review comments #1

Author: taepper

src/config/source/yaml_file.cpp

@@ -19,16 +19,9 @@ namespace {
 
 bool isSequenceOfScalars(const YAML::Node& node) {
    if (!node.IsSequence()) {
-      SPDLOG_TRACE("isSequenceOfScalars = false, node is not a sequence");
       return false;
    }
-   for (auto element : node) {
-      if (!element.IsScalar()) {
-         SPDLOG_TRACE("isSequenceOfScalars = false, list element is not a string");
-         return false;
-      }
-   }
-   return true;
+   return std::ranges::all_of(node, [](const auto& element) { return element.IsScalar(); });
 }
 
 bool isProperSingularValue(const YAML::Node& node) {

src/silo/initialize/initializer.cpp

@@ -231,7 +231,7 @@ static const std::string UNALIGNED_NUCLEOTIDE_SEQUENCE_PREFIX = "unaligned_";
 silo::schema::DatabaseSchema Initializer::createSchemaFromConfigFiles(
    config::DatabaseConfig database_config,
    ReferenceGenomes reference_genomes,
-   std::map<std::filesystem::path, common::LineageTreeAndIdMap> lineage_tree,
+   std::map<std::filesystem::path, common::LineageTreeAndIdMap> lineage_trees,
    common::PhyloTree phylo_tree_file,
    bool without_unaligned_sequences
 ) {

src/silo/initialize/initializer.h

@@ -16,7 +16,7 @@ class Initializer {
    static silo::schema::DatabaseSchema createSchemaFromConfigFiles(
       config::DatabaseConfig database_config,
       ReferenceGenomes reference_genomes,
-      std::map<std::filesystem::path, common::LineageTreeAndIdMap> lineage_tree,
+      std::map<std::filesystem::path, common::LineageTreeAndIdMap> lineage_trees,
       common::PhyloTree phylo_tree_file,
       bool without_unaligned_columns
    );