Add CodeQL workflow for GitHub code scanning (#699)

* Add CodeQL workflow for GitHub code scanning

* fix codeql error

Co-authored-by: LGTM Migrator <lgtm-migrator@users.noreply.github.com>
Co-authored-by: Co Quach <daico007@gmail.com>

.github/workflows/codeql.yml

@@ -0,0 +1,41 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  schedule:
+    - cron: "41 4 * * 6"
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ python ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+          queries: +security-and-quality
+
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v2
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
+        with:
+          category: "/language:${{ matrix.language }}"

gmso/formats/gsd.py

@@ -325,7 +325,6 @@ def _write_dihedral_information(gsd_snapshot, top):
 
 def _prepare_box_information(top):
     """Prepare the box information for writing to gsd."""
-    lx = ly = lz = xy = xz = yz = 0.0
     if allclose_units(
         top.box.angles, np.array([90, 90, 90]) * u.degree, rtol=1e-5, atol=1e-8
     ):

gmso/tests/parameterization/test_parameterization_options.py

@@ -268,6 +268,9 @@ def test_hierarchical_mol_structure(
             }
         elif match_ff_by == "group":
             ff_dict = {"sol1": oplsaa_gmso, "sol2": tip3p}
+        else:
+            raise ValueError("Unexpected value provided match_ff_by.")
+
         apply(
             top,
             ff_dict,

gmso/utils/nx_utils.py

@@ -586,7 +586,7 @@ def get_edges(networkx_graph, atom_name1, atom_name2):
         for nodes in list(networkx_graph.edges.items()):
             if nodes[1]["connection"].bond_type is None:
                 selectable_dict = create_dict_of_labels_for_edges(
-                    selectable_dict, edge
+                    selectable_dict, nodes[0]
                 )
                 mia_bond_flag = 1
         if not mia_bond_flag: