Merge branch 'develop' into testing/mypy-initial-setup

the-mr-dave · web-flow · commit f2aec5faa67e · 2026-01-14T22:48:39.000+01:00
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+pixi.lock filter=lfs diff=lfs merge=lfs -text
diff --git a/.github/workflows/basic.yml b/.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", "py314"]
                 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
 
@@ -39,44 +39,24 @@ jobs:
                 shell: bash -l {0}
 
         steps:
-        - uses: actions/checkout@v6
-        - 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
+            lfs: true
 
-        - name: Install Ubuntu compilers
-          if: matrix.os == 'ubuntu-latest'
-          run: |
-              conda install -c conda-forge gcc_linux-64
+        - name: Checkout lockfile
+          run: git lfs checkout
 
-        # Roundabout solution on macos for proper linking with mpicc
-        - name: Install macOS compilers
-          if: matrix.os == 'macos-latest'
-          run: |
-            conda install clang_osx-64
-
-        - 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/setup-pixi@v0.9.2
+          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: |
@@ -90,19 +70,19 @@ jobs:
           run: mypy
 
         - 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' || matrix.python-version == 'py314'
           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: |
@@ -119,4 +99,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v6
-        - uses: crate-ci/typos@v1.41.0
+        - uses: crate-ci/typos@v1.42.0
diff --git a/.github/workflows/extra.yml b/.github/workflows/extra.yml
@@ -144,4 +144,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v6
-        - uses: crate-ci/typos@v1.41.0
+        - uses: crate-ci/typos@v1.42.0
diff --git a/docs/conf.py b/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",
diff --git a/libensemble/gen_funcs/aposmm_localopt_support.py b/libensemble/gen_funcs/aposmm_localopt_support.py
@@ -44,9 +44,9 @@ class APOSMMException(Exception):
     if "dfols" in optimizers:
         import dfols  # noqa: F401
     if "ibcdfo_pounders" in optimizers:
-        from ibcdfo.pounders import pounders  # noqa: F401
+        from ibcdfo import run_pounders
     if "ibcdfo_manifold_sampling" in optimizers:
-        from ibcdfo.manifold_sampling import manifold_sampling_primal  # noqa: F401
+        from ibcdfo import run_MSP  # noqa: F401
     if "scipy" in optimizers:
         from scipy import optimize as sp_opt  # noqa: F401
     if "external_localopt" in optimizers:
@@ -449,7 +449,7 @@ def run_local_ibcdfo_manifold_sampling(user_specs, comm_queue, x0, f0, child_can
     # m = len(f0)
     subprob_switch = "linprog"
 
-    [X, F, hF, xkin, flag] = manifold_sampling_primal(
+    [X, F, hF, xkin, flag] = run_MSP(
         user_specs["hfun"],
         lambda x: scipy_dfols_callback_fun(x, comm_queue, child_can_read, parent_can_read, user_specs),
         x0,
@@ -507,7 +507,7 @@ def run_local_ibcdfo_pounders(user_specs, comm_queue, x0, f0, child_can_read, pa
     else:
         Options = None
 
-    [X, F, hF, flag, xkin] = pounders(
+    [X, F, hF, flag, xkin] = run_pounders(
         lambda x: scipy_dfols_callback_fun(x, comm_queue, child_can_read, parent_can_read, user_specs),
         x0,
         n,
diff --git a/libensemble/tests/regression_tests/support.py b/libensemble/tests/regression_tests/support.py
@@ -1,7 +1,6 @@
 import copy
 
 import numpy as np
-
 from libensemble.specs import input_fields, output_data
 
 branin_vals_and_minima = np.array(
diff --git a/libensemble/tests/regression_tests/test_1d_sampling.py b/libensemble/tests/regression_tests/test_1d_sampling.py
@@ -14,7 +14,6 @@
 # TESTSUITE_NPROCS: 2 4
 
 import numpy as np
-
 from libensemble import Ensemble
 from libensemble.gen_funcs.sampling import latin_hypercube_sample as gen_f
 
diff --git a/libensemble/tests/regression_tests/test_2d_sampling.py b/libensemble/tests/regression_tests/test_2d_sampling.py
@@ -14,7 +14,6 @@
 # TESTSUITE_NPROCS: 2 4
 
 import numpy as np
-
 from libensemble import Ensemble
 from libensemble.gen_funcs.sampling import latin_hypercube_sample as gen_f
 
diff --git a/libensemble/tests/regression_tests/test_GPU_variable_resources.py b/libensemble/tests/regression_tests/test_GPU_variable_resources.py
@@ -26,7 +26,6 @@
 # TESTSUITE_NPROCS: 6
 
 import numpy as np
-
 from libensemble import Ensemble
 from libensemble.alloc_funcs.start_only_persistent import only_persistent_gens as alloc_f
 from libensemble.executors.mpi_executor import MPIExecutor
diff --git a/libensemble/tests/regression_tests/test_GPU_variable_resources_multi_task.py b/libensemble/tests/regression_tests/test_GPU_variable_resources_multi_task.py
@@ -35,7 +35,6 @@
 # TESTSUITE_NPROCS: 10
 
 import numpy as np
-
 from libensemble import Ensemble
 from libensemble.alloc_funcs.start_only_persistent import only_persistent_gens as alloc_f
 from libensemble.executors.mpi_executor import MPIExecutor
diff --git a/libensemble/tests/regression_tests/test_evaluate_mixed_sample.py b/libensemble/tests/regression_tests/test_evaluate_mixed_sample.py
@@ -17,7 +17,6 @@
 import warnings
 
 import numpy as np
-
 from libensemble import Ensemble
 from libensemble.alloc_funcs.give_pregenerated_work import give_pregenerated_sim_work as alloc_f
 
diff --git a/libensemble/tests/regression_tests/test_gpCAM.py b/libensemble/tests/regression_tests/test_gpCAM.py
@@ -27,7 +27,6 @@
 import warnings
 
 import numpy as np
-
 from libensemble.alloc_funcs.start_only_persistent import only_persistent_gens as alloc_f
 from libensemble.gen_funcs.persistent_gpCAM import persistent_gpCAM, persistent_gpCAM_covar
 
diff --git a/libensemble/tests/regression_tests/test_inverse_bayes_example.py b/libensemble/tests/regression_tests/test_inverse_bayes_example.py
@@ -19,7 +19,6 @@
 # TESTSUITE_NPROCS: 3 4
 
 import numpy as np
-
 from libensemble import Ensemble
 from libensemble.alloc_funcs.inverse_bayes_allocf import only_persistent_gens_for_inverse_bayes as alloc_f
 from libensemble.gen_funcs.persistent_inverse_bayes import persistent_updater_after_likelihood as gen_f
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_dfols.py b/libensemble/tests/regression_tests/test_persistent_aposmm_dfols.py
@@ -21,9 +21,8 @@
 import multiprocessing
 import sys
 
-import numpy as np
-
 import libensemble.gen_funcs
+import numpy as np
 
 # Import libEnsemble items for this test
 from libensemble.libE import libE
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_exception.py b/libensemble/tests/regression_tests/test_persistent_aposmm_exception.py
@@ -18,9 +18,8 @@
 import multiprocessing
 import sys
 
-import numpy as np
-
 import libensemble.gen_funcs
+import numpy as np
 
 # Import libEnsemble items for this test
 from libensemble.libE import libE
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_external_localopt.py b/libensemble/tests/regression_tests/test_persistent_aposmm_external_localopt.py
@@ -26,9 +26,8 @@
 import shutil  # For copying the external_localopt script
 import sys
 
-import numpy as np
-
 import libensemble.gen_funcs
+import numpy as np
 
 # Import libEnsemble items for this test
 from libensemble.libE import libE
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_ibcdfo_manifold_sampling.py b/libensemble/tests/regression_tests/test_persistent_aposmm_ibcdfo_manifold_sampling.py
@@ -27,9 +27,8 @@
 import multiprocessing
 import sys
 
-import numpy as np
-
 import libensemble.gen_funcs
+import numpy as np
 from libensemble.libE import libE
 
 libensemble.gen_funcs.rc.aposmm_optimizers = "ibcdfo_manifold_sampling"
@@ -39,8 +38,7 @@
 from libensemble.tools import add_unique_random_streams, parse_args, save_libE_output
 
 try:
-    from ibcdfo.manifold_sampling import manifold_sampling_primal  # noqa: F401
-    from ibcdfo.manifold_sampling.h_examples import pw_maximum as hfun
+    import ibcdfo  # noqa: F401
 
 except ModuleNotFoundError:
     sys.exit("Please 'pip install ibcdfo'")
@@ -110,7 +108,7 @@ def synthetic_beamline_mapping(H, _, sim_specs):
         },
     }
 
-    gen_specs["user"]["hfun"] = hfun
+    gen_specs["user"]["hfun"] = ibcdfo.manifold_sampling.h_pw_maximum
 
     alloc_specs = {"alloc_f": alloc_f}
 
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_ibcdfo_pounders.py b/libensemble/tests/regression_tests/test_persistent_aposmm_ibcdfo_pounders.py
@@ -27,9 +27,8 @@
 import multiprocessing
 import sys
 
-import numpy as np
-
 import libensemble.gen_funcs
+import numpy as np
 from libensemble.libE import libE
 from libensemble.sim_funcs.chwirut1 import chwirut_eval
 
@@ -40,8 +39,7 @@
 from libensemble.tools import add_unique_random_streams, parse_args, save_libE_output
 
 try:
-    from ibcdfo.pounders import pounders  # noqa: F401
-    from ibcdfo.pounders.general_h_funs import emittance_combine, emittance_h
+    import ibcdfo  # noqa: F401
 except ModuleNotFoundError:
     sys.exit("Please 'pip install ibcdfo'")
 
@@ -122,8 +120,8 @@ def synthetic_beamline_mapping(H, _, sim_specs):
         }
 
         if inst == 1:
-            gen_specs["user"]["hfun"] = emittance_h
-            gen_specs["user"]["combinemodels"] = emittance_combine
+            gen_specs["user"]["hfun"] = ibcdfo.pounders.h_emittance
+            gen_specs["user"]["combinemodels"] = ibcdfo.pounders.combine_emittance
 
         alloc_specs = {"alloc_f": alloc_f}
 
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_ibcdfo_pounders_jax.py b/libensemble/tests/regression_tests/test_persistent_aposmm_ibcdfo_pounders_jax.py
@@ -27,9 +27,8 @@
 import multiprocessing
 import sys
 
-import numpy as np
-
 import libensemble.gen_funcs
+import numpy as np
 from libensemble.libE import libE
 
 libensemble.gen_funcs.rc.aposmm_optimizers = "ibcdfo_pounders"
@@ -39,8 +38,9 @@
 from libensemble.tools import add_unique_random_streams, parse_args, save_libE_output
 
 try:
-    from ibcdfo.pounders import pounders  # noqa: F401
-    from declare_hfun_and_combine_model_with_jax import hfun, combinemodels_jax
+    import ibcdfo  # noqa: F401
+
+    from declare_hfun_and_combine_model_with_jax import combinemodels_jax, hfun
 
 except ModuleNotFoundError:
     sys.exit("Please 'pip install ibcdfo'")
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_nlopt.py b/libensemble/tests/regression_tests/test_persistent_aposmm_nlopt.py
@@ -19,9 +19,8 @@
 import sys
 from math import gamma, pi, sqrt
 
-import numpy as np
-
 import libensemble.gen_funcs
+import numpy as np
 
 # Import libEnsemble items for this test
 from libensemble.libE import libE
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_periodic.py b/libensemble/tests/regression_tests/test_persistent_aposmm_periodic.py
@@ -19,9 +19,8 @@
 import multiprocessing
 import sys
 
-import numpy as np
-
 import libensemble.gen_funcs
+import numpy as np
 
 libensemble.gen_funcs.rc.aposmm_optimizers = ["nlopt", "scipy"]
 from libensemble.alloc_funcs.persistent_aposmm_alloc import persistent_aposmm_alloc as alloc_f
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_pounders.py b/libensemble/tests/regression_tests/test_persistent_aposmm_pounders.py
@@ -22,9 +22,8 @@
 import sys
 from math import ceil, gamma, pi, sqrt
 
-import numpy as np
-
 import libensemble.gen_funcs
+import numpy as np
 
 # Import libEnsemble items for this test
 from libensemble.libE import libE
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_scipy.py b/libensemble/tests/regression_tests/test_persistent_aposmm_scipy.py
@@ -18,9 +18,8 @@
 import multiprocessing
 import sys
 
-import numpy as np
-
 import libensemble.gen_funcs
+import numpy as np
 
 # Import libEnsemble items for this test
 from libensemble.libE import libE
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_tao_blmvm.py b/libensemble/tests/regression_tests/test_persistent_aposmm_tao_blmvm.py
@@ -20,9 +20,8 @@
 import sys
 from math import gamma, pi, sqrt
 
-import numpy as np
-
 import libensemble.gen_funcs
+import numpy as np
 
 # Import libEnsemble items for this test
 from libensemble.libE import libE
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_tao_nm.py b/libensemble/tests/regression_tests/test_persistent_aposmm_tao_nm.py
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_timeout.py b/libensemble/tests/regression_tests/test_persistent_aposmm_timeout.py
diff --git a/libensemble/tests/regression_tests/test_persistent_aposmm_with_grad.py b/libensemble/tests/regression_tests/test_persistent_aposmm_with_grad.py
diff --git a/libensemble/tests/regression_tests/test_persistent_fd_param_finder.py b/libensemble/tests/regression_tests/test_persistent_fd_param_finder.py
diff --git a/libensemble/tests/regression_tests/test_persistent_gp_multitask_ax.py b/libensemble/tests/regression_tests/test_persistent_gp_multitask_ax.py
diff --git a/libensemble/tests/regression_tests/test_persistent_surmise_calib.py b/libensemble/tests/regression_tests/test_persistent_surmise_calib.py
diff --git a/libensemble/tests/regression_tests/test_persistent_surmise_killsims.py b/libensemble/tests/regression_tests/test_persistent_surmise_killsims.py
diff --git a/libensemble/tests/regression_tests/test_persistent_tasmanian.py b/libensemble/tests/regression_tests/test_persistent_tasmanian.py
diff --git a/libensemble/tests/regression_tests/test_persistent_tasmanian_async.py b/libensemble/tests/regression_tests/test_persistent_tasmanian_async.py
diff --git a/libensemble/tests/regression_tests/test_with_app_persistent_aposmm_tao_nm.py b/libensemble/tests/regression_tests/test_with_app_persistent_aposmm_tao_nm.py
diff --git a/pixi.lock b/pixi.lock
diff --git a/pyproject.toml b/pyproject.toml

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+pixi.lock filter=lfs diff=lfs merge=lfs -text`