iseg, (segment, ientry) in enumerate(zip(segments, seg_index_entries)):
                 ientry['status'] = segment.status
                 ientry['endpoint_type'] = segment.endpoint_type or Segment.SEG_ENDPOINT_UNSET
                 ientry['cputime'] = segment.cputime
@@ -1021,7 +1020,7 @@ def update_segments(self, n_iter, segments):
 
             # Then we iterate over data sets and store data
             if dsets:
-                for (dsname, (shape, dtype)) in dsets.items():
+                for dsname, (shape, dtype) in dsets.items():
                     # dset = self._require_aux_dataset(iter_group, dsname, n_total_segments, shape, dtype)
                     try:
                         dsopts = self.dataset_options[dsname]
diff --git a/src/westpa/core/h5io.py b/src/westpa/core/h5io.py
index 37cc532a2..878918fb0 100644
--- a/src/westpa/core/h5io.py
+++ b/src/westpa/core/h5io.py
@@ -101,7 +101,6 @@ def tostr(b):
 
 
 def is_within_directory(directory, target):
-
     abs_directory = os.path.abspath(directory)
     abs_target = os.path.abspath(target)
 
@@ -111,7 +110,6 @@ def is_within_directory(directory, target):
 
 
 def safe_extract(tar, path=".", members=None, *, numeric_owner=False):
-
     for member in tar.getmembers():
         member_path = os.path.join(path, member.name)
         if not is_within_directory(path, member_path):
@@ -374,7 +372,6 @@ class WESTPAH5File(h5py.File):
     _this_fileformat_version = 8
 
     def __init__(self, *args, **kwargs):
-
         # These values are used for creating files or reading files where this
         # data is not stored. Otherwise, values stored as attributes on the root
         # group are used instead.
@@ -919,7 +916,6 @@ def get_iter_data(self, n_iter, seg_slice=index_exp[:]):
 class IterBlockedDataset:
     @classmethod
     def empty_like(cls, blocked_dataset):
-
         source = blocked_dataset.data if blocked_dataset.data is not None else blocked_dataset.dataset
 
         newbds = cls(
diff --git a/src/westpa/core/propagators/__init__.py b/src/westpa/core/propagators/__init__.py
index a51e0ee11..7cd526f2d 100644
--- a/src/westpa/core/propagators/__init__.py
+++ b/src/westpa/core/propagators/__init__.py
@@ -10,7 +10,6 @@ def blocked_iter(blocksize, iterable, fillvalue=None):
 
 class WESTPropagator:
     def __init__(self, rc=None):
-
         # For maximum flexibility, the basis states and initial states valid
         # at the point in the simulation when the propgator is used must be
         # available in several routines, and it is inconvenient to pass them
diff --git a/src/westpa/core/propagators/executable.py b/src/westpa/core/propagators/executable.py
index d301b2664..692ae17b4 100644
--- a/src/westpa/core/propagators/executable.py
+++ b/src/westpa/core/propagators/executable.py
@@ -372,7 +372,7 @@ def exec_child(self, executable, environ=None, stdin=None, stdout=None, stderr=N
         return (rc, rusage)
 
     def exec_child_from_child_info(self, child_info, template_args, environ):
-        for (key, value) in child_info.get('environ', {}).items():
+        for key, value in child_info.get('environ', {}).items():
             environ[key] = self.makepath(value)
         return self.exec_child(
             executable=self.makepath(child_info['executable'], template_args),
@@ -443,7 +443,6 @@ def update_args_env_segment(self, template_args, environ, segment):
             initial_state = self.initial_states[segment.initial_state_id]
 
             if initial_state.istate_type == InitialState.ISTATE_TYPE_START:
-
                 basis_state = BasisState(
                     label=f"sstate_{initial_state.state_id}", pcoord=initial_state.pcoord, probability=0.0, auxref=""
                 )
@@ -465,7 +464,6 @@ def update_args_env_segment(self, template_args, environ, segment):
                 environ[self.ENV_PARENT_DATA_REF] = environ[self.ENV_BSTATE_DATA_REF]
 
             elif initial_state.istate_type == InitialState.ISTATE_TYPE_START:
-
                 # This points to the start-state PDB
                 environ[self.ENV_PARENT_DATA_REF] = environ[self.ENV_BSTATE_DATA_REF] + '/' + initial_state.basis_auxref
             else:  # initial_state.type == InitialState.ISTATE_TYPE_GENERATED
diff --git a/src/westpa/core/sim_manager.py b/src/westpa/core/sim_manager.py
index 9e4c32021..20264574b 100644
--- a/src/westpa/core/sim_manager.py
+++ b/src/westpa/core/sim_manager.py
@@ -37,7 +37,7 @@ class PropagationError(RuntimeError):
 class WESimManager:
     def process_config(self):
         config = self.rc.config
-        for (entry, type_) in [('gen_istates', bool), ('block_size', int), ('save_transition_matrices', bool)]:
+        for entry, type_ in [('gen_istates', bool), ('block_size', int), ('save_transition_matrices', bool)]:
             config.require_type_if_present(['west', 'propagation', entry], type_)
 
         self.do_gen_istates = config.get(['west', 'propagation', 'gen_istates'], False)
@@ -136,7 +136,7 @@ def register_callback(self, hook, function, priority=0):
     def invoke_callbacks(self, hook, *args, **kwargs):
         callbacks = self._callback_table.get(hook, [])
         sorted_callbacks = sorted(callbacks)
-        for (priority, name, fn) in sorted_callbacks:
+        for priority, name, fn in sorted_callbacks:
             log.debug('invoking callback {!r} for hook {!r}'.format(fn, hook))
             fn(*args, **kwargs)
 
@@ -478,7 +478,7 @@ def prepare_iteration(self):
         for iseg, segment in enumerate(segments.values()):
             initial_pcoords[iseg] = segment.pcoord[0]
         initial_assignments = self.system.bin_mapper.assign(initial_pcoords)
-        for (segment, assignment) in zip(iter(segments.values()), initial_assignments):
+        for segment, assignment in zip(iter(segments.values()), initial_assignments):
             initial_binning[assignment].add(segment)
         self.report_bin_statistics(initial_binning, [], save_summary=True)
         del initial_pcoords, initial_binning
@@ -733,7 +733,6 @@ def run(self):
 
         iter_elapsed = 0
         while self.n_iter <= max_iter:
-
             if max_walltime and time.time() + 1.1 * iter_elapsed >= run_killtime:
                 self.rc.pstatus('Iteration {:d} would require more than the allotted time. Ending run.'.format(self.n_iter))
                 return
diff --git a/src/westpa/core/we_driver.py b/src/westpa/core/we_driver.py
index 427c5214e..93d432362 100644
--- a/src/westpa/core/we_driver.py
+++ b/src/westpa/core/we_driver.py
@@ -189,7 +189,7 @@ def current_iter_assignments(self):
     def recycling_segments(self):
         '''Segments designated for recycling'''
         if len(self.target_states):
-            for (ibin, tstate) in self.target_states.items():
+            for ibin, tstate in self.target_states.items():
                 for segment in self.final_binning[ibin]:
                     yield segment
         else:
@@ -298,14 +298,14 @@ def new_iteration(self, initial_states=None, target_states=None, new_weights=Non
             init_pcoords = np.empty((len(new_weights), self.system.pcoord_ndim), dtype=self.system.pcoord_dtype)
             prev_init_pcoords = np.empty((len(new_weights), self.system.pcoord_ndim), dtype=self.system.pcoord_dtype)
 
-            for (ientry, entry) in enumerate(new_weights):
+            for ientry, entry in enumerate(new_weights):
                 init_pcoords[ientry] = entry.new_init_pcoord
                 prev_init_pcoords[ientry] = entry.prev_init_pcoord
 
             init_assignments = self.bin_mapper.assign(init_pcoords)
             prev_init_assignments = self.bin_mapper.assign(prev_init_pcoords)
 
-            for (entry, i, j) in zip(new_weights, prev_init_assignments, init_assignments):
+            for entry, i, j in zip(new_weights, prev_init_assignments, init_assignments):
                 flux_matrix[i, j] += entry.weight
                 transition_matrix[i, j] += 1
 
@@ -351,7 +351,7 @@ def assign(self, segments, initializing=False):
         final_binning = self.final_binning
         flux_matrix = self.flux_matrix
         transition_matrix = self.transition_matrix
-        for (segment, iidx, fidx) in zip(segments, initial_assignments, final_assignments):
+        for segment, iidx, fidx in zip(segments, initial_assignments, final_assignments):
             initial_binning[iidx].add(segment)
             final_binning[fidx].add(segment)
             flux_matrix[iidx, fidx] += segment.weight
@@ -391,7 +391,7 @@ def _recycle_walkers(self):
 
         used_istate_ids = set()
         istateiter = iter(self.avail_initial_states.values())
-        for (ibin, target_state) in self.target_states.items():
+        for ibin, target_state in self.target_states.items():
             target_bin = self.next_iter_binning[ibin]
             for segment in set(target_bin):
                 initial_state = next(istateiter)
@@ -657,7 +657,7 @@ def _run_we(self):
         # Then and only then adjust for correct particle count
         total_number_of_subgroups = 0
         total_number_of_particles = 0
-        for (ibin, bin) in enumerate(self.next_iter_binning):
+        for ibin, bin in enumerate(self.next_iter_binning):
             if len(bin) == 0:
                 continue
 
@@ -740,7 +740,7 @@ def populate_initial(self, initial_states, weights, system=None):
 
         # Create dummy segments
         segments = []
-        for (seg_id, (initial_state, weight)) in enumerate(zip(initial_states, weights)):
+        for seg_id, (initial_state, weight) in enumerate(zip(initial_states, weights)):
             dummy_segment = Segment(
                 n_iter=0,
                 seg_id=seg_id,
diff --git a/src/westpa/oldtools/aframe/binning.py b/src/westpa/oldtools/aframe/binning.py
index 091d098f5..8a8698ded 100644
--- a/src/westpa/oldtools/aframe/binning.py
+++ b/src/westpa/oldtools/aframe/binning.py
@@ -92,7 +92,7 @@ def write_bin_labels(self, dest, header='# bin labels:\n', format='# bin {bin_in
         '''
         dest.write(header or '')
         max_iwidth = len(str(self.mapper.nbins - 1))
-        for (ibin, label) in enumerate(self.mapper.labels):
+        for ibin, label in enumerate(self.mapper.labels):
             dest.write(format.format(bin_index=ibin, label=label, max_iwidth=max_iwidth))
 
     def require_binning_group(self):
@@ -125,7 +125,7 @@ def assign_to_bins(self):
 
         westpa.rc.pstatus('Assigning to bins...')
 
-        for (iiter, n_iter) in enumerate(range(self.first_iter, self.last_iter + 1)):
+        for iiter, n_iter in enumerate(range(self.first_iter, self.last_iter + 1)):
             westpa.rc.pstatus('\r  Iteration {:d}'.format(n_iter), end='')
             seg_index = self.get_seg_index(n_iter)
             pcoords = self.get_iter_group(n_iter)['pcoord'][...]
diff --git a/src/westpa/oldtools/aframe/data_reader.py b/src/westpa/oldtools/aframe/data_reader.py
index cad77a6d8..86c502439 100644
--- a/src/westpa/oldtools/aframe/data_reader.py
+++ b/src/westpa/oldtools/aframe/data_reader.py
@@ -135,7 +135,7 @@ def get_segments_by_id(self, n_iter, seg_ids, include_pcoords=True):
         if include_pcoords:
             pcoords = self.get_pcoords(n_iter, seg_ids)
 
-        for (isegid, seg_id) in enumerate(seg_ids):
+        for isegid, seg_id in enumerate(seg_ids):
             row = seg_index[seg_id]
             parents_offset = row['wtg_offset']
             n_parents = row['wtg_n_parents']
@@ -313,7 +313,6 @@ def add_args(self, parser, upcall=True):
         )
 
     def process_args(self, args, upcall=True):
-
         if args.usecols:
             westpa.rc.pstatus('Using only the following columns from external input: {!s}'.format(args.usecols))
             self.ext_input_usecols = args.usecols
@@ -413,10 +412,10 @@ def text_to_h5dataset(self, fileobj, group, dsname, dtype=np.float64, skiprows=0
                 )
 
             if usecols:
-                for (ifield, iifield) in enumerate(usecols):
+                for ifield, iifield in enumerate(usecols):
                     databuffer[irow, ifield] = dtype(fields[iifield])
             else:
-                for (ifield, field) in enumerate(fields):
+                for ifield, field in enumerate(fields):
                     databuffer[irow, ifield] = dtype(field)
 
             nrows += 1
diff --git a/src/westpa/oldtools/aframe/kinetics.py b/src/westpa/oldtools/aframe/kinetics.py
index 1ee474cff..8e49b8c47 100644
--- a/src/westpa/oldtools/aframe/kinetics.py
+++ b/src/westpa/oldtools/aframe/kinetics.py
@@ -47,7 +47,6 @@ def add_args(self, parser, upcall=True):
         )
 
     def process_args(self, args, upcall=True):
-
         self.dt = args.dt
         westpa.rc.pstatus('Assuming input data timestep of {:g}'.format(self.dt))
 
diff --git a/src/westpa/oldtools/aframe/trajwalker.py b/src/westpa/oldtools/aframe/trajwalker.py
index 537aa263e..9b9d75f59 100644
--- a/src/westpa/oldtools/aframe/trajwalker.py
+++ b/src/westpa/oldtools/aframe/trajwalker.py
@@ -58,7 +58,7 @@ def get_initial_nodes(self, first_iter, last_iter, include_pcoords=True):
 
         # Convert to Segment objects
         segments = []
-        for (n_iter, id_set) in root_ids.items():
+        for n_iter, id_set in root_ids.items():
             segments.extend(self.data_reader.get_segments_by_id(n_iter, id_set, include_pcoords=include_pcoords))
         return segments
 
diff --git a/src/westpa/oldtools/aframe/transitions.py b/src/westpa/oldtools/aframe/transitions.py
index d3078464c..dd2c36cd2 100644
--- a/src/westpa/oldtools/aframe/transitions.py
+++ b/src/westpa/oldtools/aframe/transitions.py
@@ -200,9 +200,7 @@ def _accumulate_transitions(self, timepoints, assignments, weights, bin_pops, tr
         iibdisc = self.iibdisc
         iibins = self.iibins
         tdat_maxlen = self.max_acc
-        for (trans_ti, weight, ibin, fbin, ibinpops) in zip(
-            trans_timepoints, trans_weights, trans_ibin, trans_fbin, trans_ibinpops
-        ):
+        for trans_ti, weight, ibin, fbin, ibinpops in zip(trans_timepoints, trans_weights, trans_ibin, trans_fbin, trans_ibinpops):
             # Record this crossing event's data
             bin_pops_last_exit[ibin] = ibinpops[ibin]
             last_exit[ibin] = trans_ti
diff --git a/src/westpa/oldtools/cmds/w_ttimes.py b/src/westpa/oldtools/cmds/w_ttimes.py
index 3021b0699..6134844e6 100644
--- a/src/westpa/oldtools/cmds/w_ttimes.py
+++ b/src/westpa/oldtools/cmds/w_ttimes.py
@@ -85,7 +85,6 @@ def add_args(self, parser, upcall=True):
         self.add_common_output_args(output_options)
 
     def process_args(self, args, upcall=True):
-
         self.ed_stats_filename = args.ed_stats
         self.fpt_stats_filename = args.fpt_stats
         self.flux_stats_filename = args.flux_stats
@@ -201,7 +200,7 @@ def gen_stats(self):
             westpa.rc.pstatus()
             del trans_ibin
 
-        for (dsname, data) in (('duration', durations), ('fpt', fpts), ('flux', fluxes), ('rate', rates)):
+        for dsname, data in (('duration', durations), ('fpt', fpts), ('flux', fluxes), ('rate', rates)):
             try:
                 del self.ttimes_group[dsname]
             except KeyError:
@@ -234,7 +233,7 @@ def gen_stats(self):
         self.record_data_binhash(self.ttimes_group)
 
     def summarize_stats(self):
-        for (array, dsname, argname, title) in (
+        for array, dsname, argname, title in (
             (self.durations, 'duration', 'ed_stats_filename', 'event duration'),
             (self.fpts, 'fpt', 'fpt_stats_filename', 'first passage time'),
             (self.fluxes, 'flux', 'flux_stats_filename', 'flux'),
@@ -259,7 +258,6 @@ def summarize_stats(self):
                 )
 
     def summarize_ci(self, filename, array, title, confidence, headers, labels):
-
         format_2d = (
             '{ibin:{mw}d}    {fbin:{mw}d}    {0:20.15g}    {1:20.15g}    {2:20.15g}    {3:20.15g}    {4:20.15g}    {5:20.15g}\n'
         )
diff --git a/src/westpa/tools/binning.py b/src/westpa/tools/binning.py
index f6704bc49..668d18ef6 100644
--- a/src/westpa/tools/binning.py
+++ b/src/westpa/tools/binning.py
@@ -209,7 +209,6 @@ def write_bin_info(mapper, assignments, weights, n_target_states, outfile=sys.st
 
 
 def write_bin_labels(mapper, dest, header='# bin labels:\n', fmt='# bin {index:{max_iwidth}d} -- {label!s}\n'):
-
     '''Print labels for all bins in ``mapper`` to the file-like object``dest``.
 
     If provided, ``header`` is printed prior to any labels. A number of expansions
@@ -229,7 +228,7 @@ def write_bin_labels(mapper, dest, header='# bin labels:\n', fmt='# bin {index:{
         dest.write(header.format(mapper=mapper, classname=mapper.__class__.__name__, nbins=mapper.bins))
 
     max_iwidth = len(str(mapper.nbins - 1))
-    for (ibin, label) in enumerate(mapper.labels):
+    for ibin, label in enumerate(mapper.labels):
         dest.write(fmt.format(index=ibin, label=label, max_iwidth=max_iwidth))
 
 
@@ -277,7 +276,6 @@ class BinMappingComponent(WESTToolComponent):
     '''
 
     def __init__(self):
-
         # The final mapper
         self.mapper = None
         self.mapper_hash = None
@@ -368,7 +366,6 @@ def add_target_count_args(self, parser, description='bin target count options'):
         )
 
     def process_args(self, args):
-
         # User may have suppressed any of these arguments
         bins_from_system = getattr(args, 'bins_from_system', None)
         bins_from_expr = getattr(args, 'bins_from_expr', None)
diff --git a/src/westpa/tools/kinetics_tool.py b/src/westpa/tools/kinetics_tool.py
index 0b8d20bfb..39c495332 100644
--- a/src/westpa/tools/kinetics_tool.py
+++ b/src/westpa/tools/kinetics_tool.py
@@ -95,7 +95,6 @@ def __init__(self, parent):
         self.kinetics_file = None
 
     def add_args(self, parser):
-
         iogroup = parser.add_argument_group('input/output options')
         # self.default_kinetics_file will be picked up as a class attribute from the appropriate subclass
         # We can do this with the output file, too...
@@ -261,7 +260,6 @@ def print_averages(self, dataset, header, dim=1):
     def run_calculation(
         self, pi, nstates, start_iter, stop_iter, step_iter, dataset, eval_block, name, dim, do_averages=False, **extra
     ):
-
         # We want to use the same codepath to run a quick average as we do the longer evolution sets, so...
         if do_averages:
             start_pts = [start_iter, stop_iter]
@@ -279,7 +277,6 @@ def run_calculation(
         # This is appropriate for bootstrapped quantities, I think.
 
         if True:
-
             futures = []
             for iblock, start in enumerate(start_pts):
                 stop = min(start + step_iter, stop_iter)
diff --git a/src/westpa/tools/selected_segs.py b/src/westpa/tools/selected_segs.py
index 6afee8203..a1e250b91 100644
--- a/src/westpa/tools/selected_segs.py
+++ b/src/westpa/tools/selected_segs.py
@@ -30,7 +30,6 @@ def __contains__(self, pair):
         return tuple(pair) in self._segments
 
     def add(self, pair):
-
         (n_iter, seg_id) = int(pair[0]), int(pair[1])
         self._segments.add((n_iter, seg_id))
         self._segs_by_iter.setdefault(n_iter, set()).add(seg_id)
diff --git a/src/westpa/trajtree/trajtree.py b/src/westpa/trajtree/trajtree.py
index 025290598..4254320a6 100644
--- a/src/westpa/trajtree/trajtree.py
+++ b/src/westpa/trajtree/trajtree.py
@@ -28,7 +28,6 @@ def get_root_indices(self):
         return np.squeeze(np.argwhere(self.trajtable['parent_offset'] == -1))
 
     def trace_trajectories(self, visit, get_visitor_state=None, set_visitor_state=None, vargs=None, vkwargs=None):
-
         if (get_visitor_state or set_visitor_state) and not (get_visitor_state and set_visitor_state):
             raise ValueError('either both or neither of get_visitor_state and set_visitor_state must be specified')
 
@@ -67,7 +66,6 @@ def trace_trajectories(self, visit, get_visitor_state=None, set_visitor_state=No
 
 class FakeTrajTreeSet(TrajTreeSet):
     def __init__(self):
-
         # _tt_dtype = np.dtype([('n_iter', np.uint32),
         #                         ('seg_id', np.int64),
         #                         ('parent_id', np.int64),
diff --git a/src/westpa/westext/adaptvoronoi/adaptVor_driver.py b/src/westpa/westext/adaptvoronoi/adaptVor_driver.py
index 9caaa6dd8..281faad02 100644
--- a/src/westpa/westext/adaptvoronoi/adaptVor_driver.py
+++ b/src/westpa/westext/adaptvoronoi/adaptVor_driver.py
@@ -31,7 +31,6 @@ class AdaptiveVoronoiDriver:
     '''
 
     def __init__(self, sim_manager, plugin_config):
-
         if not sim_manager.work_manager.is_master:
             return
 
@@ -200,7 +199,6 @@ def update_centers(self, iter_group):
         self.centers = np.vstack((self.centers, curr_pcoords[max_ind[0][0]][-1]))
 
     def prepare_new_iteration(self):
-
         n_iter = self.sim_manager.n_iter
 
         with self.data_manager.lock:
diff --git a/src/westpa/westext/hamsm_restarting/example_overrides.py b/src/westpa/westext/hamsm_restarting/example_overrides.py
index e0124b4f7..6c82cc0da 100644
--- a/src/westpa/westext/hamsm_restarting/example_overrides.py
+++ b/src/westpa/westext/hamsm_restarting/example_overrides.py
@@ -20,7 +20,6 @@ def processCoordinates(self, coords):
         return data
 
     if self.dimReduceMethod == "pca" or self.dimReduceMethod == "vamp":
-
         ### NaCl dimensionality reduction
         log.warning("Hardcoded selection: Doing dim reduction for Na, Cl. This is only for testing!")
         indNA = self.reference_structure.topology.select("element Na")
diff --git a/src/westpa/westext/hamsm_restarting/restart_driver.py b/src/westpa/westext/hamsm_restarting/restart_driver.py
index a02ef5538..91e142d58 100644
--- a/src/westpa/westext/hamsm_restarting/restart_driver.py
+++ b/src/westpa/westext/hamsm_restarting/restart_driver.py
@@ -159,7 +159,6 @@ def prepare_coordinates(plugin_config, h5file, we_h5filename):
 
     n_iter = None
     for n_iter in tqdm.tqdm(range(1, model.maxIter + 1)):
-
         nS = model.numSegments[n_iter - 1].astype(int)
         coords = np.zeros((nS, 2, model.nAtoms, 3))
         dsetName = "/iterations/iter_%08d/auxdata/coord" % int(n_iter)
@@ -530,7 +529,6 @@ def prepare_extension_run(self, run_number, restart_state, first_extension=False
         os.symlink(f'restart0/run{run_number}/seg_logs', 'seg_logs')
 
         if first_extension:
-
             # Get lines to make a new west.cfg by extending west.propagation.max_total_iterations
             with open('west.cfg', 'r') as west_config:
                 lines = west_config.readlines()
@@ -578,7 +576,6 @@ def prepare_extension_run(self, run_number, restart_state, first_extension=False
         return
 
     def generate_plots(self, restart_directory):
-
         model = self.model
 
         log.info("Producing flux-profile, pseudocommittor, and target flux comparison plots.")
@@ -616,7 +613,6 @@ def generate_plots(self, restart_directory):
 
         # Get WE direct flux estimate
         for _file in model.fileList:
-
             run = analysis.Run(_file)
             last_iter = run.num_iterations
             recycled = list(run.iteration(last_iter - 1).recycled_walkers)
@@ -754,7 +750,6 @@ def prepare_new_we(self):
 
         # If we have more runs left to do in this marathon, prepare them
         elif not last_run:
-
             log.info(f"Run {restart_state['runs_completed']}/{self.n_runs} completed.")
 
             # TODO: Initialize a new run, from the same configuration as this run was
@@ -774,7 +769,6 @@ def prepare_new_we(self):
 
             # TODO: Implement this, and get rid of the initialization_file usage right below. Placeholder for now.
             if restart_state['runs_completed'] == 1:
-
                 # Get and write basis, target, start states and segs per state for this marathon to disk
                 pass
 
@@ -826,7 +820,6 @@ def prepare_new_we(self):
             # If we're doing an extension set
             #   Instead of w_initting a new iteration, copy the files from restart0/runXX back into ./
             elif doing_extension:
-
                 self.prepare_extension_run(run_number=restart_state['runs_completed'] + 1, restart_state=restart_state)
                 return
 
@@ -881,7 +874,6 @@ def prepare_new_we(self):
         )
         for restart_number in usable_restarts:
             for run_number in range(1, 1 + restart_state['runs_completed']):
-
                 west_file_path = f"restart{restart_number}/run{run_number}/west.h5"
                 marathon_west_files.append(west_file_path)
 
@@ -902,12 +894,10 @@ def prepare_new_we(self):
             # If you reached the target, clean up from the extensions and then continue as normal
             # If  extension_iters is set to 0, then don't do extensions.
             if target_reached or self.extension_iters == 0:
-
                 log.info("All runs reached target!")
 
                 # Do some cleanup from the extension run
                 if doing_extension and not self.extension_iters == 0:
-
                     # Remove the doing_extensions.lck lockfile
                     os.remove(EXTENSION_LOCKFILE)
 
@@ -918,7 +908,6 @@ def prepare_new_we(self):
 
             # If no runs reached the target, then we need to extend them
             elif not target_reached:
-
                 log.info("Target not reached. Preparing for extensions.")
 
                 # Create the doing_extensions.lck "lockfile" to indicate we're in extend mode (or keep if exists)
@@ -953,14 +942,12 @@ def prepare_new_we(self):
 
         flux_filename = f"{restart_directory}/JtargetSS.txt"
         with open(flux_filename, 'w') as fp:
-
             log.debug(f"Writing flux to {flux_filename}")
             fp.write(str(model.JtargetSS))
             fp.close()
 
         ss_filename = f"{restart_directory}/pSS.txt"
         with open(ss_filename, 'w') as fp:
-
             log.debug(f"Writing pSS to {ss_filename}")
             np.savetxt(fp, model.pSS)
             fp.close()
@@ -977,7 +964,6 @@ def prepare_new_we(self):
         # TODO: Include start states from previous runs
         sstates_filename = f"{restart_directory}/startstates.txt"
         with open(sstates_filename, 'w') as fp:
-
             # Track the total number of segments iterated over
             seg_idx = 0
 
@@ -988,8 +974,7 @@ def prepare_new_we(self):
             total_bin_weights = []
 
             # Loop over each set of (bin index, all the structures in that bin)
-            for (msm_bin_idx, structures) in tqdm.tqdm(model.cluster_structures.items()):
-
+            for msm_bin_idx, structures in tqdm.tqdm(model.cluster_structures.items()):
                 total_bin_weights.append(0)
 
                 # Don't put structures in the basis or target
@@ -1011,13 +996,11 @@ def prepare_new_we(self):
                 # Write each structure to disk. Loop over each structure within a bin.
                 msm_bin_we_weight_tracker = 0
                 for struct_idx, structure in enumerate(structures):
-
                     structure_filename = (
                         f"{struct_directory}/bin{msm_bin_idx}_" f"struct{struct_idx}.{STRUCT_EXTENSIONS[self.struct_filetype]}"
                     )
 
                     with self.struct_filetype(structure_filename, 'w') as struct_file:
-
                         # One structure per segment
                         seg_we_weight = model.cluster_structure_weights[msm_bin_idx][struct_idx]
                         msm_bin_we_weight_tracker += seg_we_weight
diff --git a/src/westpa/westext/stringmethod/string_driver.py b/src/westpa/westext/stringmethod/string_driver.py
index c4592553e..c4681446f 100644
--- a/src/westpa/westext/stringmethod/string_driver.py
+++ b/src/westpa/westext/stringmethod/string_driver.py
@@ -214,7 +214,6 @@ def avgpos_cartesian(self, n_iter):
         return avg_pos, sum_bin_weight
 
     def prepare_new_iteration(self):
-
         n_iter = self.sim_manager.n_iter
 
         with self.data_manager.lock:
diff --git a/src/westpa/westext/stringmethod/string_method.py b/src/westpa/westext/stringmethod/string_method.py
index 385aab26a..99c685097 100644
--- a/src/westpa/westext/stringmethod/string_method.py
+++ b/src/westpa/westext/stringmethod/string_method.py
@@ -21,7 +21,6 @@
 
 
 class WESTStringMethod:
-
     ___metaclass__ = ABCMeta
 
     def __init__(self, centers, **kwargs):
@@ -218,7 +217,6 @@ def update_string_centers(self, avgcoords, binprob):
                 avgcoords[idx] = pavg.mean(axis=0)
 
         for sid, si in enumerate(self._strindx):
-
             x = avgcoords.copy()[si]
             centers = self.centers[si]
             occupied = np.nonzero(binprob[si[0]])
diff --git a/src/westpa/westext/weed/weed_driver.py b/src/westpa/westext/weed/weed_driver.py
index dfa2b9096..41ac6483e 100644
--- a/src/westpa/westext/weed/weed_driver.py
+++ b/src/westpa/westext/weed/weed_driver.py
@@ -117,7 +117,7 @@ def prepare_new_iteration(self):
             for iseg, segment in enumerate(segments):
                 pcoords[iseg] = segment.pcoord[0]
             assignments = mapper.assign(pcoords)
-            for (segment, assignment) in zip(segments, assignments):
+            for segment, assignment in zip(segments, assignments):
                 bins[assignment].add(segment)
 
             westpa.rc.pstatus('\nReweighting using a different bin mapper than simulation:\n{}'.format(mapper))
@@ -169,7 +169,7 @@ def prepare_new_iteration(self):
             westpa.rc.pstatus('Empty bins assigned nonzero probability: {!s}.'.format(np.array_str(np.arange(n_bins)[z2nz_mask])))
         else:
             westpa.rc.pstatus('\nBin populations after reweighting:\n{!s}'.format(binprobs))
-            for (bin, newprob) in zip(bins, binprobs):
+            for bin, newprob in zip(bins, binprobs):
                 bin.reweight(newprob)
 
             weed_global_group.attrs['last_reweighting'] = n_iter
diff --git a/src/westpa/westext/wess/ProbAdjust.py b/src/westpa/westext/wess/ProbAdjust.py
index 1835ac719..0a5ce59cc 100644
--- a/src/westpa/westext/wess/ProbAdjust.py
+++ b/src/westpa/westext/wess/ProbAdjust.py
@@ -57,7 +57,6 @@ def solve_steady_state(T, U, target_bins_index):
 
 
 def prob_adjust(binprob, rates, uncert, oldindex, targets=[]):
-
     nbins = binprob.size
 
     result = solve_steady_state(rates, uncert, targets)
diff --git a/src/westpa/westext/wess/wess_driver.py b/src/westpa/westext/wess/wess_driver.py
index a3655bc25..9b523ea78 100644
--- a/src/westpa/westext/wess/wess_driver.py
+++ b/src/westpa/westext/wess/wess_driver.py
@@ -135,7 +135,7 @@ def prepare_new_iteration(self):
             for iseg, segment in enumerate(segments):
                 pcoords[iseg] = segment.pcoord[0]
             assignments = mapper.assign(pcoords)
-            for (segment, assignment) in zip(segments, assignments):
+            for segment, assignment in zip(segments, assignments):
                 bins[assignment].add(segment)
 
             target_states = list(we_driver.target_states.values())
@@ -193,7 +193,7 @@ def prepare_new_iteration(self):
             westpa.rc.pstatus('Empty bins assigned nonzero probability: {!s}.'.format(np.array_str(np.arange(n_bins)[z2nz_mask])))
         else:
             westpa.rc.pstatus('\nBin populations after reweighting:\n{!s}'.format(binprobs))
-            for (bin, newprob) in zip(bins, binprobs):
+            for bin, newprob in zip(bins, binprobs):
                 if len(bin):
                     bin.reweight(newprob)
 
diff --git a/src/westpa/work_managers/environment.py b/src/westpa/work_managers/environment.py
index 2133809ec..9a2774129 100644
--- a/src/westpa/work_managers/environment.py
+++ b/src/westpa/work_managers/environment.py
@@ -75,7 +75,6 @@ def get_val(self, name, default=None, type_=None):
                 raise ValueError('cannot convert {!r} to {!r}: {!s}'.format(val, type_, e))
 
     def add_wm_args(self, parser):
-
         wm_group = parser.add_argument_group(self.group_title, self.group_description)
         wm_mutex = wm_group.add_mutually_exclusive_group()
         wm_mutex.add_argument(
diff --git a/src/westpa/work_managers/mpi.py b/src/westpa/work_managers/mpi.py
index c8ed93f51..2834233d2 100644
--- a/src/westpa/work_managers/mpi.py
+++ b/src/westpa/work_managers/mpi.py
@@ -174,11 +174,9 @@ def _dispatcher(self):
         assert threading.currentThread().getName() == "dispatcher"
 
         while not self.shutItDown:
-
             req = []
             # do we have work and somewhere to send it?
             while self.tasks and self.dests:
-
                 with self.lock:
                     task = self.tasks.popleft()
                     sendTo = self.dests.popleft()
@@ -201,10 +199,8 @@ def _receiver(self):
         assert threading.currentThread().getName() == "receiver"
 
         while not self.shutItDown:
-
             # are we waiting on any results?
             while self.nPending:
-
                 stat = MPI.Status()
                 (tid, msg, val) = self.comm.recv(source=MPI.ANY_SOURCE, tag=self.result_tag, status=stat)
                 log.debug('Manager._receiver received task: %s' % tid)
@@ -278,7 +274,6 @@ def startup(self):
         """Clock the worker in for work."""
         log.debug('Worker.startup() %s' % self.rank)
         if not self.running:
-
             self.clockIn()
 
             self.running = True
@@ -292,14 +287,12 @@ def clockIn(self):
         comm = self.comm
 
         while True:
-
             stat = MPI.Status()
             task = comm.recv(source=self.managerID, tag=MPI.ANY_TAG, status=stat)
 
             tag = stat.Get_tag()
 
             if tag == self.task_tag:
-
                 log.debug('Worker %s received task: %s' % (self.rank, task.task_id))
 
                 # do the work
diff --git a/src/westpa/work_managers/zeromq/core.py b/src/westpa/work_managers/zeromq/core.py
index d93450ede..f9c22fdc1 100644
--- a/src/westpa/work_managers/zeromq/core.py
+++ b/src/westpa/work_managers/zeromq/core.py
@@ -93,7 +93,6 @@ class Message:
     idempotent_announcement_messages = {SHUTDOWN, TASKS_AVAILABLE, MASTER_BEACON}
 
     def __init__(self, message=None, payload=None, master_id=None, src_id=None):
-
         if isinstance(message, Message):
             self.message = message.message
             self.payload = message.payload
@@ -207,7 +206,6 @@ def __init__(self):
         self._indices = {}  # indexes into durations/started, keyed by identifier
 
     def add_timer(self, identifier, duration):
-
         if identifier in self._identifiers:
             raise KeyError('timer {!r} already present'.format(identifier))
 
@@ -266,7 +264,6 @@ def which_expired(self, at=None):
 
 
 class ZMQCore:
-
     # The overall communication topology (socket layout, etc)
     # Cannot be updated without updating configuration files, command-line parameters,
     # etc. (Changes break user scripts.)
@@ -332,7 +329,6 @@ def make_internal_endpoint(cls):
             return cls.make_tcp_endpoint()
 
     def __init__(self):
-
         # Unique identifier of this ZMQ node
         self.node_id = uuid.uuid4()
 
diff --git a/src/westpa/work_managers/zeromq/work_manager.py b/src/westpa/work_managers/zeromq/work_manager.py
index 54db5dc90..ba2df69b7 100644
--- a/src/westpa/work_managers/zeromq/work_manager.py
+++ b/src/westpa/work_managers/zeromq/work_manager.py
@@ -161,7 +161,6 @@ def from_environ(cls, wmenv=None):
         if mode == 'master':
             instance = ZMQWorkManager(n_workers)
         else:  # mode =='node'
-
             upstream_info = {}
             if read_host_info:
                 upstream_info.update(cls.read_host_info(read_host_info))
@@ -310,7 +309,7 @@ def submit_many(self, tasks):
             # We are shutting down
             raise ZMQWMEnvironmentError('work manager is shutting down')
         futures = []
-        for (fn, args, kwargs) in tasks:
+        for fn, args, kwargs in tasks:
             future = WMFuture()
             task = Task(fn, args, kwargs, task_id=future.task_id)
             self.futures[task.task_id] = future
diff --git a/src/westpa/work_managers/zeromq/worker.py b/src/westpa/work_managers/zeromq/worker.py
index b43de1ad0..dd4cb43e2 100644
--- a/src/westpa/work_managers/zeromq/worker.py
+++ b/src/westpa/work_managers/zeromq/worker.py
@@ -282,7 +282,6 @@ def __init__(self, task_endpoint, result_endpoint):
         self.result_endpoint = result_endpoint
 
     def comm_loop(self):
-
         task_socket = self.context.socket(zmq.PULL)
         result_socket = self.context.socket(zmq.PUSH)
 
diff --git a/tests/fixtures/odld/odld_system.py b/tests/fixtures/odld/odld_system.py
index 4e3d23010..3acef4faa 100644
--- a/tests/fixtures/odld/odld_system.py
+++ b/tests/fixtures/odld/odld_system.py
@@ -44,7 +44,6 @@ def gen_istate(self, basis_state, initial_state):
         return initial_state
 
     def propagate(self, segments):
-
         A, B, C, x0 = self.A, self.B, self.C, self.x0
 
         n_segs = len(segments)
diff --git a/tests/refs/odld_system.py b/tests/refs/odld_system.py
index d1a268fb7..4dc9829c9 100755
--- a/tests/refs/odld_system.py
+++ b/tests/refs/odld_system.py
@@ -44,7 +44,6 @@ def gen_istate(self, basis_state, initial_state):
         return initial_state
 
     def propagate(self, segments):
-
         A, B, C, x0 = self.A, self.B, self.C, self.x0
 
         n_segs = len(segments)
diff --git a/tests/test_binning.py b/tests/test_binning.py
index dbbff1a29..8120f4e0e 100644
--- a/tests/test_binning.py
+++ b/tests/test_binning.py
@@ -283,7 +283,6 @@ def testMegaComplexRecursion(self):
     # TODO: Fix this test
     @pytest.mark.xfail(reason="known error in assign")
     def test2dRectilinearRecursion(self):
-
         '''
          0                            1                      2
          +----------------------------+----------------------+
diff --git a/tests/test_tools/common.py b/tests/test_tools/common.py
index 384a9e71d..80ca3488a 100755
--- a/tests/test_tools/common.py
+++ b/tests/test_tools/common.py
@@ -71,7 +71,6 @@ def check_args(self, outcome, errmsg, args):
         assert outcome, str(errmsg)
 
     def check_runs_with_args(self, **kwargs):
-
         try:
             self.w.go()  # Run tool with given args
 
diff --git a/tests/test_tools/h5diff.py b/tests/test_tools/h5diff.py
index b956b434d..dcb701c20 100755
--- a/tests/test_tools/h5diff.py
+++ b/tests/test_tools/h5diff.py
@@ -4,14 +4,12 @@
 
 class H5Diff:
     def __init__(self, ref_file, test_file):
-
         self.ref_file = h5py.File(ref_file, 'r')
         self.test_file = h5py.File(test_file, 'r')
 
     # TODO: I don't love that this is hardcoded to compare the test file against the ref file, but
     #   to fix that I'd have to figure out how to pass an argument when I pass this as a callable to visititems()
     def check_in_ref(self, name, obj):
-
         # print(f"\nDiffing {name}", end='\n')
 
         test_object = obj
@@ -19,8 +17,7 @@ def check_in_ref(self, name, obj):
         assert ref_object is not None, f"Element {ref_object} did not exist in test file"
 
         # If it's a dataset, compare the actual contents
-        if type(test_object) == h5py._hl.dataset.Dataset:
-
+        if isinstance(test_object, h5py._hl.dataset.Dataset):
             if name in self.excluded_datasets:
                 return None
 
@@ -35,7 +32,6 @@ def check_in_ref(self, name, obj):
             # HACK: This if statement evaluates to False if the test_object is a single value like a float or something, since
             #   .dtype is referencing an attribute of a numpy array.
             if test_object[()].dtype.names is not None:
-
                 non_reference_test_elements = [
                     x for i, x in enumerate(test_object[()][0]) if not test_object[()].dtype.names[i] in ref_names
                 ]
@@ -59,7 +55,7 @@ def check_in_ref(self, name, obj):
             if type(non_reference_ref_elements) is ndarray and issubdtype(non_reference_ref_elements.dtype, floating):
                 comparison = isclose(non_reference_test_elements, non_reference_ref_elements, atol=self.float_thresh)
 
-            if type(comparison) == bool:
+            if isinstance(comparison, bool):
                 assert non_reference_test_elements == non_reference_ref_elements, f"Elements didn't match in {name}"
             else:
                 try:
@@ -73,7 +69,7 @@ def check_in_ref(self, name, obj):
 
         # If it's a group, do nothing
         # TODO: Is it sufficient to check only the datasets? The groups should just be organizational units
-        elif type(test_object) == h5py._hl.group.Group:
+        elif isinstance(test_object, h5py._hl.group.Group):
             pass
 
         # Returning None every loop makes visititems() iterate through every element.
@@ -89,7 +85,6 @@ def check_in_ref(self, name, obj):
     # But if it's flipped, then if there's extra junk in the test file, that wouldn't be revealed.
     # This works for the time being, and as an **extremely** janky hack fix, you could do it both ways...
     def check(self, float_thresh=1e-8, excluded_datasets=[]):
-
         self.float_thresh = float_thresh
         self.excluded_datasets = excluded_datasets
         self.test_file.visititems(self.check_in_ref)
@@ -97,7 +92,6 @@ def check(self, float_thresh=1e-8, excluded_datasets=[]):
 
 # TODO: Add some simple argument handler here
 if __name__ == "__main__":
-
     diff = H5Diff("./assign_ref.h5", "./analysis_tocompare.h5")
 
     diff.check()
diff --git a/tests/test_tools/test_w_assign.py b/tests/test_tools/test_w_assign.py
index 09650d789..6803c59c2 100755
--- a/tests/test_tools/test_w_assign.py
+++ b/tests/test_tools/test_w_assign.py
@@ -8,7 +8,6 @@
 
 class Test_W_Assign:
     def test_run_w_assign(self, ref_50iter):
-
         args = MockArgs(
             verbosity='debug',
             rcfile=self.cfg_filepath,
diff --git a/tests/test_tools/test_w_direct.py b/tests/test_tools/test_w_direct.py
index 3ef299748..e3150f17c 100755
--- a/tests/test_tools/test_w_direct.py
+++ b/tests/test_tools/test_w_direct.py
@@ -11,7 +11,6 @@
 
 
 class Test_W_Direct(unittest.TestCase):
-
     test_name = 'W_DIRECT'
 
     def test_run_w_direct(self):
@@ -30,7 +29,6 @@ def test_run_w_direct(self):
 @pytest.mark.skip(reason="work-in-progress test that uses entry point")
 class Test_W_Direct_New:
     def test_run_w_direct(self, ref_50iter):
-
         with mock.patch(
             target='argparse.ArgumentParser.parse_args',
             return_value=argparse.Namespace(
diff --git a/tests/test_tools/test_w_ipa.py b/tests/test_tools/test_w_ipa.py
index afc94cc7f..89853ca02 100755
--- a/tests/test_tools/test_w_ipa.py
+++ b/tests/test_tools/test_w_ipa.py
@@ -10,7 +10,6 @@
 
 
 class Test_W_IPA(unittest.TestCase):
-
     test_name = 'W_IPA'
 
     def test_run_w_ipa(self):
diff --git a/tests/test_tools/test_w_trace.py b/tests/test_tools/test_w_trace.py
index bc552dd72..311dfde9a 100755
--- a/tests/test_tools/test_w_trace.py
+++ b/tests/test_tools/test_w_trace.py
@@ -84,9 +84,7 @@ def test_args(self):
         return self.check_args, test_outcome, err, args
 
     def check_output(self, arg_idx):
-
         with h5py.File(self.outfile) as f:
-
             assert 'trajectories' in list(f.keys()), "'trajectories' group not in output file"
 
             traj_group = f['trajectories']
diff --git a/tests/test_we_driver.py b/tests/test_we_driver.py
index 6487a34da..9e8f69586 100644
--- a/tests/test_we_driver.py
+++ b/tests/test_we_driver.py
@@ -222,7 +222,6 @@ def test_recycle(self):
         assert segments[0].endpoint_type == Segment.SEG_ENDPOINT_RECYCLED
 
     def test_multiple_merge(self):
-
         # This weight and count combination is known to trigger a split to 51
         # followed by a count adjustment to 50 (thanks to Josh Adelman)
         segment = self.segment(0.0, 0.5, weight=0.9999999999970001)
diff --git a/tests/test_work_managers/test_zeromq/test_worker.py b/tests/test_work_managers/test_zeromq/test_worker.py
index f59c2e1e4..3d4c52674 100644
--- a/tests/test_work_managers/test_zeromq/test_worker.py
+++ b/tests/test_work_managers/test_zeromq/test_worker.py
@@ -20,7 +20,6 @@
 
 
 class TestZMQWorkerBasic(ZMQTestBase, unittest.TestCase):
-
     # endpoint_type = 'tcp'
 
     '''Tests for the core task dispersal/retrieval and shutdown operations
diff --git a/tests/test_yamlfe.py b/tests/test_yamlfe.py
index 6c401dacb..b981907cc 100644
--- a/tests/test_yamlfe.py
+++ b/tests/test_yamlfe.py
@@ -26,6 +26,7 @@ def initialize(self):
 #  - returns the correct system
 #    given both
 
+
 # A class to test both paths at the same time
 # if it works we assure we can load the driver
 # AND overwrite it properly