Check that all distances are positive or zero

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

* gn3/computations/slink.py: check that all distances between the 'somethings'
  are all either zero or positive.

* tests/unit/computations/test_slink.py:
  * Remove data with all distances positive or zero, since it would fail the
    test
  * Change the expected message to more closely correspond to the business
    logic

1 files changed, 2 insertions, 3 deletions

diff --git a/tests/unit/computations/test_slink.py b/tests/unit/computations/test_slink.py
index 207debf..6be3f33 100644
--- a/tests/unit/computations/test_slink.py
+++ b/tests/unit/computations/test_slink.py
@@ -55,15 +55,14 @@ class TestSlink(TestCase):
     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]],
+        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]]]:
             with self.subTest(lst=lst):
-                with self.assertRaises(ValueError, msg="Got an unexpected negative value!"):
+                with self.assertRaises(ValueError, msg="Distances should be positive."):
                     nearest(lst, 1, 1)
 
     def test_nearest_with_expected(self):