Merge pull request #1035 from Libensemble/refactor/remove_setup_extras

remove use/mention of pip install libensemble[extras]

docs/advanced_installation.rst

@@ -28,13 +28,6 @@ To install the latest PyPI release::
 
     pip install libensemble
 
-The above comes with required dependencies only. To install with some
-common user function dependencies (as used in the examples and tests)::
-
-    pip install libensemble[extras]
-
-Note that since ``PETSc`` will build from source, this may take a while.
-
 To pip install libEnsemble from the latest develop branch::
 
     python -m pip install --upgrade git+https://github.com/Libensemble/libensemble.git@develop

libensemble/gen_funcs/persistent_fd_param_finder.py

@@ -88,7 +88,7 @@ def fd_param_finder(H, persis_info, gen_specs, libE_info):
             for k in range(nf + 1):
                 if k != nf / 2:
                     logical_conds = (calc_in["x_ind"] == i, calc_in["f_ind"] == j, calc_in["n_ind"] == k)
-                    Fhist0[i, j, k] = calc_in["f_val"][np.logical_and.reduce(logical_conds)]
+                    Fhist0[i, j, k] = calc_in["f_val"][np.logical_and.reduce(logical_conds)][0]
 
             # Compute noise for (i, j):
             # [Fnoise(i, j), ~, inform(i, j)] = ECnoise(nf-1, Fhist0(i, j, 2:nf));

libensemble/sim_funcs/borehole.py

@@ -65,7 +65,7 @@ def borehole_func(x):
     denom1 = 2 * L * Tu / (np.log(r / rw) * rw**2 * Kw)
     denom2 = Tu / Tl
 
-    return (numer / (np.log(r / rw) * (1 + denom1 + denom2))).reshape(-1)
+    return ((numer / (np.log(r / rw) * (1 + denom1 + denom2))).reshape(-1))[0]
 
 
 def gen_borehole_input(n):

libensemble/sim_funcs/rosenbrock.py

@@ -31,7 +31,7 @@ def EvaluateFunction(x, component):
         x2 = x[2 * i + 1]
         f = 100 * (x1**2 - x2) ** 2 + (x1 - 1) ** 2
 
-    return f
+    return f[0]
 
 
 def EvaluateJacobian(x, component, const):

libensemble/tests/regression_tests/test_evaluate_mixed_sample.py

@@ -14,6 +14,8 @@
 # TESTSUITE_COMMS: mpi local tcp
 # TESTSUITE_NPROCS: 2 4
 
+import warnings
+
 import numpy as np
 
 from libensemble.alloc_funcs.give_pregenerated_work import give_pregenerated_sim_work as alloc_f
@@ -24,6 +26,8 @@
 from libensemble.sim_funcs.borehole import borehole_func, gen_borehole_input
 from libensemble.tools import parse_args, save_libE_output
 
+warnings.filterwarnings("ignore", category=DeprecationWarning)
+
 # Main block is necessary only when using local comms with spawn start method (default on macOS and Windows).
 if __name__ == "__main__":
     nworkers, is_manager, libE_specs, _ = parse_args()

libensemble/tests/regression_tests/test_ytopt_heffte.py

@@ -21,6 +21,7 @@
 warnings.filterwarnings("ignore", category=ImportWarning)
 warnings.filterwarnings("ignore", category=FutureWarning)
 warnings.filterwarnings("ignore", category=RuntimeWarning)
+warnings.filterwarnings("ignore", category=DeprecationWarning)
 
 import os
 import secrets

setup.py

@@ -69,7 +69,6 @@ def run_tests(self):
         "libensemble.tests.unit_tests",
         "libensemble.tests.regression_tests",
     ],
-    package_data={"libensemble.sim_funcs.branin": ["known_minima_and_func_values"]},
     install_requires=["numpy", "psutil", "setuptools", "pydantic", "tomli", "pyyaml"],
     # If run tests through setup.py - downloads these but does not install
     tests_require=[
@@ -80,19 +79,6 @@ def run_tests(self):
         "mock",
     ],
     extras_require={
-        "extras": [
-            "ax-platform",
-            "DFO-LS",
-            "dragonfly-opt",
-            "funcx",
-            "mpi4py",
-            "mpmath",
-            "nlopt",
-            "petsc",
-            "petsc4py",
-            "pyyaml",
-            "scipy",
-        ],
         "docs": [
             "autodoc_pydantic",
             "sphinx",