Merge branch 'ete4' of github.com:etetoolkit/ete into ete4

tests/redundant/test_arraytable.py

@@ -0,0 +1,42 @@
+import unittest
+
+import numpy as np
+
+from ete4 import ArrayTable
+from .. import datasets as ds
+
+
+class Test_Core_ArrayTable(unittest.TestCase):
+    """Tests reading clustering or phylogenetic profile data."""
+
+    def test_arraytable_parser(self):
+        """Test reading numeric tables."""
+        A = ArrayTable(ds.expression)
+
+        self.assertEqual(A.get_row_vector("A").tolist(),
+                         [-1.23, -0.81, 1.79, 0.78,-0.42,-0.69, 0.58])
+        self.assertEqual(A.get_several_row_vectors(["A", "C"]).tolist(),
+                         [[-1.23, -0.81, 1.79, 0.78, -0.42, -0.69, 0.58],
+                          [-2.19, 0.13, 0.65, -0.51, 0.52, 1.04, 0.36]])
+
+        self.assertEqual(A.get_several_column_vectors(["col2", "col7"]).tolist(),
+                         [[-0.81, -0.94, 0.13, -0.98, -0.83, -1.11, -1.17, -1.25],
+                          [0.58, 1.12, 0.36, 0.93, 0.65, 0.48, 0.26, 0.77]])
+
+        self.assertEqual(A.get_column_vector("col4").tolist(),
+                         [0.78, 0.36, -0.51, -0.76, 0.07, -0.14, 0.23, -0.3])
+
+        A.remove_column("col4")
+        self.assertTrue(A.get_column_vector("col4") is None)
+
+        Abis = A.merge_columns({"merged1": ["col1", "col2"],
+                                "merged2": ["col5", "col6"]}, "mean")
+
+        self.assertTrue((np.round(Abis.get_column_vector("merged1"), 3) ==
+                         [-1.02, -1.35, -1.03, -1.1, -1.15, -1.075, -1.37, -1.39]).all())
+        # Continue this......
+        # Sure. C'mon Jaime, you can do it!
+
+
+if __name__ == '__main__':
+    unittest.main()

tests/test_arraytable.py

@@ -1,42 +1,37 @@
-import unittest
+"""
+Tests reading clustering or phylogenetic profile data.
+"""
 
 import numpy as np
 
 from ete4 import ArrayTable
 from . import datasets as ds
 
 
-class Test_Core_ArrayTable(unittest.TestCase):
-    """Tests reading clustering or phylogenetic profile data."""
+def test_arraytable_parser():
+    """Test reading numeric tables and simple manipulations."""
+    A = ArrayTable(ds.expression)
 
-    def test_arraytable_parser(self):
-        """Test reading numeric tables."""
-        A = ArrayTable(ds.expression)
+    assert (A.get_row_vector("A").tolist() ==
+            [-1.23, -0.81, 1.79, 0.78,-0.42,-0.69, 0.58])
 
-        self.assertEqual(A.get_row_vector("A").tolist(),
-                         [-1.23, -0.81, 1.79, 0.78,-0.42,-0.69, 0.58])
-        self.assertEqual(A.get_several_row_vectors(["A", "C"]).tolist(),
-                         [[-1.23, -0.81, 1.79, 0.78, -0.42, -0.69, 0.58],
-                          [-2.19, 0.13, 0.65, -0.51, 0.52, 1.04, 0.36]])
+    assert (A.get_several_row_vectors(["A", "C"]).tolist() ==
+            [[-1.23, -0.81, 1.79, 0.78, -0.42, -0.69, 0.58],
+             [-2.19, 0.13, 0.65, -0.51, 0.52, 1.04, 0.36]])
 
-        self.assertEqual(A.get_several_column_vectors(["col2", "col7"]).tolist(),
-                         [[-0.81, -0.94, 0.13, -0.98, -0.83, -1.11, -1.17, -1.25],
-                          [0.58, 1.12, 0.36, 0.93, 0.65, 0.48, 0.26, 0.77]])
+    assert (A.get_column_vector("col4").tolist() ==
+            [0.78, 0.36, -0.51, -0.76, 0.07, -0.14, 0.23, -0.3])
 
-        self.assertEqual(A.get_column_vector("col4").tolist(),
-                         [0.78, 0.36, -0.51, -0.76, 0.07, -0.14, 0.23, -0.3])
+    assert (A.get_several_column_vectors(["col2", "col7"]).tolist() ==
+            [[-0.81, -0.94, 0.13, -0.98, -0.83, -1.11, -1.17, -1.25],
+             [0.58, 1.12, 0.36, 0.93, 0.65, 0.48, 0.26, 0.77]])
 
-        A.remove_column("col4")
-        self.assertTrue(A.get_column_vector("col4") is None)
+    A.remove_column("col4")
+    assert A.get_column_vector("col4") is None
 
-        Abis = A.merge_columns({"merged1": ["col1", "col2"],
-                                "merged2": ["col5", "col6"]}, "mean")
+    Abis = A.merge_columns({"merged1": ["col1", "col2"],
+                            "merged2": ["col5", "col6"]}, "mean")
+    assert (np.round(Abis.get_column_vector("merged1"), 3).tolist() ==
+            [-1.02, -1.35, -1.03, -1.1, -1.15, -1.075, -1.37, -1.39])
 
-        self.assertTrue((np.round(Abis.get_column_vector("merged1"), 3) ==
-                         [-1.02, -1.35, -1.03, -1.1, -1.15, -1.075, -1.37, -1.39]).all())
-        # Continue this......
-        # Sure. C'mon Jaime, you can do it!
-
-
-if __name__ == '__main__':
-    unittest.main()
+    # TODO: More tests. Jaime, you can do it!