Merge pull request #1545 from Libensemble/release/v_1.5.0

Release/v 1.5.0

Author: shuds13

.black

@@ -3,5 +3,4 @@ ignore:
   - "libensemble/tools/forkable_pdb.py"
   - "libensemble/tools/live_data/*"
   - "libensemble/sim_funcs/executor_hworld.py"
-  - "libensemble/gen_funcs/persistent_ax_multitask.py"
-  - "libensemble/gen_funcs/persistent_gpCAM.py"
+  - "libensemble/gen_funcs/persistent_tasmanian.py"

.codecov.yml

@@ -46,6 +46,3 @@ per-file-ignores =
         libensemble/tests/functionality_tests/test_active_persistent_worker_abort.py:E402
         libensemble/tests/unit_tests/test_persistent_aposmm.py:E402
         libensemble/tests/unit_tests/RENAME_test_persistent_aposmm.py:E402
-
-        # Allow undefined name '__version__'
-        setup.py:F821

.flake8

@@ -36,4 +36,3 @@ updates:
       submodule-updates:
         patterns:
           - "*"
-

.github/dependabot.yml

@@ -17,29 +17,29 @@ jobs:
             matrix:
                 os: [ubuntu-latest]
                 mpi-version: [mpich]
-                python-version: [3.9, "3.10", "3.11", "3.12", "3.13"]
-                pydantic-version: ["2.8.2"]
+                python-version: ["3.10", "3.11", "3.12", "3.13"]
+                pydantic-version: ["2.10.6"]
                 comms-type: [m, l]
                 include:
                     - os: macos-latest
                       python-version: "3.11"
                       mpi-version: mpich
-                      pydantic-version: "2.8.2"
+                      pydantic-version: "2.10.6"
                       comms-type: m
                     - os: macos-latest
                       python-version: "3.11"
                       mpi-version: mpich
-                      pydantic-version: "2.8.2"
+                      pydantic-version: "2.10.6"
                       comms-type: l
                     - os: ubuntu-latest
                       mpi-version: mpich
                       python-version: "3.10"
-                      pydantic-version: "1.10.17"
+                      pydantic-version: "1.10.21"
                       comms-type: m
                     - os: ubuntu-latest
                       mpi-version: mpich
                       python-version: "3.10"
-                      pydantic-version: "1.10.17"
+                      pydantic-version: "1.10.21"
                       comms-type: l
 
         env:
@@ -129,4 +129,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.28.2
+        - uses: crate-ci/typos@v1.31.1

.github/workflows/basic.yml

@@ -11,43 +11,43 @@ jobs:
             matrix:
                 os: [ubuntu-latest]
                 mpi-version: [mpich]
-                python-version: [3.9, "3.10", "3.11", "3.12"]
-                pydantic-version: ["2.8.2"]
+                python-version: ['3.10', '3.11', '3.12', '3.13']
+                pydantic-version: ['2.10.6']
                 comms-type: [m, l]
                 include:
                     - os: macos-latest
-                      python-version: 3.11
+                      python-version: '3.13'
                       mpi-version: mpich
-                      pydantic-version: "2.8.2"
+                      pydantic-version: '2.10.6'
                       comms-type: m
                     - os: macos-latest
-                      python-version: 3.11
+                      python-version: '3.13'
                       mpi-version: mpich
-                      pydantic-version: "2.8.2"
+                      pydantic-version: '2.10.6'
                       comms-type: l
                     - os: ubuntu-latest
-                      python-version: "3.10"
+                      python-version: '3.12'
                       mpi-version: mpich
-                      pydantic-version: "2.8.2"
+                      pydantic-version: '2.10.6'
                       comms-type: t
                     - os: ubuntu-latest
-                      mpi-version: "openmpi"
-                      pydantic-version: "2.8.2"
-                      python-version: "3.12"
+                      mpi-version: 'openmpi'
+                      pydantic-version: '2.10.6'
+                      python-version: '3.12'
                       comms-type: l
                     - os: ubuntu-latest
                       mpi-version: mpich
-                      python-version: "3.10"
-                      pydantic-version: "1.10.17"
+                      python-version: '3.12'
+                      pydantic-version: '1.10.21'
                       comms-type: m
                     - os: ubuntu-latest
                       mpi-version: mpich
-                      python-version: "3.10"
-                      pydantic-version: "1.10.17"
+                      python-version: '3.12'
+                      pydantic-version: '1.10.21'
                       comms-type: l
 
         env:
-            HYDRA_LAUNCHER: "fork"
+            HYDRA_LAUNCHER: 'fork'
             TERM: xterm-256color
             GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
@@ -61,7 +61,7 @@ jobs:
           uses: conda-incubator/setup-miniconda@v3
           with:
             activate-environment: condaenv
-            miniconda-version: "latest"
+            miniconda-version: 'latest'
             python-version: ${{ matrix.python-version }}
             channels: conda-forge
             channel-priority: flexible
@@ -75,8 +75,8 @@ jobs:
         - name: Install Ubuntu compilers
           if: matrix.os == 'ubuntu-latest'
           run: |
-              conda install gcc_linux-64
-              pip install nlopt==2.9.0
+            conda install gcc_linux-64
+            pip install nlopt==2.9.0
 
         # Roundabout solution on macos for proper linking with mpicc
         - name: Install macOS compilers
@@ -93,25 +93,25 @@ jobs:
           run: |
             conda env update --file install/gen_deps_environment.yml
 
-        - name: Install gpcam
-          if: matrix.python-version != '3.12'
+        - name: Install gpcam and octave # Neither yet support 3.13
+          if: matrix.python-version <= '3.12'
           run: |
             pip install gpcam
+            conda install octave
 
-        - name: Install surmise
+        - 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'
+          if: matrix.os == 'ubuntu-latest' && matrix.python-version <= '3.12'
           run: |
-            sudo apt-get install bc
-            pip install -r install/ubuntu_no312.txt
-            pip install Tasmanian --user
+            pip install scikit-build packaging
 
         - name: Install Balsam on Pydantic 1
-          if: matrix.pydantic-version == '1.10.17'
+          if: matrix.pydantic-version == '1.10.21'
           run: |
             conda install pyzmq
             git clone https://github.com/argonne-lcf/balsam.git
@@ -120,38 +120,37 @@ jobs:
 
         - name: Install other testing dependencies
           run: |
-            conda install octave
             pip install -r install/testing_requirements.txt
             pip install -r install/misc_feature_requirements.txt
             source install/install_ibcdfo.sh
+            conda install numpy scipy
 
         - name: Install libEnsemble, flake8, lock environment
           run: |
             pip install pydantic==${{ matrix.pydantic-version }}
             pip install -e .
             flake8 libensemble
 
-        - name: Remove test for persistent Tasmanian, Surmise on Python 3.12
-          if: matrix.python-version >= '3.12'
+        - name: Remove test using octave, gpcam on Python 3.13
+          if: matrix.python-version >= '3.13'
           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
+            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 == '2.8.2'
+          if: matrix.pydantic-version == '2.10.6'
           run: |
             pip install redis
             pip install proxystore==0.7.0
 
         - name: Remove proxystore test on Pydantic 1
-          if: matrix.pydantic-version == '1.10.17'
+          if: matrix.pydantic-version == '1.10.21'
           run: |
             rm ./libensemble/tests/regression_tests/test_proxystore_integration.py
 
         - name: Remove Balsam/Globus-compute tests on Pydantic 2
-          if: matrix.pydantic-version == '2.8.2'
+          if: matrix.pydantic-version == '2.10.6'
           run: |
             rm ./libensemble/tests/unit_tests/test_ufunc_runners.py
             rm ./libensemble/tests/unit_tests/test_executor_balsam.py
@@ -181,4 +180,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.28.2
+        - uses: crate-ci/typos@v1.31.1

.github/workflows/extra.yml

@@ -26,3 +26,4 @@ dist/
 .spyproject/
 
 .hypothesis
+.pixi

.gitignore

@@ -1,32 +1,32 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
     - id: end-of-file-fixer
       exclude: ^(.*\.xml|.*\.svg)$
     - id: trailing-whitespace
       exclude: ^(.*\.xml|.*\.svg)$
 
 - repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+  rev: 6.0.0
   hooks:
     - id: isort
       args: [--profile=black, --line-length=120]
 
 - repo: https://github.com/psf/black
-  rev: 22.12.0
+  rev: 25.1.0
   hooks:
     - id: black
       args: [--line-length=120]
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
+  rev: 7.1.1
   hooks:
   -   id: flake8
       args: [--max-line-length=120]
 
 - repo: https://github.com/asottile/blacken-docs
-  rev: v1.12.1
+  rev: 1.19.1
   hooks:
   -   id: blacken-docs
       additional_dependencies: [black==22.12.0]

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: "ubuntu-22.04"
   tools:
-    python: "3.9"
+    python: "3.10"
 
 sphinx:
     configuration: docs/conf.py