swap from log4j to logback

bethac07 commented 2 years ago

Resolves #153

All tests passing locally, and can still open bioformats-requiring files in local cellprofiler.

bethac07 commented 2 years ago

Some tests in core now failing, digging in

======================================================================================================= FAILURES =======================================================================================================
__________________________________________________________________________________________________ test_load_objects ___________________________________________________________________________________________________

    def test_load_objects():
        path = tests.modules.maybe_download_example_image(
            ["ExampleSBSImages"], "Channel2-01-A-01.tif"
        )
        target = bioformats.load_image(path, rescale=False)
        target = skimage.morphology.label(target)

        with open(path, "rb") as fd:
            md5 = hashlib.md5(fd.read()).hexdigest()
        workspace = run_workspace(
            path, cellprofiler_core.modules.namesandtypes.LOAD_AS_OBJECTS
        )
        o = workspace.object_set.get_objects(OBJECTS_NAME)
        assert isinstance(o, cellprofiler_core.object.Objects)
        areas = o.areas
        counts = numpy.bincount(target.flatten())
        assert areas[0] == counts[1]
        assert areas[1] == counts[2]
>       assert areas[2] == counts[3]
E       assert 1 == 2

tests/modules/test_namesandtypes.py:1928: AssertionError
_______________________________________________________________________________________________ test_load_single_object ________________________________________________________________________________________________

    def test_load_single_object():
        path = tests.modules.maybe_download_example_image(
            ["ExampleSBSImages"], "Channel1-01-A-01.tif"
        )
        lsi_path = tests.modules.maybe_download_example_image(
            ["ExampleSBSImages"], "Channel2-01-A-01.tif"
        )
        target = bioformats.load_image(lsi_path, rescale=False)
        target = skimage.morphology.label(target)
        with open(lsi_path, "rb") as fd:
            md5 = hashlib.md5(fd.read()).hexdigest()
        workspace = run_workspace(
            path,
            cellprofiler_core.modules.namesandtypes.LOAD_AS_GRAYSCALE_IMAGE,
            lsi=[
                {
                    "path": lsi_path,
                    "load_as_type": cellprofiler_core.modules.namesandtypes.LOAD_AS_OBJECTS,
                    "name": "lsi",
                }
            ],
        )
        o = workspace.object_set.get_objects("lsi")
        assert isinstance(o, cellprofiler_core.object.Objects)
        counts = numpy.bincount(target.flatten())
        areas = o.areas
        assert areas[0] == counts[1]
        assert areas[1] == counts[2]
>       assert areas[2] == counts[3]
E       assert 1 == 2

tests/modules/test_namesandtypes.py:2064: AssertionError

bethac07 commented 2 years ago

They... stopped failing and I don't know why?

All tests now passing in core and CellProfiler

gnodar01 commented 2 years ago

Should loci_tools.jar also be replaced in setup.cfg?

CellProfiler / python-bioformats

swap from log4j to logback #154