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Merge branch 'develop' into refactor/deprecate_from_yaml_toml_json
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‎.gitattributes‎

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pixi.lock filter=lfs diff=lfs merge=lfs -text

‎.github/workflows/basic.yml‎

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matrix:
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os: [ubuntu-latest]
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mpi-version: [mpich]
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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python-version: ["py310", "py311", "py312", "py313", "py314"]
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comms-type: [m, l]
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include:
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- os: macos-latest
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python-version: "3.11"
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python-version: "py311"
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mpi-version: mpich
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comms-type: m
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- os: macos-latest
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python-version: "3.11"
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python-version: "py311"
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mpi-version: mpich
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comms-type: l
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steps:
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- uses: actions/checkout@v6
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- name: Setup conda - Python ${{ matrix.python-version }}
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uses: conda-incubator/setup-miniconda@v3
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with:
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activate-environment: condaenv
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miniconda-version: "latest"
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python-version: ${{ matrix.python-version }}
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channels: conda-forge
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channel-priority: strict
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auto-update-conda: true
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lfs: true
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- name: Force-update certifi and pip
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run: |
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python --version
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python -m pip install --upgrade pip
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python -m pip install -I --upgrade certifi
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- name: Install Ubuntu compilers
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if: matrix.os == 'ubuntu-latest'
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run: |
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conda install -c conda-forge gcc_linux-64
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- name: Checkout lockfile
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run: git lfs checkout
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# Roundabout solution on macos for proper linking with mpicc
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- name: Install macOS compilers
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if: matrix.os == 'macos-latest'
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run: |
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conda install clang_osx-64
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- name: Install basic testing/feature dependencies
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run: |
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pip install -r install/testing_requirements.txt
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pip install -r install/misc_feature_requirements.txt
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source install/install_ibcdfo.sh
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conda install numpy scipy
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- uses: prefix-dev/setup-pixi@v0.9.4
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with:
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pixi-version: v0.55.0
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frozen: true
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environments: ${{ matrix.python-version }}
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activate-environment: ${{ matrix.python-version }}
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- name: Install mpi4py and MPI from conda
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- name: Install IBCDFO
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run: |
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conda install mpi4py ${{ matrix.mpi-version }}
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pixi run -e ${{ matrix.python-version }} ./install/install_ibcdfo.sh
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- name: Install libEnsemble, test flake8
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run: |
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pip install -e .
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flake8 libensemble
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- name: Remove various tests on newer pythons
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if: matrix.python-version >= '3.11'
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if: matrix.python-version == 'py311' || matrix.python-version == 'py312' || matrix.python-version == 'py313' || matrix.python-version == 'py314'
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run: |
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rm ./libensemble/tests/functionality_tests/test_local_sine_tutorial*.py # matplotlib errors on 3.12
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rm ./libensemble/tests/functionality_tests/test_local_sine_tutorial*.py # matplotlib errors on py312
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- name: Run simple tests, Ubuntu
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if: matrix.os == 'ubuntu-latest'
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run: |
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./libensemble/tests/run_tests.py -A "-W error" -${{ matrix.comms-type }}
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./libensemble/tests/run_tests.py -A "-W error" -${{ matrix.comms-type }}
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- name: Run simple tests, macOS
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if: matrix.os == 'macos-latest'
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run: |
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./libensemble/tests/run_tests.py -A "-W error" -${{ matrix.comms-type }}
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pixi run -e ${{ matrix.python-version }} ./libensemble/tests/run_tests.py -A "-W error" -${{ matrix.comms-type }}
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- name: Merge coverage
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run: |
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v6
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- uses: crate-ci/typos@v1.40.0
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- uses: crate-ci/typos@v1.43.0

‎.github/workflows/extra.yml‎

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matrix:
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os: [ubuntu-latest]
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mpi-version: [mpich]
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python-version: ['3.10', '3.11', '3.12', '3.13']
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python-version: ["py310e", "py311e", "py312e", "py313e", "py314e"]
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comms-type: [m, l]
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include:
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- os: macos-latest
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python-version: '3.13'
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python-version: "py312e"
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mpi-version: mpich
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comms-type: m
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- os: macos-latest
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python-version: '3.13'
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python-version: "py312e"
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- os: ubuntu-latest
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python-version: '3.12'
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python-version: "py312e"
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mpi-version: mpich
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comms-type: t
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- os: ubuntu-latest
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mpi-version: 'openmpi'
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python-version: '3.12'
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mpi-version: openmpi
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python-version: "py312e"
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env:
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steps:
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- uses: actions/checkout@v6
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- name: Setup conda - Python ${{ matrix.python-version }}
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uses: conda-incubator/setup-miniconda@v3
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with:
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activate-environment: condaenv
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miniconda-version: 'latest'
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python-version: ${{ matrix.python-version }}
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channels: conda-forge
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channel-priority: strict
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auto-update-conda: true
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- name: Force-update certifi
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run: |
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python --version
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pip install -I --upgrade certifi
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lfs: true
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- name: Install Ubuntu compilers
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if: matrix.os == 'ubuntu-latest'
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run: |
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conda install -c conda-forge gcc_linux-64
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pip install nlopt==2.9.0
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- name: Checkout lockfile
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run: git lfs checkout
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# Roundabout solution on macos for proper linking with mpicc
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- name: Install macOS compilers
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if: matrix.os == 'macos-latest'
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run: |
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conda install clang_osx-64
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pip install nlopt==2.8.0
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- name: Install mpi4py and MPI from conda
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conda install mpi4py ${{ matrix.mpi-version }}
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- name: Install generator dependencies
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conda env update --file install/gen_deps_environment.yml
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- name: Install gpcam and octave # Neither yet support 3.13
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if: matrix.python-version <= '3.12'
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run: |
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pip install gpcam==8.1.13
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conda install octave
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- name: Install surmise and Tasmanian
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if: matrix.os == 'ubuntu-latest'
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pip install --upgrade git+https://github.com/bandframework/surmise.git
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pip install Tasmanian --user
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- name: Install generator dependencies for Ubuntu tests
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if: matrix.os == 'ubuntu-latest' && matrix.python-version <= '3.12'
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run: |
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pip install scikit-build packaging
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- uses: prefix-dev/setup-pixi@v0.9.2
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with:
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pixi-version: v0.55.0
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cache: true
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frozen: true
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environments: ${{ matrix.python-version }}
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activate-environment: ${{ matrix.python-version }}
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- name: Install other testing dependencies
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pip install -r install/testing_requirements.txt
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pip install -r install/misc_feature_requirements.txt
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source install/install_ibcdfo.sh
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conda install numpy scipy
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pixi run -e ${{ matrix.python-version }} install/install_ibcdfo.sh
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- name: Install libEnsemble, flake8, lock environment
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pip install -e .
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flake8 libensemble
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- name: Remove test using octave, gpcam on Python 3.13
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if: matrix.python-version >= '3.13'
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- name: Install gpcam
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if: matrix.python-version != 'py313e' && matrix.python-version != 'py314e'
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run: |
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pixi run -e ${{ matrix.python-version }} pip install gpcam==8.1.13
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- name: Remove test using octave, gpcam, globus-compute on Python 3.13
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if: matrix.python-version == 'py313e' || matrix.python-version == 'py314e'
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rm ./libensemble/tests/unit_tests/test_ufunc_runners.py # needs globus-compute
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rm ./libensemble/tests/regression_tests/test_persistent_fd_param_finder.py # needs octave, which doesn't yet support 3.13
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rm ./libensemble/tests/regression_tests/test_persistent_aposmm_external_localopt.py # needs octave, which doesn't yet support 3.13
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rm ./libensemble/tests/regression_tests/test_gpCAM.py # needs gpcam, which doesn't build on 3.13
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- name: Install redis/proxystore
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pip install redis
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pip install proxystore==0.7.0
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rm ./libensemble/tests/regression_tests/test_persistent_gp_multitask_ax.py # needs ax-platform, which doesn't yet support 3.14
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- name: Start Redis
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- name: Run extensive tests
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- name: Run extensive tests, Ubuntu
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if: matrix.os == 'ubuntu-latest'
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./libensemble/tests/run_tests.py -e -${{ matrix.comms-type }}
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- name: Run extensive tests, macOS
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if: matrix.os == 'macos-latest'
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run: |
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pixi run -e ${{ matrix.python-version }} ./libensemble/tests/run_tests.py -e -${{ matrix.comms-type }}
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- name: Merge coverage
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mv libensemble/tests/.cov* .
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- uses: actions/checkout@v6
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- uses: crate-ci/typos@v1.40.0
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- uses: crate-ci/typos@v1.43.0

‎.readthedocs.yml‎

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os: "ubuntu-22.04"
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tools:
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commands:
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# from https://docs.readthedocs.com/platform/stable/build-customization.html#support-git-lfs-large-file-storage
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# Download and uncompress the binary
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# https://git-lfs.github.com/
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- wget https://github.com/git-lfs/git-lfs/releases/download/v3.1.4/git-lfs-linux-amd64-v3.1.4.tar.gz
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- tar xvfz git-lfs-linux-amd64-v3.1.4.tar.gz git-lfs
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# Modify LFS config paths to point where git-lfs binary was downloaded
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- git config filter.lfs.process "`pwd`/git-lfs filter-process"
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- git config filter.lfs.smudge "`pwd`/git-lfs smudge -- %f"
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- git config filter.lfs.clean "`pwd`/git-lfs clean -- %f"
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# Make LFS available in current repository
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- ./git-lfs install
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# Download content from remote
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- ./git-lfs fetch
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# Make local files to have the real content on them
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- ./git-lfs checkout
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- asdf plugin add pixi
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- asdf install pixi latest
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- asdf global pixi latest
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- pixi run -e docs build-docs
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- mkdir -p $READTHEDOCS_OUTPUT/html/
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- cp -r docs/_build/html/** $READTHEDOCS_OUTPUT/html/
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sphinx:
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- pdf
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python:
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install:
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- requirements: docs/requirements.txt
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- method: pip
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path: .
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extra_requirements:
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- docs

‎docs/conf.py‎

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autodoc_mock_imports = ["ax", "balsam", "gpcam", "IPython", "matplotlib", "pandas", "scipy", "surmise"]
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autodoc_mock_imports = ["ax", "gpcam", "IPython", "matplotlib", "pandas", "scipy", "surmise"]
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"sphinxcontrib.autodoc_pydantic",
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"sphinx_copybutton",
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"sphinx_lfs_content",
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spelling_word_list_filename = "spelling_wordlist.txt"

‎docs/examples/gen_funcs.rst‎

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gpcam
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tasmanian
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fd_param_finder
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surmise
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Modular Bayesian calibration/inference framework using Surmise_ (demonstration of cancelling previous issued simulations).
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- :doc:`Tasmanian<tasmanian>`
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- :ref:`Tasmanian<community:tasmanian-link>`
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Evaluates points generators by the Tasmanian_ sparse grid library
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‎docs/examples/tasmanian.rst‎

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‎docs/history_output_logging.rst‎

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

‎docs/requirements.txt‎

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‎install/misc_feature_requirements.txt‎

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globus-compute-sdk==4.2.0
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globus-compute-sdk==4.3.0

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