refactor: rebase followup

Author: taepper

src/silo/common/phylo_tree.cpp

@@ -34,7 +34,6 @@ std::shared_ptr<TreeNode> parse_auspice_tree(
       node->children.push_back(child_node);
    }
 
-   // Insert node into the map *after* children so it's fully constructed
    node_map[node->node_id] = node;
    return node;
 }

src/silo/common/phylo_tree.h

@@ -13,6 +13,7 @@ using silo::common::TreeNodeId;
 class TreeNode {
   public:
    TreeNodeId node_id;
+   // TODO(#815) remove these cyclic references
    std::vector<std::shared_ptr<TreeNode>> children;
    std::optional<std::shared_ptr<TreeNode>> parent;
    int depth;

src/silo/storage/column/string_column.h

@@ -108,6 +108,8 @@ template <class Archive>
 ) {
    ar & object.column_name;
    ar & object.dictionary;
+   // TODO(#815) add serialization function for phylo_tree
+   // ar & object.phylo_tree;
 }
 }  // namespace boost::serialization
 
@@ -121,10 +123,20 @@ template <class Archive>
 ) {
    std::string column_name;
    silo::common::BidirectionalMap<std::string> dictionary;
+   // TODO(#815) add serialization function for phylo_tree
+   // std::optional<silo::common::PhyloTree> phylo_tree;
    ar & column_name;
    ar & dictionary;
+   // ar & phylo_tree;
+   //   if(phylo_tree.has_value()){
+   //      object = std::make_shared<silo::storage::column::StringColumnMetadata>(
+   //         std::move(column_name), std::move(dictionary), std::move(phylo_tree)
+   //      );
+   //   }
+   //   else{
    object = std::make_shared<silo::storage::column::StringColumnMetadata>(
       std::move(column_name), std::move(dictionary)
    );
+   //   }
 }
 }  // namespace boost::serialization