Testing

.gitattributes

@@ -0,0 +1 @@
+pixi.lock filter=lfs diff=lfs merge=lfs -text

.github/workflows/basic.yml

@@ -17,29 +17,16 @@ jobs:
             matrix:
                 os: [ubuntu-latest]
                 mpi-version: [mpich]
-                python-version: ["3.10", "3.11", "3.12", "3.13"]
-                pydantic-version: ["2.10.6"]
+                python-version: ["py310", "py311", "py312", "py313", "py314"]
                 comms-type: [m, l]
                 include:
                     - os: macos-latest
-                      python-version: "3.11"
+                      python-version: "py311"
                       mpi-version: mpich
-                      pydantic-version: "2.10.6"
                       comms-type: m
                     - os: macos-latest
-                      python-version: "3.11"
+                      python-version: "py311"
                       mpi-version: mpich
-                      pydantic-version: "2.10.6"
-                      comms-type: l
-                    - os: ubuntu-latest
-                      mpi-version: mpich
-                      python-version: "3.10"
-                      pydantic-version: "1.10.21"
-                      comms-type: m
-                    - os: ubuntu-latest
-                      mpi-version: mpich
-                      python-version: "3.10"
-                      pydantic-version: "1.10.21"
                       comms-type: l
 
         env:
@@ -53,66 +40,43 @@ jobs:
 
         steps:
         - uses: actions/checkout@v4
-        - name: Setup conda - Python ${{ matrix.python-version }}
-          uses: conda-incubator/setup-miniconda@v3
           with:
-            activate-environment: condaenv
-            miniconda-version: "latest"
-            python-version: ${{ matrix.python-version }}
-            channels: conda-forge
-            channel-priority: strict
-            auto-update-conda: true
-
-        - name: Force-update certifi and pip
-          run: |
-            python --version
-            python -m pip install --upgrade pip
-            python -m pip install -I --upgrade certifi
-
-        - name: Install Ubuntu compilers
-          if: matrix.os == 'ubuntu-latest'
-          run: |
-              conda install -c conda-forge gcc_linux-64
-              pip install nlopt==2.9.0
+            lfs: true
 
-        # Roundabout solution on macos for proper linking with mpicc
-        - name: Install macOS compilers
-          if: matrix.os == 'macos-latest'
-          run: |
-            conda install clang_osx-64
-            pip install nlopt==2.8.0
+        - name: Checkout lockfile
+          run: git lfs checkout
 
-        - name: Install basic testing/feature dependencies
-          run: |
-            pip install -r install/testing_requirements.txt
-            pip install -r install/misc_feature_requirements.txt
-            source install/install_ibcdfo.sh
-            conda install numpy scipy
+        - uses: prefix-dev/[email protected]
+          with:
+            pixi-version: v0.55.0
+            cache: true
+            frozen: true
+            environments: ${{ matrix.python-version }}
+            activate-environment: ${{ matrix.python-version }}
 
-        - name: Install mpi4py and MPI from conda
+        - name: Install IBCDFO
           run: |
-            conda install mpi4py ${{ matrix.mpi-version }}
+            pixi run -e ${{ matrix.python-version }} ./install/install_ibcdfo.sh
 
         - name: Install libEnsemble, test flake8
           run: |
-            pip install pydantic==${{ matrix.pydantic-version }}
             pip install -e .
             flake8 libensemble
 
         - name: Remove various tests on newer pythons
-          if: matrix.python-version >= '3.11'
+          if: matrix.python-version == 'py311' || matrix.python-version == 'py312' || matrix.python-version == 'py313' || matrix.python-version == 'py314'
           run: |
-            rm ./libensemble/tests/functionality_tests/test_local_sine_tutorial*.py # matplotlib errors on 3.12
+            rm ./libensemble/tests/functionality_tests/test_local_sine_tutorial*.py # matplotlib errors on py312
 
         - name: Run simple tests, Ubuntu
           if: matrix.os == 'ubuntu-latest'
           run: |
-           ./libensemble/tests/run_tests.py -A "-W error" -${{ matrix.comms-type }}
+            ./libensemble/tests/run_tests.py -A "-W error" -${{ matrix.comms-type }}
 
         - name: Run simple tests, macOS
           if: matrix.os == 'macos-latest'
           run: |
-            ./libensemble/tests/run_tests.py -A "-W error" -${{ matrix.comms-type }}
+            pixi run -e ${{ matrix.python-version }} ./libensemble/tests/run_tests.py -A "-W error" -${{ matrix.comms-type }}
 
         - name: Merge coverage
           run: |
@@ -128,5 +92,5 @@ jobs:
         if: contains(github.base_ref, 'develop')
         runs-on: ubuntu-latest
         steps:
-        - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.34.0
+        - uses: actions/checkout@v6
+        - uses: crate-ci/typos@v1.42.0

.github/workflows/extra.yml

@@ -12,39 +12,24 @@ jobs:
                 os: [ubuntu-latest]
                 mpi-version: [mpich]
                 python-version: ['3.10', '3.11', '3.12', '3.13']
-                pydantic-version: ['2.10.6']
                 comms-type: [m, l]
                 include:
                     - os: macos-latest
                       python-version: '3.13'
                       mpi-version: mpich
-                      pydantic-version: '2.10.6'
                       comms-type: m
                     - os: macos-latest
                       python-version: '3.13'
                       mpi-version: mpich
-                      pydantic-version: '2.10.6'
                       comms-type: l
                     - os: ubuntu-latest
                       python-version: '3.12'
                       mpi-version: mpich
-                      pydantic-version: '2.10.6'
                       comms-type: t
                     - os: ubuntu-latest
                       mpi-version: 'openmpi'
-                      pydantic-version: '2.10.6'
                       python-version: '3.12'
                       comms-type: l
-                    - os: ubuntu-latest
-                      mpi-version: mpich
-                      python-version: '3.12'
-                      pydantic-version: '1.10.21'
-                      comms-type: m
-                    - os: ubuntu-latest
-                      mpi-version: mpich
-                      python-version: '3.12'
-                      pydantic-version: '1.10.21'
-                      comms-type: l
 
         env:
             HYDRA_LAUNCHER: 'fork'
@@ -56,7 +41,7 @@ jobs:
                 shell: bash -l {0}
 
         steps:
-        - uses: actions/checkout@v4
+        - uses: actions/checkout@v6
         - name: Setup conda - Python ${{ matrix.python-version }}
           uses: conda-incubator/setup-miniconda@v3
           with:
@@ -110,14 +95,6 @@ jobs:
           run: |
             pip install scikit-build packaging
 
-        - name: Install Balsam on Pydantic 1
-          if: matrix.pydantic-version == '1.10.21'
-          run: |
-            conda install pyzmq
-            git clone https://github.com/argonne-lcf/balsam.git
-            sed -i -e "s/pyzmq>=22.1.0,<23.0.0/pyzmq>=23.0.0,<24.0.0/" ./balsam/setup.cfg
-            cd balsam; pip install -e .; cd ..
-
         - name: Install other testing dependencies
           run: |
             pip install -r install/testing_requirements.txt
@@ -127,7 +104,6 @@ jobs:
 
         - name: Install libEnsemble, flake8, lock environment
           run: |
-            pip install pydantic==${{ matrix.pydantic-version }}
             pip install -e .
             flake8 libensemble
 
@@ -138,26 +114,14 @@ jobs:
             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
 
-        - name: Install redis/proxystore on Pydantic 2
-          if: matrix.pydantic-version == '2.10.6'
+        - name: Install redis/proxystore
           run: |
             pip install redis
             pip install proxystore==0.7.0
 
-        - name: Remove proxystore test on Pydantic 1
-          if: matrix.pydantic-version == '1.10.21'
-          run: |
-            rm ./libensemble/tests/regression_tests/test_proxystore_integration.py
-
-        - name: Remove Balsam/Globus-compute tests on Pydantic 2
-          if: matrix.pydantic-version == '2.10.6'
-          run: |
-            rm ./libensemble/tests/unit_tests/test_ufunc_runners.py
-            rm ./libensemble/tests/unit_tests/test_executor_balsam.py
-
         - name: Start Redis
           if: matrix.os == 'ubuntu-latest'
-          uses: supercharge/redis-github-action@1.8.0
+          uses: supercharge/redis-github-action@v2
           with:
             redis-version: 7
 
@@ -179,5 +143,5 @@ jobs:
         if: contains(github.base_ref, 'develop')
         runs-on: ubuntu-latest
         steps:
-        - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.34.0
+        - uses: actions/checkout@v6
+        - uses: crate-ci/typos@v1.42.0

docs/advanced_installation.rst

@@ -173,11 +173,9 @@ Optional Dependencies for Additional Features
 
 The following packages may be installed separately to enable additional features:
 
-* Balsam_ - Manage and submit applications to the Balsam service with our :ref:`BalsamExecutor<balsam-exctr>`
 * pyyaml_ and tomli_ - Parameterize libEnsemble via yaml or toml
 * `Globus Compute`_ - Submit simulation or generator function instances to remote Globus Compute endpoints
 
-.. _Balsam: https://balsam.readthedocs.io/en/latest/
 .. _conda-forge: https://conda-forge.org/
 .. _Conda: https://docs.conda.io/en/latest/
 .. _GitHub: https://github.com/Libensemble/libensemble

docs/conf.py

@@ -31,7 +31,7 @@ def __getattr__(cls, name):
         return MagicMock()
 
 
-autodoc_mock_imports = ["ax", "balsam", "gpcam", "IPython", "matplotlib", "pandas", "scipy", "surmise"]
+autodoc_mock_imports = ["ax", "gpcam", "IPython", "matplotlib", "pandas", "scipy", "surmise"]
 
 MOCK_MODULES = [
     "argparse",

docs/executor/ex_index.rst

@@ -14,4 +14,3 @@ portable interface for running and managing user applications.
    overview
    executor
    mpi_executor
-   balsam_2_executor

docs/executor/overview.rst

@@ -26,17 +26,12 @@ The **Executor** provides a portable interface for running applications on any s
     ``result()``, and ``exception()`` functions from the standard.
 
     The main ``Executor`` class can subprocess serial applications in place,
-    while the ``MPIExecutor`` is used for running MPI applications, and the
-    ``BalsamExecutor`` for submitting MPI run requests from a worker running on
-    a compute node to the Balsam service. This second approach is suitable for
-    systems that don't allow submitting MPI applications from compute nodes.
+    while the ``MPIExecutor`` is used for running MPI applications.
 
     Typically, users choose and parameterize their ``Executor`` objects in their
     calling scripts, where each executable generator or simulation application is
-    registered to it. If an alternative Executor like Balsam is used, then the
-    applications can be registered as in the example below. Once in the user-side
-    worker code (sim/gen func), the Executor can be retrieved without any need to
-    specify the type.
+    registered to it. Once in the user-side worker code (sim/gen func), the Executor
+    can be retrieved without any need to specify the type.
 
     Once the Executor is retrieved, tasks can be submitted by specifying the
     ``app_name`` from registration in the calling script alongside other optional
@@ -177,22 +172,16 @@ may resemble:
 
         print(task.state)  # state may be finished/failed/killed
 
-.. note::
-    Applications or tasks submitted via the Balsam Executor are referred to as
-    **"jobs"** within Balsam, including within Balsam's database and when
-    describing the state of a completed submission.
-
 The ``MPIExecutor`` autodetects system criteria such as the appropriate MPI launcher
 and mechanisms to poll and kill tasks. It also has access to the resource manager,
 which partitions resources among workers, ensuring that runs utilize different
 resources (e.g., nodes). Furthermore, the ``MPIExecutor`` offers resilience via the
 feature of re-launching tasks that fail to start because of system factors.
 
 Various back-end mechanisms may be used by the Executor to best interact
-with each system, including proxy launchers or task management systems such as
-Balsam_. Currently, these Executors launch at the application level within
+with each system, including proxy launchers or task management systems.
+Currently, these Executors launch at the application level within
 an existing resource pool. However, submissions to a batch scheduler may be
 supported in future Executors.
 
-.. _Balsam: https://balsam.readthedocs.io/en/latest/
 .. _concurrent futures: https://docs.python.org/library/concurrent.futures.html

docs/history_output_logging.rst

@@ -1,6 +1,15 @@
 Output Management
 =================
 
+Simulation Directories
+~~~~~~~~~~~~~~~~~~~~~~
+
+By default, libEnsemble places output files in the current working directory.
+
+See the ``Directories`` section of :ref:`libE_specs<datastruct-libe-specs>` for instructions
+on how to separate simulation runs into separate directories and copy/symlink input files into these
+locations.
+
 Default Log Files
 ~~~~~~~~~~~~~~~~~
 The history array :ref:`H<funcguides-history>` and

docs/known_issues.rst

@@ -15,7 +15,7 @@ may occur when using libEnsemble.
   we recommend using ``local`` comms in place of ``mpi4py``.
 * When using the Executor: Open-MPI does not work with direct MPI task
   submissions in mpi4py comms mode, since Open-MPI does not support nested MPI
-  executions. Use either ``local`` mode or the Balsam Executor instead.
+  executions. Use ``local`` mode instead.
 * Local comms mode (multiprocessing) may fail if MPI is initialized before
   forking processors. This is thought to be responsible for issues combining
   multiprocessing with PETSc on some platforms.

docs/overview_usecases.rst

@@ -118,8 +118,7 @@ its capabilities.
 
   * **Executor**: The executor can be used within user functions to provide a
     simple, portable interface for running and managing user tasks (applications).
-    There are multiple executors including the ``MPIExecutor`` and ``BalsamExecutor``.
-    The base ``Executor`` class allows local sub-processing of serial tasks.
+    There are multiple executors including the base ``Executor`` and ``MPIExecutor``.
 
   * **Submit**: Enqueue or indicate that one or more jobs or tasks need to be
     launched. When using the libEnsemble Executor, a *submitted* task is executed