fix: update release workflow and improve type hints in hypergraph methods

Author: yifanfeng97

.github/workflows/release.yml

@@ -5,7 +5,7 @@ on:
     types: [published]
 
 permissions:
-  contents: read
+  contents: write  # For uploading release assets
   id-token: write  # For trusted publishing to PyPI
 
 jobs:
@@ -28,10 +28,17 @@ jobs:
       run: uv python install 3.11
 
     - name: Install dependencies
-      run: uv sync --group test
+      run: uv sync --group test --group dev
+    
+    - name: Run quality checks
+      run: |
+        uv run black --check hyperdb/ tests/
+        uv run isort --check-only hyperdb/ tests/
+        uv run flake8 hyperdb/ tests/
+        uv run mypy hyperdb/ --ignore-missing-imports
     
     - name: Run tests
-      run: uv run pytest tests/ -v
+      run: uv run pytest tests/ -v --cov=hyperdb --cov-report=xml --cov-report=term
 
     - name: Build package
       run: uv build
@@ -40,19 +47,23 @@ jobs:
       run: |
         uv run pip install twine
         uv run twine check dist/*
+        
+    - name: Create package archive
+      run: |
+        cd dist
+        zip -r ../packages.zip .
+        cd ..
     
     - name: Publish to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        password: ${{ secrets.PYPI_API_TOKEN }}
         skip-existing: true
+        # Uses trusted publishing with id-token, no password needed
 
     - name: Upload Release Assets
-      uses: actions/upload-release-asset@v1
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      uses: softprops/action-gh-release@v1
       with:
-        upload_url: ${{ github.event.release.upload_url }}
-        asset_path: dist/
-        asset_name: packages
-        asset_content_type: application/zip
+        files: |
+          dist/*
+          packages.zip
+        token: ${{ secrets.GITHUB_TOKEN }}

hyperdb/base.py

@@ -93,16 +93,16 @@ def encode_e(self, e_tuple: Union[List, Set, Tuple]) -> Tuple:
         raise NotImplementedError
 
     @cached_property
-    def all_v(self) -> List[str]:
+    def all_v(self) -> Set[Any]:
         r"""
-        Return a list of all vertices in the hypergraph.
+        Return a set of all vertices in the hypergraph.
         """
         raise NotImplementedError
 
     @cached_property
-    def all_e(self) -> List[Tuple]:
+    def all_e(self) -> Set[Tuple]:
         r"""
-        Return a list of all hyperedges in the hypergraph.
+        Return a set of all hyperedges in the hypergraph.
         """
         raise NotImplementedError
 
@@ -214,7 +214,7 @@ def degree_e(self, e_tuple: Tuple) -> int:
         """
         raise NotImplementedError
 
-    def nbr_e_of_v(self, v_id: Any) -> list:
+    def nbr_e_of_v(self, v_id: Any) -> set:
         r"""
         Return the hyperedge neighbors of the vertex.
 
@@ -223,7 +223,7 @@ def nbr_e_of_v(self, v_id: Any) -> list:
         """
         raise NotImplementedError
 
-    def nbr_v_of_e(self, e_tuple: Tuple) -> list:
+    def nbr_v_of_e(self, e_tuple: Tuple) -> set:
         r"""
         Return the vertex neighbors of the hyperedge.
 
@@ -232,12 +232,13 @@ def nbr_v_of_e(self, e_tuple: Tuple) -> list:
         """
         raise NotImplementedError
 
-    def nbr_v(self, v_id: Any) -> list:
+    def nbr_v(self, v_id: Any, exclude_self: bool = True) -> set:
         r"""
         Return the vertex neighbors of the vertex.
 
         Args:
             ``v_id`` (``Any``): The vertex id.
+            ``exclude_self`` (``bool``): Whether to exclude the vertex itself from neighbors.
         """
         raise NotImplementedError
 

hyperdb/hypergraph.py

@@ -110,18 +110,18 @@ def encode_e(self, e_tuple: Union[List, Set, Tuple]) -> Tuple:
         return tuple(tmp)
 
     @cached_property
-    def all_v(self) -> List[str]:
+    def all_v(self) -> Set[Any]:
         r"""
-        Return a list of all vertices in the hypergraph.
+        Return a set of all vertices in the hypergraph.
         """
-        return list(self._v_data.keys())
+        return set(self._v_data.keys())
 
     @cached_property
-    def all_e(self) -> List[Tuple]:
+    def all_e(self) -> Set[Tuple]:
         r"""
-        Return a list of all hyperedges in the hypergraph.
+        Return a set of all hyperedges in the hypergraph.
         """
-        return list(self._e_data.keys())
+        return set(self._e_data.keys())
 
     @cached_property
     def num_v(self) -> int:
@@ -298,7 +298,7 @@ def degree_e(self, e_tuple: Union[List, Set, Tuple]) -> int:
         assert e_tuple in self._e_data, f"The hyperedge {e_tuple} does not exist in the hypergraph."
         return len(e_tuple)
 
-    def nbr_e_of_v(self, v_id: Any) -> list:
+    def nbr_e_of_v(self, v_id: Any) -> set:
         r"""
         Return the incident hyperedges of the vertex.
 
@@ -307,9 +307,9 @@ def nbr_e_of_v(self, v_id: Any) -> list:
         """
         assert isinstance(v_id, Hashable), "The vertex id must be hashable."
         assert v_id in self._v_data, f"The vertex {v_id} does not exist in the hypergraph."
-        return list(self._v_inci[v_id])
+        return set(self._v_inci[v_id])
 
-    def nbr_v_of_e(self, e_tuple: Union[List, Set, Tuple]) -> list:
+    def nbr_v_of_e(self, e_tuple: Union[List, Set, Tuple]) -> set:
         r"""
         Return the incident vertices of the hyperedge.
 
@@ -319,9 +319,9 @@ def nbr_v_of_e(self, e_tuple: Union[List, Set, Tuple]) -> list:
         assert isinstance(e_tuple, (list, set, tuple)), "The hyperedge must be a list, set, or tuple of vertex ids."
         e_tuple = self.encode_e(e_tuple)
         assert e_tuple in self._e_data, f"The hyperedge {e_tuple} does not exist in the hypergraph."
-        return list(e_tuple)
+        return set(e_tuple)
 
-    def nbr_v(self, v_id: Any, exclude_self=True) -> list:
+    def nbr_v(self, v_id: Any, exclude_self=True) -> set:
         r"""
         Return the neighbors of the vertex.
 
@@ -335,4 +335,4 @@ def nbr_v(self, v_id: Any, exclude_self=True) -> list:
             nbrs.update(e_tuple)
         if exclude_self:
             nbrs.remove(v_id)
-        return list(nbrs)
+        return nbrs

tests/test_hypergraph.py

@@ -22,18 +22,18 @@ def hg():
 
 
 def test_all_v(hg):
-    assert hg.all_v == set([1, 2, 3, 4, 5, 6])
+    assert hg.all_v == {1, 2, 3, 4, 5, 6}
     assert hg.num_v == 6
     hg.remove_v(2)
-    assert hg.all_v == set([1, 3, 4, 5, 6])
+    assert hg.all_v == {1, 3, 4, 5, 6}
     assert hg.num_v == 5
 
 
 def test_all_e(hg):
-    assert hg.all_e == set([(1, 2), (1, 3), (2, 3, 4), (1, 3, 4, 5), (4, 5, 6), (1, 5, 6)])
+    assert hg.all_e == {(1, 2), (1, 3), (1, 3, 4, 5), (1, 5, 6), (2, 3, 4), (4, 5, 6)}
     assert hg.num_e == 6
     hg.remove_v(2)
-    assert hg.all_e == set([(1, 3), (3, 4), (1, 3, 4, 5), (4, 5, 6), (1, 5, 6)])
+    assert hg.all_e == {(1, 3), (1, 3, 4, 5), (1, 5, 6), (3, 4), (4, 5, 6)}
     assert hg.num_e == 5