Pixibuild

.github/workflows/build_and_test.yaml

@@ -84,13 +84,8 @@ jobs:
       # ────────────────────────────────────────────────────────────────
       # Pytest checks
       # ────────────────────────────────────────────────────────────────
-      - name: Install Pixi Python deps
-        run: |
-          pixi --version
-          pixi install
-
       - name: Run pytest checks on HDF5 output
-        run: pixi run pytest
+        run: pixi run -e dashboard pytest
 
       - uses: actions/upload-artifact@v4
         if: failure()

.github/workflows/build_and_test_mac.yaml

@@ -88,13 +88,8 @@ jobs:
       # ────────────────────────────────────────────────────────────────
       # Pytest checks
       # ────────────────────────────────────────────────────────────────
-      - name: Install Pixi Python deps
-        run: |
-          pixi --version
-          pixi install
-
       - name: Run pytest checks on HDF5 output
-        run: pixi run pytest
+        run: pixi run -e dashboard pytest
 
       - uses: actions/upload-artifact@v4
         if: failure()

.github/workflows/pixi_build.yaml

@@ -14,12 +14,10 @@ jobs:
   build:
     name: ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
-    env:
-      FANS_BUILD_DIR: build
     strategy:
       fail-fast: false
       matrix:
-        os: [macos-latest, ubuntu-latest]
+        os: [ubuntu-latest]
     steps:
       - name: Checkout code
         uses: actions/checkout@v5
@@ -32,6 +30,12 @@ jobs:
       - name: Run pytest checks on HDF5 output
         run: pixi run test
 
+      - name: Upload test logs
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-logs
+          path: test/*.log
+
       - uses: actions/upload-artifact@v4
         if: failure()
         with:

.gitignore

@@ -210,3 +210,4 @@ test/input_files/**/*.json
 # pixi environments
 .pixi
 *.egg-info
+*.conda

CHANGELOG.md

@@ -2,6 +2,8 @@
 
 ## latest
 
+- Introduce pixi build workflow and conftest.py for pytest-fixture [#82](https://github.com/DataAnalyticsEngineering/FANS/pull/82)
+- Use dashboard environment for regular pytest [#81](https://github.com/DataAnalyticsEngineering/FANS/pull/81)
 - Fix bug in J2 plasticity routine [#80](https://github.com/DataAnalyticsEngineering/FANS/pull/80)
 
 ## v0.4.2

pixi.toml

@@ -2,6 +2,10 @@
 channels = ["conda-forge"]
 name = "FANS"
 platforms = ["linux-64", "osx-64", "osx-arm64"]
+preview = ["pixi-build"]
+
+[dependencies]
+fans = { path = "." }
 
 [feature.dashboard.dependencies]
 python = ">=3.13.5,<3.14"
@@ -23,10 +27,44 @@ precommit = "pre-commit run --all-files"
 h52xdmf = { args = ["file"], cmd = "cd \"$INIT_CWD\" && python -m fans_dashboard.plotting.h52xdmf -t -v {{file}}" }
 
 [tasks]
-test = {depends-on = [
-  { task = "pytest", environment = "dashboard" }, # Will be changed later with pixi-build
-]}
+test = { cmd = "pytest -v -s --from-pixi", cwd = "test/pytest", depends-on = ["test-fans"] }
+test-fans = { cmd = "./run_tests.sh -n {{n}}", args = [
+  { arg = "n", default = "2" }, # Number of threads
+], cwd = "test" }
 
 [environments]
 default = {features = ["dashboard"]}
 dashboard = { features = ["dashboard"], no-default-feature = true }
+
+################## Pixi build part
+
+[package]
+name = "fans"
+version = "0.4.2"
+
+[package.build]
+backend = { name = "pixi-build-cmake", version = "0.3.*" }
+
+[package.build.config]
+extra-args = [
+    "-DFANS_LIBRARY_FOR_MICRO_MANAGER=ON",
+    ]
+
+[workspace.target.osx-arm64.build-variants]
+cxx_compiler_version = ["18"]
+
+[workspace.target.linux-64.build-variants]
+cxx_compiler = ["clangxx"]
+cxx_compiler_version = ["18"]
+
+[package.build-dependencies]
+cmake = "==4.0.3"
+pybind11 = "*"
+pkg-config = "*"
+ninja = "1.13.*"
+
+[package.host-dependencies]
+hdf5 = { version = "*", build = "* mpi_openmpi*" }
+fftw = { version = "*", build = "* mpi_openmpi*" } # works
+openmpi-mpicxx = "*"
+eigen = "*"

test/README.md

@@ -31,7 +31,7 @@ This will run all test cases and generate result files in `build/test/`.
 After running the tests, the results are verified using pytest. We recommend running pytest via a pre-configured Pixi task,
 
 ```bash
-pixi run pytest
+pixi run -e dashboard pytest
 ```
 
 Note: The validation tests expect result files to be in `build/test/` directory, so make sure to run the tests first.

test/pytest/conftest.py

@@ -0,0 +1,43 @@
+import pytest
+import os
+
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--from-pixi",
+        action="store_true",
+        default=False,
+        help="Run tests from pixi task.",
+    )
+
+
+@pytest.fixture(
+    params=[
+        "test_J2Plasticity",
+        "test_LinearElastic",
+        "test_LinearThermal",
+        "test_PseudoPlastic",
+    ]
+)
+def test_files(request):
+    json_base_dir = os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "../input_files/"
+    )
+    # Determine the HDF5 base directory based on the --from-pixi option
+    # if run from pixi, use output directory; otherwise, use build/test directory, as it is the one used by ctest
+    if request.config.getoption("--from-pixi"):
+        h5_base_dir = os.path.join(
+            os.path.dirname(os.path.abspath(__file__)), "../output"
+        )
+    else:
+        h5_base_dir = os.path.join(
+            os.path.dirname(os.path.abspath(__file__)), "../../build/test/"
+        )
+
+    json_path = os.path.join(json_base_dir, f"{request.param}.json")
+    h5_path = os.path.join(h5_base_dir, f"{request.param}.h5")
+
+    if os.path.exists(json_path) and os.path.exists(h5_path):
+        return json_path, h5_path
+
+    assert False, f"Required test files not found: {json_path} or {h5_path}"

test/pytest/test_displacement_averaging.py

@@ -5,30 +5,6 @@
 from fans_dashboard.core.utils import identify_hierarchy, extract_and_organize_data
 
 
-@pytest.fixture(
-    params=[
-        "test_J2Plasticity",
-        "test_LinearElastic",
-        "test_LinearThermal",
-        "test_PseudoPlastic",
-    ]
-)
-def test_files(request):
-    json_base_dir = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), "../input_files/"
-    )
-    h5_base_dir = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), "../../build/test/"
-    )
-
-    json_path = os.path.join(json_base_dir, f"{request.param}.json")
-    h5_path = os.path.join(h5_base_dir, f"{request.param}.h5")
-
-    if os.path.exists(json_path) and os.path.exists(h5_path):
-        return json_path, h5_path
-    pytest.skip(f"Required test files not found: {json_path} or {h5_path}")
-
-
 def test_displacement_averaging(test_files):
     """
     This test verifies that the average of displacement fluctuations is zero for all

test/pytest/test_homogenization_consistency.py

@@ -5,30 +5,6 @@
 from fans_dashboard.core.utils import identify_hierarchy, extract_and_organize_data
 
 
-@pytest.fixture(
-    params=[
-        "test_J2Plasticity",
-        "test_LinearElastic",
-        "test_LinearThermal",
-        "test_PseudoPlastic",
-    ]
-)
-def test_files(request):
-    json_base_dir = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), "../input_files/"
-    )
-    h5_base_dir = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), "../../build/test/"
-    )
-
-    json_path = os.path.join(json_base_dir, f"{request.param}.json")
-    h5_path = os.path.join(h5_base_dir, f"{request.param}.h5")
-
-    if os.path.exists(json_path) and os.path.exists(h5_path):
-        return json_path, h5_path
-    pytest.skip(f"Required test files not found: {json_path} or {h5_path}")
-
-
 def test_homogenization_consistency(test_files):
     """
     This test verifies that the relationship stress_average = homogenized_tangent * strain_average

test/pytest/test_homogenized_tangent_spd.py

@@ -6,30 +6,6 @@
 from scipy.linalg import eigvalsh
 
 
-@pytest.fixture(
-    params=[
-        "test_J2Plasticity",
-        "test_LinearElastic",
-        "test_LinearThermal",
-        "test_PseudoPlastic",
-    ]
-)
-def test_files(request):
-    json_base_dir = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), "../input_files/"
-    )
-    h5_base_dir = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), "../../build/test/"
-    )
-
-    json_path = os.path.join(json_base_dir, f"{request.param}.json")
-    h5_path = os.path.join(h5_base_dir, f"{request.param}.h5")
-
-    if os.path.exists(json_path) and os.path.exists(h5_path):
-        return json_path, h5_path
-    pytest.skip(f"Required test files not found: {json_path} or {h5_path}")
-
-
 def test_homogenized_tangent_spd(test_files):
     """
     This test verifies that the homogenized tangent is strictly Symmetric Positive Definite (SPD)

test/pytest/test_homogenized_tangent_within_VRbounds.py

@@ -11,30 +11,6 @@
 )
 
 
-@pytest.fixture(
-    params=[
-        "test_J2Plasticity",
-        "test_LinearElastic",
-        "test_LinearThermal",
-        "test_PseudoPlastic",
-    ]
-)
-def test_files(request):
-    json_base_dir = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), "../input_files/"
-    )
-    h5_base_dir = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), "../../build/test/"
-    )
-
-    json_path = os.path.join(json_base_dir, f"{request.param}.json")
-    h5_path = os.path.join(h5_base_dir, f"{request.param}.h5")
-
-    if os.path.exists(json_path) and os.path.exists(h5_path):
-        return json_path, h5_path
-    pytest.skip(f"Required test files not found: {json_path} or {h5_path}")
-
-
 def test_homogenized_tangent_within_VRbounds(test_files):
     """
     This test verifies that the homogenized tangent is within Voigt and Reuss bounds

test/pytest/test_loading_to_strain_average.py

@@ -5,30 +5,6 @@
 from fans_dashboard.core.utils import identify_hierarchy, extract_and_organize_data
 
 
-@pytest.fixture(
-    params=[
-        "test_J2Plasticity",
-        "test_LinearElastic",
-        "test_LinearThermal",
-        "test_PseudoPlastic",
-    ]
-)
-def test_files(request):
-    json_base_dir = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), "../input_files/"
-    )
-    h5_base_dir = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), "../../build/test/"
-    )
-
-    json_path = os.path.join(json_base_dir, f"{request.param}.json")
-    h5_path = os.path.join(h5_base_dir, f"{request.param}.h5")
-
-    if os.path.exists(json_path) and os.path.exists(h5_path):
-        return json_path, h5_path
-    pytest.skip(f"Required test files not found: {json_path} or {h5_path}")
-
-
 def test_loading_to_strain_average(test_files):
     """
     This test verifies that the strain_average field in the results matches the macroscale_loading

test/pytest/test_strain_stress_averaging.py

@@ -5,30 +5,6 @@
 from fans_dashboard.core.utils import identify_hierarchy, extract_and_organize_data
 
 
-@pytest.fixture(
-    params=[
-        "test_J2Plasticity",
-        "test_LinearElastic",
-        "test_LinearThermal",
-        "test_PseudoPlastic",
-    ]
-)
-def test_files(request):
-    json_base_dir = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), "../input_files/"
-    )
-    h5_base_dir = os.path.join(
-        os.path.dirname(os.path.abspath(__file__)), "../../build/test/"
-    )
-
-    json_path = os.path.join(json_base_dir, f"{request.param}.json")
-    h5_path = os.path.join(h5_base_dir, f"{request.param}.h5")
-
-    if os.path.exists(json_path) and os.path.exists(h5_path):
-        return json_path, h5_path
-    pytest.skip(f"Required test files not found: {json_path} or {h5_path}")
-
-
 def test_strain_stress_averaging(test_files):
     """
     This test verifies that the average of strain/stress fields matches the strain_average/stress_average

test/run_tests.sh

@@ -8,16 +8,25 @@ fi
 
 num_processes=$2
 
+# Select executable depending on whether we're inside a conda/pixi env
+if [ -n "$CONDA_PREFIX" ]; then
+    FANS_EXEC="$CONDA_PREFIX/bin/FANS"
+else
+    FANS_EXEC="./FANS"
+fi
+
 TIME_CMD="command time -v"
 [[ "$OSTYPE" == "darwin"* ]] && TIME_CMD="command gtime -v"
 
+mkdir -p output
+
 # Run the jobs serially
-$TIME_CMD mpiexec -n $num_processes ./FANS input_files/test_LinearThermal.json test_LinearThermal.h5 > test_LinearThermal.log 2>&1
+$TIME_CMD mpiexec -n $num_processes "$FANS_EXEC" input_files/test_LinearThermal.json output/test_LinearThermal.h5 > test_LinearThermal.log 2>&1
 
-$TIME_CMD mpiexec -n $num_processes ./FANS input_files/test_LinearElastic.json test_LinearElastic.h5 > test_LinearElastic.log 2>&1
+$TIME_CMD mpiexec -n $num_processes "$FANS_EXEC" input_files/test_LinearElastic.json output/test_LinearElastic.h5 > test_LinearElastic.log 2>&1
 
-$TIME_CMD mpiexec -n $num_processes ./FANS input_files/test_PseudoPlastic.json test_PseudoPlastic.h5 > test_PseudoPlastic.log 2>&1
+$TIME_CMD mpiexec -n $num_processes "$FANS_EXEC" input_files/test_PseudoPlastic.json output/test_PseudoPlastic.h5 > test_PseudoPlastic.log 2>&1
 
-$TIME_CMD mpiexec -n $num_processes ./FANS input_files/test_J2Plasticity.json test_J2Plasticity.h5 > test_J2Plasticity.log 2>&1
+$TIME_CMD mpiexec -n $num_processes "$FANS_EXEC" input_files/test_J2Plasticity.json output/test_J2Plasticity.h5 > test_J2Plasticity.log 2>&1
 
-$TIME_CMD mpiexec -n $num_processes ./FANS input_files/test_MixedBCs.json test_MixedBCs.h5 > test_MixedBCs.log 2>&1
+$TIME_CMD mpiexec -n $num_processes "$FANS_EXEC" input_files/test_MixedBCs.json output/test_MixedBCs.h5 > test_MixedBCs.log 2>&1