💚 Parallel tests

Makefile

@@ -59,7 +59,7 @@ lint: ## check style with flake8
 	flake8 tiatoolbox tests
 
 test: ## run tests quickly with the default Python
-	pytest
+	pytest -n auto
 
 coverage: ## check code coverage quickly with the default Python
 	pytest  --cov=tiatoolbox --cov-report=term --cov-report=html --cov-report=xml

tests/models/test_arch_micronet.py

@@ -15,9 +15,7 @@
 ON_GPU = toolbox_env.has_gpu()
 
 
-def test_functionality(
-    remote_sample,
-):
+def test_functionality(remote_sample):
     """Functionality test."""
     sample_wsi = remote_sample("wsi1_2k_2k_svs")
     reader = WSIReader.open(sample_wsi)

tests/models/test_hovernetplus.py

@@ -8,9 +8,8 @@
 from tiatoolbox.utils.transforms import imresize
 
 
-def test_functionality(remote_sample, tmp_path):
+def test_functionality(remote_sample):
     """Functionality test."""
-    tmp_path = str(tmp_path)
     sample_patch = str(remote_sample("stainnorm-source"))
     patch_pre = imread(sample_patch)
     patch_pre = imresize(patch_pre, scale_factor=0.5)

tests/models/test_semantic_segmentation.py

@@ -5,6 +5,7 @@
 # ! The garbage collector
 import gc
 import multiprocessing
+import pathlib
 import shutil
 from pathlib import Path
 
@@ -258,23 +259,25 @@ def test_functional_wsi_stream_dataset(remote_sample):
 # -------------------------------------------------------------------------------------
 
 
-def test_crash_segmentor(remote_sample):
+def test_crash_segmentor(remote_sample, tmp_path):
     """Functional crash tests for segmentor."""
     # # convert to pathlib Path to prevent wsireader complaint
     mini_wsi_svs = Path(remote_sample("wsi2_4k_4k_svs"))
     mini_wsi_jpg = Path(remote_sample("wsi2_4k_4k_jpg"))
     mini_wsi_msk = Path(remote_sample("wsi2_4k_4k_msk"))
 
     model = _CNNTo1()
+
+    save_dir = pathlib.Path(f"{tmp_path}/test_crash_segmentor")
     semantic_segmentor = SemanticSegmentor(batch_size=BATCH_SIZE, model=model)
+
     # fake injection to trigger Segmentor to create parallel
     # post processing workers because baseline Semantic Segmentor does not support
     # post processing out of the box. It only contains condition to create it
     # for any subclass
     semantic_segmentor.num_postproc_workers = 1
 
     # * test basic crash
-    _rm_dir("output")  # default output dir test
     with pytest.raises(TypeError, match=r".*`mask_reader`.*"):
         semantic_segmentor.filter_coordinates(mini_wsi_msk, np.array(["a", "b", "c"]))
     with pytest.raises(ValueError, match=r".*ndarray.*integer.*"):
@@ -286,7 +289,7 @@ def test_crash_segmentor(remote_sample):
     with pytest.raises(ValueError, match=r".*must be a valid file path.*"):
         semantic_segmentor.get_reader(mini_wsi_msk, "not_exist", "wsi", True)
 
-    _rm_dir("output")  # default output dir test
+    _rm_dir(save_dir)
     with pytest.raises(ValueError, match=r".*provide.*"):
         SemanticSegmentor()
     with pytest.raises(ValueError, match=r".*valid mode.*"):
@@ -299,10 +302,16 @@ def test_crash_segmentor(remote_sample):
             mode="tile",
             on_gpu=ON_GPU,
             crash_on_exception=True,
+            save_dir=save_dir,
         )
     with pytest.raises(ValueError, match=r".*already exists.*"):
-        semantic_segmentor.predict([], mode="tile", patch_input_shape=[2048, 2048])
-    _rm_dir("output")  # default output dir test
+        semantic_segmentor.predict(
+            [],
+            mode="tile",
+            patch_input_shape=[2048, 2048],
+            save_dir=save_dir,
+        )
+    _rm_dir(save_dir)
 
     # * test not providing any io_config info when not using pretrained model
     with pytest.raises(ValueError, match=r".*provide either `ioconfig`.*"):
@@ -311,11 +320,11 @@ def test_crash_segmentor(remote_sample):
             mode="tile",
             on_gpu=ON_GPU,
             crash_on_exception=True,
+            save_dir=save_dir,
         )
-    _rm_dir("output")  # default output dir test
+    _rm_dir(save_dir)
 
     # * Test crash propagation when parallelize post processing
-    _rm_dir("output")
     semantic_segmentor.num_postproc_workers = 2
     semantic_segmentor.model.forward = _crash_func
     with pytest.raises(ValueError, match=r"Propagation Crash."):
@@ -325,17 +334,19 @@ def test_crash_segmentor(remote_sample):
             mode="wsi",
             on_gpu=ON_GPU,
             crash_on_exception=True,
+            save_dir=save_dir,
         )
-    _rm_dir("output")
+    _rm_dir(save_dir)
+
     # test ignore crash
     semantic_segmentor.predict(
         [mini_wsi_svs],
         patch_input_shape=[2048, 2048],
         mode="wsi",
         on_gpu=ON_GPU,
         crash_on_exception=False,
+        save_dir=save_dir,
     )
-    _rm_dir("output")
 
 
 def test_functional_segmentor_merging(tmp_path):