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authorMuriithi Frederick Muriuki2021-07-23 05:13:34 +0300
committerMuriithi Frederick Muriuki2021-07-23 05:13:34 +0300
commitf10c18757a097f310c011c54f31a9a4bc6e47ce5 (patch)
treea0961c7f4fb3414100688459f2e0c76292a5277e /gn3
parentb817112a878a4efa3c673a38af7b0938a70cdb9e (diff)
downloadgenenetwork3-f10c18757a097f310c011c54f31a9a4bc6e47ce5.tar.gz
Add dummy module documentation
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Add initial dummy module documentation in form of a python docstring Update the names of what would be private methods/function to start with a double-underscore (__) so that they do not show up in the default python documentation.
Diffstat (limited to 'gn3')
-rw-r--r--gn3/computations/slink.py42
1 files changed, 25 insertions, 17 deletions
diff --git a/gn3/computations/slink.py b/gn3/computations/slink.py
index fc6f479..c29ddb0 100644
--- a/gn3/computations/slink.py
+++ b/gn3/computations/slink.py
@@ -1,3 +1,11 @@
+"""
+DESCRIPTION:
+ TODO: Add a description for the module
+
+FUNCTIONS:
+slink:
+ TODO: Describe what the function does...
+"""
from functools import partial
class LengthError(BaseException):
@@ -6,29 +14,29 @@ class LengthError(BaseException):
class MirrorError(BaseException):
pass
-def is_list_or_tuple(item):
+def __is_list_or_tuple(item):
return type(item) in [list, tuple]
-def raise_valueerror_if_data_is_not_lists_or_tuples(lists):
+def __raise_valueerror_if_data_is_not_lists_or_tuples(lists):
"""Check that `lists` is a list of lists: If not, raise an exception."""
- if (not is_list_or_tuple(lists)) or (not all(map(is_list_or_tuple, lists))):
+ if (not __is_list_or_tuple(lists)) or (not all(map(__is_list_or_tuple, lists))):
raise ValueError("Expected list or tuple")
-def raise_valueerror_if_lists_empty(lists):
+def __raise_valueerror_if_lists_empty(lists):
"""Check that the list and its direct children are not empty."""
def empty(lst):
return len(lst) == 0
if (empty(lists)) or not all(map(lambda x: not empty(x), lists)):
raise ValueError("List/Tuple should NOT be empty!")
-def raise_lengtherror_if_child_lists_are_not_same_as_parent(lists):
+def __raise_lengtherror_if_child_lists_are_not_same_as_parent(lists):
def len_is_same_as_parent(lst):
return len(lst) == len(lists)
if not all(map(len_is_same_as_parent, lists)):
raise LengthError("All children lists should be same length as the parent.")
-def raise_valueerror_if_child_list_distance_from_itself_is_not_zero(lists):
+def __raise_valueerror_if_child_list_distance_from_itself_is_not_zero(lists):
def get_child_distance(child):
idx = lists.index(child)
return lists[idx][idx]
@@ -38,7 +46,7 @@ def raise_valueerror_if_child_list_distance_from_itself_is_not_zero(lists):
if not all(map(distance_is_zero, children_distances)):
raise ValueError("Distance of each child list/tuple from itself should be zero!")
-def raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists):
+def __raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists):
"""Check that the distance from A to B, is the same as the distance from B to A.
If the two distances are different, throw an exception."""
for i in range(len(lists)):
@@ -49,7 +57,7 @@ If the two distances are different, throw an exception."""
"should be the same in both directions.").format(
lists[i][j], lists[j][i]))
-def raise_valueerror_on_negative_distances(lists):
+def __raise_valueerror_on_negative_distances(lists):
"""Check that distances between 'somethings' are all positive, otherwise,
raise an exception."""
def zero_or_positive(val):
@@ -89,20 +97,20 @@ def nearest(lists, i, j):
in `j`."""
#### Guard Functions: Should we do this a different way? ####
- raise_valueerror_if_data_is_not_lists_or_tuples(lists)
- raise_valueerror_if_lists_empty(lists)
- raise_lengtherror_if_child_lists_are_not_same_as_parent(lists)
- raise_valueerror_if_child_list_distance_from_itself_is_not_zero(lists)
- raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists)
- raise_valueerror_on_negative_distances(lists)
+ __raise_valueerror_if_data_is_not_lists_or_tuples(lists)
+ __raise_valueerror_if_lists_empty(lists)
+ __raise_lengtherror_if_child_lists_are_not_same_as_parent(lists)
+ __raise_valueerror_if_child_list_distance_from_itself_is_not_zero(lists)
+ __raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists)
+ __raise_valueerror_on_negative_distances(lists)
#### END: Guard Functions ####
if type(i) == int and type(j) == int: # From member i to member j
return lists[i][j]
- elif type(i) == int and is_list_or_tuple(j):
+ elif type(i) == int and __is_list_or_tuple(j):
return min(map(lambda j_new: nearest(lists, i, j_new), j))
- elif type(j) == int and is_list_or_tuple(i):
+ elif type(j) == int and __is_list_or_tuple(i):
return min(map(lambda i_new: nearest(lists, i_new, j), i))
- elif is_list_or_tuple(i) and is_list_or_tuple(j):
+ elif __is_list_or_tuple(i) and __is_list_or_tuple(j):
partial_i = map(lambda x:partial(nearest, lists, x), i[:-1])
ns = list(map(lambda f, x: f(x), partial_i, j[:1]))
return min(ns)