adding cpu only test Github job

.github/workflows/iris.yml → .github/workflows/tests_httomo.yml

@@ -1,6 +1,7 @@
-name: Tests on IRIS
+name: HTTomo tests
 
 on:
+  workflow_dispatch:
   pull_request:
     branches:
       - main
@@ -9,48 +10,46 @@ on:
       - main
 
 jobs:
-  iris-gpu:
-    runs-on: iris-gpu
-    container:
-      image: nvidia/cuda:12.6.3-devel-ubi8
-      env:
-        NVIDIA_VISIBLE_DEVICES: ${{ env.NVIDIA_VISIBLE_DEVICES }}
-
+  tests-linux:
+    runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
-
     steps:
       - name: Checkout repository code
         uses: actions/checkout@v4
 
       - name: Create conda environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-name: httomo
           create-args: >-
-            cupy==12.3.0
+            python==3.12
+            numpy==2.4
             h5py=*=*mpi_openmpi*
             mpi4py
-            tomopy==1.15
+            tomopy==1.15.3
           post-cleanup: 'all'
           init-shell: bash
 
       - name: Install httomo libraries and httomo
         run: |
           micromamba activate httomo
-          pip install .[dev-gpu]
+          python -m pip install --no-deps pytest pytest-cov
+          python -m pip install --no-deps tomobar
+          python -m pip install --no-deps httomolibgpu
+          python -m pip install --no-deps httomolib
+          python -m pip install --no-deps httomo-backends          
+          pip install . --no-deps
           micromamba list
 
       - name: Generate full yaml pipelines using pipeline directives
         run: |
-          pip install "ruamel.yaml>0.18.0"
+          python -m pip install pyyaml pluggy Pygments iniconfig loguru tqdm graypy hdf5plugin pytest_mock plumbum click
+          python -m pip install aiofiles pillow
+          python -m pip install "ruamel.yaml>0.18.0"
           python ./docs/source/scripts/execute_pipelines_build.py -o ./docs/source/pipelines_full/
 
       - name: Run HTTomo framework tests
         run: |
-          pytest tests/
-
-      - name: Run HTTomo pipelines tests (small data)
-        run: |
-          pytest tests/test_pipeline_small.py --small_data
+          pytest tests/

tests/conftest.py

@@ -46,6 +46,12 @@ def pytest_addoption(parser):
         default=False,
         help="run performance tests only",
     )
+    parser.addoption(
+        "--cupy",
+        action="store_true",
+        default=False,
+        help="run cupy involved tests",
+    )
     parser.addoption(
         "--small_data",
         action="store_true",
@@ -79,6 +85,16 @@ def pytest_collection_modifyitems(config, items):
         for item in items:
             if "perf" in item.keywords:
                 item.add_marker(skip_perf)
+    if config.getoption("--cupy"):
+        skip_other = pytest.mark.skip(reason="not a CuPy test")
+        for item in items:
+            if "cupy" not in item.keywords:
+                item.add_marker(skip_other)
+    else:
+        skip_perf = pytest.mark.skip(reason="cupy test - use '--cupy' to run")
+        for item in items:
+            if "cupy" in item.keywords:
+                item.add_marker(skip_perf)
     if config.getoption("--small_data"):
         skip_other = pytest.mark.skip(reason="not a pipeline small data test")
         for item in items:
@@ -160,21 +176,6 @@ def test_data_path():
     return os.path.join(CUR_DIR, "test_data")
 
 
-@pytest.fixture
-def ensure_clean_memory():
-    import cupy as cp
-
-    cp.get_default_memory_pool().free_all_blocks()
-    cp.get_default_pinned_memory_pool().free_all_blocks()
-    cache = cp.fft.config.get_plan_cache()
-    cache.clear()
-    yield None
-    cp.get_default_memory_pool().free_all_blocks()
-    cp.get_default_pinned_memory_pool().free_all_blocks()
-    cache = cp.fft.config.get_plan_cache()
-    cache.clear()
-
-
 @pytest.fixture
 def standard_data_path():
     return "/entry1/tomo_entry/data/data"

tests/method_wrappers/test_dezinging.py

@@ -97,7 +97,7 @@ def remove_outlier(x, axis="auto"):
 
 
 @pytest.mark.cupy
-def test_dezinging_no_pool_memory_leak(mocker: MockerFixture, ensure_clean_memory):
+def test_dezinging_no_pool_memory_leak(mocker: MockerFixture):
     class FakeModule:
         def remove_outlier(x, axis="auto"):
             # Needs more memory than the return size

tests/method_wrappers/test_save_intermediate.py

@@ -253,7 +253,7 @@ def save_intermediate_data(
     # Create intermediate data wrapper
     mocker.patch.object(httomo.globals, "run_out_dir", tmp_path)
     wrp = make_method_wrapper(
-        make_mock_repo(mocker, implementation="gpu_cupy"),
+        make_mock_repo(mocker, implementation="cpu"),
         "httomo.methods",
         "save_intermediate_data",
         MPI.COMM_WORLD,

tests/runner/test_gpu_utils.py

@@ -26,6 +26,7 @@ def test_get_available_memory_cpu(mocker: MockerFixture):
     assert get_available_gpu_memory() > 10e9
 
 
+@pytest.mark.cupy
 @pytest.mark.parametrize(
     "nodes, gpus_per_node, global_rank, local_rank",
     [

tests/sweep_runner/test_param_sweep_runner.py

@@ -107,6 +107,7 @@ def test_after_prepare_block_attr_contains_data(mocker: MockerFixture):
     np.testing.assert_array_equal(runner.block.data, data)
 
 
+@pytest.mark.cupy
 def tests_preview_modifier_paganin(mocker: MockerFixture):
     SINO_SLICES = 100
     GLOBAL_SHAPE = PREVIEWED_SLICES_SHAPE = (1800, SINO_SLICES, 160)

tests/test_ui_layer.py

@@ -139,7 +139,7 @@ def test_build_pipeline_from_json(standard_data: str):
     },
     {
         "method": "find_center_vo",
-        "module_path": "httomolibgpu.recon.rotation",
+        "module_path": "tomopy.recon.rotation",
         "parameters": {
             "ind": "mid",
             "smin": -50,
@@ -155,8 +155,8 @@ def test_build_pipeline_from_json(standard_data: str):
         }
     },
     {
-        "method": "FBP3d_tomobar",
-        "module_path": "httomolibgpu.recon.algorithm",
+        "method": "recon",
+        "module_path": "tomopy.recon.algorithm",
         "parameters": {
             "center": "${{centering.side_outputs.centre_of_rotation}}",
             "filter_freq_cutoff": 0.6,