Merge pull request #1571 from Libensemble/develop

Merge docs into main

Author: shuds13

.flake8

@@ -37,8 +37,6 @@ per-file-ignores =
         libensemble/tests/functionality_tests/test_mpi_runners_zrw_supernode_uneven.py:E501
 
         # Need to set something before the APOSMM import
-        libensemble/tests/scaling_tests/warpx/run_libensemble_on_warpx.py:E402
-        examples/calling_scripts/run_libensemble_on_warpx.py:E402
         libensemble/tests/regression_tests/test_persistent_aposmm*: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

.github/workflows/basic.yml

@@ -60,7 +60,7 @@ jobs:
             miniconda-version: "latest"
             python-version: ${{ matrix.python-version }}
             channels: conda-forge
-            channel-priority: flexible
+            channel-priority: strict
             auto-update-conda: true
 
         - name: Force-update certifi and pip
@@ -72,7 +72,7 @@ jobs:
         - name: Install Ubuntu compilers
           if: matrix.os == 'ubuntu-latest'
           run: |
-              conda install gcc_linux-64
+              conda install -c conda-forge gcc_linux-64
               pip install nlopt==2.9.0
 
         # Roundabout solution on macos for proper linking with mpicc
@@ -129,4 +129,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.31.1
+        - uses: crate-ci/typos@v1.34.0

.github/workflows/extra.yml

@@ -64,7 +64,7 @@ jobs:
             miniconda-version: 'latest'
             python-version: ${{ matrix.python-version }}
             channels: conda-forge
-            channel-priority: flexible
+            channel-priority: strict
             auto-update-conda: true
 
         - name: Force-update certifi
@@ -75,7 +75,7 @@ jobs:
         - name: Install Ubuntu compilers
           if: matrix.os == 'ubuntu-latest'
           run: |
-            conda install gcc_linux-64
+            conda install -c conda-forge gcc_linux-64
             pip install nlopt==2.9.0
 
         # Roundabout solution on macos for proper linking with mpicc
@@ -96,7 +96,7 @@ jobs:
         - name: Install gpcam and octave # Neither yet support 3.13
           if: matrix.python-version <= '3.12'
           run: |
-            pip install gpcam
+            pip install gpcam==8.1.13
             conda install octave
 
         - name: Install surmise and Tasmanian
@@ -180,4 +180,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.31.1
+        - uses: crate-ci/typos@v1.34.0

README.rst

@@ -22,6 +22,9 @@ 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.
+
 Installation
 ============
 
@@ -182,3 +185,7 @@ 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
+
+.. |ScriptCreator| image:: https://img.shields.io/badge/Script_Creator-purple?logo=magic
+   :target: https://libensemble.github.io/script-creator/
+   :alt: Script Creator

docs/data_structures/libE_specs.rst

@@ -205,14 +205,14 @@ libEnsemble is primarily customized by setting options within a ``LibeSpecs`` cl
                 **save_H_and_persis_on_abort** [bool] = ``True``:
                     Save states of ``H`` and ``persis_info`` to file on aborting after an exception.
 
-                **save_H_on_completion** Optional[bool] = ``False``
+                **save_H_on_completion** bool | None = ``False``
                     Save state of ``H`` to file upon completing a workflow. Also enabled when either ``save_every_k_sims``
                     or ``save_every_k_gens`` is set.
 
-                **save_H_with_date** Optional[bool] = ``False``
+                **save_H_with_date** bool | None = ``False``
                     Save ``H`` filename contains date and timestamp.
 
-                **H_file_prefix** Optional[str] = ``"libE_history"``
+                **H_file_prefix** str | None = ``"libE_history"``
                     Prefix for ``H`` filename.
 
                 **use_persis_return_gen** [bool] = ``False``:

docs/tutorials/aposmm_tutorial.rst

@@ -314,6 +314,6 @@ can be found in libEnsemble's `WarpX Scaling Test`_.
 .. _PETSc/TAO: https://www.mcs.anl.gov/petsc/
 .. _SciPy: https://scipy.org/
 .. _Six-Hump Camel function: https://www.sfu.ca/~ssurjano/camel6.html
-.. _WarpX Scaling Test: https://github.com/Libensemble/libensemble/tree/main/libensemble/tests/scaling_tests/warpx
+.. _WarpX Scaling Test: https://github.com/Libensemble/libe-community-examples/tree/main/warpx
 .. |Open in Colab| image:: https://colab.research.google.com/assets/colab-badge.svg
   :target:  http://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/aposmm/aposmm_tutorial_notebook.ipynb

examples/calling_scripts/run_libensemble_on_warpx.py

@@ -348,7 +348,7 @@
     "Many common libEnsemble use-cases involve using libEnsemble's Executor to launch user\n",
     "applications with parameters requested by APOSMM, then evaluate their output using\n",
     "APOSMM, and repeat until minima are identified. A currently supported example\n",
-    "can be found in libEnsemble's [WarpX Scaling Test](https://github.com/Libensemble/libensemble/tree/main/libensemble/tests/scaling_tests/warpx)\n",
+    "can be found in libEnsemble's [WarpX Scaling Test](https://github.com/Libensemble/libe-community-examples/tree/main/warpx)\n",
     "\n",
     "Please see the [API reference](https://libensemble.readthedocs.io/en/main/examples/aposmm.html) for more APOSMM configuration options and other information."
    ]

examples/tutorials/aposmm/aposmm_tutorial_notebook.ipynb

@@ -12,4 +12,6 @@ dependencies:
   - mumps-mpi
   - DFO-LS
   - mpmath
-  - ax-platform>=0.5.0
+  - ax-platform==0.5.0
+  - petsc
+  - petsc4py

install/gen_deps_environment.yml

@@ -1 +1 @@
-globus-compute-sdk==3.3.1
+globus-compute-sdk==3.8.0