Fix tests

HISTORY.md

@@ -9,7 +9,6 @@
 **New features**
 
 * It is now possible to create Newick tree with `Taxonomy.toNewick`
-* It is now possible to clip Taxonomies with `Taxonomy.clip()`, which behaves similarly to `Taxonomy.prune()` but removes upstream nodes and reroots tree.
 
 ## 2.5.2
 

taxidTools/Taxonomy.py

@@ -681,7 +681,7 @@ def prune(self, taxid: Union[str, int], inplace: Optional[bool] = True) -> None:
             tax = self.copy()
 
         # Getting upstream nodes
-        nodes = tax.getAncestry(taxid)
+        nodes = self.getAncestry(taxid)
 
         # Unlinking other branches from upstream nodes
         # No need to change parents of the other nodes,
@@ -811,75 +811,6 @@ def write(self, path: str) -> None:
         with open(path, 'w') as fi:
             fi.write(writer)
 
-    def clip(self, taxid: Union[str, int], inplace: Optional[bool] = True) -> None:
-        """
-        Clip the Taxonomy at the given taxid
-
-        Nodes not in the lineage (upwards and downwards)
-        of the given taxid will be discarded.
-        The Ancestors of the given taxid will NOT be kept and the given
-        node will become the new root!
-
-        Parameters
-        ----------
-        taxid: str or int
-            taxid whose Lineage to keep
-        inplace: bool, optional
-            perfrom the operation inplace and mutate the underlying objects
-            or return a mutated copy of the instance, keep the original unchanged
-
-        Returns
-        -------
-        None
-
-        See Also
-        --------
-        Taxonomy.prune
-
-        Examples
-        --------
-        >>> node0 = Node(taxid = 0, name = "root",
-                         rank = "root", parent = None)
-        >>> node1 = Node(taxid = 1, name = "node1",
-                         rank = "rank1", parent = node0)
-        >>> node2 = Node(taxid = 2, name = "node2",
-                         rank = "rank1", parent = node0)
-        >>> node11 = Node(taxid = 11, name = "node11",
-                          rank = "rank2", parent = node1)
-        >>> node12 = Node(taxid = 12, name = "node12",
-                          rank = "rank2", parent = node1)
-        >>> tax = Taxonomy.from_list([node0, node1, node2, node11, node12])
-        >>> tax.clip(1)
-
-        Ancestry not kept
-
-        >>> tax.getAncestry(11)
-        Lineage([Node(11)])
-
-        Other branches are gone
-
-        >>> tax.get('2')
-        None
-        """
-        if inplace:
-            tax = self
-        else:
-            tax = self.copy()
-
-        # Getting upstream nodes
-        nodes = tax.getAncestry(taxid)
-
-        # Removing upstream nodes
-        for i in range(1, len(nodes)):
-            tax.pop(nodes[i])
-
-        # Rerooting taxonomy
-        taxid.parent = None
-        tax.root = taxid
-
-        if not inplace:
-            return tax
-
     def toNewick(self, names: str = 'name') -> str:
         """
         Generate a Newock string fro the current taxonomy

tests/test_Taxonomy.py

@@ -87,7 +87,7 @@ def test_ancestry_tests(self):
     def test_copy(self):
         self.new = self.txd.copy()
         self.txd.data = {}
-        self.assertRaises(taxidTools.InvalidNodeError, self.txd[0])
+        self.assertIsNone(self.txd.get('0'))
         self.assertIsNotNone(self.new.get('0', None))
 
     def test_InvalidNodeError(self):

tests/test_complextree.py

@@ -151,12 +151,5 @@ def test_insert_nodes_recc(self):
         self.txd.addNode(node3)
         new_nodes = _insert_nodes_recc(self.node0, ['rank3', 'rank2', 'rank1.5', 'rank1'])
         self.assertEqual(len(new_nodes), 12)
-
-        self.assertRaises(ValueError, _insert_nodes_recc, self.node0, ['root'])
-
-    def test_clip(self):
-        subtree = self.txd.clip(1)
-        self.assertEqual(self.txd.root, self.txd['1'])
-        self.assertIsNone(self.txd['1'].parent)
-        self.assertRaises(taxidTools.InvalidNodeError, self.txd.__getitem__, '0')
-        self.assertRaises(taxidTools.InvalidNodeError, self.txd.__getitem__, '2')
+        with self.assertRaises(ValueError):
+            _insert_nodes_recc(self.node0, ['root'])