Extract tests from code in GN1

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi

* gn3/computations/slink.py: Add dummy `nearest' function
* tests/unit/computations/test_slink.py: Add some tests

  This commit adds tests to try and reproduce the working of the `nearest'
  function in:
  https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py

  This commit might not yet have extracted all the expected behaviour of the
  `nearest' function, and therefore, there is a possibility of a later commit
  augmenting the work in this commit.

1 files changed, 175 insertions, 0 deletions

diff --git a/tests/unit/computations/test_slink.py b/tests/unit/computations/test_slink.py
new file mode 100644
index 0000000..816cd2f
--- /dev/null
+++ b/tests/unit/computations/test_slink.py
@@ -0,0 +1,175 @@
+"""Module contains tests for slink"""
+import unittest
+from unittest import TestCase
+
+from gn3.computations.slink import nearest
+from gn3.computations.slink import LengthError
+from gn3.computations.slink import MirrorError
+
+class TestSlink(TestCase):
+    """Class for testing slink functions"""
+
+    def test_nearest_expects_list_of_lists(self):
+        # This might be better handled with type-hints and mypy
+        for item in [9, "some string", 5.432,
+                     [1,2,3], ["test", 7.4]]:
+            with self.subTest(item=item):
+                with self.assertRaises(ValueError, msg="Expected list or tuple"):
+                    nearest(item, 1, 1)
+
+    def test_nearest_does_not_allow_empty_lists(self):
+        for lst in [[],
+                    [[],[]],
+                    [[],[],[]],
+                    [[0, 1, 2],[],[1, 2, 0]]]:
+            with self.subTest(lst=lst):
+                with self.assertRaises(ValueError):
+                    nearest(lst, 1, 1)
+
+    def test_nearest_expects_exception_if_all_child_lists_are_not_of_equal_length_to_length_of_parent_list(self):
+        for lst in [[[0,1]],
+                    [[0,1,2],[3,4,5]],
+                    [[0,1,2,3],[4,5,6],[7,8,9,0]],
+                    [[0,1,2,3,4],[5,6,7,8,9],[1,2,3,4,5],[2,3],[3,4,5,6,7]]]:
+            with self.subTest(lst=lst):
+                with self.assertRaises(LengthError):
+                    nearest(lst, 1, 1)
+
+    def test_nearest_expects_exception_if_there_is_no_zero_at_childs_list_index_corresponding_to_its_index_in_parent(self):
+        # I don't like the name of this test. Make the name clearer
+        for lst in [[[1]],
+                    [[1,2],[3,4]],
+                    [1,0,0],[0,0,5],[0,3,4],
+                    [0,0,0,0],[0,0,3,3],[0,1,2,3],[0,3,2,0]]:
+            with self.subTest(lst=lst):
+                with self.assertRaises(ValueError):
+                    nearest(lst, 1, 1)
+
+    def test_nearest_expects_exception_if_value_at_index_j_in_list_i_does_not_equals_value_at_index_i_in_list_j(self):
+        for lst in [[[0,1],[2,0]],
+                    [[0,1,2],[1,0,3],[9,7,0]],
+                    [[0,1,2,3],[7,0,2,3],[2,3,0,1],[8,9,5,0]]]:
+            with self.subTest(lst=lst):
+                with self.assertRaises(MirrorError):
+                    nearest(lst, 1, 1)
+
+    def test_nearest_expects_zero_or_positive_distances(self):
+        # Based on:
+        # https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L87-L89
+        for lst in [[[0,1,2,3],[1,0,3,4],[2,3,0,5],[3,4,5,0]],
+                    [[0,1,2,3],[-1,0,3,4],[2,3,0,5],[3,4,5,0]],
+                    [[0,1,2,3],[1,0,3,4],[-2,3,0,5],[3,4,5,0]],
+                    [[0,1,2,3],[1,0,3,4],[2,-3,0,5],[3,4,5,0]],
+                    [[0,1,2,3],[1,0,3,4],[2,3,0,5],[-3,4,5,0]],
+                    [[0,1,2,3],[1,0,3,4],[2,3,0,5],[3,-4,5,0]],
+                    [[0,1,2,3],[1,0,3,4],[2,3,0,5],[3,4,-5,0]]]:
+            with self.subTest(lst=lst):
+                with self.assertRaises(ValueError, msg="Got an unexpected negative value!"):
+                    nearest(lst, 1, 1)
+
+    def test_nearest_with_expected(self):
+        # Give this test a better name
+        # The lists in this tests are taken from:
+        # https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L39-L40
+        for lst, i, j, expected in [[[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     0,0,0],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     0,1,9],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     0,2,3],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     0,3,6],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     0,4,11],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     1,0,9],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     1,1,0],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     1,2,7],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     1,3,5],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     1,4,10],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     2,0,3],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     2,1,7],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     2,2,0],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     2,3,9],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     2,4,2],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     3,0,6],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     3,1,5],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     3,2,9],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     3,3,0],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     3,4,8],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     4,0,11],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     4,1,10],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     4,2,2],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     4,3,8],
+                                    [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
+                                     4,4,0],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     0,0,0],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     0,1,9],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     0,2,5.5],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     0,3,6],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     0,4,11],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     1,0,9],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     1,1,0],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     1,2,7],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     1,3,5],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     1,4,10],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     2,0,5.5],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     2,1,7],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     2,2,0],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     2,3,9],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     2,4,2],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     3,0,6],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     3,1,5],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     3,2,9],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     3,3,0],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     3,4,3],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     4,0,11],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     4,1,10],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     4,2,2],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     4,3,3],
+                                    [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
+                                     4,4,0]]:
+            with self.subTest(lst=lst):
+                self.assertEqual(nearest(lst, i, j), expected)