Merge branch 'develop' into deps/bump

jlnav · jlnav · commit 5979a5b97c1d · 2026-05-06T11:07:39.000-05:00
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -10,7 +10,7 @@ updates:
   - package-ecosystem: github-actions
     directory: /
     schedule:
-      interval: weekly # Reduced frequency
+      interval: monthly # Reduced frequency
     target-branch: "develop"
     groups:
       actions-updates:
@@ -20,7 +20,7 @@ updates:
   - package-ecosystem: pip
     directory: /
     schedule:
-      interval: weekly # Reduced frequency
+      interval: monthly # Reduced frequency
     target-branch: "develop"
     groups:
       python-updates:
@@ -30,7 +30,7 @@ updates:
   - package-ecosystem: gitsubmodule
     directory: /
     schedule:
-      interval: weekly # Reduced frequency
+      interval: monthly # Reduced frequency
     target-branch: "develop"
     groups:
       submodule-updates:
diff --git a/.github/workflows/basic.yml b/.github/workflows/basic.yml
@@ -98,4 +98,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v6
-        - uses: crate-ci/typos@v1.45.1
+        - uses: crate-ci/typos@v1.46.0
diff --git a/.github/workflows/extra.yml b/.github/workflows/extra.yml
@@ -111,4 +111,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v6
-        - uses: crate-ci/typos@v1.45.1
+        - uses: crate-ci/typos@v1.46.0
diff --git a/docs/data_structures/libE_specs.rst b/docs/data_structures/libE_specs.rst
@@ -209,12 +209,6 @@ libEnsemble is primarily customized by setting options within a ``LibeSpecs`` in
                 **H_file_prefix** str | None = ``"libE_history"``
                     Prefix for ``H`` filename.
 
-                **use_persis_return_gen** [bool] = ``False``:
-                    Adds persistent generator output fields to the History array on return.
-
-                **use_persis_return_sim** [bool] = ``False``:
-                    Adds persistent simulator output fields to the History array on return.
-
                 **final_gen_send** [bool] = ``False``:
                     Send final simulation results to persistent generators before shutdown.
                     The results will be sent along with the ``PERSIS_STOP`` tag.
diff --git a/docs/dev_guide/release_management/release_platforms/rel_spack.rst b/docs/dev_guide/release_management/release_platforms/rel_spack.rst
@@ -24,7 +24,7 @@ Do ONCE in your local checkout:
 
 To set upstream repo::
 
-    git remote add upstream https://github.com/spack/spack.git
+    git remote add upstream https://github.com/spack/spack-packages.git
     git remote -v # check added
 
 (Optional) To prevent accidental pushes to upstream::
@@ -80,12 +80,15 @@ See the Spack packaging_ and contribution_ guides for more info.
 Quick example to update libEnsemble
 -----------------------------------
 
+The libEnsemble ``package.py`` file can be viewed online at:
+https://github.com/spack/spack-packages/blob/develop/repos/spack_repo/builtin/packages/py_libensemble/package.py
+
 This will open the libEnsemble ``package.py`` file in your editor (given by
 environment variable ``EDITOR``)::
 
     spack edit py-libensemble  # SPACK_ROOT must be set (see above) (Python packages use "py-" prefix)
 
-Or just open it manually: ``var/spack/repos/builtin/packages/py-libensemble/package.py``.
+Or just open it manually: ``repos/spack_repo/builtin/packages/py_libensemble/package.py``.
 
 Now get the checksum for new lines:
 
@@ -119,7 +122,7 @@ Express Summary: Make Fork Identical to Upstream
 Quick summary for bringing the develop branch on a forked repo up to speed with upstream
 (YOU WILL LOSE ANY CHANGES)::
 
-    git remote add upstream https://github.com/spack/spack.git
+    git remote add upstream https://github.com/spack/spack-packages.git
     git fetch upstream
     git checkout develop
     git reset --hard upstream/develop
diff --git a/libensemble/gen_funcs/persistent_fd_param_finder.py b/libensemble/gen_funcs/persistent_fd_param_finder.py
@@ -119,4 +119,4 @@ def fd_param_finder(H, persis_info, gen_specs, libE_info):
         tag, Work, calc_in = ps.send_recv(H0)
 
     persis_info["Fnoise"] = Fnoise
-    return H0, persis_info, FINISHED_PERSISTENT_GEN_TAG
+    return None, persis_info, FINISHED_PERSISTENT_GEN_TAG
diff --git a/libensemble/gen_funcs/persistent_sampling.py b/libensemble/gen_funcs/persistent_sampling.py
@@ -121,7 +121,6 @@ def sample_corners_with_probability(corners, p, b):
                     running_total[row["corner_id"]] += row["f"]
 
     # Having received a PERSIS_STOP, update f_est field for all points and return
-    # For manager to honor final H_o return, must have set libE_specs["use_persis_return_gen"] = True
     f_est = running_total / number_of_samples
     H_o = np.zeros(len(sent), dtype=[("sim_id", int), ("corner_id", int), ("f_est", float)])
     for count, i in enumerate(sent):
diff --git a/libensemble/gen_funcs/uniform_or_localopt.py b/libensemble/gen_funcs/uniform_or_localopt.py
@@ -25,9 +25,7 @@ def uniform_or_localopt(H, persis_info, gen_specs, libE_info):
         `test_uniform_sampling_then_persistent_localopt_runs.py <https://github.com/Libensemble/libensemble/blob/develop/libensemble/tests/functionality_tests/test_uniform_sampling_then_persistent_localopt_runs.py>`_ # noqa
     """
     if libE_info.get("persistent"):
-        x_opt, persis_info_updates, tag_out = try_and_run_nlopt(H, gen_specs, libE_info)
-        H_o = []
-        return H_o, persis_info_updates, tag_out
+        return try_and_run_nlopt(H, gen_specs, libE_info)
     else:
         rng = get_rng(gen_specs, libE_info)
         ub = gen_specs["user"]["ub"]
@@ -109,10 +107,9 @@ def nlopt_obj_fun(x, grad):
         if exit_code > 0 and exit_code < 5:
             persis_info_updates["x_opt"] = x_opt
     except Exception:  # Raised when manager sent PERSIS_STOP or STOP_TAG
-        x_opt = []
         persis_info_updates = {}
 
-    return x_opt, persis_info_updates, FINISHED_PERSISTENT_GEN_TAG
+    return None, persis_info_updates, FINISHED_PERSISTENT_GEN_TAG
 
 
 def add_to_Out(H_o, x, i, ub, lb, local=False, active=False):
diff --git a/libensemble/history.py b/libensemble/history.py
@@ -68,15 +68,22 @@ def __init__(
                 H[field][: len(H0)] = H0[field]
 
             if "sim_started" not in fields:
-                logger.manager_warning("Marking entries in H0 as having been 'sim_started' and 'sim_ended'")
+                logger.manager_warning(  # type: ignore[attr-defined]
+                    "Marking entries in H0 as having been " + "'sim_started' and 'sim_ended'"
+                )
+
                 H["sim_started"][: len(H0)] = 1
                 H["sim_ended"][: len(H0)] = 1
             elif "sim_ended" not in fields:
-                logger.manager_warning("Marking entries in H0 as having been 'sim_ended' if 'sim_started'")
+                logger.manager_warning(  # type: ignore[attr-defined]
+                    "Marking entries in H0 as having been " + "'sim_ended' if 'sim_started'"
+                )
+
                 H["sim_ended"][: len(H0)] = H0["sim_started"]
 
             if "sim_id" not in fields:
-                logger.manager_warning("Assigning sim_ids to entries in H0")
+                logger.manager_warning("Assigning sim_ids to entries in H0")  # type: ignore[attr-defined]
+
                 H["sim_id"][: len(H0)] = np.arange(0, len(H0))
         else:
             H = np.zeros(L + len(H0), dtype=specs_dtype_list)
@@ -130,8 +137,11 @@ def update_history_f(self, D: dict, kill_canceled_sims: bool = False) -> None:
 
         for j, ind in enumerate(new_inds):
             for field in fields:
-                if self.safe_mode:
-                    assert field not in protected_libE_fields, "The field '" + field + "' is protected"
+                if field in protected_libE_fields:
+                    if self.safe_mode:
+                        assert False, "The field '" + field + "' is protected"
+                    continue
+
                 if np.isscalar(returned_H[field][j]) or returned_H.dtype[field].hasobject:
                     self.H[field][ind] = returned_H[field][j]
                 else:
@@ -194,9 +204,10 @@ def update_history_to_gen(self, q_inds: npt.NDArray):
                     self.H["gen_informed"][ind] = True
 
             if self.using_H0 and not self.given_back_warned:
-                logger.manager_warning(
-                    "Giving entries in H0 back to gen. Marking entries in H0 as 'gen_informed' if 'sim_ended'."
+                logger.manager_warning(  # type: ignore[attr-defined]
+                    "Giving entries in H0 back to gen. Marking entries in " + "H0 as 'gen_informed' if 'sim_ended'."
                 )
+
                 self.given_back_warned = True
 
             self.H["gen_informed_time"][q_inds] = t
@@ -250,8 +261,11 @@ def update_history_x_in(self, gen_worker: int, D: npt.NDArray, gen_started_time:
             update_inds = D["sim_id"]
 
         for field in D.dtype.names:
-            if self.safe_mode:
-                assert field not in protected_libE_fields, "The field '" + field + "' is protected"
+            if field in protected_libE_fields:
+                if self.safe_mode:
+                    assert False, "The field '" + field + "' is protected"
+                continue
+
             self.H[field][update_inds] = D[field]
 
         first_gen_inds = update_inds[self.H["gen_ended_time"][update_inds] == 0]
diff --git a/libensemble/manager.py b/libensemble/manager.py
@@ -34,7 +34,7 @@
 )
 from libensemble.resources.resources import Resources
 from libensemble.tools.fields_keys import protected_libE_fields
-from libensemble.tools.tools import _PERSIS_RETURN_WARNING, _USER_CALC_DIR_WARNING
+from libensemble.tools.tools import _USER_CALC_DIR_WARNING
 from libensemble.utils.misc import _WorkerIndexer, extract_H_ranges
 from libensemble.utils.output_directory import EnsembleDirectory
 from libensemble.utils.timer import Timer
@@ -488,13 +488,11 @@ def _update_state_on_worker_msg(self, persis_info: dict, D_recv: dict, w: int) -
         if calc_status in [FINISHED_PERSISTENT_SIM_TAG, FINISHED_PERSISTENT_GEN_TAG]:
             final_data = D_recv.get("calc_out", None)
             if isinstance(final_data, np.ndarray):
-                if calc_status is FINISHED_PERSISTENT_GEN_TAG and self.libE_specs.get("use_persis_return_gen", False):
+                if calc_status is FINISHED_PERSISTENT_GEN_TAG:
                     self._ensure_sim_id_in_persis_in(final_data)
                     self.hist.update_history_x_in(w, final_data, self.W[w]["gen_started_time"])
-                elif calc_status is FINISHED_PERSISTENT_SIM_TAG and self.libE_specs.get("use_persis_return_sim", False):
+                elif calc_status is FINISHED_PERSISTENT_SIM_TAG:
                     self.hist.update_history_f(D_recv, self.kill_canceled_sims)
-                else:
-                    logger.info(_PERSIS_RETURN_WARNING)
             self.W[w]["persis_state"] = 0
             if self.W[w]["active_recv"]:
                 self.W[w]["active"] = 0
diff --git a/libensemble/sim_funcs/six_hump_camel.py b/libensemble/sim_funcs/six_hump_camel.py
@@ -94,15 +94,13 @@ def persistent_six_hump_camel(H, persis_info, sim_specs, libE_info):
 
         tag, Work, calc_in = ps.send_recv(H_o)
 
-    final_return = None
-
     # Overwrite final point - for testing only
     if sim_specs["user"].get("replace_final_fields", 0):
         calc_in = np.ones(1, dtype=[("x", float, (2,))])
         H_o, persis_info = six_hump_camel(calc_in, persis_info, sim_specs, libE_info)
-        final_return = H_o
+        return H_o, persis_info, FINISHED_PERSISTENT_SIM_TAG
 
-    return final_return, persis_info, FINISHED_PERSISTENT_SIM_TAG
+    return None, persis_info, FINISHED_PERSISTENT_SIM_TAG
 
 
 def six_hump_camel_func(x):
diff --git a/libensemble/specs.py b/libensemble/specs.py
@@ -686,12 +686,6 @@ def set_calc_dirs_on_input_dir(self):
     ``manager_port``, ``authkey``, and ``workerID``. ``nworkers`` is specified normally.
     """
 
-    use_persis_return_gen: bool | None = False
-    """ Adds persistent generator output fields to the History array on return. """
-
-    use_persis_return_sim: bool | None = False
-    """ Adds persistent simulator output fields to the History array on return. """
-
     final_gen_send: bool | None = False
     """
     Send final simulation results to persistent generators before shutdown.
diff --git a/libensemble/tests/functionality_tests/test_persistent_sim_uniform_sampling.py b/libensemble/tests/functionality_tests/test_persistent_sim_uniform_sampling.py
@@ -36,9 +36,6 @@
     nworkers, is_manager, libE_specs, _ = parse_args()
     libE_specs["num_resource_sets"] = nworkers - 1  # Only matters if sims use resources.
 
-    # Only used to test returning/overwriting a point at the end of the persistent sim.
-    libE_specs["use_persis_return_sim"] = True
-
     if nworkers < 2:
         sys.exit("Cannot run with a persistent worker if only one worker -- aborting...")
 
diff --git a/libensemble/tests/functionality_tests/test_persistent_uniform_sampling_running_mean.py b/libensemble/tests/functionality_tests/test_persistent_uniform_sampling_running_mean.py
@@ -29,8 +29,6 @@
 if __name__ == "__main__":
     nworkers, is_manager, libE_specs, _ = parse_args()
 
-    libE_specs["use_persis_return_gen"] = True
-
     if nworkers < 2:
         sys.exit("Cannot run with a persistent worker if only one worker -- aborting...")
 
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
@@ -119,7 +119,7 @@ def synthetic_beamline_mapping(H, _, sim_specs):
     H, persis_info, flag = libE(sim_specs, gen_specs, exit_criteria, alloc_specs=alloc_specs, libE_specs=libE_specs)
 
     if is_manager:
-        assert np.min(H["f"]) == 2.0, "The best is 2"
+        assert np.min(H["f"][H["f"] > 0]) == 2.0, "The best is 2"  # nonzero
         assert persis_info[0].get("run_order"), "Run_order should have been given back"
         assert flag == 0
 
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_scipy.py b/libensemble/tests/regression_tests/test_persistent_aposmm_scipy.py
@@ -127,4 +127,4 @@
     H, persis_info, flag = libE(sim_specs, gen_specs, exit_criteria, alloc_specs=alloc_specs, libE_specs=libE_specs)
 
     if is_manager:
-        assert np.sum(H["sim_ended"]) >= exit_criteria["sim_max"], "Run didn't finish"
+        assert np.sum(H["sim_ended"]) >= exit_criteria["sim_max"] - 10, "Not enough runs finished"
diff --git a/libensemble/tools/tools.py b/libensemble/tools/tools.py
@@ -62,20 +62,6 @@
     + "\n\n"
 )
 
-# ==================== Warning that persistent return data is not used ==========
-
-_PERSIS_RETURN_WARNING = (
-    "\n"
-    + 79 * "*"
-    + "\n"
-    + "A persistent worker has returned history data on shutdown. This data is\n"
-    + "not currently added to the manager's history to avoid possibly overwriting, but\n"
-    + "will be added to the manager's history in a future release. If you want to\n"
-    + "overwrite/append, you can set the libE_specs option ``use_persis_return_gen``\n"
-    + "or ``use_persis_return_sim``"
-    "\n" + 79 * "*" + "\n\n"
-)
-
 
 def _get_shortname(basename):
     script_name = os.path.splitext(os.path.basename(basename))[0]
