From b817112a878a4efa3c673a38af7b0938a70cdb9e Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Fri, 23 Jul 2021 05:01:52 +0300
Subject: Add docstring for `nearest' function

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

* gn3/computations/slink.py: add documentation for the `nearest` function in
  the `gn3.computations.slink` module in the form of a (hopefully correct)
  python docstring.
---
 gn3/computations/slink.py | 29 ++++++++++++++++++++++++++---
 1 file changed, 26 insertions(+), 3 deletions(-)

(limited to 'gn3/computations/slink.py')

diff --git a/gn3/computations/slink.py b/gn3/computations/slink.py
index 880ce9f..fc6f479 100644
--- a/gn3/computations/slink.py
+++ b/gn3/computations/slink.py
@@ -60,10 +60,33 @@ raise an exception."""
         raise ValueError("Distances should be positive.")
 
 def nearest(lists, i, j):
-    """Computes some form of distance.
-This is 'copied' over from genenetwork1, from https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L42-L64.
+    """
+    Computes shortest distance between member(s) in `i` and member(s) in `j`.
 
-This description should be updated once the form/type of 'distance' identified."""
+    Description:
+    This is 'copied' over from genenetwork1, from https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L42-L64.
+
+    This description should be updated to better describe what 'member' means in
+    the context where the function is used.
+
+    Parameters:
+    lists (list of lists of distances): Represents a list of members and their
+        distances from each other.
+        Each inner list represents the distances the member at that coordinate
+        is from other members in the list: for example, a member at index 0 with
+        the values [0, 9, 1, 7] indicates that the member is:
+        - 0 units of distance away from itself
+        - 9 units of distance away from member at coordinate 1
+        - 1 unit of distance away from member at coordinate 2
+        - 7 units of distance away from member at coordinate 3
+    i (int or list of ints): Represents the coordinate of a member, or a list of
+        coordinates of members on the `lists` list.
+    j (int or list of ints): Represents the coordinate of a member, or a list of
+        coordinates of members on the `lists` list.
+
+    Returns:
+    int: Represents the shortest distance between member(s) in `i` and member(s)
+        in `j`."""
 
     #### Guard Functions: Should we do this a different way? ####
     raise_valueerror_if_data_is_not_lists_or_tuples(lists)
-- 
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