Remove submodule logger

.gitmodules

@@ -16,9 +16,6 @@
 [submodule "vendor/rampler"]
 	path = vendor/rampler
 	url = https://github.com/rvaser/rampler
-[submodule "vendor/logger"]
-	path = vendor/logger
-	url = https://github.com/rvaser/logger
 [submodule "vendor/ClaraGenomicsAnalysis"]
 	path = vendor/ClaraGenomicsAnalysis
 	url = https://github.com/clara-genomics/ClaraGenomicsAnalysis

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.2)
 project(racon)
-set(racon_version 1.4.9)
+set(racon_version 1.4.10)
 
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
@@ -30,6 +30,7 @@ include_directories(${PROJECT_SOURCE_DIR}/src)
 
 set(racon_sources
     src/main.cpp
+    src/logger.cpp
     src/polisher.cpp
     src/overlap.cpp
     src/sequence.cpp
@@ -58,9 +59,6 @@ endif()
 if (NOT TARGET edlib)
     add_subdirectory(vendor/edlib EXCLUDE_FROM_ALL)
 endif()
-if (NOT TARGET logger)
-    add_subdirectory(vendor/logger EXCLUDE_FROM_ALL)
-endif()
 if (racon_enable_cuda)
     if (DEFINED CLARAGENOMICSANALYSIS_SDK_PATH)
         list(APPEND CMAKE_PREFIX_PATH "${CLARAGENOMICSANALYSIS_SDK_PATH}/cmake")
@@ -90,7 +88,7 @@ if (racon_enable_cuda)
     endif()
 endif()
 
-target_link_libraries(racon bioparser spoa thread_pool edlib_static logger)
+target_link_libraries(racon bioparser spoa thread_pool edlib_static)
 if (racon_enable_cuda)
     target_link_libraries(racon cudapoa cudaaligner)
 endif()
@@ -106,6 +104,7 @@ if (racon_build_tests)
 
     set(racon_test_sources
         test/racon_test.cpp
+        src/logger.cpp
         src/polisher.cpp
         src/overlap.cpp
         src/sequence.cpp
@@ -123,7 +122,7 @@ if (racon_build_tests)
         add_subdirectory(vendor/googletest/googletest EXCLUDE_FROM_ALL)
     endif()
 
-    target_link_libraries(racon_test bioparser spoa thread_pool edlib_static logger gtest_main)
+    target_link_libraries(racon_test bioparser spoa thread_pool edlib_static gtest_main)
     if (racon_enable_cuda)
         target_link_libraries(racon_test cudapoa cudaaligner)
     endif()

src/cuda/cudapolisher.cpp

@@ -10,11 +10,11 @@
 #include <cuda_profiler_api.h>
 
 #include "sequence.hpp"
+#include "logger.hpp"
 #include "cudapolisher.hpp"
 #include <claragenomics/utils/cudautils.hpp>
 
 #include "bioparser/bioparser.hpp"
-#include "logger/logger.hpp"
 
 namespace racon {
 

src/logger.cpp

@@ -0,0 +1,56 @@
+/*!
+ * @file logger.cpp
+ *
+ * @brief Logger source file
+ */
+
+#include <iostream>
+
+#include "logger.hpp"
+
+namespace racon {
+
+Logger::Logger()
+        : time_(0.), bar_(0), time_point_() {
+}
+
+Logger::~Logger() {
+}
+
+void Logger::log() {
+    auto now = std::chrono::steady_clock::now();
+    if (time_point_ != std::chrono::time_point<std::chrono::steady_clock>()) {
+        time_ += std::chrono::duration_cast<std::chrono::duration<double>>(now - time_point_).count();
+    }
+    time_point_ = now;
+}
+
+void Logger::log(const std::string& msg) const {
+    std::cerr << msg << " " << std::fixed
+        << std::chrono::duration_cast<std::chrono::duration<double>>(std::chrono::steady_clock::now() - time_point_).count()
+        << " s" << std::endl;
+}
+
+void Logger::bar(const std::string& msg) {
+    ++bar_;
+    std::string progress_bar = "[" + std::string(bar_, '=') + (bar_ == 20 ? "" : ">" + std::string(19 - bar_, ' ')) + "]";
+
+    std::cerr << msg << " " << progress_bar << " " << std::fixed
+        << std::chrono::duration_cast<std::chrono::duration<double>>(std::chrono::steady_clock::now() - time_point_).count()
+        << " s";
+
+    bar_ %= 20;
+    if (bar_ == 0) {
+        std::cerr << std::endl;
+    } else {
+        std::cerr << "\r";
+    }
+}
+
+void Logger::total(const std::string& msg) const {
+    std::cerr << msg << " " << std::fixed
+        << time_ + std::chrono::duration_cast<std::chrono::duration<double>>(std::chrono::steady_clock::now() - time_point_).count()
+        << " s" << std::endl;
+}
+
+}

src/logger.hpp

@@ -0,0 +1,56 @@
+/*!
+ * @file logger.hpp
+ *
+ * @brief Logger header file
+ */
+
+#pragma once
+
+#include <cstdint>
+#include <chrono>
+#include <string>
+
+namespace racon {
+
+static const std::string version = "v1.0.0";
+
+class Logger {
+public:
+    Logger();
+
+    Logger(const Logger&) = default;
+    Logger& operator=(const Logger&) = default;
+
+    Logger(Logger&&) = default;
+    Logger& operator=(Logger&&) = default;
+
+    ~Logger();
+
+    /*!
+     * @brief Resets the time point
+     */
+    void log();
+
+    /*!
+     * @brief Prints the elapsed time from last time point to stderr
+     */
+    void log(const std::string& msg) const;
+
+    /*!
+     * @brief Prints a progress bar and the elapsed time from last time to
+     * stderr (the progress bar resets after 20 calls)
+     */
+    void bar(const std::string& msg);
+
+    /*!
+     * @brief Prints the total elapsed time from the first log() call
+     */
+    void total(const std::string& msg) const;
+
+private:
+    double time_;
+    std::uint32_t bar_;
+    std::chrono::time_point<std::chrono::steady_clock> time_point_;
+};
+
+}

src/polisher.cpp

@@ -11,6 +11,7 @@
 #include "overlap.hpp"
 #include "sequence.hpp"
 #include "window.hpp"
+#include "logger.hpp"
 #include "polisher.hpp"
 #ifdef CUDA_ENABLED
 #include "cuda/cudapolisher.hpp"
@@ -19,7 +20,6 @@
 #include "bioparser/bioparser.hpp"
 #include "thread_pool/thread_pool.hpp"
 #include "spoa/spoa.hpp"
-#include "logger/logger.hpp"
 
 namespace racon {
 
@@ -170,7 +170,7 @@ Polisher::Polisher(std::unique_ptr<bioparser::Parser<Sequence>> sparser,
         alignment_engines_(), sequences_(), dummy_quality_(window_length, '!'),
         window_length_(window_length), windows_(),
         thread_pool_(thread_pool::createThreadPool(num_threads)),
-        thread_to_id_(), logger_(new logger::Logger()) {
+        thread_to_id_(), logger_(new Logger()) {
 
     uint32_t id = 0;
     for (const auto& it: thread_pool_->thread_identifiers()) {

src/polisher.hpp

@@ -25,15 +25,13 @@ namespace spoa {
     class AlignmentEngine;
 }
 
-namespace logger {
-    class Logger;
-}
 
 namespace racon {
 
 class Sequence;
 class Overlap;
 class Window;
+class Logger;
 
 enum class PolisherType {
     kC, // Contig polishing
@@ -95,7 +93,7 @@ class Polisher {
     std::unique_ptr<thread_pool::ThreadPool> thread_pool_;
     std::unordered_map<std::thread::id, uint32_t> thread_to_id_;
 
-    std::unique_ptr<logger::Logger> logger_;
+    std::unique_ptr<Logger> logger_;
 };
 
 }