ensure cellfinder-core can run on single cpu (#198)

pyproject.toml

@@ -48,6 +48,7 @@ dev = [
     "pyinstrument",
     "pytest",
     "pytest-cov",
+    "pytest-lazy-fixture",
     "pytest-mock",
     "pytest-timeout",
     "tox",
@@ -118,6 +119,7 @@ module = [
     "tifffile.*",
     "pyinstrument.*",
     "pytest.*",
+    "pytest_lazyfixture.*",
     "scipy.*",
     "skimage.*",
     "sklearn.*",

src/cellfinder_core/detect/detect.py

@@ -88,7 +88,7 @@ def main(
             f"{signal_array.dtype}"
         )
     n_processes = get_num_processes(min_free_cpu_cores=n_free_cpus)
-    n_ball_procs = n_processes - 1
+    n_ball_procs = max(n_processes - 1, 1)
     start_time = datetime.now()
 
     (

tests/tests/conftest.py

@@ -1,3 +1,4 @@
+import os
 from typing import Tuple
 
 import numpy as np
@@ -9,13 +10,25 @@
 
 
 @pytest.fixture(scope="session")
-def n_free_cpus() -> int:
+def no_free_cpus() -> int:
     """
-    Set number of free CPUs while the tests are running.
+    Set number of free CPUs so all available CPUs are used by the tests.
     """
     return 0
 
 
+@pytest.fixture(scope="session")
+def run_on_one_cpu_only() -> int:
+    """
+    Set number of free CPUs so tests can use exactly one CPU.
+    """
+    cpus = os.cpu_count()
+    if cpus is not None:
+        return cpus - 1
+    else:
+        raise ValueError("No CPUs available.")
+
+
 @pytest.fixture(scope="session")
 def download_default_model():
     """

tests/tests/test_integration/test_detection.py

@@ -44,6 +44,13 @@ def background_array():
 
 # FIXME: This isn't a very good example
 @pytest.mark.slow
+@pytest.mark.parametrize(
+    "n_free_cpus",
+    [
+        pytest.lazy_fixture("no_free_cpus"),
+        pytest.lazy_fixture("run_on_one_cpu_only"),
+    ],
+)
 def test_detection_full(signal_array, background_array, n_free_cpus):
     cells_test = main(
         signal_array,
@@ -72,10 +79,10 @@ def test_detection_full(signal_array, background_array, n_free_cpus):
 
 
 def test_detection_small_planes(
-    signal_array, background_array, n_free_cpus, mocker
+    signal_array, background_array, no_free_cpus, mocker
 ):
     # Check that processing works when number of planes < number of processes
-    nproc = get_num_processes(n_free_cpus)
+    nproc = get_num_processes(no_free_cpus)
     n_planes = 2
 
     # Don't want to bother classifying in this test, so mock classifcation
@@ -92,11 +99,11 @@ def test_detection_small_planes(
         background_array[0:n_planes],
         voxel_sizes,
         ball_z_size=5,
-        n_free_cpus=n_free_cpus,
+        n_free_cpus=no_free_cpus,
     )
 
 
-def test_callbacks(signal_array, background_array, n_free_cpus):
+def test_callbacks(signal_array, background_array, no_free_cpus):
     # 20 is minimum number of planes needed to find > 0 cells
     signal_array = signal_array[0:20]
     background_array = background_array[0:20]
@@ -121,7 +128,7 @@ def detect_finished_callback(points):
         detect_callback=detect_callback,
         classify_callback=classify_callback,
         detect_finished_callback=detect_finished_callback,
-        n_free_cpus=n_free_cpus,
+        n_free_cpus=no_free_cpus,
     )
 
     np.testing.assert_equal(planes_done, np.arange(len(signal_array)))
@@ -139,13 +146,13 @@ def test_floating_point_error(signal_array, background_array):
         main(signal_array, background_array, voxel_sizes)
 
 
-def test_synthetic_data(synthetic_bright_spots, n_free_cpus):
+def test_synthetic_data(synthetic_bright_spots, no_free_cpus):
     signal_array, background_array = synthetic_bright_spots
     detected = main(
         signal_array,
         background_array,
         voxel_sizes,
-        n_free_cpus=n_free_cpus,
+        n_free_cpus=no_free_cpus,
     )
     assert len(detected) == 8
 

tox.ini

@@ -14,6 +14,7 @@ commands = python -m pytest -v --color=yes
 deps =
     pytest
     pytest-cov
+    pytest-lazy-fixture
     pytest-mock
     pytest-timeout
 passenv =