tests

.github/workflows/run_tests.yaml

@@ -0,0 +1,75 @@
+name: Tests with Spark
+
+on:
+  push:
+    branches:
+      - tests
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python:
+          - '3.10'
+          - '3.11'
+          - '3.12'
+        spark:
+          - 3.4.0
+
+    env:
+      ANTS_PATH: $HOME/ants-2.5.3/bin
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+
+      - uses: actions/setup-java@v4
+        with:
+          java-version: '21'
+          distribution: temurin
+
+      # https://github.com/marketplace/actions/setup-apache-spark
+      - uses: vemonet/setup-spark@v1
+        with:
+          spark-version: ${{ matrix.spark }}
+          hadoop-version: '3'
+
+      - run: spark-submit --version
+
+      # Download and install ANTs
+      - name: Install ANTs
+        run: |
+          wget https://github.com/ANTsX/ANTs/releases/download/v2.5.3/ants-2.5.3-ubuntu-20.04-X64-gcc.zip
+          unzip ants-2.5.3-ubuntu-20.04-X64-gcc.zip -d $HOME/
+          rm ants-2.5.3-ubuntu-20.04-X64-gcc.zip
+          echo "ANTs installed successfully"
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r tests/requirements.txt --no-cache-dir
+
+      - name: Install voluseg
+        run: |
+          pip install . --no-cache-dir
+
+      - name: Run tests with pytest
+        run: |
+          pytest --cov=voluseg --cov-report=term-missing
+
+      - name: Upload coverage report
+        if: success()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-report
+          path: htmlcov/

app/app.py

@@ -5,16 +5,16 @@
 
 # set and save parameters
 parameters0 = voluseg.parameter_dictionary()
-parameters0['dir_ants'] = '/ants-2.5.3/bin/'
-parameters0['dir_input'] = '/voluseg/data/'
-parameters0['dir_output'] = '/voluseg/output/'
-parameters0['registration'] = 'high'
-parameters0['diam_cell'] = 5.0
-parameters0['f_volume'] = 2.0
+parameters0["dir_ants"] = "/ants-2.5.3/bin/"
+parameters0["dir_input"] = "/voluseg/data/"
+parameters0["dir_output"] = "/voluseg/output/"
+parameters0["registration"] = "high"
+parameters0["diam_cell"] = 5.0
+parameters0["f_volume"] = 2.0
 voluseg.step0_process_parameters(parameters0)
 
 # load and print parameters
-filename_parameters = os.path.join(parameters0['dir_output'], 'parameters.pickle')
+filename_parameters = os.path.join(parameters0["dir_output"], "parameters.pickle")
 parameters = voluseg.load_parameters(filename_parameters)
 pprint.pprint(parameters)
 
@@ -31,4 +31,4 @@
 voluseg.step4_detect_cells(parameters)
 
 print("clean cells.")
-voluseg.step5_clean_cells(parameters)
+voluseg.step5_clean_cells(parameters)

tests/README.md

@@ -0,0 +1,7 @@
+# Tests
+
+Run tests locally with `pytest`:
+
+```bash
+pytest -s
+```

tests/requirements.txt

@@ -0,0 +1,2 @@
+pytest==8.3.2
+pytest-cov==5.0.0

tests/test_voluseg.py

@@ -0,0 +1,97 @@
+import os
+import pprint
+import voluseg
+import pytest
+from pathlib import Path
+
+from voluseg._tools import download_sample_data
+
+
+@pytest.fixture
+def setup_parameters(tmp_path):
+    # Define parameters and paths
+    parameters = voluseg.parameter_dictionary()
+
+    # Download sample data, only if running in GitHub Actions
+    if os.environ.get("GITHUB_ACTIONS") == "true":
+        data_path = download_sample_data()
+    else:
+        data_path = "/change_path_to/sample_data"
+    parameters["dir_input"] = data_path
+    parameters["dir_ants"] = os.environ.get("ANTS_PATH")
+    parameters["dir_output"] = str(tmp_path)  # Use pytest's tmp_path fixture for output
+    parameters["registration"] = "high"
+    parameters["diam_cell"] = 5.0
+    parameters["f_volume"] = 2.0
+
+    # Save parameters
+    voluseg.step0_process_parameters(parameters)
+
+    # Return parameters for further use in tests
+    return parameters
+
+
+def test_load_parameters(setup_parameters):
+    # Load parameters
+    file_path = str(Path(setup_parameters["dir_output"] / "parameters.pickle"))
+    file_parameters = voluseg.load_parameters(file_path)
+
+    all_keys = set(setup_parameters.keys()).union(set(file_parameters.keys()))
+
+    for key in all_keys:
+        assert key in setup_parameters, f"Key '{key}' is missing in setup_parameters"
+        assert key in file_parameters, f"Key '{key}' is missing in file_parameters"
+        if key in setup_parameters and key in file_parameters:
+            assert (
+                setup_parameters[key] == file_parameters[key]
+            ), f"Value differs for key '{key}': setup_parameters has {setup_parameters[key]}, file_parameters has {file_parameters[key]}"
+
+
+def test_voluseg_pipeline_h5_dir(setup_parameters):
+
+    # Test step 1 - process volumes
+    print("Process volumes.")
+    voluseg.step1_process_volumes(setup_parameters)
+    n_files_input = len([p for p in Path(setup_parameters["dir_input"]).glob("*.h5")])
+    n_files_output = len(
+        [
+            p
+            for p in (Path(setup_parameters["dir_output"]) / "volumes/0/").glob(
+                "*.nii.gz"
+            )
+        ]
+    )
+    assert (
+        n_files_input == n_files_output
+    ), f"Number of input files ({n_files_input}) does not match number of output files ({n_files_output})"
+
+    # Test step 2 - align volumes
+    print("Align volumes.")
+    voluseg.step2_align_volumes(setup_parameters)
+    n_files_transform = len(
+        [
+            p
+            for p in (Path(setup_parameters["dir_output"]) / "transforms/0/").glob(
+                "*.mat"
+            )
+        ]
+    )
+    assert (
+        n_files_output == n_files_transform
+    ), f"Number of output files ({n_files_output}) does not match number of transform files ({n_files_transform})"
+
+    # Test step 3 - mask volumes
+    print("Mask volumes.")
+    voluseg.step3_mask_volumes(setup_parameters)
+    assert (
+        Path(setup_parameters["dir_output"]) / "masks_plots/0/histogram.png"
+    ).exists(), "Histogram plot does not exist"
+    assert (
+        Path(setup_parameters["dir_output"]) / "masks_plots/0/mask_z000.png"
+    ).exists(), "Mask plot does not exist"
+
+    # print("Detect cells.")
+    # voluseg.step4_detect_cells(setup_parameters)
+
+    # print("Clean cells.")
+    # voluseg.step5_clean_cells(setup_parameters)

voluseg/_tools/sample_data.py

@@ -2,9 +2,10 @@
 import zipfile
 import os
 from pathlib import Path
+from typing import Union
 
 
-def download_sample_data(destination_folder: str = ".") -> None:
+def download_sample_data(destination_folder: str = ".") -> Union[str, None]:
     """
     Download sample data for Voluseg.
 
@@ -16,7 +17,8 @@ def download_sample_data(destination_folder: str = ".") -> None:
 
     Returns
     -------
-    None
+    str or None
+        Path to the folder where the data was extracted, or None if the download failed.
     """
     # Download the ZIP file
     download_url = "https://drive.usercontent.google.com/download"
@@ -47,6 +49,7 @@ def download_sample_data(destination_folder: str = ".") -> None:
         # Remove the ZIP file
         os.remove(filename)
         print(f"Removed the ZIP file: {filename}")
-
+        return extract_folder
     else:
         print(f"Failed to download file. Status code: {response.status_code}")
+        return None