fix: remove deprecated edge methods from SimplicialComplex

.github/workflows/coverage.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: [main]
+    branches: [main, dev]
 
 jobs:
   build:

.github/workflows/test-code.yml

@@ -7,6 +7,7 @@ on:
   pull_request:
     branches:
       - main
+      - dev
 
 jobs:
   test:

.github/workflows/test-tutorials.yml

@@ -7,6 +7,7 @@ on:
   pull_request:
     branches:
       - main
+      - dev
 
 jobs:
   test:

xgi/core/hypergraph.py

@@ -1040,7 +1040,7 @@ def random_edge_shuffle(self, e_id1=None, e_id2=None, seed=None):
 
         # randomly redistribute nodes between the two edges
         nodes_list = list(nodes)
-        chosen = rng.choice(nodes_list, size=len(e1), replace=False)
+        chosen = rng.choice(nodes_list, size=len(e1), replace=False).tolist()
         e1_new = set(chosen)
         e2_new = nodes - e1_new
 

xgi/core/simplicialcomplex.py

@@ -122,46 +122,35 @@ def __str__(self):
                 f" nodes and {self.num_edges} simplices"
             )
 
-    def add_edge(self, edge, idx=None, **attr):
-        """Deprecated in SimplicialComplex. Use add_simplex instead"""
-        warn("add_edge is deprecated in SimplicialComplex. Use add_simplex instead")
-        return self.add_simplex(edge, idx=None, **attr)
-
-    def add_edges_from(self, ebunch_to_add, max_order=None, **attr):
-        """Deprecated in SimplicialComplex. Use add_simplices_from instead"""
-        warn(
-            "add_edges_from is deprecated in SimplicialComplex. "
-            "Use add_simplices_from instead"
+    def add_edge(self, *args, **kwargs):
+        raise XGIError(
+            "add_edge is not available for SimplicialComplex. "
+            "Use add_simplex instead."
         )
-        return self.add_simplices_from(ebunch_to_add, max_order=None, **attr)
 
-    def add_weighted_edges_from(
-        self, ebunch_to_add, max_order=None, weight="weight", **attr
-    ):
-        """Deprecated in SimplicialComplex. Use add_weighted_simplices_from instead"""
-        warn(
-            "add_weighted_edges_from is deprecated in SimplicialComplex."
-            " Use add_weighted_simplices_from instead"
+    def add_edges_from(self, *args, **kwargs):
+        raise XGIError(
+            "add_edges_from is not available for SimplicialComplex. "
+            "Use add_simplices_from instead."
         )
-        return self.add_weighted_simplices_from(
-            ebunch_to_add, max_order=max_order, weight=weight, **attr
+
+    def add_weighted_edges_from(self, *args, **kwargs):
+        raise XGIError(
+            "add_weighted_edges_from is not available for SimplicialComplex. "
+            "Use add_weighted_simplices_from instead."
         )
 
-    def remove_edge(self, idx):
-        """Deprecated in SimplicialComplex. Use remove_simplex_id instead"""
-        warn(
-            "remove_edge is deprecated in SimplicialComplex. "
-            "Use remove_simplex_id instead"
+    def remove_edge(self, *args, **kwargs):
+        raise XGIError(
+            "remove_edge is not available for SimplicialComplex. "
+            "Use remove_simplex_id instead."
         )
-        return self.remove_simplex_id(idx)
 
-    def remove_edges_from(self, ebunch):
-        """Deprecated in SimplicialComplex. Use remove_simplex_ids_from instead"""
-        warn(
-            "remove_edges_from is deprecated in SimplicialComplex. "
-            "Use remove_simplex_ids_from instead"
+    def remove_edges_from(self, *args, **kwargs):
+        raise XGIError(
+            "remove_edges_from is not available for SimplicialComplex. "
+            "Use remove_simplex_ids_from instead."
         )
-        return self.remove_simplex_ids_from(ebunch)
 
     def remove_node(self, n):
         """Remove a single node.

xgi/readwrite/__init__.py

@@ -21,6 +21,8 @@
     "write_hif_collection",
     "read_incidence_matrix",
     "write_incidence_matrix",
+    "read_json",
+    "write_json",
     "load_xgi_data",
     "download_xgi_data",
 ]