Merge branch 'develop' into experimental/jlnav_plus_shuds_asktell

Libensemble · Sep 12, 2024 · fe7629e · fe7629e
2 parents 345aea3 + 1b44c81
commit fe7629e
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Showing 22 changed files with 32 additions and 921 deletions.
diff --git a/.flake8 b/.flake8
@@ -39,7 +39,6 @@ per-file-ignores =
         examples/calling_scripts/run_libensemble_on_warpx.py:E402
         libensemble/tests/regression_tests/test_persistent_aposmm*:E402
         libensemble/tests/regression_tests/test_persistent_gp_multitask_ax.py:E402
-        libensemble/tests/regression_tests/test_ytopt_heffte.py:E402
         libensemble/tests/functionality_tests/test_uniform_sampling_then_persistent_localopt_runs.py:E402
         libensemble/tests/functionality_tests/test_stats_output.py:E402
         libensemble/tests/functionality_tests/test_active_persistent_worker_abort.py:E402

diff --git a/.github/workflows/basic.yml b/.github/workflows/basic.yml
@@ -63,19 +63,6 @@ jobs:
             channel-priority: flexible
             auto-update-conda: true
 
-        - uses: actions/cache/restore@v4
-          name: Restore cached dependencies
-          id: cache
-          if: matrix.os == 'ubuntu-latest'
-          with:
-            path: |
-              /home/runner/.local
-              /usr/share/miniconda3/envs/condaenv
-              /usr/share/miniconda3/bin
-              /usr/share/miniconda3/lib
-              /usr/share/miniconda3/include
-            key: libe-${{ github.ref_name }}-${{ matrix.python-version }}-${{ matrix.comms-type }}-${{ matrix.pydantic-version }}-basic
-
         - name: Force-update certifi
           run: |
             python --version
@@ -95,15 +82,7 @@ jobs:
           run: |
             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
+            source install/install_ibcdfo.sh
 
         - name: Install mpi4py and MPI from conda
           run: |
@@ -115,18 +94,6 @@ jobs:
             pip install mpmath matplotlib
             conda install numpy nlopt scipy
 
-        - uses: actions/cache/save@v4
-          name: Save dependencies to cache
-          if: matrix.os == 'ubuntu-latest'
-          with:
-            path: |
-              /home/runner/.local
-              /usr/share/miniconda3/envs/condaenv
-              /usr/share/miniconda3/bin
-              /usr/share/miniconda3/lib
-              /usr/share/miniconda3/include
-            key: libe-${{ github.ref_name }}-${{ matrix.python-version }}-${{ matrix.comms-type }}
-
         - name: Install libEnsemble, flake8
           run: |
             pip install pydantic==${{ matrix.pydantic-version }}
@@ -163,4 +130,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/[email protected].1
+        - uses: crate-ci/[email protected].5
diff --git a/.github/workflows/extra.yml b/.github/workflows/extra.yml
@@ -67,20 +67,6 @@ jobs:
             channel-priority: flexible
             auto-update-conda: true
 
-        - uses: actions/cache/restore@v4
-          name: Restore cached dependencies
-          id: cache
-          if: matrix.os == 'ubuntu-latest'
-          with:
-            path: |
-              /home/runner/work/libensemble/libensemble/heffte/build/
-              /home/runner/.local
-              /usr/share/miniconda3/envs/condaenv
-              /usr/share/miniconda3/bin
-              /usr/share/miniconda3/lib
-              /usr/share/miniconda3/include
-            key: libe-${{ github.ref_name }}-${{ matrix.python-version }}-${{ matrix.comms-type }}-${{ matrix.pydantic-version }}-extra
-
         - name: Force-update certifi
           run: |
             python --version
@@ -97,65 +83,29 @@ jobs:
             conda install clang_osx-64
 
         - name: Install mpi4py and MPI from conda
-          if: (matrix.python-version != '3.10' && matrix.os == 'ubuntu-latest') || matrix.os == 'macos-latest'
           run: |
             conda install mpi4py ${{ matrix.mpi-version }}
 
-        - name: Install mpi4py from pip, MPI from conda
-          if: matrix.python-version == '3.10' && matrix.os == 'ubuntu-latest'
-          run: |
-            conda install ${{ matrix.mpi-version }}
-            pip install mpi4py
-
         - name: Install generator dependencies
           run: |
-            python -m pip install --upgrade pip
-            pip install mpmath
-            pip install matplotlib
             conda env update --file install/gen_deps_environment.yml
 
-        #- name: Install ax-platform
-        #  run: pip install "ax-platform<=0.4.0"
-
         - name: Install gpcam
           if: matrix.python-version != '3.12'
           run: |
             pip install gpcam
 
         - name: Install surmise
-          if: matrix.os != 'macos-latest'
+          if: matrix.os == 'ubuntu-latest'
           run: |
             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'
-          run: |
-            pip install scikit-learn==1.4.0
-            pip install pandas==2.2.1
-            pip install ConfigSpace
-            pip install "ray[default]"
-            git clone https://github.com/ytopt-team/scikit-optimize.git
-            cd scikit-optimize
-            pip install .
-            cd ..
-            git clone -b version1 https://github.com/ytopt-team/autotune.git
-            cd autotune
-            pip install .
-            cd ..
-            git clone -b main https://github.com/ytopt-team/ytopt.git
-            cd ytopt
-            pip install .
-            cd ..
-
         - name: Install generator dependencies for Ubuntu tests
           if: matrix.os == 'ubuntu-latest' && matrix.python-version != '3.12'
           run: |
             sudo apt-get install bc
-
-            # 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
-            pip install scikit-build packaging Tasmanian --user
+            pip install -r install/ubuntu_no312.txt
+            pip install Tasmanian --user
 
         - name: Install Balsam on Pydantic 1
           if: matrix.pydantic-version == '1.10.17'
@@ -170,43 +120,7 @@ jobs:
             conda install octave
             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" >> $GITHUB_ENV
-            popd
-            pushd IBCDFO/ibcdfo_pypkg/
-            pip install -e .
-            popd
-
-        - name: Build heffte
-          if: matrix.os != 'macos-latest'
-          run: |
-            # begin heffte build and dependencies
-            sudo apt install libfftw3-dev
-            git clone https://github.com/icl-utk-edu/heffte.git
-            mkdir heffte/build
-            cd heffte/build
-            pwd
-            cmake -D CMAKE_BUILD_TYPE=Release -D BUILD_SHARED_LIBS=ON -D CMAKE_INSTALL_PREFIX=./ -D Heffte_ENABLE_AVX=ON -D Heffte_ENABLE_FFTW=ON ../
-            make -j 4
-            make install
-            cp ./benchmarks/speed3d_c2c ../../libensemble/tests/regression_tests/
-            # end heffte build and dependencies
-
-        - uses: actions/cache/save@v4
-          name: Save dependencies to cache
-          if: matrix.os == 'ubuntu-latest'
-          with:
-            path: |
-              /home/runner/work/libensemble/libensemble/heffte/build/
-              /home/runner/.local
-              /usr/share/miniconda3/envs/condaenv
-              /usr/share/miniconda3/bin
-              /usr/share/miniconda3/lib
-              /usr/share/miniconda3/include
-            key: libe-${{ github.ref_name }}-${{ matrix.python-version }}-${{ matrix.comms-type }}
+            source install/install_ibcdfo.sh
 
         - name: Install libEnsemble, flake8, lock environment
           run: |
@@ -217,25 +131,26 @@ jobs:
         - name: Remove various tests on newer pythons
           if: matrix.python-version >= '3.11'
           run: |
-            rm ./libensemble/tests/regression_tests/test_ytopt_heffte.py
             # rm ./libensemble/tests/regression_tests/test_gpCAM.py
             # rm ./libensemble/tests/regression_tests/test_gpCAM_class.py
             rm ./libensemble/tests/regression_tests/test_persistent_gp.py
 
-        - name: Remove test for persistent Tasmanian on Python 3.12
+        - name: Remove test for persistent Tasmanian, Surmise on Python 3.12
           if: matrix.python-version >= '3.12'
           run: |
             rm ./libensemble/tests/regression_tests/test_persistent_tasmanian.py
             rm ./libensemble/tests/regression_tests/test_persistent_tasmanian_async.py
+            rm ./libensemble/tests/regression_tests/test_persistent_surmise_calib.py
+            rm ./libensemble/tests/regression_tests/test_persistent_surmise_killsims.py
 
         - name: Install redis/proxystore on Pydantic 2
-          if: matrix.pydantic-version == '2.6.4'
+          if: matrix.pydantic-version == '2.8.2'
           run: |
             pip install redis
             pip install proxystore==0.7.0
 
         - name: Remove proxystore test on Pydantic 1
-          if: matrix.pydantic-version == '1.10.13'
+          if: matrix.pydantic-version == '1.10.17'
           run: |
             rm ./libensemble/tests/regression_tests/test_proxystore_integration.py
 
@@ -251,16 +166,10 @@ jobs:
           with:
             redis-version: 7
 
-        - name: Run extensive tests, Ubuntu
-          if: matrix.os == 'ubuntu-latest'
+        - name: Run extensive tests
           run: |
            ./libensemble/tests/run-tests.sh -e -z -${{ matrix.comms-type }}
 
-        - name: Run extensive tests, macOS
-          if: matrix.os == 'macos-latest'
-          run: |
-            ./libensemble/tests/run-tests.sh -e -z -${{ matrix.comms-type }}
-
         - name: Merge coverage
           run: |
             mv libensemble/tests/.cov* .
@@ -276,4 +185,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/[email protected].1
+        - uses: crate-ci/[email protected].5
diff --git a/install/gen_deps_environment.yml b/install/gen_deps_environment.yml
@@ -6,7 +6,7 @@ channels:
 dependencies:
   - pip
   - numpy>=2
-  - nlopt
+  - nlopt==2.7.1
   - scipy
   - superlu_dist
   - hypre

diff --git a/install/install_ibcdfo.sh b/install/install_ibcdfo.sh
@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+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
diff --git a/install/misc_feature_requirements.txt b/install/misc_feature_requirements.txt
@@ -1 +1 @@
-globus-compute-sdk==2.27.0
+globus-compute-sdk==2.27.1
diff --git a/install/testing_requirements.txt b/install/testing_requirements.txt
@@ -1,9 +1,10 @@
 flake8==7.1.1
 coverage==7.3.1
-pytest==8.3.2
+pytest==8.3.3
 pytest-cov==5.0.0
 pytest-timeout==2.3.1
 mock==5.1.0
 python-dateutil==2.9.0.post0
 anyio==4.4.0
 matplotlib==3.9.2
+mpmath==1.3.0
diff --git a/install/ubuntu_no312.txt b/install/ubuntu_no312.txt
@@ -0,0 +1,5 @@
+gpcam==8.1.6
+scikit-build==0.18.1
+packaging==24.1
+git+https://github.com/jlnav/dragonfly.git@fix/remove_npobject
+git+https://github.com/bandframework/surmise.git
diff --git a/libensemble/gen_funcs/ytopt_asktell.py b/libensemble/gen_funcs/ytopt_asktell.py
diff --git a/libensemble/sim_funcs/heffte.py b/libensemble/sim_funcs/heffte.py