start of tests (towards #3)

Author: Scott Warchal

tests/test_colfuncs.py

@@ -0,0 +1,37 @@
+"""
+tests for meld.colfuncs
+"""
+
+import os
+import pandas as pd
+import meld.colfuncs
+
+CURRENT_PATH = os.path.dirname(__file__)
+TEST_PATH = os.path.join(CURRENT_PATH, "test_data", "test_run0/DATA.csv")
+
+def test_collapse_cols():
+    """meld.colfuncs.collapse_cols(dataframe, sep)"""
+    example_df = pd.read_csv(TEST_PATH, header=[0,1])
+    collapsed_colnames = meld.colfuncs.collapse_cols(example_df, sep="_")
+    example_df.columns = collapsed_colnames
+    expected_colnames = ["Image_ImageNumber",
+                         "Image_Intensity_channel_1",
+                         "Cell_Area",
+                         "Cell_Eccentricity",
+                         "Nucleus_Area",
+                         "Nucleus_Eccentricity",
+                         "Metadata_Well"]
+    assert collapsed_colnames == expected_colnames
+
+
+def test_inflate_cols():
+    """meld.colfuncs.inflate_cols(dataframe)"""
+    # create example dataframe
+    example_df = pd.DataFrame(
+        {"Image_ImageNumber": [1, 2, 3],
+         "Cell_Area"        : [20, 20, 20],
+         "Nuclei_Perimeter" : [15, 15, 15]}
+    )
+    example_df.columns = meld.colfuncs.inflate_cols(example_df, sep="_")
+    # check the columns are MultiIndexed
+    assert isinstance(example_df.columns, pd.core.index.MultiIndex)

tests/test_data/test_run0/DATA.csv

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+Image,Image,Cell,Cell,Nucleus,Nucleus,Metadata
+ImageNumber,Intensity_channel_1,Area,Eccentricity,Area,Eccentricity,Well
+1,0.1,10,0.5,2,0.2,A01
+1,0.1,10,0.5,2,0.2,A01
+1,0.3,10,0.5,2,0.2,A01
+2,0.2,20,0.5,3,0.2,A01
+2,0.3,20,0.5,3,0.2,A01
+2,0.5,30,0.5,3,0.2,A01

tests/test_data/test_run0/Image.csv

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+Image,Image,Cell,Cell,Nucleus,Nucleus,Metadata
+ImageNumber,Intensity_channel_1,Area,Eccentricity,Area,Eccentricity,Well
+1,0.1,5,0.5,2,0.1,A02
+1,0.1,5,0.5,2,0.1,A02
+1,0.3,10,0.5,2,0.2,A02
+2,0.2,15,0.5,3,0.1,A02
+2,0.3,15,0.5,3,0.2,A02
+2,0.5,15,0.5,3,0.1,A02

tests/test_data/test_run1/DATA.csv

@@ -0,0 +1,8 @@
+Image,Image,Cell,Cell,Nucleus,Nucleus,Metadata
+ImageNumber,Intensity_channel_1,Area,Eccentricity,Area,Eccentricity,Well
+1,0.3,10,0.5,2,0.2,A03
+1,0.2,10,0.5,2,0.2,A03
+1,0.1,10,0.5,2,0.2,A03
+2,0.5,20,0.5,3,0.2,A03
+2,0.4,20,0.5,3,0.2,A03
+2,0.5,30,0.5,3,0.2,A03

tests/test_data/test_run1/Image.csv

@@ -0,0 +1,8 @@
+Image,Image,Cell,Cell,Nucleus,Nucleus,Metadata
+ImageNumber,Intensity_channel_1,Area,Eccentricity,Area,Eccentricity,Well
+1,0.1,10,0.5,2,0.1,A04
+1,0.1,10,0.5,2,0.1,A04
+1,0.3,10,0.5,2,0.1,A04
+2,0.2,20,0.5,3,0.1,A04
+2,0.3,20,0.5,3,0.1,A04
+2,0.5,30,0.5,3,0.1,A04

tests/test_data/test_run2/DATA.csv

@@ -0,0 +1,20 @@
+"""
+tests for meld.merge_to_db
+"""
+
+
+def test_create_db():
+    """meld.merge_to_db.Merger.create_db(location, db_name)"""
+    assert False
+
+
+# TODO
+def test_to_db():
+    """meld.merge_to_db.Merger.to_db(select, header)"""
+    assert False
+
+
+# TODO
+def test_to_db_agg():
+    """meld.merge_to_db.Merger.to_db_agg(select, header, by, method, prefix)"""
+    assert False

tests/test_data/test_run2/Image.csv

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+"""
+tests for meld.utils
+"""
+
+
+def test_aggregate():
+    """meld.utils.aggregate(data, on, method)"""
+    assert False
+
+
+# TODO
+def test__check_inputs():
+    """meld.utils._check_inputs(data, on, method)"""
+    assert False
+
+
+# TODO
+def test__check_featuredata():
+    """meld.utils._check_featuredata(data, on)"""
+    assert False
+
+
+# TODO
+def test_get_featuredata():
+    """meld.utils.get_featuredata(data, metadata_string, prefix)"""
+    assert False
+
+
+# TODO
+def test_get_metadata():
+    """meld.utils.get_metadata(data, metadata_string, prefix=False)"""
+    assert False