Merge branch 'develop' into docs/generator_section_refactor

Author: jlnav

.github/workflows/basic.yml

@@ -129,4 +129,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.28.4
+        - uses: crate-ci/typos@v1.29.4

.github/workflows/extra.yml

@@ -181,4 +181,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.28.4
+        - uses: crate-ci/typos@v1.29.4

docs/conf.py

@@ -30,32 +30,18 @@ class Mock(MagicMock):
     def __getattr__(cls, name):
         return MagicMock()
 
+autodoc_mock_imports = ["ax", "balsam", "gpcam", "IPython", "matplotlib", "pandas", "scipy", "surmise"]
 
 MOCK_MODULES = [
     "argparse",
     "dfols",
-    "IPython",
-    "IPython.display",
-    "IPython.core",
-    "IPython.core.pylabtools",
     "math",
-    "matplotlib",
-    "matplotlib.pyplot",
     "mpi4py",
     "mpmath",
     "nlopt",
     "PETSc",
     "petsc4py",
     "psutil",
-    "scipy",
-    "scipy.io",
-    "scipy.sparse",
-    "scipy.spatial",
-    "scipy.spatial.distance",
-    # "scipy.special",  # Adding this raises many more errors
-    "scipy.stats",
-    "surmise.calibration",
-    "surmise.emulation",
     "Tasmanian",
 ]
 
@@ -132,7 +118,6 @@ def __getattr__(cls, name):
 
 autodoc_pydantic_model_show_json = False
 
-autodoc_mock_imports = ["balsam"]
 extlinks = {
     "duref": ("http://docutils.sourceforge.net/docs/ref/rst/" "restructuredtext.html#%s", ""),
     "durole": ("http://docutils.sourceforge.net/docs/ref/rst/" "roles.html#%s", ""),

docs/examples/gen_funcs.rst

@@ -27,6 +27,7 @@ Here we list many generator functions included with libEnsemble.
   :maxdepth: 2
   :caption: Modeling and Approximation
 
+  gpcam
   tasmanian
   fd_param_finder
   surmise

docs/tutorials/executor_forces_tutorial.rst

@@ -380,7 +380,7 @@ Running forces application with input file
 Many applications read an input file instead of being given parameters directly on the run line.
 
 forces_simple_with_input_file_ directory contains a variant of this example, where a templated
-input file is parametized for each evaluation.
+input file is parameterized for each evaluation.
 
 This requires **jinja2** to be installed::
 

libensemble/gen_funcs/persistent_ax_multitask.py

@@ -41,6 +41,8 @@
 from libensemble.message_numbers import EVAL_GEN_TAG, FINISHED_PERSISTENT_GEN_TAG, PERSIS_STOP, STOP_TAG
 from libensemble.tools.persistent_support import PersistentSupport
 
+__all__ = ["persistent_gp_mt_ax_gen_f"]
+
 
 def persistent_gp_mt_ax_gen_f(H, persis_info, gen_specs, libE_info):
     """

libensemble/tools/tools.py

@@ -83,8 +83,7 @@ def _get_shortname(calling_file):
 
 # =================== save libE output to pickle and np ========================
 
-
-def save_libE_output(H, persis_info, calling_file, nworkers, dest_path=os.getcwd(), mess="Run completed"):
+def save_libE_output(H, persis_info, calling_file, nworkers, dest_path=None, mess="Run completed"):
     """
     Writes out history array and persis_info to files.
 
@@ -121,6 +120,9 @@ def save_libE_output(H, persis_info, calling_file, nworkers, dest_path=os.getcwd
         A message to print/log when saving the file.
 
     """
+    if dest_path is None:
+        dest_path = os.getcwd()
+
     short_name = _get_shortname(calling_file)
     prob_str = "length=" + str(len(H)) + "_evals=" + str(sum(H["sim_ended"])) + "_workers=" + str(nworkers)