Merge pull request #72 from fmi-faim/update-test-cellpose

Relax test for cellpose segmentation

.github/workflows/test.yml

@@ -26,7 +26,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v3

pyproject.toml

@@ -10,7 +10,7 @@ build-backend = "hatchling.build"
 name = "faim-wako-searchfirst"
 description = ''
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = "MIT"
 keywords = []
 authors = [
@@ -19,16 +19,18 @@ authors = [
 classifiers = [
   "Development Status :: 4 - Beta",
   "Programming Language :: Python",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: Implementation :: CPython",
   "Programming Language :: Python :: Implementation :: PyPy",
 ]
 dependencies = [
   "cellpose",
   "confuse",
+  "numpy",
+  "pandas",
   "rich",
   "scikit-image",
   "tqdm",
@@ -50,6 +52,7 @@ dependencies = [
   "pytest",
   "pytest-cov",
 ]
+
 [tool.hatch.envs.default.scripts]
 cov = "pytest --cov-report=term-missing --cov-config=pyproject.toml --cov=faim_wako_searchfirst --cov=tests {args}"
 no-cov = "cov --no-cov {args}"

tests/test_cellpose.py

@@ -29,9 +29,9 @@ def test_cellpose(_data_path):
         reader = csv.reader(csv_file, quoting=csv.QUOTE_NONNUMERIC)
         entries = list(reader)
         assert len(entries) == 3, "Incorrect number of objects detected."
-        assert entries[0] == pytest.approx([1, 40.5, 30.5])
-        assert entries[1] == pytest.approx([2, 158.5, 58.5])
-        assert entries[2] == pytest.approx([3, 79.5287, 146.4483])
+        assert entries[0] == pytest.approx([1, 40.5, 30.5], rel=1e-2)
+        assert entries[1] == pytest.approx([2, 158.5, 58.5], rel=1e-2)
+        assert entries[2] == pytest.approx([3, 79.5, 146.5], rel=1e-2)
 
     segmentation_folder = _data_path.parent / (_data_path.name + "_segmentation")
     assert sum(1 for _ in segmentation_folder.glob("*")) == 1