test: Add tests files to calcualate coverage

.github/workflows/test_prereleases.yml

@@ -47,6 +47,7 @@ jobs:
         with:
           python-version: ${{ matrix.python }}
           cache: 'pip'
+          cache-dependency-path: 'requirements/requirements_pyinstaller.txt'
 
       - name: Install Windows OpenGL
         if: runner.os == 'Windows'
@@ -104,7 +105,6 @@ jobs:
       name: Install Python 3.9
       with:
         python-version: 3.9
-        cache: 'pip'
     - name: Install ubuntu libraries
       if: runner.os == 'Linux'
       run: |

codecov.yml

@@ -17,5 +17,9 @@ coverage:
         target: auto
         threshold: 0.5%  # coverage can drop by up to 0.5% while still posting success
         paths: [ 'package/PartSegImage/.*' ]
+      Tests:
+        target: auto
+        threshold: 1%  # coverage can drop by up to 0.5% while still posting success
+        paths: [ 'package/tests/.*' ]
 comment:
   require_changes: true  # if true: only post the PR comment if coverage changes

package/tests/test_PartSeg/conftest.py

@@ -1,7 +1,7 @@
 from contextlib import suppress
 
 import pytest
-from qtpy.QtWidgets import QApplication, QDialog, QMessageBox
+from qtpy.QtWidgets import QDialog, QMessageBox
 
 from PartSeg._roi_analysis.partseg_settings import PartSettings
 from PartSeg._roi_mask.main_window import ChosenComponents
@@ -133,16 +133,6 @@ def clean_settings():
         yield
 
 
-@pytest.fixture
-def leaked_widgets():
-    initial = QApplication.topLevelWidgets()
-    yield
-    QApplication.processEvents()
-    leak = set(QApplication.topLevelWidgets()).difference(initial)
-    if any(n.__class__.__name__ != "CanvasBackendDesktop" for n in leak):
-        raise AssertionError(f"Widgets ({len(leak)}) leaked!: {leak}")
-
-
 @pytest.fixture(autouse=True)
 def reset_napari_settings(monkeypatch, tmp_path):
     def _mock_save(self, path=None, **dict_kwargs):
@@ -161,7 +151,7 @@ def _mock_save(self, path=None, **dict_kwargs):
 @pytest.fixture(autouse=True)
 def block_message_box(monkeypatch, request):
     def raise_on_call(*_, **__):
-        raise RuntimeError("exec_ call")
+        raise RuntimeError("exec_ call")  # pragma: no cover
 
     monkeypatch.setattr(QMessageBox, "exec_", raise_on_call)
     monkeypatch.setattr(QMessageBox, "critical", raise_on_call)

package/tests/test_PartSeg/test_check_release.py

@@ -24,11 +24,7 @@ def urlopen_mock(url):
             )
         )
 
-    def message_box_block(self, *args):
-        raise RuntimeError(f"call of message box {self.text()}")
-
     monkeypatch.setattr(urllib.request, "urlopen", urlopen_mock)
-    monkeypatch.setattr(check_version.QMessageBox, "exec_", message_box_block)
     assert packaging.version.parse("0.10.0") < packaging.version.parse("0.11.0")
     chk_thr = check_version.CheckVersionThread(package_name, base_version="0.11.0")
     chk_thr.release = "0.10.0"

package/tests/test_PartSeg/test_common_backend.py

@@ -325,11 +325,11 @@ def __init__(self, raise_=False, return_none=False):
 
     @classmethod
     def support_time(cls):
-        return False
+        return False  # for class interfce, # pragma: no cover
 
     @classmethod
     def support_z(cls):
-        return True
+        return True  # for class interfce, # pragma: no cover
 
     def calculation_run(self, report_fun: Callable[[str, int], None]) -> Optional[ROIExtractionResult]:
         if self.raise_:
@@ -389,14 +389,8 @@ class TestDict(partially_const_dict.PartiallyConstDict):
 
 
 class TestLoadBackup:
-    @staticmethod
-    def block_exec(*args, **kwargs):
-        raise RuntimeError("aa")
-
     def test_no_backup(self, monkeypatch, tmp_path):
         monkeypatch.setattr(load_backup.state_store, "save_folder", tmp_path)
-        monkeypatch.setattr(load_backup.QMessageBox, "exec_", self.block_exec)
-        monkeypatch.setattr(load_backup.QMessageBox, "question", self.block_exec)
         monkeypatch.setattr(load_backup, "parsed_version", parse("0.13.13"))
         load_backup.import_config()
 
@@ -405,8 +399,6 @@ def test_no_backup(self, monkeypatch, tmp_path):
 
     def test_no_backup_old(self, monkeypatch, tmp_path):
         monkeypatch.setattr(load_backup.state_store, "save_folder", tmp_path / "0.13.13")
-        monkeypatch.setattr(load_backup.QMessageBox, "exec_", self.block_exec)
-        monkeypatch.setattr(load_backup.QMessageBox, "question", self.block_exec)
         monkeypatch.setattr(load_backup, "parsed_version", parse("0.13.13"))
         (tmp_path / "0.13.14").mkdir()
         (tmp_path / "0.13.15").mkdir()
@@ -425,7 +417,6 @@ def question(*args, **kwargs):
             return response
 
         monkeypatch.setattr(load_backup.state_store, "save_folder", tmp_path / "0.13.13")
-        monkeypatch.setattr(load_backup.QMessageBox, "exec_", self.block_exec)
         monkeypatch.setattr(load_backup.QMessageBox, "question", question)
         monkeypatch.setattr(load_backup, "parsed_version", parse("0.13.13"))
         create_file(tmp_path / "0.13.14" / "14.txt")
@@ -441,12 +432,6 @@ def question(*args, **kwargs):
             assert not (tmp_path / "0.13.13").exists()
 
 
-class NapariSettingsMock:
-    @staticmethod
-    def load():
-        return 1
-
-
 @pytest.fixture
 def image(tmp_path):
     data = np.random.random((10, 10, 2))

package/tests/test_PartSeg/test_window_import.py

@@ -7,21 +7,21 @@
 def test_analysis_import():
     try:
         import PartSeg._roi_analysis.main_window  # noqa: F401
-    except ImportError:
+    except ImportError:  # pragma: no cover
         pytest.fail("Error in importing segmentation ui")
 
 
 def test_launcher_import():
     try:
         import PartSeg._launcher.main_window  # noqa: F401
-    except ImportError:
+    except ImportError:  # pragma: no cover
         pytest.fail("Error in importing launcher ui")
 
 
 def test_segmentation_import():
     try:
         import PartSeg._roi_mask.main_window  # noqa: F401
-    except ImportError:
+    except ImportError:  # pragma: no cover
         pytest.fail("Error in importing mask segmentation ui")
 
 

package/tests/test_PartSegCore/test_algorithm_describe_base.py

@@ -315,6 +315,7 @@ def get_fields(cls) -> typing.List[typing.Union[AlgorithmProperty, str]]:
                 ]
 
         assert SampleSubAlgorithm.get_name() == "sample2"
+        assert SampleAlgorithm.get_name() == "sample"
         with pytest.warns(FutureWarning, match=r"Class has __argument_class__ defined"):
             assert len(SampleSubAlgorithm.get_fields()) == 3
         with pytest.warns(FutureWarning, match=r"Class has __argument_class__ defined"):

package/tests/test_PartSegCore/test_analysis_batch.py

@@ -4,9 +4,9 @@
 import shutil
 import sys
 import time
+import warnings
 from glob import glob
 
-import numpy as np
 import pandas as pd
 import pytest
 
@@ -40,8 +40,8 @@
 from PartSegCore.mask_create import MaskProperty
 from PartSegCore.segmentation.noise_filtering import DimensionType
 from PartSegCore.segmentation.restartable_segmentation_algorithms import LowerThresholdFlowAlgorithm
-from PartSegCore.universal_const import UNIT_SCALE, Units
-from PartSegImage import Image, ImageWriter, TiffImageReader
+from PartSegCore.universal_const import Units
+from PartSegImage import TiffImageReader
 
 ENGINE = None if pd.__version__ == "0.24.0" else "openpyxl"
 
@@ -51,25 +51,6 @@ def __init__(self, file_path):
         self.file_path = file_path
 
 
-@pytest.fixture
-def create_test_data(tmpdir):
-    # for future use
-    spacing = tuple(x / UNIT_SCALE[Units.nm.value] for x in (210, 70, 70))
-    res = []
-    for i in range(8):
-        mask_data = np.zeros((10, 20, 20 + i), dtype=np.uint8)
-        mask_data[1:-1, 2:-2, 2:-2] = 1
-        data = np.zeros(mask_data.shape + (2,), dtype=np.uint16)
-        data[1:-1, 2:-2, 2:-2] = 15000
-        data[2:-2, 3:-3, 3:7] = 33000
-        data[2:-2, 3:-3, -7:-3] = 33000
-        image = Image(data, spacing, "", mask=mask_data, axes_order="ZYXC")
-        ImageWriter.save(image, os.path.join(str(tmpdir), f"file_{i}.tif"))
-        res.append(os.path.join(str(tmpdir), f"file_{i}.tif"))
-        ImageWriter.save_mask(image, os.path.join(str(tmpdir), f"file_{i}_mask.tif"))
-    return res
-
-
 # TODO add check of per component measurements
 
 # noinspection DuplicatedCode
@@ -453,13 +434,13 @@ def test_full_pipeline(self, tmpdir, data_test_dir, monkeypatch):
                 time.sleep(0.1)
             else:
                 break
-        else:
+        else:  # pragma: no cover
             manager.kill_jobs()
             pytest.fail("jobs hanged")
 
         manager.writer.finish()
         if sys.platform == "darwin":
-            time.sleep(2)
+            time.sleep(2)  # pragma: no cover
         else:
             time.sleep(0.4)
         assert os.path.exists(os.path.join(tmpdir, "test.xlsx"))
@@ -503,7 +484,7 @@ def test_full_pipeline_error(self, tmp_path, data_test_dir, monkeypatch):
             manager.get_results()
         manager.writer.finish()
         if sys.platform == "darwin":
-            time.sleep(2)
+            time.sleep(2)  # pragma: no cover
         else:
             time.sleep(0.4)
         assert os.path.exists(os.path.join(result_dir, "test.xlsx"))
@@ -538,7 +519,7 @@ def test_full_pipeline_mask_project(self, tmpdir, data_test_dir):
             time.sleep(0.1)
             manager.get_results()
         if sys.platform == "darwin":
-            time.sleep(2)
+            time.sleep(2)  # pragma: no cover
         else:
             time.sleep(0.4)
         manager.writer.finish()
@@ -660,9 +641,9 @@ def test_full_pipeline_component_split(self, tmpdir, data_test_dir):
             time.sleep(0.1)
             res = manager.get_results()
             if res.errors:
-                print(res.errors, file=sys.stderr)
+                warnings.warn(str(res.errors))  # pragma: no cover
         if sys.platform == "darwin":
-            time.sleep(2)
+            time.sleep(2)  # pragma: no cover
         else:
             time.sleep(0.4)
         manager.writer.finish()

package/tests/test_PartSegCore/test_io.py

@@ -267,7 +267,7 @@ def test_profile_load(self, data_test_dir):
             with open(profile_path) as ff:
                 data = json.load(ff, object_hook=partseg_object_hook)
             assert check_loaded_dict(data)
-        except Exception:  # pylint: disable=W0703
+        except Exception:  # pylint: disable=W0703  # pragma: no cover
             pytest.fail("Fail in loading profile")
 
     def test_measure_load(self, data_test_dir):
@@ -277,7 +277,7 @@ def test_measure_load(self, data_test_dir):
             with open(profile_path) as ff:
                 data = json.load(ff, object_hook=partseg_object_hook)
             assert check_loaded_dict(data)
-        except Exception:  # pylint: disable=W0703
+        except Exception:  # pylint: disable=W0703  # pragma: no cover
             pytest.fail("Fail in loading profile")
 
     def test_json_dump(self):

package/tests/test_PartSegCore/test_measurements.py

@@ -73,16 +73,6 @@ def cube_image_fixture():
     return get_cube_image()
 
 
-@pytest.fixture
-def cube_mask_40(cube_image):
-    return cube_image.get_channel(0)[0] > 40
-
-
-@pytest.fixture
-def cube_mask_60(cube_image):
-    return cube_image.get_channel(0)[0] > 60
-
-
 def get_square_image():
     return Image(get_cube_array()[:, 25:26], (100, 50, 50), "", axes_order="TZYX")
 

package/tests/test_PartSegCore/test_mso.py

@@ -521,7 +521,7 @@ def test_two_components_bridge(self):
         arr[2:8, 2:8, 11:18] = 3
         assert np.all(res == arr)
 
-    def _test_background_simple(self):
+    def test_background_simple(self):
         components = np.ones((20, 20, 20), dtype=np.uint8)
         components[1:-1, 1:-1, 1:-1] = 0
         components[9:11, 9:11, 9:11] = 2

package/tests/test_PartSegCore/test_segmentation_proceses.py

@@ -14,7 +14,7 @@
 
 
 def empty(_a, _b):
-    pass
+    pass  # pragma: no cover
 
 
 class TestSegmentation:
@@ -24,7 +24,7 @@ def test_profile_execute(self, data_test_dir):
         try:
             data = load_metadata_base(profile_path)
             assert check_loaded_dict(data)
-        except Exception:  # pylint: disable=W0703
+        except Exception:  # pylint: disable=W0703  # pragma: no cover
             pytest.fail("Fail in loading profile")
             return
         image = TiffImageReader.read_image(

package/tests/test_PartSegCore/test_utils.py

@@ -51,11 +51,11 @@ def fun(self):  # pylint: disable=R0201
 
 def test_get_callback():
     def call_fun():
-        return 1
+        raise NotImplementedError
 
     class A:
         def fun(self):  # pylint: disable=R0201
-            return 1
+            raise NotImplementedError
 
     a = A()
 

setup.cfg

@@ -121,7 +121,7 @@ test =
     tox
 
 [tool:pytest]
-addopts = --cov=PartSeg --cov=PartSegCore --cov PartSegImage --maxfail=5 --durations=5
+addopts = --maxfail=5 --durations=5
 testpaths = package/tests
 junit_family = legacy
 timeout = 900
@@ -159,6 +159,7 @@ exclude_lines =
     pragma: no cover
     raise NotImplementedError
     if typing.TYPE_CHECKING
+    raise RuntimeError()
 
 [flake8]
 max-line-length = 120

tox.ini

@@ -73,13 +73,13 @@ deps =
     repo: git+https://github.com/napari/napari.git
 commands =
     !repo: python -m pytest -v package/tests/test_PartSeg/test_napari_widgets.py  --no-cov
-    repo: python -m pytest --no-cov
+    repo: python -m pytest --no-cov .
 
 [testenv:py{37,38,39}-PyQt5-coverage]
 deps =
     {[testenv]deps}
 commands =
-    python -m pytest --cov-report=xml --cov-report html --cov-append --cov {envsitepackagesdir}/PartSeg --cov {envsitepackagesdir}/PartSegCore --cov {envsitepackagesdir}/PartSegImage
+    python -m pytest --cov-report=xml --cov-report html --cov-append --cov {envsitepackagesdir}/PartSeg --cov {envsitepackagesdir}/PartSegCore --cov {envsitepackagesdir}/PartSegImage --cov package/tests
     codecov
 
 [testenv:py37-PyQt5-minimal]