fix: fmt::format inconsistencies leading to errors in v10

GenSpectrum · Jun 14, 2024 · b5f7a71 · b5f7a71
1 parent d927f23
commit b5f7a71
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Showing 10 changed files with 40 additions and 37 deletions.
diff --git a/include/silo/config/database_config.h b/include/silo/config/database_config.h
@@ -7,7 +7,7 @@
 #include <string_view>
 #include <vector>
 
-#include <fmt/core.h>
+#include <fmt/format.h>
 
 namespace silo::config {
 
@@ -52,32 +52,39 @@ class DatabaseConfigReader {
 }  // namespace silo::config
 
 template <>
-struct [[maybe_unused]] fmt::formatter<silo::config::DatabaseConfig> : fmt::formatter<std::string> {
+class [[maybe_unused]] fmt::formatter<silo::config::DatabaseConfig> : fmt::formatter<std::string> {
+  public:
+   constexpr auto parse(format_parse_context& ctx) { return ctx.begin(); }
    [[maybe_unused]] static auto format(
       const silo::config::DatabaseConfig& database_config,
-      format_context& ctx
+      fmt::format_context& ctx
    ) -> decltype(ctx.out());
 };
 
 template <>
-struct [[maybe_unused]] fmt::formatter<silo::config::DatabaseSchema> : fmt::formatter<std::string> {
+class [[maybe_unused]] fmt::formatter<silo::config::DatabaseSchema> {
+  public:
+   constexpr auto parse(format_parse_context& ctx) { return ctx.begin(); }
    [[maybe_unused]] static auto format(
       const silo::config::DatabaseSchema& database_schema,
-      format_context& ctx
+      fmt::format_context& ctx
    ) -> decltype(ctx.out());
 };
 
 template <>
-struct [[maybe_unused]] fmt::formatter<silo::config::DatabaseMetadata>
-    : fmt::formatter<std::string> {
+class [[maybe_unused]] fmt::formatter<silo::config::DatabaseMetadata> {
+  public:
+   constexpr auto parse(format_parse_context& ctx) { return ctx.begin(); }
    [[maybe_unused]] static auto format(
       const silo::config::DatabaseMetadata& database_metadata,
       format_context& ctx
    ) -> decltype(ctx.out());
 };
 
 template <>
-struct [[maybe_unused]] fmt::formatter<silo::config::ValueType> : fmt::formatter<std::string> {
+class [[maybe_unused]] fmt::formatter<silo::config::ValueType> {
+  public:
+   constexpr auto parse(format_parse_context& ctx) { return ctx.begin(); }
    [[maybe_unused]] static auto format(
       const silo::config::ValueType& value_type,
       format_context& ctx

diff --git a/include/silo/config/preprocessing_config.h b/include/silo/config/preprocessing_config.h
@@ -7,7 +7,7 @@
 #include <string_view>
 #include <unordered_map>
 
-#include <fmt/core.h>
+#include <fmt/format.h>
 
 #include "silo/config/util/abstract_config_source.h"
 

diff --git a/include/silo/database_info.h b/include/silo/database_info.h
@@ -21,7 +21,9 @@ struct DatabaseInfo {
 }  // namespace silo
 
 template <>
-struct [[maybe_unused]] fmt::formatter<silo::DatabaseInfo> : fmt::formatter<std::string> {
+class [[maybe_unused]] fmt::formatter<silo::DatabaseInfo> {
+  public:
+   constexpr auto parse(format_parse_context& ctx) { return ctx.begin(); }
    [[maybe_unused]] static auto format(silo::DatabaseInfo database_info, format_context& ctx)
       -> decltype(ctx.out()) {
       return fmt::format_to(

diff --git a/include/silo/storage/position.h b/include/silo/storage/position.h
@@ -6,7 +6,7 @@
 #include <utility>
 #include <vector>
 
-#include <fmt/core.h>
+#include <fmt/format.h>
 #include <roaring/roaring.hh>
 
 #include "silo/common/aa_symbols.h"

diff --git a/include/silo/storage/sequence_store.h b/include/silo/storage/sequence_store.h
@@ -8,10 +8,11 @@
 #include <utility>
 #include <vector>
 
-#include <fmt/core.h>
+#include <fmt/format.h>
 #include <roaring/roaring.hh>
 
 #include "silo/common/aa_symbols.h"
+#include "silo/common/format_number.h"
 #include "silo/common/nucleotide_symbols.h"
 #include "silo/common/symbol_map.h"
 #include "silo/storage/insertion_index.h"
@@ -108,9 +109,19 @@ class SequenceStore {
 }  // namespace silo
 
 template <>
-struct [[maybe_unused]] fmt::formatter<silo::SequenceStoreInfo> : fmt::formatter<std::string> {
+class [[maybe_unused]] fmt::formatter<silo::SequenceStoreInfo> {
+  public:
+   constexpr auto parse(format_parse_context& ctx) { return ctx.begin(); }
    [[maybe_unused]] static auto format(
-      silo::SequenceStoreInfo sequence_store_info,
+      const silo::SequenceStoreInfo& sequence_store_info,
       format_context& ctx
-   ) -> decltype(ctx.out());
-};
+   ) -> decltype(ctx.out()) {
+      return fmt::format_to(
+         ctx.out(),
+         "SequenceStoreInfo[sequence count: {}, size: {}, N bitmaps size: {}]",
+         sequence_store_info.sequence_count,
+         sequence_store_info.size,
+         silo::formatNumber(sequence_store_info.n_bitmaps_size)
+      );
+   }
+};
diff --git a/src/silo/config/database_config.cpp b/src/silo/config/database_config.cpp
@@ -6,7 +6,6 @@
 #include <string_view>
 
 #include <fmt/format.h>
-#include <spdlog/spdlog.h>
 #include <yaml-cpp/yaml.h>
 
 #include "silo/config/util/config_exception.h"
@@ -69,7 +68,7 @@ struct convert<silo::config::DatabaseConfig> {
          config.default_nucleotide_sequence = "main";
       }
 
-      SPDLOG_TRACE("Resulting database config: {}", config);
+      // SPDLOG_TRACE(fmt::format("Resulting database config: {}", config));
 
       return true;
    }
@@ -193,13 +192,13 @@ std::optional<DatabaseMetadata> DatabaseConfig::getMetadata(const std::string& n
 
 void DatabaseConfig::writeConfig(const std::filesystem::path& config_path) const {
    const YAML::Node node = YAML::convert<DatabaseConfig>::encode(*this);
-   SPDLOG_DEBUG("Writing database config to {}", config_path.string());
+   // SPDLOG_DEBUG("Writing database config to {}", config_path.string());
    std::ofstream out_file(config_path);
    out_file << YAML::Dump(node);
 }
 
 DatabaseConfig DatabaseConfigReader::readConfig(const std::filesystem::path& config_path) const {
-   SPDLOG_INFO("Reading database config from {}", config_path.string());
+   // SPDLOG_INFO("Reading database config from {}", config_path.string());
    try {
       return YAML::LoadFile(config_path.string()).as<DatabaseConfig>();
    } catch (const YAML::Exception& e) {

diff --git a/src/silo/database.cpp b/src/silo/database.cpp
@@ -17,7 +17,7 @@
 #include <utility>
 #include <vector>
 
-#include <fmt/core.h>
+#include <fmt/format.h>
 #include <oneapi/tbb/blocked_range.h>
 #include <oneapi/tbb/parallel_for.h>
 #include <oneapi/tbb/parallel_for_each.h>

diff --git a/src/silo/query_engine/actions/fasta_aligned.cpp b/src/silo/query_engine/actions/fasta_aligned.cpp
@@ -4,7 +4,6 @@
 #include <optional>
 #include <utility>
 
-#include <fmt/core.h>
 #include <fmt/format.h>
 #include <oneapi/tbb/blocked_range.h>
 #include <oneapi/tbb/parallel_for.h>

diff --git a/src/silo/query_engine/filter_expressions/bool_equals.cpp b/src/silo/query_engine/filter_expressions/bool_equals.cpp
@@ -1,5 +1,4 @@
 #include "silo/query_engine/filter_expressions/bool_equals.h"
-#include <fmt/core.h>
 
 #include <utility>
 

diff --git a/src/silo/storage/sequence_store.cpp b/src/silo/storage/sequence_store.cpp
@@ -12,7 +12,6 @@
 #include <roaring/roaring.hh>
 
 #include "silo/common/aa_symbols.h"
-#include "silo/common/format_number.h"
 #include "silo/common/nucleotide_symbols.h"
 #include "silo/common/string_utils.h"
 #include "silo/common/symbol_map.h"
@@ -129,19 +128,6 @@ void silo::SequenceStorePartition<SymbolType>::finalize() {
    );
 }
 
-[[maybe_unused]] auto fmt::formatter<silo::SequenceStoreInfo>::format(
-   silo::SequenceStoreInfo sequence_store_info,
-   fmt::format_context& ctx
-) -> decltype(ctx.out()) {
-   return fmt::format_to(
-      ctx.out(),
-      "SequenceStoreInfo[sequence count: {}, size: {}, N bitmaps size: {}]",
-      sequence_store_info.sequence_count,
-      sequence_store_info.size,
-      silo::formatNumber(sequence_store_info.n_bitmaps_size)
-   );
-}
-
 template <typename SymbolType>
 silo::SequenceStoreInfo silo::SequenceStorePartition<SymbolType>::getInfo() const {
    size_t n_bitmaps_size = 0;