Update tests (#348)

* Remove unused test data dir * Remove another unused test data directory * Register custom pytest marker * lint * Add coverage --------- Co-authored-by: Will Graham <[email protected]> Co-authored-by: willGraham01 <[email protected]>
brainglobe · Jan 4, 2024 · d94a73b · d94a73b
1 parent 84784e2
commit d94a73b
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Showing 297 changed files with 37 additions and 1,604 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -103,6 +103,10 @@ include = ["cellfinder*"]
 
 [tool.setuptools_scm]
 
+[tool.pytest.ini_options]
+addopts = "--cov=cellfinder"
+markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"]
+
 [tool.tox]
 legacy_tox_ini = """
 # For more information about tox, see https://tox.readthedocs.io/en/latest/

diff --git a/tests/core/test_unit/test_tools/test_IO.py b/tests/core/test_unit/test_tools/test_IO.py
@@ -2,8 +2,8 @@
 
 from cellfinder.core.tools import IO
 
-BRAIN_DIR = "tests/data/brain"
-BRAIN_PATHS = f"{BRAIN_DIR}/brain_paths.txt"
+BRAIN_DIR = "tests/data/background"
+BRAIN_PATHS = f"{BRAIN_DIR}/background_paths.txt"
 
 
 def test_read_with_dask_txt():

diff --git a/tests/core/test_unit/test_tools/test_system.py b/tests/core/test_unit/test_tools/test_system.py
@@ -14,18 +14,18 @@
 
 def test_get_subdirectories():
     subdirs = system.get_subdirectories(data_dir)
-    assert len(subdirs) == 9
+    assert len(subdirs) == 7
     assert Path(data_dir / "cells") in subdirs
-    assert Path(data_dir / "brain") in subdirs
+    assert Path(data_dir / "background") in subdirs
 
     subdir_names = system.get_subdirectories(data_dir, names_only=True)
-    assert len(subdir_names) == 9
+    assert len(subdir_names) == 7
     assert "cells" in subdir_names
-    assert "brain" in subdir_names
+    assert "background" in subdir_names
 
 
 def test_get_number_of_files_in_dir():
-    assert system.get_number_of_files_in_dir(background_im_dir) == 26
+    assert system.get_number_of_files_in_dir(background_im_dir) == 27
 
 
 def write_file_single_size(directory, file_size):

diff --git a/tests/data/background/background_paths.txt b/tests/data/background/background_paths.txt
@@ -0,0 +1,26 @@
+tests/data/background/background_ch010010.tif
+tests/data/background/background_ch010023.tif
+tests/data/background/background_ch010019.tif
+tests/data/background/background_ch010022.tif
+tests/data/background/background_ch010015.tif
+tests/data/background/background_ch010002.tif
+tests/data/background/background_ch010005.tif
+tests/data/background/background_ch010021.tif
+tests/data/background/background_ch010000.tif
+tests/data/background/background_ch010008.tif
+tests/data/background/background_ch010007.tif
+tests/data/background/background_ch010006.tif
+tests/data/background/background_ch010004.tif
+tests/data/background/background_ch010014.tif
+tests/data/background/background_ch010011.tif
+tests/data/background/background_ch010017.tif
+tests/data/background/background_ch010003.tif
+tests/data/background/background_ch010018.tif
+tests/data/background/background_ch010020.tif
+tests/data/background/background_ch010025.tif
+tests/data/background/background_ch010013.tif
+tests/data/background/background_ch010009.tif
+tests/data/background/background_ch010016.tif
+tests/data/background/background_ch010012.tif
+tests/data/background/background_ch010001.tif
+tests/data/background/background_ch010024.tif
diff --git a/tests/data/brain/brain_paths.txt b/tests/data/brain/brain_paths.txt
diff --git a/tests/data/brain/image_0000.tif b/tests/data/brain/image_0000.tif
diff --git a/tests/data/brain/image_0001.tif b/tests/data/brain/image_0001.tif
diff --git a/tests/data/brain/image_0002.tif b/tests/data/brain/image_0002.tif
diff --git a/tests/data/brain/image_0003.tif b/tests/data/brain/image_0003.tif
diff --git a/tests/data/brain/image_0004.tif b/tests/data/brain/image_0004.tif
diff --git a/tests/data/brain/image_0005.tif b/tests/data/brain/image_0005.tif
diff --git a/tests/data/brain/image_0006.tif b/tests/data/brain/image_0006.tif
diff --git a/tests/data/brain/image_0007.tif b/tests/data/brain/image_0007.tif
diff --git a/tests/data/brain/image_0008.tif b/tests/data/brain/image_0008.tif
diff --git a/tests/data/brain/image_0009.tif b/tests/data/brain/image_0009.tif
diff --git a/tests/data/brain/image_0010.tif b/tests/data/brain/image_0010.tif
diff --git a/tests/data/brain/image_0011.tif b/tests/data/brain/image_0011.tif
diff --git a/tests/data/brain/image_0012.tif b/tests/data/brain/image_0012.tif
diff --git a/tests/data/brain/image_0013.tif b/tests/data/brain/image_0013.tif
diff --git a/tests/data/brain/image_0014.tif b/tests/data/brain/image_0014.tif
diff --git a/tests/data/brain/image_0015.tif b/tests/data/brain/image_0015.tif
diff --git a/tests/data/brain/image_0016.tif b/tests/data/brain/image_0016.tif
diff --git a/tests/data/brain/image_0017.tif b/tests/data/brain/image_0017.tif
diff --git a/tests/data/brain/image_0018.tif b/tests/data/brain/image_0018.tif
diff --git a/tests/data/brain/image_0019.tif b/tests/data/brain/image_0019.tif
diff --git a/tests/data/brain/image_0020.tif b/tests/data/brain/image_0020.tif
diff --git a/tests/data/brain/image_0021.tif b/tests/data/brain/image_0021.tif
diff --git a/tests/data/brain/image_0022.tif b/tests/data/brain/image_0022.tif
diff --git a/tests/data/brain/image_0023.tif b/tests/data/brain/image_0023.tif
diff --git a/tests/data/brain/image_0024.tif b/tests/data/brain/image_0024.tif
diff --git a/tests/data/brain/image_0025.tif b/tests/data/brain/image_0025.tif
diff --git a/tests/data/brain/image_0026.tif b/tests/data/brain/image_0026.tif
diff --git a/tests/data/brain/image_0027.tif b/tests/data/brain/image_0027.tif
diff --git a/tests/data/brain/image_0028.tif b/tests/data/brain/image_0028.tif
diff --git a/tests/data/brain/image_0029.tif b/tests/data/brain/image_0029.tif
diff --git a/tests/data/brain/image_0030.tif b/tests/data/brain/image_0030.tif
diff --git a/tests/data/brain/image_0031.tif b/tests/data/brain/image_0031.tif
diff --git a/tests/data/brain/image_0032.tif b/tests/data/brain/image_0032.tif
diff --git a/tests/data/brain/image_0033.tif b/tests/data/brain/image_0033.tif
diff --git a/tests/data/brain/image_0034.tif b/tests/data/brain/image_0034.tif
diff --git a/tests/data/brain/image_0035.tif b/tests/data/brain/image_0035.tif
diff --git a/tests/data/brain/image_0036.tif b/tests/data/brain/image_0036.tif
diff --git a/tests/data/brain/image_0037.tif b/tests/data/brain/image_0037.tif
diff --git a/tests/data/brain/image_0038.tif b/tests/data/brain/image_0038.tif
diff --git a/tests/data/brain/image_0039.tif b/tests/data/brain/image_0039.tif
diff --git a/tests/data/brain/image_0040.tif b/tests/data/brain/image_0040.tif
diff --git a/tests/data/brain/image_0041.tif b/tests/data/brain/image_0041.tif
diff --git a/tests/data/brain/image_0042.tif b/tests/data/brain/image_0042.tif
diff --git a/tests/data/brain/image_0043.tif b/tests/data/brain/image_0043.tif
diff --git a/tests/data/brain/image_0044.tif b/tests/data/brain/image_0044.tif
diff --git a/tests/data/brain/image_0045.tif b/tests/data/brain/image_0045.tif
diff --git a/tests/data/brain/image_0046.tif b/tests/data/brain/image_0046.tif
diff --git a/tests/data/brain/image_0047.tif b/tests/data/brain/image_0047.tif
diff --git a/tests/data/brain/image_0048.tif b/tests/data/brain/image_0048.tif
diff --git a/tests/data/brain/image_0049.tif b/tests/data/brain/image_0049.tif
diff --git a/tests/data/brain/image_0050.tif b/tests/data/brain/image_0050.tif
diff --git a/tests/data/brain/image_0051.tif b/tests/data/brain/image_0051.tif
diff --git a/tests/data/brain/image_0052.tif b/tests/data/brain/image_0052.tif
diff --git a/tests/data/brain/image_0053.tif b/tests/data/brain/image_0053.tif
diff --git a/tests/data/brain/image_0054.tif b/tests/data/brain/image_0054.tif
diff --git a/tests/data/brain/image_0055.tif b/tests/data/brain/image_0055.tif
diff --git a/tests/data/brain/image_0056.tif b/tests/data/brain/image_0056.tif
diff --git a/tests/data/brain/image_0057.tif b/tests/data/brain/image_0057.tif
diff --git a/tests/data/brain/image_0058.tif b/tests/data/brain/image_0058.tif
diff --git a/tests/data/brain/image_0059.tif b/tests/data/brain/image_0059.tif
diff --git a/tests/data/brain/image_0060.tif b/tests/data/brain/image_0060.tif
diff --git a/tests/data/brain/image_0061.tif b/tests/data/brain/image_0061.tif
diff --git a/tests/data/brain/image_0062.tif b/tests/data/brain/image_0062.tif
diff --git a/tests/data/brain/image_0063.tif b/tests/data/brain/image_0063.tif
diff --git a/tests/data/brain/image_0064.tif b/tests/data/brain/image_0064.tif
diff --git a/tests/data/brain/image_0065.tif b/tests/data/brain/image_0065.tif
diff --git a/tests/data/brain/image_0066.tif b/tests/data/brain/image_0066.tif
diff --git a/tests/data/brain/image_0067.tif b/tests/data/brain/image_0067.tif
diff --git a/tests/data/brain/image_0068.tif b/tests/data/brain/image_0068.tif
diff --git a/tests/data/brain/image_0069.tif b/tests/data/brain/image_0069.tif
diff --git a/tests/data/brain/image_0070.tif b/tests/data/brain/image_0070.tif
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diff --git a/tests/data/brain/image_0073.tif b/tests/data/brain/image_0073.tif
diff --git a/tests/data/brain/image_0074.tif b/tests/data/brain/image_0074.tif
diff --git a/tests/data/brain/image_0075.tif b/tests/data/brain/image_0075.tif
diff --git a/tests/data/brain/image_0076.tif b/tests/data/brain/image_0076.tif
diff --git a/tests/data/brain/image_0077.tif b/tests/data/brain/image_0077.tif
diff --git a/tests/data/brain/image_0078.tif b/tests/data/brain/image_0078.tif
diff --git a/tests/data/brain/image_0079.tif b/tests/data/brain/image_0079.tif
diff --git a/tests/data/brain/image_0080.tif b/tests/data/brain/image_0080.tif
diff --git a/tests/data/brain/image_0081.tif b/tests/data/brain/image_0081.tif
diff --git a/tests/data/brain/image_0082.tif b/tests/data/brain/image_0082.tif
diff --git a/tests/data/brain/image_0083.tif b/tests/data/brain/image_0083.tif
diff --git a/tests/data/brain/image_0084.tif b/tests/data/brain/image_0084.tif
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diff --git a/tests/data/brain/image_0088.tif b/tests/data/brain/image_0088.tif
diff --git a/tests/data/brain/image_0089.tif b/tests/data/brain/image_0089.tif
diff --git a/tests/data/brain/image_0090.tif b/tests/data/brain/image_0090.tif
diff --git a/tests/data/brain/image_0091.tif b/tests/data/brain/image_0091.tif
diff --git a/tests/data/brain/image_0092.tif b/tests/data/brain/image_0092.tif
diff --git a/tests/data/brain/image_0093.tif b/tests/data/brain/image_0093.tif
diff --git a/tests/data/brain/image_0094.tif b/tests/data/brain/image_0094.tif
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diff --git a/tests/data/brain/image_0096.tif b/tests/data/brain/image_0096.tif
diff --git a/tests/data/brain/image_0097.tif b/tests/data/brain/image_0097.tif
diff --git a/tests/data/brain/image_0098.tif b/tests/data/brain/image_0098.tif
diff --git a/tests/data/brain/image_0099.tif b/tests/data/brain/image_0099.tif
diff --git a/tests/data/brain/image_0100.tif b/tests/data/brain/image_0100.tif
diff --git a/tests/data/brain/image_0101.tif b/tests/data/brain/image_0101.tif
diff --git a/tests/data/brain/image_0102.tif b/tests/data/brain/image_0102.tif
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diff --git a/tests/data/brain/image_0113.tif b/tests/data/brain/image_0113.tif
diff --git a/tests/data/brain/image_0114.tif b/tests/data/brain/image_0114.tif
diff --git a/tests/data/brain/image_0115.tif b/tests/data/brain/image_0115.tif
diff --git a/tests/data/brain/image_0116.tif b/tests/data/brain/image_0116.tif
diff --git a/tests/data/brain/image_0117.tif b/tests/data/brain/image_0117.tif
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diff --git a/tests/data/brain/image_0120.tif b/tests/data/brain/image_0120.tif
diff --git a/tests/data/brain/image_0121.tif b/tests/data/brain/image_0121.tif
diff --git a/tests/data/brain/image_0122.tif b/tests/data/brain/image_0122.tif
diff --git a/tests/data/brain/image_0123.tif b/tests/data/brain/image_0123.tif
diff --git a/tests/data/brain/image_0124.tif b/tests/data/brain/image_0124.tif
diff --git a/tests/data/brain/image_0125.tif b/tests/data/brain/image_0125.tif
diff --git a/tests/data/brain/image_0126.tif b/tests/data/brain/image_0126.tif
diff --git a/tests/data/brain/image_0127.tif b/tests/data/brain/image_0127.tif
diff --git a/tests/data/brain/image_0128.tif b/tests/data/brain/image_0128.tif
diff --git a/tests/data/brain/image_0129.tif b/tests/data/brain/image_0129.tif
diff --git a/tests/data/brain/image_0130.tif b/tests/data/brain/image_0130.tif
diff --git a/tests/data/brain/image_0131.tif b/tests/data/brain/image_0131.tif
diff --git a/tests/data/brain/image_0132.tif b/tests/data/brain/image_0132.tif
diff --git a/tests/data/brain/image_0133.tif b/tests/data/brain/image_0133.tif
diff --git a/tests/data/brain/image_0134.tif b/tests/data/brain/image_0134.tif
diff --git a/tests/data/brain/image_0135.tif b/tests/data/brain/image_0135.tif
diff --git a/tests/data/brain/image_0136.tif b/tests/data/brain/image_0136.tif
diff --git a/tests/data/brain/image_0137.tif b/tests/data/brain/image_0137.tif
diff --git a/tests/data/brain/image_0138.tif b/tests/data/brain/image_0138.tif
diff --git a/tests/data/brain/image_0139.tif b/tests/data/brain/image_0139.tif
diff --git a/tests/data/brain/image_0140.tif b/tests/data/brain/image_0140.tif
diff --git a/tests/data/brain/image_0141.tif b/tests/data/brain/image_0141.tif
diff --git a/tests/data/brain/image_0142.tif b/tests/data/brain/image_0142.tif
diff --git a/tests/data/brain/image_0143.tif b/tests/data/brain/image_0143.tif
diff --git a/tests/data/brain/image_0144.tif b/tests/data/brain/image_0144.tif
diff --git a/tests/data/brain/image_0145.tif b/tests/data/brain/image_0145.tif
diff --git a/tests/data/brain/image_0146.tif b/tests/data/brain/image_0146.tif
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diff --git a/tests/data/brain/image_0148.tif b/tests/data/brain/image_0148.tif
diff --git a/tests/data/brain/image_0149.tif b/tests/data/brain/image_0149.tif
diff --git a/tests/data/brain/image_0150.tif b/tests/data/brain/image_0150.tif
diff --git a/tests/data/brain/image_0151.tif b/tests/data/brain/image_0151.tif
diff --git a/tests/data/brain/image_0152.tif b/tests/data/brain/image_0152.tif
diff --git a/tests/data/brain/image_0153.tif b/tests/data/brain/image_0153.tif
diff --git a/tests/data/brain/image_0154.tif b/tests/data/brain/image_0154.tif
diff --git a/tests/data/brain/image_0155.tif b/tests/data/brain/image_0155.tif
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diff --git a/tests/data/brain/image_0200.tif b/tests/data/brain/image_0200.tif
diff --git a/tests/data/brain/image_0201.tif b/tests/data/brain/image_0201.tif
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diff --git a/tests/data/brain/image_0211.tif b/tests/data/brain/image_0211.tif
diff --git a/tests/data/brain/image_0212.tif b/tests/data/brain/image_0212.tif
diff --git a/tests/data/brain/image_0213.tif b/tests/data/brain/image_0213.tif
diff --git a/tests/data/brain/image_0214.tif b/tests/data/brain/image_0214.tif
diff --git a/tests/data/brain/image_0215.tif b/tests/data/brain/image_0215.tif
diff --git a/tests/data/brain/image_0216.tif b/tests/data/brain/image_0216.tif
diff --git a/tests/data/brain/image_0217.tif b/tests/data/brain/image_0217.tif
diff --git a/tests/data/brain/image_0218.tif b/tests/data/brain/image_0218.tif
diff --git a/tests/data/brain/image_0219.tif b/tests/data/brain/image_0219.tif
diff --git a/tests/data/brain/image_0220.tif b/tests/data/brain/image_0220.tif
diff --git a/tests/data/brain/image_0221.tif b/tests/data/brain/image_0221.tif
diff --git a/tests/data/brain/image_0222.tif b/tests/data/brain/image_0222.tif
diff --git a/tests/data/brain/image_0223.tif b/tests/data/brain/image_0223.tif
diff --git a/tests/data/brain/image_0224.tif b/tests/data/brain/image_0224.tif
diff --git a/tests/data/brain/image_0225.tif b/tests/data/brain/image_0225.tif
diff --git a/tests/data/brain/image_0226.tif b/tests/data/brain/image_0226.tif
diff --git a/tests/data/brain/image_0227.tif b/tests/data/brain/image_0227.tif
diff --git a/tests/data/brain/image_0228.tif b/tests/data/brain/image_0228.tif
diff --git a/tests/data/brain/image_0229.tif b/tests/data/brain/image_0229.tif
diff --git a/tests/data/brain/image_0230.tif b/tests/data/brain/image_0230.tif
diff --git a/tests/data/brain/image_0231.tif b/tests/data/brain/image_0231.tif
diff --git a/tests/data/brain/image_0232.tif b/tests/data/brain/image_0232.tif
diff --git a/tests/data/brain/image_0233.tif b/tests/data/brain/image_0233.tif
diff --git a/tests/data/brain/image_0234.tif b/tests/data/brain/image_0234.tif
diff --git a/tests/data/brain/image_0235.tif b/tests/data/brain/image_0235.tif
diff --git a/tests/data/brain/image_0236.tif b/tests/data/brain/image_0236.tif
diff --git a/tests/data/brain/image_0237.tif b/tests/data/brain/image_0237.tif
diff --git a/tests/data/brain/image_0238.tif b/tests/data/brain/image_0238.tif
diff --git a/tests/data/brain/image_0239.tif b/tests/data/brain/image_0239.tif
diff --git a/tests/data/brain/image_0240.tif b/tests/data/brain/image_0240.tif
diff --git a/tests/data/brain/image_0241.tif b/tests/data/brain/image_0241.tif
diff --git a/tests/data/brain/image_0242.tif b/tests/data/brain/image_0242.tif
diff --git a/tests/data/brain/image_0243.tif b/tests/data/brain/image_0243.tif
diff --git a/tests/data/brain/image_0244.tif b/tests/data/brain/image_0244.tif
diff --git a/tests/data/brain/image_0245.tif b/tests/data/brain/image_0245.tif
diff --git a/tests/data/brain/image_0246.tif b/tests/data/brain/image_0246.tif
diff --git a/tests/data/brain/image_0247.tif b/tests/data/brain/image_0247.tif
diff --git a/tests/data/brain/image_0248.tif b/tests/data/brain/image_0248.tif
diff --git a/tests/data/brain/image_0249.tif b/tests/data/brain/image_0249.tif
diff --git a/tests/data/brain/image_0250.tif b/tests/data/brain/image_0250.tif
diff --git a/tests/data/brain/image_0251.tif b/tests/data/brain/image_0251.tif
diff --git a/tests/data/brain/image_0252.tif b/tests/data/brain/image_0252.tif
diff --git a/tests/data/brain/image_0253.tif b/tests/data/brain/image_0253.tif
diff --git a/tests/data/brain/image_0254.tif b/tests/data/brain/image_0254.tif
diff --git a/tests/data/brain/image_0255.tif b/tests/data/brain/image_0255.tif
diff --git a/tests/data/brain/image_0256.tif b/tests/data/brain/image_0256.tif
diff --git a/tests/data/brain/image_0257.tif b/tests/data/brain/image_0257.tif
diff --git a/tests/data/brain/image_0258.tif b/tests/data/brain/image_0258.tif
diff --git a/tests/data/brain/image_0259.tif b/tests/data/brain/image_0259.tif
diff --git a/tests/data/brain/image_0260.tif b/tests/data/brain/image_0260.tif
diff --git a/tests/data/brain/image_0261.tif b/tests/data/brain/image_0261.tif
diff --git a/tests/data/brain/image_0262.tif b/tests/data/brain/image_0262.tif
diff --git a/tests/data/brain/image_0263.tif b/tests/data/brain/image_0263.tif
diff --git a/tests/data/brain/image_0264.tif b/tests/data/brain/image_0264.tif
diff --git a/tests/data/brain/image_0265.tif b/tests/data/brain/image_0265.tif
diff --git a/tests/data/brain/image_0266.tif b/tests/data/brain/image_0266.tif
diff --git a/tests/data/brain/image_0267.tif b/tests/data/brain/image_0267.tif
diff --git a/tests/data/brain/image_0268.tif b/tests/data/brain/image_0268.tif
diff --git a/tests/data/brain/image_0269.tif b/tests/data/brain/image_0269.tif
diff --git a/tests/data/registration_output/Linux/boundaries.tiff b/tests/data/registration_output/Linux/boundaries.tiff
diff --git a/tests/data/registration_output/Linux/deformation_field_0.tiff b/tests/data/registration_output/Linux/deformation_field_0.tiff
diff --git a/tests/data/registration_output/Linux/deformation_field_1.tiff b/tests/data/registration_output/Linux/deformation_field_1.tiff
diff --git a/tests/data/registration_output/Linux/deformation_field_2.tiff b/tests/data/registration_output/Linux/deformation_field_2.tiff
diff --git a/tests/data/registration_output/Linux/downsampled.tiff b/tests/data/registration_output/Linux/downsampled.tiff
diff --git a/tests/data/registration_output/Linux/downsampled_channel_0.tiff b/tests/data/registration_output/Linux/downsampled_channel_0.tiff
diff --git a/tests/data/registration_output/Linux/downsampled_standard.tiff b/tests/data/registration_output/Linux/downsampled_standard.tiff
diff --git a/tests/data/registration_output/Linux/downsampled_standard_channel_0.tiff b/tests/data/registration_output/Linux/downsampled_standard_channel_0.tiff
diff --git a/tests/data/registration_output/Linux/registered_atlas.tiff b/tests/data/registration_output/Linux/registered_atlas.tiff
diff --git a/tests/data/registration_output/Linux/registered_hemispheres.tiff b/tests/data/registration_output/Linux/registered_hemispheres.tiff