hictk: support replaying warnings right before app exit

src/hictk/cli/cli.cpp

@@ -5,6 +5,7 @@
 #include "hictk/tools/cli.hpp"
 
 #include <fmt/format.h>
+#include <spdlog/spdlog.h>
 
 #include <CLI/CLI.hpp>
 #include <cassert>
@@ -25,6 +26,13 @@
   return Cli::subcommand_to_str(get_subcommand());
 }
 
+void Cli::log_warnings() const noexcept {
+  for (const auto& w : _warnings) {
+    SPDLOG_WARN(FMT_STRING("{}"), w);
+  }
+  _warnings.clear();
+}
+
 auto Cli::parse_arguments() -> Config {
   try {
     _cli.name(_exec_name);

src/hictk/cli/cli_dump.cpp

@@ -145,7 +145,6 @@
 void Cli::validate_dump_subcommand() const {
   assert(_cli.get_subcommand("dump")->parsed());
 
-  std::vector<std::string> warnings;
   std::vector<std::string> errors;
   const auto& c = std::get<DumpConfig>(_config);
 
@@ -164,26 +163,26 @@
   const auto resolution_parsed = !subcmd.get_option("--resolution")->empty();
 
   if ((is_cooler || is_scool) && resolution_parsed) {
-    warnings.emplace_back("--resolution is ignored when file is in .[s]cool format.");
+    _warnings.emplace_back("--resolution is ignored when file is in .[s]cool format.");
   }
 
   const auto range_parsed = !subcmd.get_option("--range")->empty();
   if (range_parsed && c.table != "chroms" && c.table != "bins" && c.table != "pixels" &&
       c.table != "weights") {
-    warnings.emplace_back(
+    _warnings.emplace_back(
         "--range and --range2 are ignored when --table is not bins, chroms, pixels, or weights");
   }
 
   const auto query_file_parsed = !subcmd.get_option("--query-file")->empty();
   if (query_file_parsed && c.table != "bins" && c.table != "pixels") {
-    warnings.emplace_back("--query-file is ignored when --table is not bins or pixels");
+    _warnings.emplace_back("--query-file is ignored when --table is not bins or pixels");
   }
 
   const auto matrix_type_parsed = !subcmd.get_option("--matrix-type")->empty();
   const auto matrix_unit_parsed = !subcmd.get_option("--matrix-unit")->empty();
 
   if (!is_hic && (matrix_type_parsed || matrix_unit_parsed)) {
-    warnings.emplace_back(
+    _warnings.emplace_back(
         "--matrix-type and --matrix-unit are ignored when input file is not in .hic format.");
   }
 
@@ -205,10 +204,6 @@
     errors.emplace_back("--balance requires --table=pixels.");
   }
 
-  for (const auto& w : warnings) {
-    SPDLOG_WARN(FMT_STRING("{}"), w);
-  }
-
   if (!errors.empty()) {
     throw std::runtime_error(
         fmt::format(FMT_STRING("the following error(s) where encountered while validating CLI "

src/hictk/cli/cli_fix_mcool.cpp

@@ -103,7 +103,6 @@
 void Cli::validate_fix_mcool_subcommand() const {
   const auto& c = std::get<FixMcoolConfig>(_config);
   std::vector<std::string> errors;
-  std::vector<std::string> warnings{};
 
   if (!c.force && std::filesystem::exists(c.path_to_output)) {
     errors.emplace_back(fmt::format(
@@ -113,20 +112,20 @@
   if (c.skip_balancing) {
     const auto* sc = _cli.get_subcommand("fix-mcool");
     if (!sc->get_option("--tmpdir")->empty()) {
-      warnings.emplace_back("option --tmpdir is ignored when --skip-balancing is provided.");
+      _warnings.emplace_back("option --tmpdir is ignored when --skip-balancing is provided.");
     }
     if (!sc->get_option("--in-memory")->empty()) {
-      warnings.emplace_back("option --in-memory is ignored when --skip-balancing is provided.");
+      _warnings.emplace_back("option --in-memory is ignored when --skip-balancing is provided.");
     }
     if (!sc->get_option("--compression-lvl")->empty()) {
-      warnings.emplace_back(
+      _warnings.emplace_back(
           "option --compression-lvl is ignored when --skip-balancing is provided.");
     }
     if (!sc->get_option("--chunk-size")->empty()) {
-      warnings.emplace_back("option --chunk-size is ignored when --skip-balancing is provided.");
+      _warnings.emplace_back("option --chunk-size is ignored when --skip-balancing is provided.");
     }
     if (!sc->get_option("--threads")->empty()) {
-      warnings.emplace_back("option --threads is ignored when --skip-balancing is provided.");
+      _warnings.emplace_back("option --threads is ignored when --skip-balancing is provided.");
     }
   }
 
@@ -137,10 +136,6 @@
         FMT_STRING("fixing .mcool with storage-mode=\"{}\" is not supported"), *storage_mode));
   }
 
-  for (const auto& w : warnings) {
-    SPDLOG_WARN(FMT_STRING("{}"), w);
-  }
-
   if (!errors.empty()) {
     throw std::runtime_error(fmt::format(
         FMT_STRING(

src/hictk/cli/cli_load.cpp

@@ -197,7 +197,6 @@
 void Cli::validate_load_subcommand() const {
   assert(_cli.get_subcommand("load")->parsed());
 
-  std::vector<std::string> warnings;
   std::vector<std::string> errors;
   const auto& c = std::get<LoadConfig>(_config);
   const auto& sc = *_cli.get_subcommand("load");
@@ -230,14 +229,10 @@
   }
 
   if (c.format == "4dn" && c.format == "validpairs" && c.assume_sorted) {
-    warnings.emplace_back(
+    _warnings.emplace_back(
         "--assume-sorted has no effect when ingesting interactions in 4dn or validpairs format.");
   }
 
-  for (const auto& w : warnings) {
-    SPDLOG_WARN(FMT_STRING("{}"), w);
-  }
-
   if (!errors.empty()) {
     throw std::runtime_error(
         fmt::format(FMT_STRING("the following error(s) where encountered while validating CLI "

src/hictk/cli/cli_zoomify.cpp

@@ -175,7 +175,6 @@
 void Cli::validate_zoomify_subcommand() const {
   assert(_cli.get_subcommand("zoomify")->parsed());
 
-  std::vector<std::string> warnings;
   std::vector<std::string> errors;
   const auto& c = std::get<ZoomifyConfig>(_config);
 
@@ -206,7 +205,7 @@
 
   if (base_resolution == 0) {  // Variable bin size
     errors.clear();
-    warnings.clear();
+    _warnings.clear();
     errors.emplace_back("Zoomifying files with variable bin size is currently not supported.");
   } else {
     if (const auto dupl = detect_duplicate_resolutions(c.resolutions); !dupl.empty()) {
@@ -226,16 +225,12 @@
     const auto nice_or_pow2_steps_parsed =
         !sc->get_option("--nice-steps")->empty() || !sc->get_option("--pow2-steps")->empty();
     if (!c.resolutions.empty() && nice_or_pow2_steps_parsed) {
-      warnings.emplace_back(
+      _warnings.emplace_back(
           "--nice-steps and --pow2-steps are ignored when resolutions are explicitly set with "
           "--resolutions.");
     }
   }
 
-  for (const auto& w : warnings) {
-    SPDLOG_WARN(FMT_STRING("{}"), w);
-  }
-
   if (!errors.empty()) {
     throw std::runtime_error(
         fmt::format(FMT_STRING("the following error(s) where encountered while validating CLI "

src/hictk/include/hictk/tools/cli.hpp

@@ -220,6 +220,7 @@ class Cli {
   [[nodiscard]] int exit(const CLI::ParseError& e) const;
   [[nodiscard]] int exit() const noexcept;
   [[nodiscard]] static std::string_view subcommand_to_str(subcommand s) noexcept;
+  void log_warnings() const noexcept;
 
  private:
   int _argc;
@@ -229,6 +230,7 @@ class Cli {
   Config _config{};
   CLI::App _cli{};
   subcommand _subcommand{subcommand::help};
+  mutable std::vector<std::string> _warnings{};
 
   void make_balance_subcommand();
   void make_ice_balance_subcommand(CLI::App& app);