Merge pull request #1 from queens-py/github-actions

GitHub actions

.github/workflows/.github-ci.yml

@@ -0,0 +1,48 @@
+# yamllint disable
+---
+#---------------------------------------------------------------------------------------------------
+env:
+  TEST_TIMING_OPTION: ""  # Set the option if local test should be timed or not. Default is off.
+  PYTHON_PACKAGE_MANAGER: "conda"  # Python package manager to create the python environments
+name: github_ci
+
+on: [push]
+
+jobs:
+  run_tests:
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/4c-multiphysics/4c:latest
+      options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+      - name: build
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y rsync
+          ln -s /home/user/4C/build/4C config/4C
+          ln -s /home/user/4C/build/post_ensight config/post_ensight
+          ln -s /home/user/4C/build/post_processor config/post_processor
+          # /usr/bin/mpirun --bind-to none --use-hwthread-cpus -np 2 config/4C /home/user/4C/tests/input_files/solid_runtime_hex8.dat out
+          $PYTHON_PACKAGE_MANAGER env create -f environment.yml
+          $PYTHON_PACKAGE_MANAGER activate queens
+          pip install -e .[develop]
+          $PYTHON_PACKAGE_MANAGER env export > pipeline_conda_environment.yml
+          $PYTHON_PACKAGE_MANAGER list
+      - name: codechecks
+        run: |
+          $PYTHON_PACKAGE_MANAGER activate queens
+          isort --check-only queens tests > track_isort.txt 2>&1
+          black --check queens tests > track_black.txt 2>&1
+          pylint --rcfile=.pylintrc_ci queens tests | tee track_pylint.txt 2>&1
+          pylint queens tests --rcfile=.pylintrc --output-format=json:pylint_warnings.json --fail-under 0
+          python .gitlab/pipeline_utils/code_quality_creator.py pylint_warnings.json
+          pydocstyle --match-dir='^(?!.*test).*$' queens > track_pydocstyle.txt 2>&1
+      - name: tests
+        run: |
+          $PYTHON_PACKAGE_MANAGER activate queens
+          pytest -v -m "unit_tests or integration_tests or integration_tests_fourc" -o log_cli=true --log-cli-level=INFO --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes --junitxml=test_junit.xml

tests/input_files/queens/bmfia_rpvi_park_gp_template.yml

@@ -67,7 +67,7 @@ mf_approx:
   stochastic_optimizer_name: gp_optimizer
 bmfia_interface:
   type: bmfia_interface
-  num_processors_multi_processing: 4
+  num_processors_multi_processing: 2
   probabilistic_mapping_type: per_coordinate
 bmfia_iterator:
   type: bmfia

tests/input_files/queens/bmfia_smc_park.yml

@@ -42,7 +42,7 @@ mf_approx:
   mean_function_type: identity_multi_fidelity
 bmfia_interface:
   type: bmfia_interface
-  num_processors_multi_processing: 4
+  num_processors_multi_processing: 2
   probabilistic_mapping_type: per_coordinate
 optimizer:
   type: adam

tests/input_files/third_party/fourc/coarse_plate_dirichlet_template.dat

@@ -11,8 +11,8 @@ created by pre_exodus
 DIM           3
 -----------------------------------------------------DISCRETISATION
 NUMSTRUCDIS                     1
---------------------------------------------------------PROBLEM TYP
-PROBLEMTYP                      Structure
+--------------------------------------------------------PROBLEM TYPE
+PROBLEMTYPE                      Structure
 RESTART                         0
 SHAPEFCT                        Polynomial
 -----------------------------------------------------------------IO
@@ -23,7 +23,7 @@ STRUCT_STRAIN                   Yes
 FILESTEPS                       1000
 ----------------------------------------------------------STRUCTURAL DYNAMIC
 LINEAR_SOLVER                   1
-DYNAMICTYP                      Statics
+DYNAMICTYPE                      Statics
 RESULTSEVRY                     1
 RESTARTEVRY                     0
 NLNSOL                          fullnewton
@@ -484,5 +484,3 @@ NODE       121 COORD -1.2500000000000000e+01 -1.2500000000000000e+01  0.00000000
 ---------------------------------------------------CELLSCATRA ELEMENTS
 ---------------------------------------------------ELECTROMAGNETIC ELEMENTS
 -------------------------------------------------------ARTERY ELEMENTS
----------------------------------------------------------------END
-// END

tests/input_files/third_party/fourc/solid_runtime_hex8.dat

@@ -2,9 +2,9 @@
 This is a simple test that tests the extrapolation of stressees from Gauss points to nodes for a
 hex8 discretization
 
-4C git SHA1: b23a601ba839ee3749c44a8d4436fb7c509f9d69
--------------------------------------------------------------------PROBLEM TYP
-PROBLEMTYP                      Structure
+tested date: 19.12.2024
+-------------------------------------------------------------------PROBLEM TYPE
+PROBLEMTYPE                      Structure
 ----------------------------------------------------------------------------IO
 OUTPUT_BIN                      yes
 STRUCT_DISP                     yes
@@ -29,7 +29,7 @@ NAME                            Structure_Solver
 SOLVER                          Superlu
 ------------------------------------------------------------STRUCTURAL DYNAMIC
 INT_STRATEGY                    Standard
-DYNAMICTYP                      Statics
+DYNAMICTYPE                      Statics
 PRESTRESSTOLDISP                1e-9
 RESULTSEVRY                     1
 RESTARTEVRY                     1
@@ -85,4 +85,3 @@ NODE 12 COORD 2.0 1.0 1.0
 ------------------------------------------------------------STRUCTURE ELEMENTS
 1 SOLID HEX8 1 5 6 2 3 7 8 4 MAT 1 KINEM nonlinear
 2 SOLID HEX8 5 9 10 6 7 11 12 8 MAT 1 KINEM nonlinear
----------------------------------------------------------------------------END

tests/integration_tests/fourc/test_fourc_mc.py

@@ -14,6 +14,8 @@
 #
 """Test 4C run."""
 
+import logging
+
 import numpy as np
 
 from queens.data_processor.data_processor_pvd import DataProcessorPvd
@@ -24,7 +26,10 @@
 from queens.models.simulation_model import SimulationModel
 from queens.parameters.parameters import Parameters
 from queens.schedulers.local_scheduler import LocalScheduler
-from queens.utils.io_utils import load_result
+from queens.utils.config_directories import experiment_directory
+from queens.utils.io_utils import load_result, read_file
+
+_logger = logging.getLogger(__name__)
 
 
 def test_fourc_mc(
@@ -59,6 +64,7 @@ def test_fourc_mc(
         input_templates=fourc_input_file_template,
         executable=fourc_executable,
         data_processor=data_processor,
+        mpi_cmd="/usr/bin/mpirun --bind-to none --use-hwthread-cpus",
     )
     model = SimulationModel(scheduler=scheduler, driver=driver)
     iterator = MonteCarloIterator(
@@ -76,7 +82,18 @@ def test_fourc_mc(
     # Load results
     results = load_result(global_settings.result_file(".pickle"))
 
-    # assert statements
-    np.testing.assert_array_almost_equal(
-        results["raw_output_data"]["result"], fourc_example_expected_output, decimal=6
-    )
+    try:
+        # assert statements
+        np.testing.assert_array_almost_equal(
+            results["raw_output_data"]["result"], fourc_example_expected_output, decimal=6
+        )
+    except (AssertionError, KeyError) as error:
+        experiment_dir = experiment_directory(global_settings.experiment_name)
+        job_dir = experiment_dir / "0"
+        _logger.info(list(job_dir.iterdir()))
+        output_dir = job_dir / "output"
+        _logger.info(list(output_dir.iterdir()))
+
+        _logger.info(read_file(output_dir / "test_fourc_mc_0.err"))
+        _logger.info(read_file(output_dir / "test_fourc_mc_0.log"))
+        raise error

tests/integration_tests/fourc/test_fourc_mc_random_field_ensight.py

@@ -14,6 +14,8 @@
 #
 """Test 4C with RF materials."""
 
+import logging
+
 import numpy as np
 import pytest
 
@@ -26,7 +28,10 @@
 from queens.parameters.fields.kl_field import KarhunenLoeveRandomField
 from queens.parameters.parameters import Parameters
 from queens.schedulers.local_scheduler import LocalScheduler
-from queens.utils.io_utils import load_result
+from queens.utils.config_directories import experiment_directory
+from queens.utils.io_utils import load_result, read_file
+
+_logger = logging.getLogger(__name__)
 
 
 class DummyKLField(KarhunenLoeveRandomField):
@@ -128,9 +133,20 @@ def test_write_random_material_to_dat(
     # Load results
     results = load_result(global_settings.result_file(".pickle"))
 
-    # Check if we got the expected results
-    np.testing.assert_array_almost_equal(results["mean"], expected_mean, decimal=8)
-    np.testing.assert_array_almost_equal(results["var"], expected_var, decimal=8)
+    try:
+        # Check if we got the expected results
+        np.testing.assert_array_almost_equal(results["mean"], expected_mean, decimal=8)
+        np.testing.assert_array_almost_equal(results["var"], expected_var, decimal=8)
+    except (AssertionError, KeyError) as error:
+        experiment_dir = experiment_directory(global_settings.experiment_name)
+        job_dir = experiment_dir / "0"
+        _logger.info(list(job_dir.iterdir()))
+        output_dir = job_dir / "output"
+        _logger.info(list(output_dir.iterdir()))
+
+        _logger.info(read_file(output_dir / "test_write_random_material_to_dat_0.err"))
+        _logger.info(read_file(output_dir / "test_write_random_material_to_dat_0.log"))
+        raise error
 
 
 @pytest.fixture(name="expected_mean")

tests/integration_tests/python/test_bmfia_park.py

@@ -74,7 +74,7 @@ def test_bmfia_smc_park(
         coordinate_labels=["x3", "x4"],
     )
     mf_interface = BmfiaInterface(
-        num_processors_multi_processing=4,
+        num_processors_multi_processing=2,
         probabilistic_mapping_type="per_coordinate",
     )
     stochastic_optimizer = Adam(
@@ -181,7 +181,7 @@ def test_bmfia_rpvi_gp_park(
         coordinate_labels=["x3", "x4"],
     )
     mf_interface = BmfiaInterface(
-        num_processors_multi_processing=4,
+        num_processors_multi_processing=2,
         probabilistic_mapping_type="per_coordinate",
     )
     stochastic_optimizer = Adam(

tests/integration_tests/python/test_constrained_gp_ip.py

@@ -79,9 +79,9 @@ def fixture_likelihood_model(parameters, global_settings):
 def fixture_expected_mean():
     """Expected mean values."""
     expected_mean = {
-        "GPMAP-I": [0.30465568, 0.52168328],
-        "CGPMAP-II": [0.29862195, 0.74123874],
-        "CFBGP": [0.29330584, 0.96121542],
+        "GPMAP-I": [0.301425, 0.653193],
+        "CGPMAP-II": [0.301557, 0.64682],
+        "CFBGP": [0.301444, 0.653865],
     }
     return expected_mean
 
@@ -90,9 +90,9 @@ def fixture_expected_mean():
 def fixture_expected_std():
     """Expected standard deviation values."""
     expected_std = {
-        "GPMAP-I": [0.00105374, 0.03230814],
-        "CGPMAP-II": [0.00197814, 0.04068283],
-        "CFBGP": [0.00156066, 0.02839873],
+        "GPMAP-I": [0.00086233, 0.02220657],
+        "CGPMAP-II": [0.00087329, 0.02323444],
+        "CFBGP": [0.001561, 0.028399],
     }
     return expected_std
 
@@ -106,15 +106,12 @@ def test_constrained_gp_ip_park(
     global_settings,
 ):
     """Test for constrained GP with IP park."""
-    num_steps = 3
+    num_steps = 4
     num_new_samples = 4
     num_initial_samples = int(num_new_samples * 2)
     quantile = 0.90
     seed = 41
 
-    if approx_type == "CFBGP":
-        num_steps = 2
-
     logpdf_gp_model = LogpdfGPModel(
         approx_type=approx_type,
         num_hyper=10,

tests/unit_tests/interfaces/test_bmfia_interface.py

@@ -194,7 +194,7 @@ def test_init():
 def test__init__():
     """Test the instantiation of the interface object."""
     instantiate_probabilistic_mappings = BmfiaInterface.instantiate_per_coordinate
-    num_processors_multi_processing = 3
+    num_processors_multi_processing = 2
     evaluate_method = BmfiaInterface.evaluate_per_coordinate
     evaluate_and_gradient_method = BmfiaInterface.evaluate_and_gradient_per_coordinate
     update_mappings_method = BmfiaInterface.update_mappings_per_coordinate
@@ -245,7 +245,7 @@ def test_build_approximation(
         return_value=dummy_plot_instance,
     )
 
-    default_bmfia_interface.num_processors_multi_processing = 3
+    default_bmfia_interface.num_processors_multi_processing = 2
 
     # Test with wrong input dimensions (2D Tensor) --> ValueError
     with pytest.raises(IndexError):
@@ -371,7 +371,7 @@ def test_train_probabilistic_mappings_in_parallel(
 
     # test with valid configuration
     num_coords = Z_LF_train.T.shape[0]
-    num_processors_multi_processing = 3
+    num_processors_multi_processing = 2
     return_state_list = BmfiaInterface.train_probabilistic_mappings_in_parallel(
         num_coords, num_processors_multi_processing, default_probabilistic_obj_lst
     )

tests/unit_tests/models/test_model.py

@@ -41,15 +41,15 @@ def fixture_model():
 def test_init(model):
     """Test init."""
     assert model.response is None
-    assert model.evaluate_and_gradient_bool is False
+    assert not model.evaluate_and_gradient_bool
 
 
 def test_evaluate_and_gradient(model):
     """Test evaluate_and_gradient method."""
-    assert model.evaluate_and_gradient_bool is False
+    assert not model.evaluate_and_gradient_bool
 
     def model_eval(self, x):
-        assert self.evaluate_and_gradient_bool is True
+        assert self.evaluate_and_gradient_bool
         return {"result": np.sum(x**2, axis=1, keepdims=True)}
 
     model.grad = Mock(
@@ -81,4 +81,4 @@ def model_eval(self, x):
             model.grad.call_args.kwargs["upstream_gradient"], upstream_[:, np.newaxis]
         )
 
-        assert model.evaluate_and_gradient_bool is False
+        assert not model.evaluate_and_gradient_bool