From db3537a843e91d19fd3faea4c964538825856bc3 Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Thu, 1 Feb 2024 14:56:59 +0000
Subject: [PATCH 01/14] Add skimage missing dependency and boot broken
 pytest-lazy-fixture

---
 pyproject.toml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 92cad582..0277bab5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -46,11 +46,11 @@ dev = [
     "pre-commit",
     "pyinstrument",
     "pytest-cov",
-    "pytest-lazy-fixture",
     "pytest-mock",
     "pytest-qt",
     "pytest-timeout",
     "pytest",
+    "scikit-image",
     "tox",
 ]
 napari = [
@@ -125,7 +125,6 @@ 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

From f4f4b04dac0e3b48adff13e21235b511e8dfe02c Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Thu, 1 Feb 2024 14:58:18 +0000
Subject: [PATCH 02/14] Remove lazy-fixture dependent fixtures

---
 tests/core/test_integration/test_detection.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/tests/core/test_integration/test_detection.py b/tests/core/test_integration/test_detection.py
index ed289d10..a29ada9f 100644
--- a/tests/core/test_integration/test_detection.py
+++ b/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,

From 67caf8256f3bb1f6d904b69799738acbb8fa975b Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Tue, 6 Feb 2024 10:19:02 +0000
Subject: [PATCH 03/14] Clarify problem fixture docstrings

---
 .gitignore             |  1 +
 tests/core/conftest.py | 14 +++++++++++---
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/.gitignore b/.gitignore
index 7a8b1bc9..607743bb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -143,3 +143,4 @@ benchmarks/env
 */_version.py
 
 .idea/
+.vscode/
\ No newline at end of file
diff --git a/tests/core/conftest.py b/tests/core/conftest.py
index f05ec88a..9a8a6544 100644
--- a/tests/core/conftest.py
+++ b/tests/core/conftest.py
@@ -9,18 +9,26 @@
 from cellfinder.core.tools.prep import DEFAULT_INSTALL_PATH
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture()
 def no_free_cpus() -> int:
     """
-    Set number of free CPUs so all available CPUs are used by the tests.
+    Set number of free CPUs,
+    so all available CPUs are used by the tests.
+
+    Note that this is passed to min_cpus_to_keep_free,
+    so a value of 0 implies no CPUs will be kept free,
+    IE all will be used.
     """
     return 0
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture()
 def run_on_one_cpu_only() -> int:
     """
     Set number of free CPUs so tests can use exactly one CPU.
+
+    Note that this is passed to min_cpus_to_keep_free,
+    so a value of #cpus-1 implies all but one CPU will be kept free.
     """
     cpus = os.cpu_count()
     if cpus is not None:

From dd0e519332baa6afe04fa3b3a4d49e16e0016947 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 6 Feb 2024 10:19:33 +0000
Subject: [PATCH 04/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .gitignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 607743bb..31dec9e3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -143,4 +143,4 @@ benchmarks/env
 */_version.py
 
 .idea/
-.vscode/
\ No newline at end of file
+.vscode/

From 125fa9def89620eb7b172f881399c9afe08714ac Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Tue, 6 Feb 2024 10:52:35 +0000
Subject: [PATCH 05/14] Remove fixtures and get pytest to check for cpu
 availability at runtime

---
 tests/core/conftest.py                        | 28 ---------
 tests/core/test_integration/test_detection.py | 58 +++++++++++++++----
 2 files changed, 46 insertions(+), 40 deletions(-)

diff --git a/tests/core/conftest.py b/tests/core/conftest.py
index 9a8a6544..f68f3a26 100644
--- a/tests/core/conftest.py
+++ b/tests/core/conftest.py
@@ -9,34 +9,6 @@
 from cellfinder.core.tools.prep import DEFAULT_INSTALL_PATH
 
 
-@pytest.fixture()
-def no_free_cpus() -> int:
-    """
-    Set number of free CPUs,
-    so all available CPUs are used by the tests.
-
-    Note that this is passed to min_cpus_to_keep_free,
-    so a value of 0 implies no CPUs will be kept free,
-    IE all will be used.
-    """
-    return 0
-
-
-@pytest.fixture()
-def run_on_one_cpu_only() -> int:
-    """
-    Set number of free CPUs so tests can use exactly one CPU.
-
-    Note that this is passed to min_cpus_to_keep_free,
-    so a value of #cpus-1 implies all but one CPU will be kept free.
-    """
-    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():
     """
diff --git a/tests/core/test_integration/test_detection.py b/tests/core/test_integration/test_detection.py
index a29ada9f..1a43dca5 100644
--- a/tests/core/test_integration/test_detection.py
+++ b/tests/core/test_integration/test_detection.py
@@ -45,14 +45,43 @@ def background_array():
 # FIXME: This isn't a very good example
 @pytest.mark.slow
 @pytest.mark.parametrize(
-    "free_cpus",
+    "cpus_to_leave_available",
     [
-        pytest.param("no_free_cpus", id="No free CPUs"),
-        pytest.param("run_on_one_cpu_only", id="One CPU"),
+        pytest.param(0, id="Leave no CPUS free"),
+        pytest.param(-1, id="Only use one CPU"),
     ],
 )
-def test_detection_full(signal_array, background_array, free_cpus, request):
-    n_free_cpus = request.getfixturevalue(free_cpus)
+def test_detection_full(
+    signal_array, background_array, cpus_to_leave_available: int
+):
+    """
+    cpus_to_leave_available is interpreted as follows:
+
+    - For values >=0, this is the number of CPUs to leave available
+    to the system when running this test.
+    - For values <0, this is HOW MANY CPUS to request be used to
+    run the test.
+
+    In each case, we check that we will be running on at least one CPU,
+    and not requesting more CPUs than the system can provide.
+    """
+    # Determine the number of CPUs to leave available
+    system_cpus = os.cpu_count()
+    # How many CPUs do we want to leave free?
+    if cpus_to_leave_available >= 0:
+        n_free_cpus = cpus_to_leave_available
+    else:
+        # Number of CPUs to keep free is <0, interpret as
+        # number of CPUs _to use_. Thus;
+        # n_free_cpus = system_cpus - |cpus_to_leave_available|
+        n_free_cpus = system_cpus - abs(cpus_to_leave_available)
+    # Check that there are enough CPUs
+    if not 0 <= n_free_cpus < system_cpus:
+        RuntimeError(
+            f"Not enough CPUS available (you want to leave {n_free_cpus} "
+            f"available, but there are only {system_cpus} on the system)."
+        )
+
     cells_test = main(
         signal_array,
         background_array,
@@ -80,10 +109,13 @@ def test_detection_full(signal_array, background_array, free_cpus, request):
 
 
 def test_detection_small_planes(
-    signal_array, background_array, no_free_cpus, mocker
+    signal_array,
+    background_array,
+    mocker,
+    cpus_to_leave_free: int = 0,
 ):
     # Check that processing works when number of planes < number of processes
-    nproc = get_num_processes(no_free_cpus)
+    nproc = get_num_processes(cpus_to_leave_free)
     n_planes = 2
 
     # Don't want to bother classifying in this test, so mock classifcation
@@ -100,11 +132,13 @@ def test_detection_small_planes(
         background_array[0:n_planes],
         voxel_sizes,
         ball_z_size=5,
-        n_free_cpus=no_free_cpus,
+        n_free_cpus=cpus_to_leave_free,
     )
 
 
-def test_callbacks(signal_array, background_array, no_free_cpus):
+def test_callbacks(
+    signal_array, background_array, cpus_to_leave_free: int = 0
+):
     # 20 is minimum number of planes needed to find > 0 cells
     signal_array = signal_array[0:20]
     background_array = background_array[0:20]
@@ -129,7 +163,7 @@ def detect_finished_callback(points):
         detect_callback=detect_callback,
         classify_callback=classify_callback,
         detect_finished_callback=detect_finished_callback,
-        n_free_cpus=no_free_cpus,
+        n_free_cpus=cpus_to_leave_free,
     )
 
     np.testing.assert_equal(planes_done, np.arange(len(signal_array)))
@@ -147,13 +181,13 @@ def test_floating_point_error(signal_array, background_array):
         main(signal_array, background_array, voxel_sizes)
 
 
-def test_synthetic_data(synthetic_bright_spots, no_free_cpus):
+def test_synthetic_data(synthetic_bright_spots, cpus_to_leave_free: int = 0):
     signal_array, background_array = synthetic_bright_spots
     detected = main(
         signal_array,
         background_array,
         voxel_sizes,
-        n_free_cpus=no_free_cpus,
+        n_free_cpus=cpus_to_leave_free,
     )
     assert len(detected) == 8
 

From bdd0d91d5fbb0a0eeb5daceb7073629cc2d2a568 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 6 Feb 2024 10:52:54 +0000
Subject: [PATCH 06/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/core/conftest.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/core/conftest.py b/tests/core/conftest.py
index f68f3a26..83778a9f 100644
--- a/tests/core/conftest.py
+++ b/tests/core/conftest.py
@@ -1,4 +1,3 @@
-import os
 from typing import Tuple
 
 import numpy as np

From 1545b1b86e739fd0a159f605a56ebbf01f6bd9b9 Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Tue, 6 Feb 2024 10:55:00 +0000
Subject: [PATCH 07/14] Actually raise the exception for not enough CPUs

---
 tests/core/test_integration/test_detection.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/core/test_integration/test_detection.py b/tests/core/test_integration/test_detection.py
index 1a43dca5..f7dffdc0 100644
--- a/tests/core/test_integration/test_detection.py
+++ b/tests/core/test_integration/test_detection.py
@@ -77,7 +77,7 @@ def test_detection_full(
         n_free_cpus = system_cpus - abs(cpus_to_leave_available)
     # Check that there are enough CPUs
     if not 0 <= n_free_cpus < system_cpus:
-        RuntimeError(
+        raise RuntimeError(
             f"Not enough CPUS available (you want to leave {n_free_cpus} "
             f"available, but there are only {system_cpus} on the system)."
         )

From 2753abb7a184f13a169de0ac111eb8bef80a2c1e Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Tue, 6 Feb 2024 11:03:11 +0000
Subject: [PATCH 08/14] try attempting garbage collector to run at end of test

---
 tests/core/test_integration/test_detection.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/core/test_integration/test_detection.py b/tests/core/test_integration/test_detection.py
index f7dffdc0..a2e9bc9b 100644
--- a/tests/core/test_integration/test_detection.py
+++ b/tests/core/test_integration/test_detection.py
@@ -1,3 +1,4 @@
+import gc
 import os
 from math import isclose
 
@@ -107,6 +108,9 @@ def test_detection_full(
         num_cells_validation, num_cells_test, abs_tol=DETECTION_TOLERANCE
     )
 
+    # Force explicit memory cleanup
+    gc.collect()
+
 
 def test_detection_small_planes(
     signal_array,

From 4d19fb6fb0aea5e10b81fda68d849a7317adaa50 Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Tue, 6 Feb 2024 16:07:54 +0000
Subject: [PATCH 09/14] Remove double dependency

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0277bab5..17f6d235 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,7 +50,6 @@ dev = [
     "pytest-qt",
     "pytest-timeout",
     "pytest",
-    "scikit-image",
     "tox",
 ]
 napari = [

From 448170bc9f76b3fbc4f46a87da18a5dd3421e67d Mon Sep 17 00:00:00 2001
From: Alessandro Felder <alessandrofelder@users.noreply.github.com>
Date: Wed, 7 Feb 2024 09:23:14 +0000
Subject: [PATCH 10/14] 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>
---
 cellfinder/core/detect/detect.py                       | 8 ++++----
 cellfinder/core/detect/filters/volume/volume_filter.py | 5 +++++
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/cellfinder/core/detect/detect.py b/cellfinder/core/detect/detect.py
index cd4e22c5..7c614d4e 100644
--- a/cellfinder/core/detect/detect.py
+++ b/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
 
 
diff --git a/cellfinder/core/detect/filters/volume/volume_filter.py b/cellfinder/core/detect/filters/volume/volume_filter.py
index a3e4d98f..d64ae71a 100644
--- a/cellfinder/core/detect/filters/volume/volume_filter.py
+++ b/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
 
 

From 4b840b3d0f03057cdbb928b79caeb6972e425684 Mon Sep 17 00:00:00 2001
From: Will Graham <32364977+willGraham01@users.noreply.github.com>
Date: Wed, 7 Feb 2024 11:56:20 +0000
Subject: [PATCH 11/14] 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 2753abb7a184f13a169de0ac111eb8bef80a2c1e.

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

This reverts commit 1545b1b86e739fd0a159f605a56ebbf01f6bd9b9.

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

This reverts commit bdd0d91d5fbb0a0eeb5daceb7073629cc2d2a568.

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

This reverts commit 125fa9def89620eb7b172f881399c9afe08714ac.

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

This reverts commit dd0e519332baa6afe04fa3b3a4d49e16e0016947.

* Revert "Clarify problem fixture docstrings"

This reverts commit 67caf8256f3bb1f6d904b69799738acbb8fa975b.

* Add a timeout to CI for runs
---
 .github/workflows/test_and_deploy.yml         |  1 +
 .gitignore                                    |  1 -
 tests/core/conftest.py                        | 21 +++++++
 tests/core/test_integration/test_detection.py | 62 ++++---------------
 4 files changed, 34 insertions(+), 51 deletions(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 79e765b4..8c53d434 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -35,6 +35,7 @@ jobs:
   test:
     needs: [linting, manifest]
     name: Run package tests
+    timeout-minutes: 20
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
diff --git a/.gitignore b/.gitignore
index 31dec9e3..7a8b1bc9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -143,4 +143,3 @@ benchmarks/env
 */_version.py
 
 .idea/
-.vscode/
diff --git a/tests/core/conftest.py b/tests/core/conftest.py
index 83778a9f..f05ec88a 100644
--- a/tests/core/conftest.py
+++ b/tests/core/conftest.py
@@ -1,3 +1,4 @@
+import os
 from typing import Tuple
 
 import numpy as np
@@ -8,6 +9,26 @@
 from cellfinder.core.tools.prep import DEFAULT_INSTALL_PATH
 
 
+@pytest.fixture(scope="session")
+def no_free_cpus() -> int:
+    """
+    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():
     """
diff --git a/tests/core/test_integration/test_detection.py b/tests/core/test_integration/test_detection.py
index a2e9bc9b..a29ada9f 100644
--- a/tests/core/test_integration/test_detection.py
+++ b/tests/core/test_integration/test_detection.py
@@ -1,4 +1,3 @@
-import gc
 import os
 from math import isclose
 
@@ -46,43 +45,14 @@ def background_array():
 # FIXME: This isn't a very good example
 @pytest.mark.slow
 @pytest.mark.parametrize(
-    "cpus_to_leave_available",
+    "free_cpus",
     [
-        pytest.param(0, id="Leave no CPUS free"),
-        pytest.param(-1, id="Only use one CPU"),
+        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, cpus_to_leave_available: int
-):
-    """
-    cpus_to_leave_available is interpreted as follows:
-
-    - For values >=0, this is the number of CPUs to leave available
-    to the system when running this test.
-    - For values <0, this is HOW MANY CPUS to request be used to
-    run the test.
-
-    In each case, we check that we will be running on at least one CPU,
-    and not requesting more CPUs than the system can provide.
-    """
-    # Determine the number of CPUs to leave available
-    system_cpus = os.cpu_count()
-    # How many CPUs do we want to leave free?
-    if cpus_to_leave_available >= 0:
-        n_free_cpus = cpus_to_leave_available
-    else:
-        # Number of CPUs to keep free is <0, interpret as
-        # number of CPUs _to use_. Thus;
-        # n_free_cpus = system_cpus - |cpus_to_leave_available|
-        n_free_cpus = system_cpus - abs(cpus_to_leave_available)
-    # Check that there are enough CPUs
-    if not 0 <= n_free_cpus < system_cpus:
-        raise RuntimeError(
-            f"Not enough CPUS available (you want to leave {n_free_cpus} "
-            f"available, but there are only {system_cpus} on the system)."
-        )
-
+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,
@@ -108,18 +78,12 @@ def test_detection_full(
         num_cells_validation, num_cells_test, abs_tol=DETECTION_TOLERANCE
     )
 
-    # Force explicit memory cleanup
-    gc.collect()
-
 
 def test_detection_small_planes(
-    signal_array,
-    background_array,
-    mocker,
-    cpus_to_leave_free: int = 0,
+    signal_array, background_array, no_free_cpus, mocker
 ):
     # Check that processing works when number of planes < number of processes
-    nproc = get_num_processes(cpus_to_leave_free)
+    nproc = get_num_processes(no_free_cpus)
     n_planes = 2
 
     # Don't want to bother classifying in this test, so mock classifcation
@@ -136,13 +100,11 @@ def test_detection_small_planes(
         background_array[0:n_planes],
         voxel_sizes,
         ball_z_size=5,
-        n_free_cpus=cpus_to_leave_free,
+        n_free_cpus=no_free_cpus,
     )
 
 
-def test_callbacks(
-    signal_array, background_array, cpus_to_leave_free: int = 0
-):
+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]
@@ -167,7 +129,7 @@ def detect_finished_callback(points):
         detect_callback=detect_callback,
         classify_callback=classify_callback,
         detect_finished_callback=detect_finished_callback,
-        n_free_cpus=cpus_to_leave_free,
+        n_free_cpus=no_free_cpus,
     )
 
     np.testing.assert_equal(planes_done, np.arange(len(signal_array)))
@@ -185,13 +147,13 @@ def test_floating_point_error(signal_array, background_array):
         main(signal_array, background_array, voxel_sizes)
 
 
-def test_synthetic_data(synthetic_bright_spots, cpus_to_leave_free: int = 0):
+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=cpus_to_leave_free,
+        n_free_cpus=no_free_cpus,
     )
     assert len(detected) == 8
 

From e6b233cf6b56b185861d7b4fba72e7d899588b1a Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Wed, 7 Feb 2024 11:57:36 +0000
Subject: [PATCH 12/14] ignore vscode configs in git

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 7a8b1bc9..607743bb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -143,3 +143,4 @@ benchmarks/env
 */_version.py
 
 .idea/
+.vscode/
\ No newline at end of file

From ae0e847a6c10cb31fb37675b2fa0ebd02d4fb608 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 7 Feb 2024 12:00:09 +0000
Subject: [PATCH 13/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .gitignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 607743bb..31dec9e3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -143,4 +143,4 @@ benchmarks/env
 */_version.py
 
 .idea/
-.vscode/
\ No newline at end of file
+.vscode/

From 4c20e9bb62b76ca5a652af5c3638410542498306 Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Wed, 7 Feb 2024 13:04:42 +0000
Subject: [PATCH 14/14] Bump timeout to 60 mins

---
 .github/workflows/test_and_deploy.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 8c53d434..4f941175 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -35,7 +35,7 @@ jobs:
   test:
     needs: [linting, manifest]
     name: Run package tests
-    timeout-minutes: 20
+    timeout-minutes: 60
     runs-on: ${{ matrix.os }}
     strategy:
       matrix: