Fix verbosity

paulsengroup · Jun 21, 2023 · bb73da6 · bb73da6
1 parent f0536f7
commit bb73da6
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Showing 4 changed files with 16 additions and 3 deletions.
diff --git a/src/cooler/balancing_impl.hpp b/src/cooler/balancing_impl.hpp
@@ -39,6 +39,7 @@ inline Weights::Weights(const BinTable& bins, const Dataset& dset, bool rescale)
 
 inline Weights::Weights(const BinTable& bins, const Dataset& dset, Type type, bool rescale)
     : _weights(dset.read_all<std::vector<double>>()), _type(type) {
+  [[maybe_unused]] const HighFive::SilenceHDF5 silencer{}; // NOLINT
   if (_type == Type::INFER || type == Type::UNKNOWN) {
     if (dset.has_attribute("divisive_weights")) {
       _type = dset.read_attribute<bool>("divisive_weights") ? Type::DIVISIVE : Type::MULTIPLICATIVE;

diff --git a/src/cooler/dataset_read_impl.hpp b/src/cooler/dataset_read_impl.hpp
@@ -216,7 +216,7 @@ inline hictk::internal::GenericVariant Dataset::read_last() const {
 template <typename T>
 inline T Dataset::read_attribute(std::string_view key) const {
   if constexpr (std::is_same_v<T, bool>) {
-    return static_cast<bool>(this->_dataset.getAttribute(std::string{key}).read<int>());
+    return static_cast<bool>(this->_dataset.getAttribute(std::string{key}).read<std::uint8_t>());
   } else {
     return Attribute::read<T>(this->_dataset, key);
   }

diff --git a/src/hictk/include/hictk/tools/config.hpp b/src/hictk/include/hictk/tools/config.hpp
@@ -45,6 +45,7 @@ struct DumpConfig {
   hic::MatrixType matrix_type{hic::MatrixType::observed};
   hic::MatrixUnit matrix_unit{hic::MatrixUnit::BP};
   std::uint32_t resolution{};
+  std::uint8_t verbosity{3};
 };
 
 struct LoadConfig {
@@ -57,6 +58,7 @@ struct LoadConfig {
   bool count_as_float{false};
   bool assume_sorted{true};
   bool force{false};
+  std::uint8_t verbosity{3};
 };
 
 struct MergeConfig {
@@ -65,6 +67,7 @@ struct MergeConfig {
   std::size_t chunk_size{1'000'000};
 
   bool force{false};
+  std::uint8_t verbosity{3};
 };
 
 // clang-format off

diff --git a/src/hictk/main.cpp b/src/hictk/main.cpp
@@ -14,6 +14,7 @@
 #include <stdexcept>
 #include <string_view>
 
+#include "hictk/common.hpp"
 #include "hictk/tools/cli.hpp"
 #include "hictk/tools/tools.hpp"
 #include "hictk/version.hpp"
@@ -51,8 +52,16 @@ static std::tuple<int, Cli::subcommand, Config> parse_cli_and_setup_logger(int a
     cli = std::make_unique<Cli>(argc, argv);
     auto config = cli->parse_arguments();
     const auto subcmd = cli->get_subcommand();
-    setup_logger_console(1,  // config.verbosity,
-                         subcmd != Cli::subcommand::help);
+    std::visit(
+        [&](const auto& config_) {
+          using T = hictk::remove_cvref_t<decltype(config_)>;
+          constexpr auto is_monostate = std::is_same_v<T, std::monostate>;
+          if constexpr (!is_monostate) {
+            setup_logger_console(config_.verbosity, subcmd != Cli::subcommand::help &&
+                                                        subcmd != Cli::subcommand::dump);
+          }
+        },
+        config);
 
     return std::make_tuple(0, subcmd, config);
   } catch (const CLI::ParseError& e) {