Merge branch 'develop' into refactor/deprecate_from_yaml_toml_json

Author: jlnav

.codecov.yml

@@ -4,3 +4,4 @@ ignore:
   - "libensemble/tools/live_data/*"
   - "libensemble/sim_funcs/executor_hworld.py"
   - "libensemble/gen_funcs/persistent_tasmanian.py"
+  - "libensemble/gen_classes/gpCAM.py"

.flake8

@@ -38,6 +38,7 @@ per-file-ignores =
 
         # Need to set something before the APOSMM import
         libensemble/tests/regression_tests/test_persistent_aposmm*:E402
+        libensemble/tests/regression_tests/test_asktell_aposmm_nlopt.py:E402
         libensemble/tests/regression_tests/test_persistent_gp_multitask_ax.py:E402
         libensemble/tests/functionality_tests/test_uniform_sampling_then_persistent_localopt_runs.py:E402
         libensemble/tests/functionality_tests/test_stats_output.py:E402

.github/workflows/basic.yml

@@ -62,6 +62,12 @@ jobs:
             pip install -e .
             flake8 libensemble
 
+        - name: Install mypy
+          run: pip install mypy
+
+        - name: Run mypy (limited scope)
+          run: mypy
+
         - name: Remove various tests on newer pythons
           if: matrix.python-version == 'py311' || matrix.python-version == 'py312' || matrix.python-version == 'py313' || matrix.python-version == 'py314'
           run: |
@@ -92,4 +98,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v6
-        - uses: crate-ci/typos@v1.43.0
+        - uses: crate-ci/typos@v1.44.0

.github/workflows/extra.yml

@@ -48,7 +48,7 @@ jobs:
         - name: Checkout lockfile
           run: git lfs checkout
 
-        - uses: prefix-dev/setup-pixi@v0.9.2
+        - uses: prefix-dev/setup-pixi@v0.9.4
           with:
             pixi-version: v0.55.0
             cache: true
@@ -70,14 +70,22 @@ jobs:
           run: |
             pixi run -e ${{ matrix.python-version }} pip install gpcam==8.1.13
 
+        - name: Remove xopt tests on old python
+          if: matrix.python-version == 'py310e'
+          run: |
+            rm ./libensemble/tests/regression_tests/test_xopt_EI_xopt_sim.py
+            rm ./libensemble/tests/regression_tests/test_xopt_EI.py
+            rm ./libensemble/tests/regression_tests/test_xopt_nelder_mead.py
+
         - name: Remove test using octave, gpcam, globus-compute on Python 3.13
           if: matrix.python-version == 'py313e' || matrix.python-version == 'py314e'
           run: |
             rm ./libensemble/tests/unit_tests/test_ufunc_runners.py # needs globus-compute
-            rm ./libensemble/tests/regression_tests/test_persistent_fd_param_finder.py # needs octave, which doesn't yet support 3.13
-            rm ./libensemble/tests/regression_tests/test_persistent_aposmm_external_localopt.py # needs octave, which doesn't yet support 3.13
             rm ./libensemble/tests/regression_tests/test_gpCAM.py # needs gpcam, which doesn't build on 3.13
+            rm ./libensemble/tests/regression_tests/test_asktell_gpCAM.py # needs gpcam, which doesn't build on 3.13
             rm ./libensemble/tests/regression_tests/test_persistent_gp_multitask_ax.py # needs ax-platform, which doesn't yet support 3.14
+            rm ./libensemble/tests/regression_tests/test_optimas_ax_mf.py # needs ax-platform, which doesn't yet support 3.14
+            rm ./libensemble/tests/regression_tests/test_optimas_ax_sf.py # needs ax-platform, which doesn't yet support 3.14
 
         - name: Start Redis
           if: matrix.os == 'ubuntu-latest'
@@ -110,4 +118,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v6
-        - uses: crate-ci/typos@v1.43.0
+        - uses: crate-ci/typos@v1.44.0

.pre-commit-config.yaml

@@ -1,32 +1,32 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
     - id: end-of-file-fixer
       exclude: ^(.*\.xml|.*\.svg)$
     - id: trailing-whitespace
       exclude: ^(.*\.xml|.*\.svg)$
 
 - repo: https://github.com/pycqa/isort
-  rev: 6.0.0
+  rev: 7.0.0
   hooks:
     - id: isort
       args: [--profile=black, --line-length=120]
 
 - repo: https://github.com/psf/black
-  rev: 25.1.0
+  rev: 25.12.0
   hooks:
     - id: black
       args: [--line-length=120]
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 7.1.1
+  rev: 7.3.0
   hooks:
   -   id: flake8
       args: [--max-line-length=120]
 
 - repo: https://github.com/asottile/blacken-docs
-  rev: 1.19.1
+  rev: 1.20.0
   hooks:
   -   id: blacken-docs
       additional_dependencies: [black==22.12.0]

.wci.yml

@@ -16,8 +16,8 @@ description: |
 language: Python
 
 release:
-  version: 1.5.0
-  date: 2025-04-10
+  version: 1.6.0
+  date: 2026-03-04
 
 documentation:
   general: https://libensemble.readthedocs.io

CHANGELOG.rst

@@ -8,6 +8,45 @@ GitHub issues are referenced, and can be viewed with hyperlinks on the `github r
 
 .. _`github releases page`: https://github.com/Libensemble/libensemble/releases
 
+Release 1.6.0
+--------------
+
+:Date: March 04, 2026
+
+General Updates:
+
+* Support for ``gest-api`` generators (https://gest-api.readthedocs.io). #1307
+
+  * Support for any Xopt (v3.0+) and Optimas generators.
+  * libEnsemble's APOSMM, gpCAM, and random sampling generators are supplied in ``gest-api`` format.
+  * Support dictionary (Xopt-style) simulator functions.
+
+* Simulation container support - Executor precedent accepts ``%LIBENSEMBLE_SIM_DIR%`` placeholder. #1672
+
+Examples:
+
+* Adding test for ibcdfo with jax. #1591
+* Optimas/Xopt examples. #1620 / #1635 
+* Bayesian Optimization with Xopt tutorial / notebook.
+* Tasmanian generators moved to community examples.
+
+Dependencies:
+
+* ``gest-api`` is now a required dependency. #1666 
+* Remove Pydantic v1 support and Balsam. #1573
+* Python 3.14 supported. #1609 
+
+
+:Note:
+
+* Tests were run on Linux and MacOS with Python versions 3.10, 3.11, 3.12, 3.13, 3.14
+* Heterogeneous workflows tested on Aurora (ALCF) and Perlmutter (NERSC).
+
+:Known Issues:
+
+* See known issues section in the documentation.
+
+
 Release 1.5.0
 --------------
 

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2018-2025, UChicago Argonne, LLC and the libEnsemble Development Team
+Copyright (c) 2018-2026, UChicago Argonne, LLC and the libEnsemble Development Team
 All Rights Reserved.
 
 Redistribution and use in source and binary forms, with or without

README.rst

@@ -22,8 +22,11 @@ and inference problems on the world's leading supercomputers such as Frontier, A
 
 `Quickstart`_
 
-**New:** Try out the |ScriptCreator| to generate customized scripts for running
-ensembles with your MPI applications.
+**New:** libEnsemble nows supports the `gest-api`_ generator standard, and can run with 
+Optimas and Xopt generators.
+
+The |ScriptCreator| to generate customized scripts for running ensembles with your
+MPI applications.
 
 Installation
 ============
@@ -100,6 +103,8 @@ Try some other examples live in Colab.
 +---------------------------------------------------------------+-------------------------------------+
 | Surrogate model generation with gpCAM.                        | |Surrogate Modeling|                |
 +---------------------------------------------------------------+-------------------------------------+
+| Bayesian Optimization with Xopt.                              | |Bayesian Optimization with Xopt|   |
++---------------------------------------------------------------+-------------------------------------+
 
 There are many more examples in the `regression tests`_ and `Community Examples repository`_.
 
@@ -161,6 +166,7 @@ Resources
 .. _conda-forge: https://conda-forge.org/
 .. _Contributions: https://github.com/Libensemble/libensemble/blob/main/CONTRIBUTING.rst
 .. _docs: https://libensemble.readthedocs.io/en/main/advanced_installation.html
+.. _gest-api: https://gest-api.readthedocs.io
 .. _GitHub: https://github.com/Libensemble/libensemble
 .. _libEnsemble mailing list: https://lists.mcs.anl.gov/mailman/listinfo/libensemble
 .. _libEnsemble Slack page: https://libensemble.slack.com
@@ -186,6 +192,9 @@ Resources
 .. |Surrogate Modeling| image:: https://colab.research.google.com/assets/colab-badge.svg
   :target:  https://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/gpcam_surrogate_model/gpcam.ipynb
 
+.. |Bayesian Optimization with Xopt| image:: https://colab.research.google.com/assets/colab-badge.svg
+  :target:  https://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/xopt_bayesian_gen/xopt_EI_example.ipynb
+
 .. |ScriptCreator| image:: https://img.shields.io/badge/Script_Creator-purple?logo=magic
    :target: https://libensemble.github.io/script-creator/
    :alt: Script Creator

docs/advanced_installation.rst

@@ -1,23 +1,20 @@
 Advanced Installation
 =====================
 
-libEnsemble can be installed from ``pip``, ``Conda``, or ``Spack``.
+libEnsemble can be installed from ``pip``, ``uv``, ``Conda``, or ``Spack``.
 
 libEnsemble requires the following dependencies, which are typically
 automatically installed alongside libEnsemble:
 
 * Python_       ``>= 3.10``
 * NumPy_        ``>= 1.21``
 * psutil_       ``>= 5.9.4``
-* `pydantic`_   ``>= 1.10.12``
+* `pydantic`_   ``>= 2``
 * pyyaml_       ``>= v6.0``
 * tomli_        ``>= 1.2.1``
+* gest-api_     ``>= 0.1,<0.2``
 
-Given libEnsemble's compiled dependencies, the following installation
-methods each offer a trade-off between convenience and the ability
-to customize builds, including platform-specific optimizations.
-
-We always recommend installing in a virtual environment from Conda or another source.
+We recommend installing in a virtual environment from ``uv``, ``conda`` or another source.
 
 Further recommendations for selected HPC systems are given in the
 :ref:`HPC platform guides<platform-index>`.
@@ -53,6 +50,12 @@ Further recommendations for selected HPC systems are given in the
 
             CC=mpicc MPICC=mpicc pip install mpi4py --no-binary mpi4py
 
+    .. tab-item:: uv
+
+        To install the latest PyPI_ release via uv_::
+
+            uv pip install libensemble
+
     .. tab-item:: conda
 
         Install libEnsemble with Conda_ from the conda-forge channel::
@@ -178,6 +181,7 @@ The following packages may be installed separately to enable additional features
 
 .. _conda-forge: https://conda-forge.org/
 .. _Conda: https://docs.conda.io/en/latest/
+.. _gest-api: https://github.com/campa-consortium/gest-api
 .. _GitHub: https://github.com/Libensemble/libensemble
 .. _Globus Compute: https://www.globus.org/compute
 .. _MPICH: https://www.mpich.org/
@@ -192,3 +196,4 @@ The following packages may be installed separately to enable additional features
 .. _spack_libe: https://github.com/Libensemble/spack_libe
 .. _tomli: https://pypi.org/project/tomli/
 .. _tqdm: https://tqdm.github.io/
+.. _uv: https://docs.astral.sh/uv/