Merge pull request #1488 from Libensemble/release/v_1.4.3

Release/v 1.4.3

Author: shuds13

.flake8

@@ -14,6 +14,8 @@ exclude =
         # Keeping bad python format to match PETSc source code
         libensemble/sim_funcs/chwirut1.py
         examples/sim_funcs/chwirut1.py
+        # test runner
+        libensemble/tests/run_tests.py
 
 # Note that you can use wildcard exceptions with something such as
 # libensemble/libensemble/tests/regression_tests/*:F401
@@ -39,7 +41,6 @@ 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

.github/dependabot.yml

@@ -10,17 +10,30 @@ updates:
   - package-ecosystem: github-actions
     directory: /
     schedule:
-      interval: daily
+      interval: weekly # Reduced frequency
     target-branch: "develop"
+    groups:
+      actions-updates:
+        patterns:
+          - "actions/*"
 
   - package-ecosystem: pip
     directory: /
     schedule:
-      interval: daily
+      interval: weekly # Reduced frequency
     target-branch: "develop"
+    groups:
+      python-updates:
+        patterns:
+          - "*"
 
   - package-ecosystem: gitsubmodule
     directory: /
     schedule:
-      interval: daily
+      interval: weekly # Reduced frequency
     target-branch: "develop"
+    groups:
+      submodule-updates:
+        patterns:
+          - "*"
+

.github/workflows/basic.yml

@@ -17,29 +17,29 @@ jobs:
             matrix:
                 os: [ubuntu-latest]
                 mpi-version: [mpich]
-                python-version: [3.9, "3.10", "3.11", "3.12"]
-                pydantic-version: ["2.6.4"]
+                python-version: [3.9, "3.10", "3.11", "3.12", "3.13"]
+                pydantic-version: ["2.8.2"]
                 comms-type: [m, l]
                 include:
                     - os: macos-latest
                       python-version: "3.11"
                       mpi-version: mpich
-                      pydantic-version: "2.6.4"
+                      pydantic-version: "2.8.2"
                       comms-type: m
                     - os: macos-latest
                       python-version: "3.11"
                       mpi-version: mpich
-                      pydantic-version: "2.6.4"
+                      pydantic-version: "2.8.2"
                       comms-type: l
                     - os: ubuntu-latest
                       mpi-version: mpich
                       python-version: "3.10"
-                      pydantic-version: "1.10.13"
+                      pydantic-version: "1.10.17"
                       comms-type: m
                     - os: ubuntu-latest
                       mpi-version: mpich
                       python-version: "3.10"
-                      pydantic-version: "1.10.13"
+                      pydantic-version: "1.10.17"
                       comms-type: l
 
         env:
@@ -63,71 +63,37 @@ 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
+        - name: Force-update certifi and pip
           run: |
             python --version
-            pip install -I --upgrade certifi
+            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 gcc_linux-64
+          run: |
+              conda install 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 basic testing/feature dependencies
           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
+            conda install numpy scipy
 
         - name: Install mpi4py and MPI from conda
           run: |
             conda install mpi4py ${{ matrix.mpi-version }}
 
-        - name: Install generator dependencies
-          run: |
-            python -m pip install --upgrade pip
-            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 }}-${{ matrix.comms-type }}
-
-        - name: Install libEnsemble, flake8
+        - name: Install libEnsemble, test flake8
           run: |
             pip install pydantic==${{ matrix.pydantic-version }}
             pip install -e .
@@ -141,19 +107,19 @@ jobs:
         - name: Run simple tests, Ubuntu
           if: matrix.os == 'ubuntu-latest'
           run: |
-           ./libensemble/tests/run-tests.sh -A "-W error" -z -${{ matrix.comms-type }}
+           ./libensemble/tests/run_tests.py -A "-W error" -${{ matrix.comms-type }}
 
         - name: Run simple tests, macOS
           if: matrix.os == 'macos-latest'
           run: |
-            ./libensemble/tests/run-tests.sh -A "-W error" -z -${{ matrix.comms-type }}
+            ./libensemble/tests/run_tests.py -A "-W error" -${{ matrix.comms-type }}
 
         - name: Merge coverage
           run: |
             mv libensemble/tests/.cov* .
 
         - name: Upload coverage reports to Codecov
-          uses: codecov/codecov-action@v4
+          uses: codecov/codecov-action@v5
           env:
             CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
@@ -163,4 +129,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.23.6
+        - uses: crate-ci/typos@v1.28.2