Merge pull request #1685 from Libensemble/release/v_1.6.0

Release/v 1.6.0

Author: shuds13

.codecov.yml

@@ -4,3 +4,4 @@ ignore:
   - "libensemble/tools/live_data/*"
   - "libensemble/sim_funcs/executor_hworld.py"
   - "libensemble/gen_funcs/persistent_tasmanian.py"
+  - "libensemble/gen_classes/gpCAM.py"

.flake8

@@ -38,6 +38,7 @@ per-file-ignores =
 
         # Need to set something before the APOSMM import
         libensemble/tests/regression_tests/test_persistent_aposmm*:E402
+        libensemble/tests/regression_tests/test_asktell_aposmm_nlopt.py: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
         libensemble/tests/functionality_tests/test_stats_output.py:E402

.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:
@@ -52,67 +39,43 @@ jobs:
                 shell: bash -l {0}
 
         steps:
-        - uses: actions/checkout@v4
-        - name: Setup conda - Python ${{ matrix.python-version }}
-          uses: conda-incubator/setup-miniconda@v3
+        - uses: actions/checkout@v6
           with:
-            activate-environment: condaenv
-            miniconda-version: "latest"
-            python-version: ${{ matrix.python-version }}
-            channels: conda-forge
-            channel-priority: strict
-            auto-update-conda: true
+            lfs: 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
+        - name: Checkout lockfile
+          run: git lfs checkout
 
-        # 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: 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/setup-pixi@v0.9.4
+          with:
+            pixi-version: v0.55.0
+            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 +91,5 @@ 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@v1.44.0

.github/workflows/extra.yml

@@ -11,39 +11,24 @@ 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: ["py310e", "py311e", "py312e", "py313e", "py314e"]
                 comms-type: [m, l]
                 include:
                     - os: macos-latest
-                      python-version: '3.13'
+                      python-version: "py312e"
                       mpi-version: mpich
-                      pydantic-version: '2.10.6'
                       comms-type: m
                     - os: macos-latest
-                      python-version: '3.13'
+                      python-version: "py312e"
                       mpi-version: mpich
-                      pydantic-version: '2.10.6'
                       comms-type: l
                     - os: ubuntu-latest
-                      python-version: '3.12'
+                      python-version: "py312e"
                       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'
+                      mpi-version: openmpi
+                      python-version: "py312e"
                       comms-type: l
 
         env:
@@ -56,115 +41,68 @@ jobs:
                 shell: bash -l {0}
 
         steps:
-        - uses: actions/checkout@v4
-        - name: Setup conda - Python ${{ matrix.python-version }}
-          uses: conda-incubator/setup-miniconda@v3
+        - uses: actions/checkout@v6
           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
-          run: |
-            python --version
-            pip install -I --upgrade certifi
+            lfs: true
 
-        - name: Install Ubuntu compilers
-          if: matrix.os == 'ubuntu-latest'
-          run: |
-            conda install -c conda-forge gcc_linux-64
-            pip install nlopt==2.9.0
+        - name: Checkout lockfile
+          run: git lfs checkout
 
-        # 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: Install mpi4py and MPI from conda
-          run: |
-            conda install mpi4py ${{ matrix.mpi-version }}
-
-        - name: Install generator dependencies
-          run: |
-            conda env update --file install/gen_deps_environment.yml
-
-        - name: Install gpcam and octave # Neither yet support 3.13
-          if: matrix.python-version <= '3.12'
-          run: |
-            pip install gpcam==8.1.13
-            conda install octave
-
-        - name: Install surmise and Tasmanian
-          if: matrix.os == 'ubuntu-latest'
-          run: |
-            pip install --upgrade git+https://github.com/bandframework/surmise.git
-            pip install Tasmanian --user
-
-        - name: Install generator dependencies for Ubuntu tests
-          if: matrix.os == 'ubuntu-latest' && matrix.python-version <= '3.12'
-          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 ..
+        - uses: prefix-dev/setup-pixi@v0.9.4
+          with:
+            pixi-version: v0.55.0
+            cache: true
+            frozen: true
+            environments: ${{ matrix.python-version }}
+            activate-environment: ${{ matrix.python-version }}
 
         - name: Install other testing 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
+            pixi run -e ${{ matrix.python-version }} install/install_ibcdfo.sh
 
         - name: Install libEnsemble, flake8, lock environment
           run: |
-            pip install pydantic==${{ matrix.pydantic-version }}
             pip install -e .
             flake8 libensemble
 
-        - name: Remove test using octave, gpcam on Python 3.13
-          if: matrix.python-version >= '3.13'
+        - name: Install gpcam
+          if: matrix.python-version != 'py313e' && matrix.python-version != 'py314e'
           run: |
-            rm ./libensemble/tests/regression_tests/test_persistent_fd_param_finder.py # needs octave, which doesn't yet support 3.13
-            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'
-          run: |
-            pip install redis
-            pip install proxystore==0.7.0
+            pixi run -e ${{ matrix.python-version }} pip install gpcam==8.1.13
 
-        - name: Remove proxystore test on Pydantic 1
-          if: matrix.pydantic-version == '1.10.21'
+        - name: Remove xopt tests on old python
+          if: matrix.python-version == 'py310e'
           run: |
-            rm ./libensemble/tests/regression_tests/test_proxystore_integration.py
+            rm ./libensemble/tests/regression_tests/test_xopt_EI_xopt_sim.py
+            rm ./libensemble/tests/regression_tests/test_xopt_EI.py
+            rm ./libensemble/tests/regression_tests/test_xopt_nelder_mead.py
 
-        - name: Remove Balsam/Globus-compute tests on Pydantic 2
-          if: matrix.pydantic-version == '2.10.6'
+        - name: Remove test using octave, gpcam, globus-compute on Python 3.13
+          if: matrix.python-version == 'py313e' || matrix.python-version == 'py314e'
           run: |
-            rm ./libensemble/tests/unit_tests/test_ufunc_runners.py
-            rm ./libensemble/tests/unit_tests/test_executor_balsam.py
+            rm ./libensemble/tests/unit_tests/test_ufunc_runners.py # needs globus-compute
+            rm ./libensemble/tests/regression_tests/test_gpCAM.py # needs gpcam, which doesn't build on 3.13
+            rm ./libensemble/tests/regression_tests/test_asktell_gpCAM.py # needs gpcam, which doesn't build on 3.13
+            rm ./libensemble/tests/regression_tests/test_persistent_gp_multitask_ax.py # needs ax-platform, which doesn't yet support 3.14
+            rm ./libensemble/tests/regression_tests/test_optimas_ax_mf.py # needs ax-platform, which doesn't yet support 3.14
+            rm ./libensemble/tests/regression_tests/test_optimas_ax_sf.py # needs ax-platform, which doesn't yet support 3.14
 
         - 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
 
-        - name: Run extensive tests
+        - name: Run extensive tests, Ubuntu
+          if: matrix.os == 'ubuntu-latest'
           run: |
            ./libensemble/tests/run_tests.py -e -${{ matrix.comms-type }}
 
+        - name: Run extensive tests, macOS
+          if: matrix.os == 'macos-latest'
+          run: |
+           pixi run -e ${{ matrix.python-version }} ./libensemble/tests/run_tests.py -e -${{ matrix.comms-type }}
+
         - name: Merge coverage
           run: |
             mv libensemble/tests/.cov* .
@@ -179,5 +117,5 @@ 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@v1.44.0

.pre-commit-config.yaml

@@ -1,32 +1,32 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
     - id: end-of-file-fixer
       exclude: ^(.*\.xml|.*\.svg)$
     - id: trailing-whitespace
       exclude: ^(.*\.xml|.*\.svg)$
 
 - repo: https://github.com/pycqa/isort
-  rev: 6.0.0
+  rev: 7.0.0
   hooks:
     - id: isort
       args: [--profile=black, --line-length=120]
 
 - repo: https://github.com/psf/black
-  rev: 25.1.0
+  rev: 25.12.0
   hooks:
     - id: black
       args: [--line-length=120]
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 7.1.1
+  rev: 7.3.0
   hooks:
   -   id: flake8
       args: [--max-line-length=120]
 
 - repo: https://github.com/asottile/blacken-docs
-  rev: 1.19.1
+  rev: 1.20.0
   hooks:
   -   id: blacken-docs
       additional_dependencies: [black==22.12.0]