Cleanup/2026 03 10 (#1692)

jmlarson1 · web-flow · commit 12a47d72cbcd · 2026-03-10T16:01:29.000-05:00
* isort and slight ipynb cleanup
diff --git a/examples/tutorials/aposmm/aposmm_tutorial_notebook.ipynb b/examples/tutorials/aposmm/aposmm_tutorial_notebook.ipynb
@@ -369,8 +369,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.13.1"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/examples/tutorials/xopt_bayesian_gen/xopt_EI_example.ipynb b/examples/tutorials/xopt_bayesian_gen/xopt_EI_example.ipynb
@@ -256,8 +256,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.11"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/libensemble/tests/functionality_tests/test_asktell_sampling_external_gen.py b/libensemble/tests/functionality_tests/test_asktell_sampling_external_gen.py
@@ -18,15 +18,16 @@
 import numpy as np
 from gest_api.vocs import VOCS
 
-# from gest_api.vocs import ContinuousVariable
+from libensemble import Ensemble
 
 # Import libEnsemble items for this test
 from libensemble.alloc_funcs.start_only_persistent import only_persistent_gens as alloc_f
 
 # from libensemble.gen_classes.external.sampling import UniformSampleArray
 from libensemble.gen_classes.external.sampling import UniformSample
-from libensemble import Ensemble
-from libensemble.specs import GenSpecs, SimSpecs, AllocSpecs, ExitCriteria, LibeSpecs
+from libensemble.specs import AllocSpecs, ExitCriteria, GenSpecs, LibeSpecs, SimSpecs
+
+# from gest_api.vocs import ContinuousVariable
 
 
 def sim_f_array(In):
diff --git a/libensemble/tests/regression_tests/support.py b/libensemble/tests/regression_tests/support.py
@@ -1,6 +1,7 @@
 import copy
 
 import numpy as np
+
 from libensemble.specs import input_fields, output_data
 
 branin_vals_and_minima = np.array(
diff --git a/libensemble/tests/regression_tests/test_1d_sampling.py b/libensemble/tests/regression_tests/test_1d_sampling.py
@@ -14,6 +14,7 @@
 # TESTSUITE_NPROCS: 2 4
 
 import numpy as np
+
 from libensemble import Ensemble
 from libensemble.gen_funcs.sampling import latin_hypercube_sample as gen_f
 
diff --git a/libensemble/tests/regression_tests/test_2d_sampling.py b/libensemble/tests/regression_tests/test_2d_sampling.py
@@ -14,6 +14,7 @@
 # TESTSUITE_NPROCS: 2 4
 
 import numpy as np
+
 from libensemble import Ensemble
 from libensemble.gen_funcs.sampling import latin_hypercube_sample as gen_f
 
diff --git a/libensemble/tests/regression_tests/test_GPU_variable_resources.py b/libensemble/tests/regression_tests/test_GPU_variable_resources.py
@@ -26,6 +26,7 @@
 # TESTSUITE_NPROCS: 6
 
 import numpy as np
+
 from libensemble import Ensemble
 from libensemble.alloc_funcs.start_only_persistent import only_persistent_gens as alloc_f
 from libensemble.executors.mpi_executor import MPIExecutor
diff --git a/libensemble/tests/regression_tests/test_GPU_variable_resources_multi_task.py b/libensemble/tests/regression_tests/test_GPU_variable_resources_multi_task.py
@@ -35,6 +35,7 @@
 # TESTSUITE_NPROCS: 10
 
 import numpy as np
+
 from libensemble import Ensemble
 from libensemble.alloc_funcs.start_only_persistent import only_persistent_gens as alloc_f
 from libensemble.executors.mpi_executor import MPIExecutor
diff --git a/libensemble/tests/regression_tests/test_evaluate_mixed_sample.py b/libensemble/tests/regression_tests/test_evaluate_mixed_sample.py
@@ -17,6 +17,7 @@
 import warnings
 
 import numpy as np
+
 from libensemble import Ensemble
 from libensemble.alloc_funcs.give_pregenerated_work import give_pregenerated_sim_work as alloc_f
 
diff --git a/libensemble/tests/regression_tests/test_gpCAM.py b/libensemble/tests/regression_tests/test_gpCAM.py
@@ -27,6 +27,7 @@
 import warnings
 
 import numpy as np
+
 from libensemble.alloc_funcs.start_only_persistent import only_persistent_gens as alloc_f
 from libensemble.gen_funcs.persistent_gpCAM import persistent_gpCAM, persistent_gpCAM_covar
 
diff --git a/libensemble/tests/regression_tests/test_inverse_bayes_example.py b/libensemble/tests/regression_tests/test_inverse_bayes_example.py
@@ -19,6 +19,7 @@
 # TESTSUITE_NPROCS: 3 4
 
 import numpy as np
+
 from libensemble import Ensemble
 from libensemble.alloc_funcs.inverse_bayes_allocf import only_persistent_gens_for_inverse_bayes as alloc_f
 from libensemble.gen_funcs.persistent_inverse_bayes import persistent_updater_after_likelihood as gen_f
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_dfols.py b/libensemble/tests/regression_tests/test_persistent_aposmm_dfols.py
@@ -21,9 +21,10 @@
 import multiprocessing
 import sys
 
-import libensemble.gen_funcs
 import numpy as np
 
+import libensemble.gen_funcs
+
 # Import libEnsemble items for this test
 from libensemble.libE import libE
 from libensemble.sim_funcs.chwirut1 import chwirut_eval as sim_f
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_exception.py b/libensemble/tests/regression_tests/test_persistent_aposmm_exception.py
@@ -18,9 +18,10 @@
 import multiprocessing
 import sys
 
-import libensemble.gen_funcs
 import numpy as np
 
+import libensemble.gen_funcs
+
 # Import libEnsemble items for this test
 from libensemble.libE import libE
 from libensemble.sim_funcs.periodic_func import func_wrapper as sim_f
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_external_localopt.py b/libensemble/tests/regression_tests/test_persistent_aposmm_external_localopt.py
@@ -26,9 +26,10 @@
 import shutil  # For copying the external_localopt script
 import sys
 
-import libensemble.gen_funcs
 import numpy as np
 
+import libensemble.gen_funcs
+
 # Import libEnsemble items for this test
 from libensemble.libE import libE
 from libensemble.sim_funcs.six_hump_camel import six_hump_camel as sim_f
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_ibcdfo_manifold_sampling.py b/libensemble/tests/regression_tests/test_persistent_aposmm_ibcdfo_manifold_sampling.py
@@ -27,8 +27,9 @@
 import multiprocessing
 import sys
 
-import libensemble.gen_funcs
 import numpy as np
+
+import libensemble.gen_funcs
 from libensemble.libE import libE
 
 libensemble.gen_funcs.rc.aposmm_optimizers = "ibcdfo_manifold_sampling"
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_ibcdfo_pounders.py b/libensemble/tests/regression_tests/test_persistent_aposmm_ibcdfo_pounders.py
@@ -27,8 +27,9 @@
 import multiprocessing
 import sys
 
-import libensemble.gen_funcs
 import numpy as np
+
+import libensemble.gen_funcs
 from libensemble.libE import libE
 from libensemble.sim_funcs.chwirut1 import chwirut_eval
 
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_ibcdfo_pounders_jax.py b/libensemble/tests/regression_tests/test_persistent_aposmm_ibcdfo_pounders_jax.py
@@ -27,8 +27,9 @@
 import multiprocessing
 import sys
 
-import libensemble.gen_funcs
 import numpy as np
+
+import libensemble.gen_funcs
 from libensemble.libE import libE
 
 libensemble.gen_funcs.rc.aposmm_optimizers = "ibcdfo_pounders"
@@ -39,7 +40,6 @@
 
 try:
     import ibcdfo  # noqa: F401
-
     from declare_hfun_and_combine_model_with_jax import combinemodels_jax, hfun
 
 except ModuleNotFoundError:
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_periodic.py b/libensemble/tests/regression_tests/test_persistent_aposmm_periodic.py
@@ -19,9 +19,10 @@
 import multiprocessing
 import sys
 
-import libensemble.gen_funcs
 import numpy as np
 
+import libensemble.gen_funcs
+
 libensemble.gen_funcs.rc.aposmm_optimizers = ["nlopt", "scipy"]
 from libensemble.alloc_funcs.persistent_aposmm_alloc import persistent_aposmm_alloc as alloc_f
 from libensemble.gen_funcs.persistent_aposmm import aposmm as gen_f
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_pounders.py b/libensemble/tests/regression_tests/test_persistent_aposmm_pounders.py
@@ -22,9 +22,10 @@
 import sys
 from math import ceil, gamma, pi, sqrt
 
-import libensemble.gen_funcs
 import numpy as np
 
+import libensemble.gen_funcs
+
 # Import libEnsemble items for this test
 from libensemble.libE import libE
 from libensemble.sim_funcs.chwirut1 import chwirut_eval as sim_f
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_scipy.py b/libensemble/tests/regression_tests/test_persistent_aposmm_scipy.py
@@ -18,9 +18,10 @@
 import multiprocessing
 import sys
 
-import libensemble.gen_funcs
 import numpy as np
 
+import libensemble.gen_funcs
+
 # Import libEnsemble items for this test
 from libensemble.libE import libE
 from libensemble.sim_funcs.six_hump_camel import six_hump_camel as sim_f
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_tao_blmvm.py b/libensemble/tests/regression_tests/test_persistent_aposmm_tao_blmvm.py
@@ -20,9 +20,10 @@
 import sys
 from math import gamma, pi, sqrt
 
-import libensemble.gen_funcs
 import numpy as np
 
+import libensemble.gen_funcs
+
 # Import libEnsemble items for this test
 from libensemble.libE import libE
 from libensemble.sim_funcs.six_hump_camel import six_hump_camel as sim_f
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_tao_nm.py b/libensemble/tests/regression_tests/test_persistent_aposmm_tao_nm.py
@@ -19,9 +19,10 @@
 import multiprocessing
 import sys
 
-import libensemble.gen_funcs
 import numpy as np
 
+import libensemble.gen_funcs
+
 # Import libEnsemble items for this test
 from libensemble.libE import libE
 from libensemble.sim_funcs.six_hump_camel import six_hump_camel as sim_f
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_timeout.py b/libensemble/tests/regression_tests/test_persistent_aposmm_timeout.py
@@ -20,9 +20,10 @@
 import multiprocessing
 import sys
 
-import libensemble.gen_funcs
 import numpy as np
 
+import libensemble.gen_funcs
+
 libensemble.gen_funcs.rc.aposmm_optimizers = "nlopt"
 
 from libensemble.alloc_funcs.persistent_aposmm_alloc import persistent_aposmm_alloc as alloc_f
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_with_grad.py b/libensemble/tests/regression_tests/test_persistent_aposmm_with_grad.py
@@ -21,9 +21,10 @@
 import sys
 from math import gamma, pi, sqrt
 
-import libensemble.gen_funcs
 import numpy as np
 
+import libensemble.gen_funcs
+
 # Import libEnsemble items for this test
 from libensemble.libE import libE
 from libensemble.sim_funcs.six_hump_camel import six_hump_camel as sim_f
diff --git a/libensemble/tests/regression_tests/test_persistent_fd_param_finder.py b/libensemble/tests/regression_tests/test_persistent_fd_param_finder.py
@@ -20,6 +20,7 @@
 import shutil  # For ECnoise.m
 
 import numpy as np
+
 from libensemble import Ensemble
 from libensemble.alloc_funcs.start_fd_persistent import finite_diff_alloc as alloc_f
 from libensemble.gen_funcs.persistent_fd_param_finder import fd_param_finder as gen_f
diff --git a/libensemble/tests/regression_tests/test_persistent_gp_multitask_ax.py b/libensemble/tests/regression_tests/test_persistent_gp_multitask_ax.py
@@ -24,6 +24,7 @@
 import warnings
 
 import numpy as np
+
 from libensemble import logger
 from libensemble.alloc_funcs.start_only_persistent import only_persistent_gens
 from libensemble.libE import libE
diff --git a/libensemble/tests/regression_tests/test_persistent_surmise_calib.py b/libensemble/tests/regression_tests/test_persistent_surmise_calib.py
@@ -31,6 +31,7 @@
 #   Install Surmise package
 
 import numpy as np
+
 from libensemble import Ensemble
 from libensemble.alloc_funcs.start_only_persistent import only_persistent_gens as alloc_f
 from libensemble.gen_funcs.persistent_surmise_calib import surmise_calib as gen_f
diff --git a/libensemble/tests/regression_tests/test_persistent_surmise_killsims.py b/libensemble/tests/regression_tests/test_persistent_surmise_killsims.py
@@ -33,6 +33,7 @@
 import os
 
 import numpy as np
+
 from libensemble.alloc_funcs.start_only_persistent import only_persistent_gens as alloc_f
 from libensemble.executors.executor import Executor
 from libensemble.gen_funcs.persistent_surmise_calib import surmise_calib as gen_f
diff --git a/libensemble/tests/regression_tests/test_with_app_persistent_aposmm_tao_nm.py b/libensemble/tests/regression_tests/test_with_app_persistent_aposmm_tao_nm.py
@@ -24,6 +24,7 @@
 import sys
 
 import numpy as np
+
 from libensemble.alloc_funcs.persistent_aposmm_alloc import persistent_aposmm_alloc as alloc_f
 from libensemble.executors import MPIExecutor
 from libensemble.gen_funcs.persistent_aposmm import aposmm as gen_f
diff --git a/libensemble/tests/scaling_tests/forces/forces_simple_xopt/run_libe_forces.py b/libensemble/tests/scaling_tests/forces/forces_simple_xopt/run_libe_forces.py
@@ -4,8 +4,6 @@
 
 import numpy as np
 from forces_simf import run_forces  # Classic libEnsemble sim_f.
-# from forces_simf import run_forces_dict  # gest-api/xopt style simulator.
-
 from gest_api.vocs import VOCS
 from xopt.generators.random import RandomGenerator
 
@@ -14,6 +12,9 @@
 from libensemble.executors import MPIExecutor
 from libensemble.specs import AllocSpecs, ExitCriteria, GenSpecs, LibeSpecs, SimSpecs
 
+# from forces_simf import run_forces_dict  # gest-api/xopt style simulator.
+
+
 if __name__ == "__main__":
     # Initialize MPI Executor
     exctr = MPIExecutor()
diff --git a/libensemble/tests/unit_tests/test_aposmm_starting_point_finder.py b/libensemble/tests/unit_tests/test_aposmm_starting_point_finder.py
@@ -1,8 +1,9 @@
 import numpy as np
+
 from libensemble.gen_funcs.persistent_aposmm import (
+    decide_where_to_start_localopt,
     initialize_APOSMM,
     update_history_dist,
-    decide_where_to_start_localopt,
 )
 from libensemble.sim_funcs.six_hump_camel import six_hump_camel_func
 from libensemble.tests.regression_tests.support import six_hump_camel_minima as known_minima
diff --git a/libensemble/tests/unit_tests/test_asktell.py b/libensemble/tests/unit_tests/test_asktell.py
@@ -1,4 +1,5 @@
 import numpy as np
+
 from libensemble.utils.misc import unmap_numpy_array
 
 
diff --git a/libensemble/tests/unit_tests/test_models.py b/libensemble/tests/unit_tests/test_models.py
@@ -1,8 +1,8 @@
 import numpy as np
+from gest_api.vocs import VOCS
 from pydantic import ValidationError
 
 import libensemble.tests.unit_tests.setup as setup
-from gest_api.vocs import VOCS
 from libensemble.gen_funcs.sampling import latin_hypercube_sample
 from libensemble.sim_funcs.simple_sim import norm_eval
 from libensemble.specs import ExitCriteria, GenSpecs, LibeSpecs, SimSpecs, _EnsembleSpecs
