Merge pull request #1237 from Libensemble/release/v_1.2.0

Release/v 1.2.0
Libensemble · Feb 8, 2024 · ce47158 · ce47158
2 parents 22d654d + eb15167
commit ce47158
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Showing 148 changed files with 3,101 additions and 1,971 deletions.
diff --git a/.github/workflows/basic.yml b/.github/workflows/basic.yml
@@ -18,15 +18,28 @@ jobs:
                 os: [ubuntu-latest]
                 mpi-version: [mpich]
                 python-version: [3.9, "3.10", "3.11", "3.12"]
+                pydantic-version: ["2.5.2"]
                 comms-type: [m, l]
                 include:
                     - os: macos-latest
-                      python-version: 3.11
+                      python-version: "3.11"
                       mpi-version: "mpich=4.0.3"
+                      pydantic-version: "2.5.2"
                       comms-type: m
                     - os: macos-latest
-                      python-version: 3.11
+                      python-version: "3.11"
                       mpi-version: "mpich=4.0.3"
+                      pydantic-version: "2.5.2"
+                      comms-type: l
+                    - os: ubuntu-latest
+                      mpi-version: mpich
+                      python-version: "3.10"
+                      pydantic-version: "1.10.13"
+                      comms-type: m
+                    - os: ubuntu-latest
+                      mpi-version: mpich
+                      python-version: "3.10"
+                      pydantic-version: "1.10.13"
                       comms-type: l
 
         env:
@@ -41,7 +54,7 @@ jobs:
         steps:
         - uses: actions/checkout@v4
         - name: Setup conda - Python ${{ matrix.python-version }}
-          uses: conda-incubator/setup-miniconda@v2
+          uses: conda-incubator/setup-miniconda@v3
           with:
             activate-environment: condaenv
             miniconda-version: "latest"
@@ -50,7 +63,7 @@ jobs:
             channel-priority: flexible
             auto-update-conda: true
 
-        - uses: actions/cache/restore@v3
+        - uses: actions/cache/restore@v4
           name: Restore cached dependencies
           id: cache
           if: matrix.os == 'ubuntu-latest'
@@ -61,7 +74,7 @@ jobs:
               /usr/share/miniconda3/bin
               /usr/share/miniconda3/lib
               /usr/share/miniconda3/include
-            key: libe-${{ github.ref_name }}-${{ matrix.python-version }}-${{ matrix.comms-type }}
+            key: libe-${{ github.ref_name }}-${{ matrix.python-version }}-${{ matrix.comms-type }}-${{ matrix.pydantic-version }}-basic
 
         - name: Force-update certifi
           run: |
@@ -85,18 +98,26 @@ jobs:
             pip install -r install/testing_requirements.txt
             pip install -r install/misc_feature_requirements.txt
 
+            git clone --recurse-submodules -b develop https://github.com/POptUS/IBCDFO.git
+            pushd IBCDFO/minq/py/minq5/
+            export PYTHONPATH="$PYTHONPATH:$(pwd)"
+            echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
+            popd
+            pushd IBCDFO/ibcdfo_pypkg/
+            pip install -e .
+            popd
+
         - name: Install mpi4py and MPI from conda
           run: |
             conda install mpi4py ${{ matrix.mpi-version }}
 
         - name: Install generator dependencies
-          if: matrix.os != 'windows-latest' && steps.cache.outputs.cache-hit != 'true'
           run: |
             python -m pip install --upgrade pip
-            pip install mpmath
+            pip install mpmath matplotlib
             conda install numpy nlopt scipy
 
-        - uses: actions/cache/save@v3
+        - uses: actions/cache/save@v4
           name: Save dependencies to cache
           if: matrix.os == 'ubuntu-latest'
           with:
@@ -108,11 +129,17 @@ jobs:
               /usr/share/miniconda3/include
             key: libe-${{ github.ref_name }}-${{ matrix.python-version }}-${{ matrix.comms-type }}
 
-        - name: Install libEnsemble, flake8, lock environment
+        - name: Install libEnsemble, 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'
+          run: |
+            rm ./libensemble/tests/functionality_tests/test_local_sine_tutorial*.py # matplotlib errors on 3.12
+
         - name: Run simple tests, Ubuntu
           if: matrix.os == 'ubuntu-latest'
           run: |
@@ -130,7 +157,7 @@ jobs:
             mv libensemble/tests/.cov* .
 
         - name: Upload coverage reports to Codecov
-          uses: codecov/codecov-action@v3
+          uses: codecov/codecov-action@v4
           env:
             CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
@@ -140,4 +167,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.16.23
+        - uses: crate-ci/typos@v1.18.1
diff --git a/.github/workflows/extra.yml b/.github/workflows/extra.yml
@@ -12,23 +12,38 @@ jobs:
                 os: [ubuntu-latest]
                 mpi-version: [mpich]
                 python-version: [3.9, "3.10", "3.11", "3.12"]
+                pydantic-version: ["2.5.2"]
                 comms-type: [m, l]
                 include:
                     - os: macos-latest
                       python-version: 3.11
                       mpi-version: "mpich=4.0.3"
+                      pydantic-version: "2.5.2"
                       comms-type: m
                     - os: macos-latest
                       python-version: 3.11
                       mpi-version: "mpich=4.0.3"
+                      pydantic-version: "2.5.2"
                       comms-type: l
                     - os: ubuntu-latest
                       python-version: "3.10"
                       mpi-version: "mpich"
+                      pydantic-version: "2.5.2"
                       comms-type: t
                     - os: ubuntu-latest
                       mpi-version: "openmpi"
-                      python-version: "3.11"
+                      pydantic-version: "2.5.2"
+                      python-version: "3.12"
+                      comms-type: l
+                    - os: ubuntu-latest
+                      mpi-version: mpich
+                      python-version: "3.10"
+                      pydantic-version: "1.10.13"
+                      comms-type: m
+                    - os: ubuntu-latest
+                      mpi-version: mpich
+                      python-version: "3.10"
+                      pydantic-version: "1.10.13"
                       comms-type: l
 
         env:
@@ -43,7 +58,7 @@ jobs:
         steps:
         - uses: actions/checkout@v4
         - name: Setup conda - Python ${{ matrix.python-version }}
-          uses: conda-incubator/setup-miniconda@v2
+          uses: conda-incubator/setup-miniconda@v3
           with:
             activate-environment: condaenv
             miniconda-version: "latest"
@@ -52,7 +67,7 @@ jobs:
             channel-priority: flexible
             auto-update-conda: true
 
-        - uses: actions/cache/restore@v3
+        - uses: actions/cache/restore@v4
           name: Restore cached dependencies
           id: cache
           if: matrix.os == 'ubuntu-latest'
@@ -64,7 +79,7 @@ jobs:
               /usr/share/miniconda3/bin
               /usr/share/miniconda3/lib
               /usr/share/miniconda3/include
-            key: libe-${{ github.ref_name }}-${{ matrix.python-version }}-${{ matrix.comms-type }}
+            key: libe-${{ github.ref_name }}-${{ matrix.python-version }}-${{ matrix.comms-type }}-${{ matrix.pydantic-version }}-extra
 
         - name: Force-update certifi
           run: |
@@ -95,20 +110,21 @@ jobs:
             pip install mpi4py
 
         - name: Install generator dependencies
-          if: steps.cache.outputs.cache-hit != 'true'
           run: |
             python -m pip install --upgrade pip
+            pip install mpmath matplotlib
             conda env update --file install/gen_deps_environment.yml
 
         - name: Install ax-platform
           if: matrix.python-version != '3.12'
           run: |
             pip install ax-platform==0.2.8
+            pip install gpcam
 
         - name: Install surmise
-          if: matrix.os != 'macos-latest' && steps.cache.outputs.cache-hit != 'true'
+          if: matrix.os != 'macos-latest'
           run: |
-            pip install --upgrade git+https://github.com/bandframework/surmise.git@develop
+            pip install --upgrade git+https://github.com/bandframework/surmise.git
 
         - name: Build ytopt and dependencies
           if: matrix.python-version <= '3.10' && matrix.os != 'macos-latest'
@@ -131,33 +147,14 @@ jobs:
             cd ..
 
         - name: Install generator dependencies for Ubuntu tests
-          if: matrix.os == 'ubuntu-latest' && steps.cache.outputs.cache-hit != 'true' && matrix.python-version != '3.12'
+          if: matrix.os == 'ubuntu-latest' && matrix.python-version != '3.12'
           run: |
             sudo apt-get install bc
 
-            # begin heffte build and dependencies
-            sudo apt install libfftw3-dev
-            git clone https://github.com/icl-utk-edu/heffte.git
-            mkdir heffte/build
-            cd heffte/build
-            pwd
-            cmake -D CMAKE_BUILD_TYPE=Release -D BUILD_SHARED_LIBS=ON -D CMAKE_INSTALL_PREFIX=./ -D Heffte_ENABLE_AVX=ON -D Heffte_ENABLE_FFTW=ON ../
-            make -j 4
-            make install
-            cp ./benchmarks/speed3d_c2c ../../libensemble/tests/regression_tests/
-            # end heffte build and dependencies
-
             # pip install dragonfly-opt
             # pip install git+https://github.com/dragonfly/dragonfly.git
             pip install git+https://github.com/jlnav/dragonfly.git@fix/remove_npobject
 
-
-        - name: Copy heffte exe on cache-hit
-          if: matrix.os == 'ubuntu-latest' && steps.cache.outputs.cache-hit != 'false' && matrix.python-version != '3.12'
-          run: |
-            cd /home/runner/work/libensemble/libensemble
-            cp ./heffte/build/benchmarks/speed3d_c2c ./libensemble/tests/regression_tests/
-
         - name: Install other testing dependencies
           run: |
             conda install octave
@@ -169,7 +166,31 @@ jobs:
             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: actions/cache/save@v3
+            git clone --recurse-submodules -b develop https://github.com/POptUS/IBCDFO.git
+            pushd IBCDFO/minq/py/minq5/
+            export PYTHONPATH="$PYTHONPATH:$(pwd)"
+            echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
+            popd
+            pushd IBCDFO/ibcdfo_pypkg/
+            pip install -e .
+            popd
+
+        - name: Build heffte
+          if: matrix.os != 'macos-latest'
+          run: |
+            # begin heffte build and dependencies
+            sudo apt install libfftw3-dev
+            git clone https://github.com/icl-utk-edu/heffte.git
+            mkdir heffte/build
+            cd heffte/build
+            pwd
+            cmake -D CMAKE_BUILD_TYPE=Release -D BUILD_SHARED_LIBS=ON -D CMAKE_INSTALL_PREFIX=./ -D Heffte_ENABLE_AVX=ON -D Heffte_ENABLE_FFTW=ON ../
+            make -j 4
+            make install
+            cp ./benchmarks/speed3d_c2c ../../libensemble/tests/regression_tests/
+            # end heffte build and dependencies
+
+        - uses: actions/cache/save@v4
           name: Save dependencies to cache
           if: matrix.os == 'ubuntu-latest'
           with:
@@ -184,17 +205,24 @@ jobs:
 
         - name: Install libEnsemble, flake8, lock environment
           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'
           run: |
-            rm ./libensemble/tests/regression_tests/test_heffte.py
             rm ./libensemble/tests/regression_tests/test_ytopt_heffte.py
+            rm ./libensemble/tests/regression_tests/test_gpCAM.py
             rm ./libensemble/tests/regression_tests/test_persistent_gp.py
             rm ./libensemble/tests/regression_tests/test_persistent_gp_multitask_ax.py
 
+        - name: Remove Balsam/Globus-compute tests on Pydantic 2
+          if: matrix.pydantic-version == '2.5.2'
+          run: |
+            rm ./libensemble/tests/unit_tests/test_ufunc_runners.py
+            rm ./libensemble/tests/unit_tests/test_executor_balsam.py
+
         - name: Run extensive tests, Ubuntu
           if: matrix.os == 'ubuntu-latest'
           run: |
@@ -212,7 +240,7 @@ jobs:
             mv libensemble/tests/.cov* .
 
         - name: Upload coverage reports to Codecov
-          uses: codecov/codecov-action@v3
+          uses: codecov/codecov-action@v4
           env:
             CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
@@ -222,4 +250,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.16.23
+        - uses: crate-ci/typos@v1.18.1
diff --git a/.wci.yml b/.wci.yml
@@ -16,8 +16,8 @@ description: |
 language: Python
 
 release:
-  version: 1.1.0
-  date: 2023-11-08
+  version: 1.2.0
+  date: 2024-02-08
 
 documentation:
   general: https://libensemble.readthedocs.io