Testing/pixi in testing

.gitattributes

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

.github/workflows/basic.yml

@@ -17,15 +17,15 @@ jobs:
             matrix:
                 os: [ubuntu-latest]
                 mpi-version: [mpich]
-                python-version: ["3.10", "3.11", "3.12", "3.13"]
+                python-version: ["py310", "py311", "py312", "py313"]
                 comms-type: [m, l]
                 include:
                     - os: macos-latest
-                      python-version: "3.11"
+                      python-version: "py311"
                       mpi-version: mpich
                       comms-type: m
                     - os: macos-latest
-                      python-version: "3.11"
+                      python-version: "py311"
                       mpi-version: mpich
                       comms-type: l
 
@@ -39,66 +39,44 @@ jobs:
                 shell: bash -l {0}
 
         steps:
-        - uses: actions/checkout@v5
-        - name: Setup conda - Python ${{ matrix.python-version }}
-          uses: conda-incubator/setup-miniconda@v3
+        - uses: actions/checkout@v4
           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 -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'
           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: |

.github/workflows/extra.yml

@@ -11,24 +11,24 @@ jobs:
             matrix:
                 os: [ubuntu-latest]
                 mpi-version: [mpich]
-                python-version: ['3.10', '3.11', '3.12', '3.13']
+                python-version: ["py310e", "py311e", "py312e", "py313e"]
                 comms-type: [m, l]
                 include:
                     - os: macos-latest
-                      python-version: '3.13'
+                      python-version: "py313e"
                       mpi-version: mpich
                       comms-type: m
                     - os: macos-latest
-                      python-version: '3.13'
+                      python-version: "py313e"
                       mpi-version: mpich
                       comms-type: l
                     - os: ubuntu-latest
-                      python-version: '3.12'
+                      python-version: "py312e"
                       mpi-version: mpich
                       comms-type: t
                     - os: ubuntu-latest
                       mpi-version: 'openmpi'
-                      python-version: '3.12'
+                      python-version: 'py312e'
                       comms-type: l
 
         env:
@@ -41,84 +41,42 @@ jobs:
                 shell: bash -l {0}
 
         steps:
-        - uses: actions/checkout@v5
-        - name: Setup conda - Python ${{ matrix.python-version }}
-          uses: conda-incubator/setup-miniconda@v3
+        - uses: actions/checkout@v4
           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
-
-        - name: Install Ubuntu compilers
-          if: matrix.os == 'ubuntu-latest'
-          run: |
-            conda install -c conda-forge gcc_linux-64
-            pip install nlopt==2.9.0
-
-        # 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 }}
+            lfs: true
 
-        - name: Install generator dependencies
-          run: |
-            conda env update --file install/gen_deps_environment.yml
+        - name: Checkout lockfile
+          run: git lfs checkout
 
-        - 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
+        - uses: prefix-dev/[email protected]
+          with:
+            pixi-version: v0.45.0
+            environments: ${{ matrix.python-version }}
+            activate-environment: ${{ matrix.python-version }}
 
-        - name: Install surmise and Tasmanian
+        - name: Install surmise
           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
+            pixi run -e ${{ matrix.python-version }} pip install Tasmanian
 
         - 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 }} pip install gpcam==8.2.0
+            pixi run -e ${{ matrix.python-version }} ./install/install_ibcdfo.sh
 
         - name: Install libEnsemble, flake8, lock environment
           run: |
             pip install -e .
             flake8 libensemble
 
         - name: Remove test using octave, gpcam on Python 3.13
-          if: matrix.python-version >= '3.13'
+          if: matrix.python-version == 'py313e'
           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
-          run: |
-            pip install redis
-            pip install proxystore==0.7.0
-
         - name: Start Redis
           if: matrix.os == 'ubuntu-latest'
           uses: supercharge/[email protected]
@@ -127,7 +85,7 @@ jobs:
 
         - name: Run extensive tests
           run: |
-           ./libensemble/tests/run_tests.py -e -${{ matrix.comms-type }}
+            pixi run -e ${{ matrix.python-version }} ./libensemble/tests/run_tests.py -e -${{ matrix.comms-type }}
 
         - name: Merge coverage
           run: |

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",