Remove tcp/ssh comms throughout the codebase, docs, and tests.

.claude/skills/generate-scripts/references/results_metadata.md

@@ -39,4 +39,3 @@ If the minimum objective value is exactly 0.0, check whether those rows have
 `sim_ended == True`. Unevaluated rows often have fields initialized to zero.
 This is common for the last few rows when the simulation budget is exhausted — they were
 allocated by the generator but never evaluated.
-

.github/workflows/extra.yml

@@ -22,10 +22,6 @@ jobs:
             python-version: "py312e"
             mpi-version: mpich
             comms-type: l
-          - os: ubuntu-latest
-            python-version: "py312e"
-            mpi-version: mpich
-            comms-type: t
           - os: ubuntu-latest
             mpi-version: openmpi
             python-version: "py312e"

.readthedocs.yml

@@ -23,7 +23,8 @@ build:
     - asdf plugin add pixi
     - asdf install pixi latest
     - asdf global pixi latest
-    - pixi run -e docs build-docs
+    - pixi run -e docs sphinx-build -b html docs docs/_build/html -W --keep-going
+    - pixi run -e docs sphinx-build -b linkcheck docs docs/_build/linkcheck
     - mkdir -p $READTHEDOCS_OUTPUT/html/
     - cp -r docs/_build/html/** $READTHEDOCS_OUTPUT/html/
     - pixi run -e docs build-pdf

README.rst

@@ -144,7 +144,6 @@ Resources
 
 - Ask questions or report issues on GitHub_.
 - Email ``libEnsemble@lists.mcs.anl.gov`` to request `libEnsemble Slack page`_.
-- Join the `libEnsemble mailing list`_ for updates about new releases.
 
 **Further Information:**
 
@@ -197,7 +196,6 @@ Resources
 .. _docs: https://libensemble.readthedocs.io/en/main/advanced_installation.html
 .. _gest-api: https://gest-api.readthedocs.io/en/latest/
 .. _GitHub: https://github.com/Libensemble/libensemble
-.. _libEnsemble mailing list: https://lists.mcs.anl.gov/mailman/listinfo/libensemble
 .. _libEnsemble Slack page: https://libensemble.slack.com
 .. _MPICH: http://www.mpich.org/
 .. _mpmath: http://mpmath.org/

SUPPORT.rst

@@ -5,10 +5,6 @@ Open issues on Github at:
 
 * https://github.com/Libensemble/libensemble/issues
 
-Join the libEnsemble mailing list at:
-
-* https://lists.mcs.anl.gov/mailman/listinfo/libensemble
-
 or email questions to:
 
 * libensemble@lists.mcs.anl.gov

docs/FAQ.rst

@@ -145,8 +145,6 @@ HPC Errors and Questions
   is to either switch fabric or turn off matching probes. See the answer to "Why
   does libEnsemble hang on certain systems when running with MPI?"
 
-  For more information see https://bitbucket.org/mpi4py/mpi4py/issues/102/unpicklingerror-on-commrecv-after-iprobe.
-
 .. dropdown:: **srun: Job \*\*\*\*\*\* step creation temporarily disabled, retrying (Requested nodes are busy)**
 
   Note that this message has been observed on Perlmutter when none of the problems
@@ -161,7 +159,7 @@ HPC Errors and Questions
     See question **can't open hfi unit: -1 (err=23)** for more info.
 
   - All the memory is assigned to the first job-step (srun application), due to a default
-    exclusive mode scheduling policy. This has been observed on `Perlmutter`_ and `SDF`_.
+    exclusive mode scheduling policy. This has been observed on `Perlmutter`_.
 
     In some cases using these environment variables will stop the issue::
 
@@ -302,6 +300,5 @@ macOS and Windows Errors
 .. _option to srun: https://docs.nersc.gov/systems/perlmutter/running-jobs/#single-gpu-tasks-in-parallel
 .. _Perlmutter: https://docs.nersc.gov/systems/perlmutter/architecture/
 .. _Python multiprocessing docs: https://docs.python.org/3/library/multiprocessing.html
-.. _SDF: https://sdf.slac.stanford.edu/public/doc/#/?id=what-is-the-sdf
 .. _Support: https://libensemble.readthedocs.io/en/main/introduction.html#resources
 .. _xQuartz: https://www.xquartz.org/

docs/advanced_installation/advanced_installation.rst

@@ -1,7 +1,7 @@
 Advanced Installation
 =====================
 
-`pip <advanced_installation_pip.html>`__ || `uv <advanced_installation_uv.html>`__ || `pixi <advanced_installation_pixi.html>`__ || `conda <advanced_installation_conda.html>`__ || `Spack <advanced_installation_spack.html>`__
+:doc:`pip <advanced_installation_pip>` || :doc:`uv <advanced_installation_uv>` || :doc:`pixi <advanced_installation_pixi>` || :doc:`conda <advanced_installation_conda>` || :doc:`Spack <advanced_installation_spack>`
 
 libEnsemble can be installed from ``pip``, ``uv``, ``pixi``, ``Conda``, or ``Spack``.
 

docs/advanced_installation/advanced_installation_conda.rst

@@ -1,7 +1,7 @@
 conda
 =====
 
-`Advanced Installation <advanced_installation.html>`__ \|\| `pip <advanced_installation_pip.html>`__ \|\| `uv <advanced_installation_uv.html>`__ \|\| `pixi <advanced_installation_pixi.html>`__ \|\| **conda** \|\| `Spack <advanced_installation_spack.html>`__
+:doc:`Advanced Installation <advanced_installation>` || :doc:`pip <advanced_installation_pip>` || :doc:`uv <advanced_installation_uv>` || :doc:`pixi <advanced_installation_pixi>` || **conda** || :doc:`Spack <advanced_installation_spack>`
 
 Install libEnsemble with Conda_ from the conda-forge channel::
 

docs/advanced_installation/advanced_installation_pip.rst

@@ -1,7 +1,7 @@
 pip
 ===
 
-`Advanced Installation <advanced_installation.html>`__ \|\| **pip** \|\| `uv <advanced_installation_uv.html>`__ \|\| `pixi <advanced_installation_pixi.html>`__ \|\| `conda <advanced_installation_conda.html>`__ \|\| `Spack <advanced_installation_spack.html>`__
+:doc:`Advanced Installation <advanced_installation>` || **pip** || :doc:`uv <advanced_installation_uv>` || :doc:`pixi <advanced_installation_pixi>` || :doc:`conda <advanced_installation_conda>` || :doc:`Spack <advanced_installation_spack>`
 
 To install the latest PyPI_ release::
 

docs/advanced_installation/advanced_installation_pixi.rst

@@ -1,7 +1,7 @@
 pixi
 ====
 
-`Advanced Installation <advanced_installation.html>`__ \|\| `pip <advanced_installation_pip.html>`__ \|\| `uv <advanced_installation_uv.html>`__ \|\| **pixi** \|\| `conda <advanced_installation_conda.html>`__ \|\| `Spack <advanced_installation_spack.html>`__
+:doc:`Advanced Installation <advanced_installation>` || :doc:`pip <advanced_installation_pip>` || :doc:`uv <advanced_installation_uv>` || **pixi** || :doc:`conda <advanced_installation_conda>` || :doc:`Spack <advanced_installation_spack>`
 
 Add to your pixi_ environment::
 

docs/advanced_installation/advanced_installation_spack.rst

@@ -1,7 +1,7 @@
 Spack
 =====
 
-`Advanced Installation <advanced_installation.html>`__ \|\| `pip <advanced_installation_pip.html>`__ \|\| `uv <advanced_installation_uv.html>`__ \|\| `pixi <advanced_installation_pixi.html>`__ \|\| `conda <advanced_installation_conda.html>`__ \|\| **Spack**
+:doc:`Advanced Installation <advanced_installation>` || :doc:`pip <advanced_installation_pip>` || :doc:`uv <advanced_installation_uv>` || :doc:`pixi <advanced_installation_pixi>` || :doc:`conda <advanced_installation_conda>` || **Spack**
 
 Install libEnsemble using the Spack_ distribution::
 

docs/advanced_installation/advanced_installation_uv.rst

@@ -1,7 +1,7 @@
 uv
 ==
 
-`Advanced Installation <advanced_installation.html>`__ \|\| `pip <advanced_installation_pip.html>`__ \|\| **uv** \|\| `pixi <advanced_installation_pixi.html>`__ \|\| `conda <advanced_installation_conda.html>`__ \|\| `Spack <advanced_installation_spack.html>`__
+:doc:`Advanced Installation <advanced_installation>` || :doc:`pip <advanced_installation_pip>` || **uv** || :doc:`pixi <advanced_installation_pixi>` || :doc:`conda <advanced_installation_conda>` || :doc:`Spack <advanced_installation_spack>`
 
 To install the latest PyPI_ release via uv_::
 

docs/conf.py

@@ -118,6 +118,16 @@ class AxParameterWarning(Warning):  # Ensure it's a real warning subclass
     "community": ("https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/", None)
 }
 
+# These hosts reject automated requests from Sphinx linkcheck with HTTP 403.
+linkcheck_ignore = [
+    r"https://(docs|www)\.(alcf|lcrc)\.anl\.gov/.*",
+    r"https://www\.mcs\.anl\.gov/.*",
+    r"https://link\.aps\.org/.*",
+    r"https://libensemble\.slack\.com(?:/.*)?$",
+    r"https://software\.intel\.com/.*",
+    r"https://stackoverflow\.com/.*",
+]
+
 autodoc_pydantic_model_show_json = False
 
 extlinks = {

docs/data_structures/libE_specs/libE_specs.rst

@@ -1,6 +1,6 @@
 .. _datastruct-libe-specs:
 
-**Introduction** \|\| `General <libE_specs_general.html>`__ \|\| `Directories <libE_specs_directories.html>`__ \|\| `Profiling <libE_specs_profiling.html>`__ \|\| `TCP <libE_specs_tcp.html>`__ \|\| `History <libE_specs_history.html>`__ \|\| `Resources <libE_specs_resources.html>`__
+**Introduction** || :doc:`General <libE_specs_general>` || :doc:`Directories <libE_specs_directories>` || :doc:`Profiling <libE_specs_profiling>` || :doc:`History <libE_specs_history>` || :doc:`Resources <libE_specs_resources>`
 
 LibE Specs
 ==========
@@ -19,7 +19,6 @@ libEnsemble is primarily customized by setting options within a ``LibeSpecs`` in
     libE_specs_general
     libE_specs_directories
     libE_specs_profiling
-    libE_specs_tcp
     libE_specs_history
     libE_specs_resources
 

docs/data_structures/libE_specs/libE_specs_directories.rst

@@ -1,7 +1,7 @@
 Directories
 ===========
 
-`Introduction <libE_specs.html>`__ \|\| `General <libE_specs_general.html>`__ \|\| **Directories** \|\| `Profiling <libE_specs_profiling.html>`__ \|\| `TCP <libE_specs_tcp.html>`__ \|\| `History <libE_specs_history.html>`__ \|\| `Resources <libE_specs_resources.html>`__
+:doc:`Introduction <libE_specs>` || :doc:`General <libE_specs_general>` || **Directories** || :doc:`Profiling <libE_specs_profiling>` || :doc:`History <libE_specs_history>` || :doc:`Resources <libE_specs_resources>`
 
 .. tab-set::
 

docs/data_structures/libE_specs/libE_specs_general.rst

@@ -1,15 +1,15 @@
 General
 =======
 
-`Introduction <libE_specs.html>`__ \|\| **General** \|\| `Directories <libE_specs_directories.html>`__ \|\| `Profiling <libE_specs_profiling.html>`__ \|\| `TCP <libE_specs_tcp.html>`__ \|\| `History <libE_specs_history.html>`__ \|\| `Resources <libE_specs_resources.html>`__
+:doc:`Introduction <libE_specs>` || **General** || :doc:`Directories <libE_specs_directories>` || :doc:`Profiling <libE_specs_profiling>` || :doc:`History <libE_specs_history>` || :doc:`Resources <libE_specs_resources>`
 
 **comms** [str] = ``"mpi"``:
-    Manager/Worker communications mode: ``'mpi'``, ``'local'``, ``'threads'``, or ``'tcp'``.
+    Manager/Worker communications mode: ``'mpi'``, ``'local'``, or ``'threads'``.
     If ``nworkers`` is specified, then ``local`` comms will be used unless a
     parallel MPI environment is detected.
 
 **nworkers** [int]:
-    Number of worker processes in ``"local"``, ``"threads"``, or ``"tcp"``.
+    Number of worker processes in ``"local"`` or ``"threads"``.
 
 **gen_on_worker** [bool] = False
     Instructs Worker process to run generator instead of Manager.

docs/data_structures/libE_specs/libE_specs_history.rst

@@ -1,7 +1,7 @@
 History
 =======
 
-`Introduction <libE_specs.html>`__ \|\| `General <libE_specs_general.html>`__ \|\| `Directories <libE_specs_directories.html>`__ \|\| `Profiling <libE_specs_profiling.html>`__ \|\| `TCP <libE_specs_tcp.html>`__ \|\| **History** \|\| `Resources <libE_specs_resources.html>`__
+:doc:`Introduction <libE_specs>` || :doc:`General <libE_specs_general>` || :doc:`Directories <libE_specs_directories>` || :doc:`Profiling <libE_specs_profiling>` || **History** || :doc:`Resources <libE_specs_resources>`
 
 **save_every_k_sims** [int]:
     Save history array to file after every k simulated points.

docs/data_structures/libE_specs/libE_specs_profiling.rst

@@ -1,7 +1,7 @@
 Profiling
 =========
 
-`Introduction <libE_specs.html>`__ \|\| `General <libE_specs_general.html>`__ \|\| `Directories <libE_specs_directories.html>`__ \|\| **Profiling** \|\| `TCP <libE_specs_tcp.html>`__ \|\| `History <libE_specs_history.html>`__ \|\| `Resources <libE_specs_resources.html>`__
+:doc:`Introduction <libE_specs>` || :doc:`General <libE_specs_general>` || :doc:`Directories <libE_specs_directories>` || **Profiling** || :doc:`History <libE_specs_history>` || :doc:`Resources <libE_specs_resources>`
 
 **profile** [bool] = ``False``:
     Profile manager and worker logic using ``cProfile``.

docs/data_structures/libE_specs/libE_specs_resources.rst

@@ -1,7 +1,7 @@
 Resources
 =========
 
-`Introduction <libE_specs.html>`__ \|\| `General <libE_specs_general.html>`__ \|\| `Directories <libE_specs_directories.html>`__ \|\| `Profiling <libE_specs_profiling.html>`__ \|\| `TCP <libE_specs_tcp.html>`__ \|\| `History <libE_specs_history.html>`__ \|\| **Resources**
+:doc:`Introduction <libE_specs>` || :doc:`General <libE_specs_general>` || :doc:`Directories <libE_specs_directories>` || :doc:`Profiling <libE_specs_profiling>` || :doc:`History <libE_specs_history>` || **Resources**
 
 **disable_resource_manager** [bool] = ``False``:
     Disable the built-in resource manager, including automatic resource detection

docs/data_structures/platform_specs.rst

@@ -102,6 +102,15 @@ E.g., in the command line or batch submission script:
 Known Platforms List
 --------------------
 
+.. autopydantic_model:: libensemble.resources.platforms.FluxAllocation
+    :model-show-validator-members: False
+    :model-show-validator-summary: False
+    :model-show-field-summary: False
+    :field-list-validators: False
+    :field-show-required: False
+    :field-show-default: False
+    :field-show-alias: False
+
 .. dropdown:: ``Known_platforms``
     :open:
 

docs/examples/calling_scripts.rst

@@ -43,10 +43,10 @@ This example from the regression tests demonstrates the gest-api interface with
 standardized ``APOSMM`` generator class parameterized by a ``VOCS`` object, and
 paired with a gest-api ``simulator`` callable.
 
-..  literalinclude:: ../../libensemble/tests/regression_tests/test_asktell_aposmm_nlopt.py
+..  literalinclude:: ../../libensemble/tests/regression_tests/test_aposmm_nlopt.py
     :language: python
-    :caption: tests/regression_tests/test_asktell_aposmm_nlopt.py
+    :caption: tests/regression_tests/test_aposmm_nlopt.py
     :linenos:
-    :end-at: workflow.exit_criteria = ExitCriteria(sim_max=2000, wallclock_max=600)
+    :end-before:     # Perform the run
 
 .. _regression tests: https://github.com/Libensemble/libensemble/tree/develop/libensemble/tests/regression_tests

docs/examples/gen_funcs.rst

@@ -41,7 +41,6 @@ Optimization
 
   aposmm
   uniform_or_localopt
-  ax_multitask<ax_multitask>
   VTMOP<https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/generators.html#module-vtmop>
   ytopt<https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/generators.html#module-ytopt_heffte.ytopt_asktell>
   consensus<https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/generators.html#gens.persistent_independent_optimize>
@@ -51,10 +50,6 @@ Optimization
 
   Asynchronously Parallel Optimization Solver for finding Multiple Minima (APOSMM_).
 
-- :doc:`Ax Multitask<ax_multitask>`
-
-  Bayesian optimization with a Gaussian process driven by an Ax_ multi-task algorithm.
-
 - :ref:`DEAP-NSGA-II<community:deap-link>`
 
   Distributed evolutionary algorithms (*community example*)

docs/examples/gest_api/aposmm.rst

@@ -10,7 +10,7 @@ APOSMM
 APOSMM with libEnsemble
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-.. literalinclude:: ../../../libensemble/tests/regression_tests/test_asktell_aposmm_nlopt.py
+.. literalinclude:: ../../../libensemble/tests/regression_tests/test_aposmm_nlopt.py
     :linenos:
     :start-at:        workflow = Ensemble(parse_args=True)
     :end-before:         # Perform the run

docs/executor/ex_base.rst

@@ -1,13 +1,15 @@
 Base Executor
 =============
 
-`Overview <ex_overview.html>`__ \|\| **Base Executor** \|\| `MPI Executor <ex_mpi.html>`__ \|\| `Flux Executor <ex_flux.html>`__
+:doc:`Overview <ex_overview>` || **Base Executor** || :doc:`MPI Executor <ex_mpi>` || :doc:`Flux Executor <ex_flux>`
 
 .. automodule:: executor
     :no-undoc-members:
 
+.. autoexception:: libensemble.executors.executor.ExecutorException
+
 Only for running local serial-launched applications.
-To run MPI applications and use detected resources, use the `MPI Executor <ex_mpi.html>`__ tab.
+To run MPI applications and use detected resources, use the :doc:`MPI Executor <ex_mpi>` tab.
 
 .. tab-set::
 

docs/executor/ex_flux.rst

@@ -1,7 +1,7 @@
 Flux Executor
 ==============
 
-`Overview <ex_overview.html>`__ \|\| `Base Executor <ex_base.html>`__ \|\| `MPI Executor <ex_mpi.html>`__ \|\| **Flux Executor**
+:doc:`Overview <ex_overview>` || :doc:`Base Executor <ex_base>` || :doc:`MPI Executor <ex_mpi>` || **Flux Executor**
 
 .. automodule:: flux_executor
     :no-undoc-members:

docs/executor/ex_globus_compute.rst

@@ -1,7 +1,7 @@
 Globus Compute Executor
 =======================
 
-`Overview <ex_overview.html>`__ || `Base Executor <ex_base.html>`__ || `MPI Executor <ex_mpi.html>`__ || **Globus Compute Executor**
+:doc:`Overview <ex_overview>` || :doc:`Base Executor <ex_base>` || :doc:`MPI Executor <ex_mpi>` || **Globus Compute Executor**
 
 The :class:`GlobusComputeExecutor<libensemble.executors.globus_compute_executor.GlobusComputeExecutor>`
 submits Python callables to a remote `Globus Compute`_ endpoint instead of

docs/executor/ex_index.rst

@@ -1,6 +1,6 @@
 .. _executor_index:
 
-**Overview** || `Base Executor <ex_base.html>`__ || `MPI Executor <ex_mpi.html>`__ || `Flux Executor <ex_flux.html>`__ || `Globus Compute Executor <ex_globus_compute.html>`__
+**Overview** || :doc:`Base Executor <ex_base>` || :doc:`MPI Executor <ex_mpi>` || :doc:`Flux Executor <ex_flux>` || :doc:`Globus Compute Executor <ex_globus_compute>`
 
 Executors
 =========

docs/executor/ex_mpi.rst

@@ -1,7 +1,7 @@
 MPI Executor
 ============
 
-`Overview <ex_overview.html>`__ \|\| `Base Executor <ex_base.html>`__ \|\| **MPI Executor** \|\| `Flux Executor <ex_flux.html>`__
+:doc:`Overview <ex_overview>` || :doc:`Base Executor <ex_base>` || **MPI Executor** || :doc:`Flux Executor <ex_flux>`
 
 .. automodule:: mpi_executor
     :no-undoc-members:

docs/executor/ex_overview.rst

@@ -1,7 +1,7 @@
 Overview
 ========
 
-**Overview** || `Base Executor <ex_base.html>`__ || `MPI Executor <ex_mpi.html>`__ || `Flux Executor <ex_flux.html>`__ || `Globus Compute Executor <ex_globus_compute.html>`__
+**Overview** || :doc:`Base Executor <ex_base>` || :doc:`MPI Executor <ex_mpi>` || :doc:`Flux Executor <ex_flux>` || :doc:`Globus Compute Executor <ex_globus_compute>`
 
 The **Executor** provides a portable interface for running applications on any system and
 any number of compute resources.

docs/function_guides/generator.rst

@@ -3,7 +3,7 @@
 Generators
 ==========
 
-**Introduction** \|\| `Standardized Generator (gest-api) <generator_standardized.html>`__ \|\| `Legacy Generator Function <generator_legacy.html>`__
+**Introduction** || :doc:`Standardized Generator (gest-api) <generator_standardized>` || :doc:`Legacy Generator Function <generator_legacy>`
 
 Writing a Generator
 -------------------

docs/function_guides/generator_legacy.rst

@@ -1,7 +1,7 @@
 Legacy Generator Function
 =========================
 
-`Introduction <generator.html>`__ \|\| `Standardized Generator (gest-api) <generator_standardized.html>`__ \|\| **Legacy Generator Function**
+:doc:`Introduction <generator>` || :doc:`Standardized Generator (gest-api) <generator_standardized>` || **Legacy Generator Function**
 
 .. code-block:: python
 

docs/function_guides/generator_standardized.rst

@@ -1,7 +1,7 @@
 Standardized Generator (gest-api)
 =================================
 
-`Introduction <generator.html>`__ \|\| **Standardized Generator (gest-api)** \|\| `Legacy Generator Function <generator_legacy.html>`__
+:doc:`Introduction <generator>` || **Standardized Generator (gest-api)** || :doc:`Legacy Generator Function <generator_legacy>`
 
 Standardized generators are classes that inherit from ``gest_api.Generator``.
 They adhere to the ``gest-api`` standard and are parameterized by a ``VOCS``