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Merge pull request #1160 from Libensemble/release/v_1.1.0
Release/v 1.1.0
2 parents f0cecc6 + 6199ef2 commit 06ae667

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‎.flake8‎

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libensemble/tests/regression_tests/test_persistent_gp_multitask_ax.py:E402
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libensemble/tests/regression_tests/test_ytopt_heffte.py:E402
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libensemble/tests/functionality_tests/test_uniform_sampling_then_persistent_localopt_runs.py:E402
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libensemble/tests/functionality_tests/test_stats_output.py:E402
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libensemble/tests/functionality_tests/test_active_persistent_worker_abort.py:E402
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libensemble/tests/unit_tests/test_persistent_aposmm.py:E402
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‎.github/workflows/basic.yml‎

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name: libEnsemble-simple-CI
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on:
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pull_request:
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types:
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- ready_for_review
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- opened
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- reopened
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- synchronize
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jobs:
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test-libE:
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if: '! github.event.pull_request.draft'
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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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: [3.9, "3.10", "3.11", "3.12"]
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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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mpi-version: "mpich=4.0.3"
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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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mpi-version: "mpich=4.0.3"
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comms-type: l
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env:
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HYDRA_LAUNCHER: "fork"
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TERM: xterm-256color
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v4
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- name: Setup conda - Python ${{ matrix.python-version }}
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uses: conda-incubator/setup-miniconda@v2
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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: ${{ matrix.python-version }}
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channels: conda-forge
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channel-priority: flexible
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auto-update-conda: true
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- uses: actions/cache/restore@v3
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name: Restore cached dependencies
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id: cache
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if: matrix.os == 'ubuntu-latest'
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with:
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path: |
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/home/runner/.local
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/usr/share/miniconda3/envs/condaenv
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/usr/share/miniconda3/bin
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/usr/share/miniconda3/lib
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/usr/share/miniconda3/include
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key: libe-${{ github.ref_name }}-${{ matrix.python-version }}-${{ matrix.comms-type }}
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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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- name: Install Ubuntu compilers
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if: matrix.os == 'ubuntu-latest'
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run: conda install gcc_linux-64
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# Roundabout solution on macos for proper linking with mpicc
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- name: Install macOS compilers and older SDK
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if: matrix.os == 'macos-latest'
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run: |
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wget https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX10.15.sdk.tar.xz
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mkdir ../sdk; tar xf MacOSX10.15.sdk.tar.xz -C ../sdk
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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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- name: Install mpi4py and MPI from conda
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run: |
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conda install mpi4py ${{ matrix.mpi-version }}
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- name: Install generator dependencies
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if: matrix.os != 'windows-latest' && steps.cache.outputs.cache-hit != 'true'
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run: |
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python -m pip install --upgrade pip
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pip install mpmath
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conda install numpy nlopt scipy
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- uses: actions/cache/save@v3
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name: Save dependencies to cache
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if: matrix.os == 'ubuntu-latest'
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with:
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path: |
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/home/runner/.local
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/usr/share/miniconda3/envs/condaenv
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/usr/share/miniconda3/bin
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/usr/share/miniconda3/lib
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/usr/share/miniconda3/include
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key: libe-${{ github.ref_name }}-${{ matrix.python-version }}-${{ matrix.comms-type }}
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- name: Install libEnsemble, flake8, lock environment
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run: |
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pip install -e .
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flake8 libensemble
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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.sh -A "-W error" -z -${{ matrix.comms-type }}
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- name: Run simple tests, macOS
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if: matrix.os == 'macos-latest'
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env:
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CONDA_BUILD_SYSROOT: /Users/runner/work/libensemble/sdk/MacOSX10.15.sdk
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run: |
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./libensemble/tests/run-tests.sh -A "-W error" -z -${{ matrix.comms-type }}
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- name: Merge coverage
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run: |
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mv libensemble/tests/.cov* .
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@v3
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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spellcheck:
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name: Spellcheck release branch
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if: contains(github.base_ref, 'develop')
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: crate-ci/typos@v1.16.23

.github/workflows/ci.yml renamed to .github/workflows/extra.yml

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name: libEnsemble-CI
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name: libEnsemble-complete-CI
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on:
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pull_request:
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types:
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- ready_for_review
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- opened
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- reopened
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- synchronize
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workflow_dispatch:
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jobs:
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test-libE:
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if: '! github.event.pull_request.draft'
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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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: [3.8, 3.9, "3.10", "3.11"]
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python-version: [3.9, "3.10", "3.11", "3.12"]
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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: 3.9
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python-version: 3.11
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mpi-version: "mpich=4.0.3"
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comms-type: m
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- os: macos-latest
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python-version: 3.9
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python-version: 3.11
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mpi-version: "mpich=4.0.3"
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comms-type: l
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- os: ubuntu-latest
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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: "3.10"
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python-version: "3.11"
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comms-type: l
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env:
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HYDRA_LAUNCHER: "fork"
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TERM: xterm-256color
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Setup conda - Python ${{ matrix.python-version }}
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uses: conda-incubator/setup-miniconda@v2
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with:
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python --version
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pip install -I --upgrade certifi
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# - name: Windows - Add clang path to $PATH env
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# shell: bash
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# if: matrix.os == 'windows-latest'
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# run: |
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# echo "PATH=$PATH:C:\msys64\mingw64\bin" >> $GITHUB_ENV
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# echo "PATH=$PATH:C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\bin\amd64" >> $GITHUB_ENV
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- name: Install Ubuntu compilers
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if: matrix.os == 'ubuntu-latest'
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run: conda install gcc_linux-64
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mkdir ../sdk; tar xf MacOSX10.15.sdk.tar.xz -C ../sdk
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conda install clang_osx-64
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# - name: Setup MPI (${{ matrix.mpi-version }})
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# uses: mpi4py/setup-mpi@v1
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# if: matrix.os == 'windows-latest'
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# with:
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# mpi: ${{ matrix.mpi-version }}
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# - name: Install mpi4py on Windows
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# if: matrix.os == 'windows-latest'
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# run: pip install mpi4py
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- name: Install mpi4py and MPI from conda
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if: (matrix.python-version != '3.10' && matrix.os == 'ubuntu-latest') || matrix.os == 'macos-latest'
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run: |
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pip install mpi4py
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- name: Install generator dependencies
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if: matrix.os != 'windows-latest' && steps.cache.outputs.cache-hit != 'true'
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if: steps.cache.outputs.cache-hit != 'true'
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run: |
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python -m pip install --upgrade pip
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conda env update --file install/gen_deps_environment.yml
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- name: Install ax-platform
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if: matrix.python-version != '3.12'
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run: |
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pip install ax-platform==0.2.8
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- name: Install surmise
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pip install --upgrade git+https://github.com/bandframework/surmise.git@develop
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- name: Build ytopt and dependencies
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if: matrix.python-version != '3.11' && matrix.os != 'windows-latest' && matrix.os != 'macos-latest'
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if: matrix.python-version <= '3.10' && matrix.os != 'macos-latest'
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run: |
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pip install scikit-learn==1.1.2
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pip install pandas==1.5.3
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pip install .
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cd ..
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# - name: Install some generator dependencies on Windows
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# if: matrix.os == 'windows-latest'
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# run: |
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# python -m pip install --upgrade pip
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# conda install nlopt
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# conda install scipy
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# pip install mpmath
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- name: Install generator dependencies for Ubuntu tests
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if: matrix.os == 'ubuntu-latest' && steps.cache.outputs.cache-hit != 'true'
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if: matrix.os == 'ubuntu-latest' && steps.cache.outputs.cache-hit != 'true' && matrix.python-version != '3.12'
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conda install octave
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sudo apt-get install bc
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# begin heffte build and dependencies
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# pip install git+https://github.com/dragonfly/dragonfly.git
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pip install git+https://github.com/jlnav/dragonfly.git@fix/remove_npobject
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pip install scikit-build packaging Tasmanian --user
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- name: Copy heffte exe on cache-hit
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if: matrix.os == 'ubuntu-latest' && steps.cache.outputs.cache-hit != 'false'
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if: matrix.os == 'ubuntu-latest' && steps.cache.outputs.cache-hit != 'false' && matrix.python-version != '3.12'
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run: |
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cd /home/runner/work/libensemble/libensemble
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cp ./heffte/build/benchmarks/speed3d_c2c ./libensemble/tests/regression_tests/
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- name: Install other testing dependencies
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run: |
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conda install octave
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pip install scikit-build packaging Tasmanian --user
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conda install pyzmq
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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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pip install -e .
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flake8 libensemble
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- name: Remove ytopt-heffte test on Python 3.11 (easy way)
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if: matrix.python-version == '3.11'
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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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run: |
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rm ./libensemble/tests/regression_tests/test_heffte.py
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rm ./libensemble/tests/regression_tests/test_ytopt_heffte.py
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rm ./libensemble/tests/regression_tests/test_persistent_gp.py
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rm ./libensemble/tests/regression_tests/test_persistent_gp_multitask_ax.py
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- name: Run extensive tests, Ubuntu
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if: matrix.os == 'ubuntu-latest'
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run: |
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./libensemble/tests/run-tests.sh -e -A "-W error" -z -${{ matrix.comms-type }}
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# - name: Run simple tests, Windows
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# if: matrix.os == 'windows-latest'
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# run: |
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# ./libensemble/tests/run-tests.sh -A "-W error" -z -${{ matrix.comms-type }}
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./libensemble/tests/run-tests.sh -e -z -${{ 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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env:
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CONDA_BUILD_SYSROOT: /Users/runner/work/libensemble/sdk/MacOSX10.15.sdk
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run: |
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./libensemble/tests/run-tests.sh -e -A "-W error" -z -${{ matrix.comms-type }}
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./libensemble/tests/run-tests.sh -e -z -${{ matrix.comms-type }}
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- name: Merge coverage, run Coveralls
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env:
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COVERALLS_PARALLEL: true
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- name: Merge coverage
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mv libensemble/tests/.cov* .
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coveralls --service=github
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coveralls:
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name: Notify coveralls of all jobs completing
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needs: [test-libE]
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if: '! github.event.pull_request.draft'
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runs-on: ubuntu-latest
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container: python:3-slim
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steps:
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- name: Finished
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run: |
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pip3 install --upgrade coveralls
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coveralls --finish
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@v3
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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spellcheck:
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name: Spellcheck release branch
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if: contains(github.base_ref, 'main')
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if: contains(github.base_ref, 'develop')
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: crate-ci/typos@v1.0.4
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- uses: actions/checkout@v4
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- uses: crate-ci/typos@v1.16.23

‎.typos.toml‎

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[default]
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extend-ignore-identifiers-re = [
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".*NDArray.*",
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"8ba9de56.*"
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]
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[default.extend-words]
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als = "als"
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datas = "datas"
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numer = "numer"
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inout = "inout"
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[files]
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extend-exclude = ["*.bib", "*.xml"]
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extend-exclude = ["*.bib", "*.xml", "docs/nitpicky"]

‎.wci.yml‎

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language: Python
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release:
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version: 1.0.0
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date: 2023-09-25
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version: 1.1.0
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date: 2023-11-08
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documentation:
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general: https://libensemble.readthedocs.io

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