Merge pull request #57 from TheJacksonLaboratory/release-v0.4.1post0

Release v0.4.2

.gitignore

@@ -1,3 +1,6 @@
+# Benches
+benches/history/
+
 # IDE stuff
 .idea/
 *.iml

HOW_TO_RELEASE.md

@@ -44,7 +44,7 @@ tox run
 python3 -m build
 
 # Deploy
-python3 -m twine upload --sign --identity <YOUR_GPG_KEY_HERE> dist/*
+python3 -m twine upload dist/*
 
 # Clear the deployed files
 rm -rf dist

benches/graph_traversal.py

@@ -41,6 +41,7 @@ def bench_base_graph(fpath_hpo: str,
 
     results = defaultdict(list)
 
+    root = graph.root
     for curie, label in CURIE2LABEL.items():
         term_id = hpotk.TermId.from_curie(curie)
         label = ontology.get_term_name(curie)
@@ -52,6 +53,11 @@ def bench_base_graph(fpath_hpo: str,
             'get_ancestors': lambda: list(graph.get_ancestors(term_id)),
             'get_children': lambda: list(graph.get_children(term_id)),
             'get_descendants': lambda: list(graph.get_descendants(term_id)),
+
+            'is_parent_of': lambda: graph.is_parent_of(root, term_id),
+            'is_ancestor_of': lambda: graph.is_ancestor_of(root, term_id),
+            'is_child_of': lambda: graph.is_child_of(term_id, root),
+            'is_descendant_of': lambda: graph.is_descendant_of(term_id, root),
         }
 
         for method in benches:
@@ -66,12 +72,14 @@ def bench_base_graph(fpath_hpo: str,
 
 
 def bench_indexed_graph(fpath_hpo: str,
-                        number: int = 1000) -> typing.Mapping[str, typing.Mapping[str, float]]:
+                        number: int = 1000) -> typing.Mapping[str, typing.Sequence]:
     factory = hpotk.graph.CsrIndexedGraphFactory()
     ontology = hpotk.load_minimal_ontology(fpath_hpo, graph_factory=factory)
     graph: hpotk.graph.IndexedOntologyGraph = ontology.graph
 
     results = defaultdict(list)
+    root = graph.root
+    root_idx = graph.root_idx
     for curie, label in CURIE2LABEL.items():
         term_id = hpotk.TermId.from_curie(curie)
         idx = graph.node_to_idx(term_id)
@@ -87,6 +95,15 @@ def bench_indexed_graph(fpath_hpo: str,
             'get_children': lambda: list(graph.get_children(term_id)),
             'get_descendant_idx': lambda: list(graph.get_descendant_idx(idx)),
             'get_descendants': lambda: list(graph.get_descendants(term_id)),
+
+            'is_parent_of_idx': lambda: graph.is_parent_of_idx(root_idx, idx),
+            'is_parent_of': lambda: graph.is_parent_of(root, term_id),
+            'is_ancestor_of_idx': lambda: graph.is_ancestor_of_idx(root_idx, idx),
+            'is_ancestor_of': lambda: graph.is_ancestor_of(root, term_id),
+            'is_child_of_idx': lambda: graph.is_child_of_idx(idx, root_idx),
+            'is_child_of': lambda: graph.is_child_of(term_id, root),
+            'is_descendant_of_idx': lambda: graph.is_descendant_of_idx(idx, root_idx),
+            'is_descendant_of': lambda: graph.is_descendant_of(term_id, root),
         }
 
         for method in benches:
@@ -121,9 +138,10 @@ def bench(fpath_hpo: str, number: int, revision: str):
 
     df = pd.concat(results)
     df['revision'] = revision
-    df = df.set_index(['revision', 'method', 'group', 'payload']).sort_index()
+    df = df.set_index(['group', 'method', 'payload', 'revision']).sort_index()
 
     fpath_df = f'graph_traversal-{number}-{revision}.csv'
+    logger.info('Storing results at `%s`', fpath_df)
     df.to_csv(fpath_df)
 
 
@@ -145,7 +163,7 @@ def main() -> int:
 
     args = parser.parse_args(argv)
     if args.revision is None:
-        revision = datetime.datetime.now().strftime('%Y-%m-%d')
+        revision = datetime.datetime.now().strftime('%Y-%m-%d-%H%M%S')
     else:
         revision = args.revision
     bench(args.hpo, args.number, revision)

recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "hpo-toolkit" %}
-{% set version = "0.4.1" %}
+{% set version = "0.4.2" %}
 
 package:
   name: {{ name|lower }}

src/hpotk/__init__.py

@@ -2,7 +2,7 @@
 HPO toolkit is a library for working with Human Phenotype Ontology and the HPO annotation data.
 """
 
-__version__ = "0.4.1"
+__version__ = "0.4.2"
 
 from . import algorithm
 from . import annotations

src/hpotk/graph/_api.py

@@ -91,7 +91,7 @@ def is_leaf(self, node: typing.Union[str, NODE, Identified]) -> bool:
         :return: `True` if the `node` is a leaf node or `False` otherwise.
         :raises ValueError: if `node` is not present in the graph.
         """
-        for _ in self.get_descendants(node):
+        for _ in self.get_children(node):
             return False
         return True
 
@@ -273,33 +273,149 @@ def get_ancestors(self, source: typing.Union[str, NODE, Identified],
                       include_source: bool = False) -> typing.Iterator[NODE]:
         return self._map_with_iter_func(source, include_source, self.get_ancestor_idx)
 
+    def is_leaf(self, node: typing.Union[str, NODE, Identified]) -> bool:
+        node_idx = self._map_to_term_idx(node)
+        if node_idx is None:
+            raise ValueError(f'No graph node found for {node}')
+
+        for _ in self.get_children_idx(node_idx):
+            return True
+        return False
+
+    def is_parent_of_idx(self, sub: int, obj: int) -> bool:
+        """
+        Return `True` if the subject `sub` is a parent of the object `obj`.
+
+        :param sub: index of a graph node.
+        :param obj: index of the other graph node.
+        :return: `True` if the `sub` is a parent of the `obj`.
+        :raises ValueError: if no such node exists for the `obj` index.
+        """
+        return any(sub == idx for idx in self.get_parents_idx(obj))
+
+    def is_parent_of(self, sub: typing.Union[str, NODE, Identified],
+                     obj: typing.Union[str, NODE, Identified]) -> bool:
+        obj_idx = self._map_to_term_idx(obj)
+        if obj_idx is None:
+            raise ValueError(f'No graph node found for {obj}')
+
+        sub_idx = self._map_to_term_idx(sub)
+        if sub_idx is None:
+            return False
+
+        return any(sub_idx == idx for idx in self.get_parents_idx(obj_idx))
+
+    def is_ancestor_of_idx(self, sub: int, obj: int) -> bool:
+        """
+        Return `True` if the subject `sub` is an ancestor of the object `obj`.
+
+        :param sub: index of a graph node.
+        :param obj: index of the other graph node.
+        :return: `True` if the `sub` is an ancestor of the `obj`.
+        :raises ValueError: if no such node exists for the `obj` index.
+        """
+        return any(sub == idx for idx in self.get_ancestor_idx(obj))
+
+    def is_ancestor_of(self, sub: typing.Union[str, NODE, Identified],
+                       obj: typing.Union[str, NODE, Identified]) -> bool:
+        obj_idx = self._map_to_term_idx(obj)
+        if obj_idx is None:
+            raise ValueError(f'No graph node found for {obj}')
+
+        sub_idx = self._map_to_term_idx(sub)
+        if sub_idx is None:
+            return False
+
+        return any(sub_idx == idx for idx in self.get_ancestor_idx(obj_idx))
+
+    def is_child_of_idx(self, sub: int, obj: int) -> bool:
+        """
+        Return `True` if the subject `sub` is a child of the object `obj`.
+
+        :param sub: index of a graph node.
+        :param obj: index of the other graph node.
+        :return: `True` if the `sub` is a child of the `obj`.
+        :raises ValueError: if no such node exists for the `sub` index.
+        """
+        # TODO: ValueError for `sub` may break the pattern
+        return any(obj == idx for idx in self.get_parents_idx(sub))
+
+    def is_child_of(self, sub: typing.Union[str, NODE, Identified],
+                    obj: typing.Union[str, NODE, Identified]) -> bool:
+        obj_idx = self._map_to_term_idx(obj)
+        if obj_idx is None:
+            raise ValueError(f'No graph node found for {obj}')
+
+        sub_idx = self._map_to_term_idx(sub)
+        if sub_idx is None:
+            return False
+
+        # Exploit the fact that a term has usually fewer parents than children.
+        return any(obj_idx == idx for idx in self.get_parents_idx(sub_idx))
+
+    def is_descendant_of_idx(self, sub: int, obj: int) -> bool:
+        """
+        Return `True` if the subject `sub` is a descendant of the object `obj`.
+
+        :param sub: index of a graph node.
+        :param obj: index of the other graph node.
+        :return: `True` if the `sub` is a descendant of the `obj`.
+        :raises ValueError: if no such node exists for the `sub` index.
+        """
+        # TODO: ValueError for `sub` may break the pattern
+        return any(obj == idx for idx in self.get_ancestor_idx(sub))
+
+    def is_descendant_of(self, sub: typing.Union[str, NODE, Identified],
+                         obj: typing.Union[str, NODE, Identified]) -> bool:
+        obj_idx = self._map_to_term_idx(obj)
+        if obj_idx is None:
+            raise ValueError(f'No graph node found for {obj}')
+
+        sub_idx = self._map_to_term_idx(sub)
+        if sub_idx is None:
+            return False
+
+        # Exploit the fact that a term has usually fewer parents than children.
+        return any(obj_idx == idx for idx in self.get_ancestor_idx(sub_idx))
+
     def _map_with_iter_func(self, node: typing.Union[str, NODE, Identified],
                             include_source: bool,
                             func: typing.Callable[[int], typing.Iterator[int]]) -> typing.Iterator[NODE]:
-        term_id = self._map_to_term_id(node)
-        idx = self.node_to_idx(term_id)
+        idx = self._map_to_term_idx(node)
         if idx is not None:
             if include_source:
-                return itertools.chain((term_id,), map(lambda i: self.idx_to_node(i), func(idx)))
+                return itertools.chain(
+                    (self.idx_to_node(idx),),
+                    map(self.idx_to_node, func(idx)))
             else:
-                return map(lambda i: self.idx_to_node(i), func(idx))
+                return map(self.idx_to_node, func(idx))
         else:
             raise ValueError(f'{node} is not present in the graph!')
 
     def _map_with_seq_func(self, node: typing.Union[str, NODE, Identified],
                            include_source: bool,
                            func: typing.Callable[[int], typing.Sequence[int]]) -> typing.Iterator[NODE]:
-        term_id = self._map_to_term_id(node)
-        idx = self.node_to_idx(term_id)
+        idx = self._map_to_term_idx(node)
         if idx is not None:
             if include_source:
-                return itertools.chain((term_id,), map(lambda i: self.idx_to_node(i), func(idx)))
+                return itertools.chain(
+                    (self.idx_to_node(idx),),
+                    map(self.idx_to_node, func(idx)))
             else:
-                return map(lambda i: self.idx_to_node(i), func(idx))
+                return map(self.idx_to_node, func(idx))
         else:
             raise ValueError(f'{node} is not present in the graph!')
 
-    # TODO: possibly override is_parent, is_leaf, is_ancestor, etc.
+    def _map_to_term_idx(self, node: typing.Union[str, NODE, Identified]) -> typing.Optional[int]:
+        """
+        A convenience method to convert a `node` into the node index.
+
+        :param node: one of the expected node types, including CURIE `str`, NODE, or an :class:`Identified` item.
+        :return: the node index or `None` if the node is not present in the graph.
+        :raises ValueError: if the node is not in one of the expected types.
+        """
+        term_id = self._map_to_term_id(node)
+        return self.node_to_idx(term_id)
 
     # The rest