actions

.github/workflows/ci.yml

@@ -15,12 +15,12 @@ jobs:
         os: [ubuntu-latest, macos-latest, windows-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Set up poetry
-        uses: abatilo/actions-poetry@v2.0.0
+        uses: abatilo/actions-poetry@v3
         with:
           poetry-version: ${{ matrix.poetry-version }}
       - name: Poetry install

.github/workflows/docs.yml

@@ -14,7 +14,7 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
 
@@ -31,7 +31,7 @@ jobs:
       #          pip3 install -e .
       #          python -m ipykernel install --user --name=py38
       - name: Set up poetry
-        uses: abatilo/actions-poetry@v2.0.0
+        uses: abatilo/actions-poetry@v3
         with:
           poetry-version: "1.8.3"
 

CONTRIBUTING.md

@@ -2,9 +2,9 @@ Deploying to pypi:
 
 ```
 poetry check
-poetry version <major,minor,patch>
 poetry run coverage run
 poetry run coverage report
+poetry version <major,minor,patch>
 poetry build
 poetry deploy
 ```

picea/dag.py

@@ -132,9 +132,6 @@ def __iter__(self) -> Iterable[DAGElement]:
         except StopIteration:
             return
 
-    def __len__(self):
-        return len(self._elements.keys())
-
     @property
     def elements(self) -> List[DAGElement]:
         return list(self)
@@ -163,9 +160,9 @@ def groupby(
                 subclasses
         """
         grouped = defaultdict(self.__class__)
-        for interval in self:
-            grouped[group_func(interval)][interval.ID] = interval
-            interval._container = self
+        for element in self:
+            grouped[group_func(element)][element.ID] = element
+            element._container = self
         return grouped
 
     def filter(
@@ -185,7 +182,7 @@ def filter(
             DirectedAcyclicGraph subclass with unwanted elements removed
         """
         result = self.__class__()
-        for interval in self:
-            if filter_func(interval):
-                result[interval.ID] = interval
+        for element in self:
+            if filter_func(element):
+                result[element.ID] = element
         return result

tests/tree_tests.py

@@ -22,6 +22,10 @@ def test_root(self):
         deep_node = tree.loc["a"]
         self.assertEqual(deep_node.root, tree)
 
+    #def test_number_of_elements(self):
+    #    tree = Tree.from_newick(self.newick)
+    #    self.assertEqual(10, len(tree))
+
     """
     def test_quoted_fasttree_newick(self):
         print(__file__)