Remove pytest-lazy-fixture due to incompatibility with pytest v8.0.0 (#369)

* Add skimage missing dependency and boot broken pytest-lazy-fixture

* Remove lazy-fixture dependent fixtures

* Clarify problem fixture docstrings

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Remove fixtures and get pytest to check for cpu availability at runtime

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Actually raise the exception for not enough CPUs

* try attempting garbage collector to run at end of test

* Remove double dependency

* improve detection debug logs (#375)

* improve detection debug logs

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* remove too wordy debug logs

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Searching for min. segfault example (#376) 

Reverting apparently un-neccessary changes due to conflation with a bad cache fetch. 

* Revert "try attempting garbage collector to run at end of test"

This reverts commit 2753abb.

* Revert "Actually raise the exception for not enough CPUs"

This reverts commit 1545b1b.

* Revert "[pre-commit.ci] auto fixes from pre-commit.com hooks"

This reverts commit bdd0d91.

* Revert "Remove fixtures and get pytest to check for cpu availability at runtime"

This reverts commit 125fa9d.

* Revert "[pre-commit.ci] auto fixes from pre-commit.com hooks"

This reverts commit dd0e519.

* Revert "Clarify problem fixture docstrings"

This reverts commit 67caf82.

* Add a timeout to CI for runs

* ignore vscode configs in git

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Bump timeout to 60 mins

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alessandro Felder <[email protected]>

Author: 3 people

.github/workflows/test_and_deploy.yml

@@ -35,6 +35,7 @@ jobs:
   test:
     needs: [linting, manifest]
     name: Run package tests
+    timeout-minutes: 60
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:

.gitignore

@@ -143,3 +143,4 @@ benchmarks/env
 */_version.py
 
 .idea/
+.vscode/

cellfinder/core/detect/detect.py

@@ -179,11 +179,11 @@ def main(
         # processes.
         cells = mp_3d_filter.process(async_results, locks, callback=callback)
 
-    print(
-        "Detection complete - all planes done in : {}".format(
-            datetime.now() - start_time
-        )
+    time_elapsed = datetime.now() - start_time
+    logger.debug(
+        f"All Planes done. Found {len(cells)} cells in {format(time_elapsed)}"
     )
+    print("Detection complete - all planes done in : {}".format(time_elapsed))
     return cells
 
 

cellfinder/core/detect/filters/volume/volume_filter.py

@@ -142,6 +142,10 @@ def get_results(self) -> List[Cell]:
         )
 
         cells = []
+
+        logger.debug(
+            f"Processing {len(self.cell_detector.coords_maps.items())} cells"
+        )
         for cell_id, cell_points in self.cell_detector.coords_maps.items():
             cell_volume = len(cell_points)
 
@@ -191,6 +195,7 @@ def get_results(self) -> List[Cell]:
                         )
                     )
 
+        logger.debug("Finished splitting cell clusters.")
         return cells
 
 

pyproject.toml

@@ -46,7 +46,6 @@ dev = [
     "pre-commit",
     "pyinstrument",
     "pytest-cov",
-    "pytest-lazy-fixture",
     "pytest-mock",
     "pytest-qt",
     "pytest-timeout",
@@ -125,7 +124,6 @@ commands = python -m pytest -v --color=yes
 deps =
     pytest
     pytest-cov
-    pytest-lazy-fixture
     pytest-mock
     pytest-timeout
     # Even though napari is a requirement for cellfinder.napari, we have to

tests/core/test_integration/test_detection.py

@@ -45,13 +45,14 @@ def background_array():
 # FIXME: This isn't a very good example
 @pytest.mark.slow
 @pytest.mark.parametrize(
-    "n_free_cpus",
+    "free_cpus",
     [
-        pytest.lazy_fixture("no_free_cpus"),
-        pytest.lazy_fixture("run_on_one_cpu_only"),
+        pytest.param("no_free_cpus", id="No free CPUs"),
+        pytest.param("run_on_one_cpu_only", id="One CPU"),
     ],
 )
-def test_detection_full(signal_array, background_array, n_free_cpus):
+def test_detection_full(signal_array, background_array, free_cpus, request):
+    n_free_cpus = request.getfixturevalue(free_cpus)
     cells_test = main(
         signal_array,
         background_array,