Merge pull request #74 from Matthew-Jennings/mj-implement-pytest-tmppath

Thanks for proposing the changes. I am merging these into the dev2.2.1 branch instead of the master branch.

.coveragerc

@@ -0,0 +1,3 @@
+[run]
+concurrency = multiprocessing
+parallel = true

test/basic_test.py

@@ -124,15 +124,11 @@ def run_experiment(image, roi, **kwargs):
     return data
 
 
-def test_xml_configurations():
+def test_xml_configurations(tmp_path):
     # Read the data settings xml file, and update path to image and mask.
     from xml.etree import ElementTree as ElemTree
     from mirp.extract_features_and_images import extract_features
 
-    # Remove temporary data xml file if it exists.
-    if os.path.exists(os.path.join(CURRENT_DIR, "data", "configuration_files", "temp_test_config_data.xml")):
-        os.remove(os.path.join(CURRENT_DIR, "data", "configuration_files", "temp_test_config_data.xml"))
-
     # Load xml.
     tree = ElemTree.parse(os.path.join(CURRENT_DIR, "data", "configuration_files", "test_config_data.xml"))
     paths_branch = tree.getroot()
@@ -144,12 +140,12 @@ def test_xml_configurations():
         mask.text = str(os.path.join(CURRENT_DIR, "data", "sts_images"))
 
     # Save as temporary xml file.
-    tree.write(os.path.join(CURRENT_DIR, "data", "configuration_files", "temp_test_config_data.xml"))
+    tree.write(tmp_path / "temp_test_config_data.xml")
 
     data = extract_features(
         write_features=False,
         export_features=True,
-        image=os.path.join(CURRENT_DIR, "data", "configuration_files", "temp_test_config_data.xml"),
+        image=str(tmp_path / "temp_test_config_data.xml"),
         settings=os.path.join(CURRENT_DIR, "data", "configuration_files", "test_config_settings.xml")
     )
 
@@ -162,9 +158,6 @@ def test_xml_configurations():
     assert all(data["image_voxel_size_y"].values == 3.0)
     assert all(data["image_voxel_size_z"].values == 3.0)
 
-    # Clean up
-    os.remove(os.path.join(CURRENT_DIR, "data", "configuration_files", "temp_test_config_data.xml"))
-
 
 def test_edge_cases_basic_pipeline():
     """

test/configuration_test.py

@@ -16,19 +16,16 @@ def _type_converter(type_str: str):
         raise ValueError(f"type could not be linked to an object type: {type_str}")
 
 
-def test_general_settings_configuration():
+def test_general_settings_configuration(tmp_path):
     from xml.etree import ElementTree as ElemTree
     from mirp import get_settings_xml
     from mirp.settings.general_parameters import get_general_settings
     from mirp.settings.import_config_parameters import create_settings_object
     from mirp.settings.generic import SettingsClass
 
-    temp_file = os.path.join(CURRENT_DIR, "data", "configuration_files", "settings.xml")
+    temp_file = tmp_path / "settings.xml"
 
-    # Remove temporary data xml file if it exists.
-    if os.path.exists(temp_file):
-        os.remove(temp_file)
-    get_settings_xml(os.path.join(CURRENT_DIR, "data", "configuration_files"))
+    get_settings_xml(tmp_path)
 
     settings_definitions = get_general_settings()
 
@@ -80,23 +77,17 @@ def test_general_settings_configuration():
         assert getattr(settings_keyword.general, class_key) == test_value
         assert isinstance(test_value, value_type)
 
-    if os.path.exists(temp_file):
-        os.remove(temp_file)
 
-
-def test_post_processing_settings_configuration():
+def test_post_processing_settings_configuration(tmp_path):
     from xml.etree import ElementTree as ElemTree
     from mirp import get_settings_xml
     from mirp.settings.image_processing_parameters import get_post_processing_settings
     from mirp.settings.import_config_parameters import create_settings_object
     from mirp.settings.generic import SettingsClass
 
-    temp_file = os.path.join(CURRENT_DIR, "data", "configuration_files", "settings.xml")
+    temp_file = tmp_path / "settings.xml"
 
-    # Remove temporary data xml file if it exists.
-    if os.path.exists(temp_file):
-        os.remove(temp_file)
-    get_settings_xml(os.path.join(CURRENT_DIR, "data", "configuration_files"))
+    get_settings_xml(tmp_path)
 
     settings_definitions = get_post_processing_settings()
 
@@ -157,23 +148,17 @@ def test_post_processing_settings_configuration():
             assert getattr(settings_keyword.post_process, class_key) == test_value
             assert isinstance(test_value, value_type)
 
-    if os.path.exists(temp_file):
-        os.remove(temp_file)
-
 
-def test_interpolation_settings_configuration():
+def test_interpolation_settings_configuration(tmp_path):
     from xml.etree import ElementTree as ElemTree
     from mirp import get_settings_xml
     from mirp.settings.interpolation_parameters import get_image_interpolation_settings, get_mask_interpolation_settings
     from mirp.settings.import_config_parameters import create_settings_object
     from mirp.settings.generic import SettingsClass
 
-    temp_file = os.path.join(CURRENT_DIR, "data", "configuration_files", "settings.xml")
+    temp_file = tmp_path / "settings.xml"
 
-    # Remove temporary data xml file if it exists.
-    if os.path.exists(temp_file):
-        os.remove(temp_file)
-    get_settings_xml(os.path.join(CURRENT_DIR, "data", "configuration_files"))
+    get_settings_xml(tmp_path)
 
     # All default settings.
     tree = ElemTree.parse(temp_file)
@@ -270,23 +255,17 @@ def test_interpolation_settings_configuration():
             assert getattr(settings_keyword.roi_interpolate, class_key) == test_value
             assert isinstance(test_value, value_type)
 
-    if os.path.exists(temp_file):
-        os.remove(temp_file)
 
-
-def test_perturbation_settings_configuration():
+def test_perturbation_settings_configuration(tmp_path):
     from xml.etree import ElementTree as ElemTree
     from mirp import get_settings_xml
     from mirp.settings.perturbation_parameters import get_perturbation_settings
     from mirp.settings.import_config_parameters import create_settings_object
     from mirp.settings.generic import SettingsClass
 
-    temp_file = os.path.join(CURRENT_DIR, "data", "configuration_files", "settings.xml")
+    temp_file = tmp_path / "settings.xml"
 
-    # Remove temporary data xml file if it exists.
-    if os.path.exists(temp_file):
-        os.remove(temp_file)
-    get_settings_xml(os.path.join(CURRENT_DIR, "data", "configuration_files"))
+    get_settings_xml(tmp_path)
 
     settings_definitions = get_perturbation_settings()
 
@@ -347,23 +326,17 @@ def test_perturbation_settings_configuration():
             assert getattr(settings_keyword.perturbation, class_key) == test_value
             assert isinstance(test_value, value_type)
 
-    if os.path.exists(temp_file):
-        os.remove(temp_file)
-
 
-def test_mask_resegmentation_settings_configuration():
+def test_mask_resegmentation_settings_configuration(tmp_path):
     from xml.etree import ElementTree as ElemTree
     from mirp import get_settings_xml
     from mirp.settings.resegmentation_parameters import get_mask_resegmentation_settings
     from mirp.settings.import_config_parameters import create_settings_object
     from mirp.settings.generic import SettingsClass
 
-    temp_file = os.path.join(CURRENT_DIR, "data", "configuration_files", "settings.xml")
+    temp_file = tmp_path / "settings.xml"
 
-    # Remove temporary data xml file if it exists.
-    if os.path.exists(temp_file):
-        os.remove(temp_file)
-    get_settings_xml(os.path.join(CURRENT_DIR, "data", "configuration_files"))
+    get_settings_xml(tmp_path)
 
     settings_definitions = get_mask_resegmentation_settings()
 
@@ -424,23 +397,17 @@ def test_mask_resegmentation_settings_configuration():
             assert getattr(settings_keyword.roi_resegment, class_key) == test_value
             assert isinstance(test_value, value_type)
 
-    if os.path.exists(temp_file):
-        os.remove(temp_file)
 
-
-def test_feature_extraction_settings_configuration():
+def test_feature_extraction_settings_configuration(tmp_path):
     from xml.etree import ElementTree as ElemTree
     from mirp import get_settings_xml
     from mirp.settings.feature_parameters import get_feature_extraction_settings
     from mirp.settings.import_config_parameters import create_settings_object
     from mirp.settings.generic import SettingsClass
 
-    temp_file = os.path.join(CURRENT_DIR, "data", "configuration_files", "settings.xml")
+    temp_file = tmp_path / "settings.xml"
 
-    # Remove temporary data xml file if it exists.
-    if os.path.exists(temp_file):
-        os.remove(temp_file)
-    get_settings_xml(os.path.join(CURRENT_DIR, "data", "configuration_files"))
+    get_settings_xml(tmp_path)
 
     settings_definitions = get_feature_extraction_settings()
 
@@ -504,23 +471,17 @@ def test_feature_extraction_settings_configuration():
             assert getattr(settings_keyword.feature_extr, class_key) == test_value
             assert isinstance(test_value, value_type)
 
-    if os.path.exists(temp_file):
-        os.remove(temp_file)
-
 
-def test_image_transformation_settings_configuration():
+def test_image_transformation_settings_configuration(tmp_path):
     from xml.etree import ElementTree as ElemTree
     from mirp import get_settings_xml
     from mirp.settings.transformation_parameters import get_image_transformation_settings
     from mirp.settings.import_config_parameters import create_settings_object
     from mirp.settings.generic import SettingsClass
 
-    temp_file = os.path.join(CURRENT_DIR, "data", "configuration_files", "settings.xml")
+    temp_file = tmp_path / "settings.xml"
 
-    # Remove temporary data xml file if it exists.
-    if os.path.exists(temp_file):
-        os.remove(temp_file)
-    get_settings_xml(os.path.join(CURRENT_DIR, "data", "configuration_files"))
+    get_settings_xml(tmp_path)
 
     settings_definitions = get_image_transformation_settings()
 
@@ -597,6 +558,3 @@ def test_image_transformation_settings_configuration():
         else:
             assert getattr(settings_keyword.img_transform, class_key) == test_value
             assert isinstance(test_value, value_type)
-
-    if os.path.exists(temp_file):
-        os.remove(temp_file)

test/export_image_and_mask_test.py

@@ -6,37 +6,28 @@
 CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
 
 
-def test_basic_ct_feature_extraction():
-    import shutil
-
-    write_dir = os.path.join(CURRENT_DIR, "data", "temp_data")
-    if os.path.exists(write_dir):
-        shutil.rmtree(write_dir)
-
+def test_basic_ct_feature_extraction(tmp_path):
     image = np.zeros((128, 128), dtype=float)
     image[32:64, 32:64] = 1.0
 
     mask = np.zeros((128, 128), dtype=bool)
     mask[48:64, 48:64] = True
 
-    data = extract_features_and_images(
+    extract_features_and_images(
         write_features=True,
         export_features=True,
         write_images=True,
         export_images=False,
-        write_dir=write_dir,
+        write_dir=tmp_path,
         image=image,
         mask=mask,
         base_feature_families="statistics"
     )
 
     # Check that files exist.
-    file_names = [file for file in os.listdir(write_dir) if os.path.isfile(os.path.join(write_dir, file))]
+    file_names = [file for file in os.listdir(tmp_path) if (tmp_path / file).is_file()]
 
     assert len(file_names) == 3
     assert len([file for file in file_names if file.endswith(".csv")]) == 1
     assert len([file for file in file_names if file.endswith(".nii.gz")]) == 2
     assert len([file for file in file_names if "mask" in file]) == 1
-
-    if os.path.exists(write_dir):
-        shutil.rmtree(write_dir)