Changing how CXXFLAGS is configured

Makefile.am

@@ -17,22 +17,16 @@
 EXTRA_DIST = README.md LICENSE Configuration example.fq test
 
 ACLOCAL_AMFLAGS = -I m4
-AM_CPPFLAGS = -I $(top_srcdir)/src
 
-### ADS: use AM_CXXFLAGS if these are needed
-## AM_CXXFLAGS = -Wall -Wextra -Wpedantic -Wno-unknown-attributes
-
-TESTS = test/falco.test
-TEST_EXTENSIONS = .test
-
-bin_PROGRAMS = falco
-
-falco_CXXFLAGS = $(OPENMP_CXXFLAGS) $(AM_CXXFLAGS)
-falco_CPPFLAGS = -DPROGRAM_PATH=\"$(abspath $(top_srcdir))\"
+# ADS: fix the order of user and project set vars; shouldn't need to worry about
+# setting CXXFLAGS in configure.ac
+AM_CXXFLAGS = -Wall -Wextra -Wpedantic
 if ENABLE_HTS
-falco_CPPFLAGS += -DUSE_HTS
+CPPFLAGS += -DUSE_HTS
 endif
 
+bin_PROGRAMS = falco
+
 falco_SOURCES = \
 	src/falco.cpp \
 	src/FastqStats.cpp \
@@ -52,4 +46,6 @@ falco_SOURCES = \
 	src/smithlab_utils.hpp \
 	src/aux.hpp
 
+TESTS = test/falco.test
+TEST_EXTENSIONS = .test
 CLEANFILES = tests_build/test_data.tgz

configure.ac

@@ -31,8 +31,11 @@ AS_IF([test "x$CXXFLAGS_set" != "xset"], [
 ])
 AC_MSG_NOTICE([CXXFLAGS is $CXXFLAGS])
 
+AC_DEFINE_UNQUOTED([PROGRAM_PATH], ["$srcdir"],
+  [The PROGRAM_PATH variable])
+
 AX_CXX_COMPILE_STDCXX_17([noext], [mandatory])
-AC_OPENMP([C++]) dnl make sure we have openmp for multi-core in falco
+dnl AC_OPENMP([C++]) dnl make sure we have openmp for multi-core in falco
 
 dnl check for the Zlib library
 AC_CHECK_LIB([z], [zlibVersion], [],

src/FalcoConfig.cpp

@@ -17,6 +17,8 @@
 #include "FastqStats.hpp"
 #include "html_template.hpp"
 
+#include "config.h"
+
 #include <sys/stat.h>
 #include <unistd.h>
 
@@ -25,7 +27,7 @@
 #include <fstream>
 #include <sstream>
 
-const std::string FalcoConfig::FalcoVersion = "1.2.5";
+const std::string FalcoConfig::FalcoVersion = VERSION;
 
 /*********************************************************/
 /************** DEFAULT VALUES FOR FILES *****************/

src/HtmlMaker.cpp

@@ -15,10 +15,13 @@
 
 #include "HtmlMaker.hpp"
 
+#include "config.h"
+
 #include <algorithm>
 #include <chrono>
 #include <fstream>
 #include <sstream>
+#include <regex>
 
 void
 HtmlMaker::put_data(const std::string &placeholder, const std::string &data) {
@@ -29,38 +32,42 @@ HtmlMaker::put_data(const std::string &placeholder, const std::string &data) {
 
   // at least one placeholder found
   while (pos != std::string::npos) {
-    html_boilerplate.replace(pos, placeholder.size(), data);
+    html_boilerplate.replace(pos, std::size(placeholder), data);
     pos = html_boilerplate.find(placeholder, pos + 1);
   }
 }
 
 // Comments out html pieces if analyses were skipped
 void
 HtmlMaker::put_comment(std::string &comment_begin, std::string &comment_end,
-                       bool done) {
-  // put html comments if analysis was skipped
-  if (!done) {
+                       const bool done) {
+  if (!done) { // put html comments if analysis was skipped
     put_data(comment_begin, "<!--");
     put_data(comment_end, "-->");
   }
-
-  // otherwise delete placeholder
-  else {
+  else { // otherwise delete placeholder
     put_data(comment_begin, "");
     put_data(comment_end, "");
   }
 }
 
 void
 HtmlMaker::put_file_details(const FalcoConfig &falco_config) {
-  // Put file name in filename placeholder
-  put_data("{{filename}}", falco_config.filename_stripped);
+  using namespace std::string_literals;
+  static const auto left_tag = "\\{\\{"s;
+  static const auto right_tag = "\\}\\}"s;
 
-  // Put date on date placeholder
-  auto tmp =
-    std::chrono::system_clock::to_time_t(std::chrono::system_clock::now());
-  std::string time_fmt = std::string(ctime(&tmp));
-  put_data("{{date}}", time_fmt);
-}
+  std::regex filename_re(left_tag + "filename"s + right_tag);
+  std::regex_replace(html_boilerplate, filename_re,
+                     falco_config.filename_stripped);
 
-HtmlMaker::HtmlMaker() { html_boilerplate = FalcoConfig::html_template; }
+  using system_clock = std::chrono::system_clock;
+  auto time_unformatted = system_clock::to_time_t(system_clock::now());
+  std::string time_formatted = std::string(ctime(&time_unformatted));
+
+  std::regex date_re(left_tag + "date"s + right_tag);
+  std::regex_replace(html_boilerplate, date_re, time_formatted);
+
+  std::regex version_re(left_tag + "version"s + right_tag);
+  std::regex_replace(html_boilerplate, version_re, VERSION);
+}

src/HtmlMaker.hpp

@@ -28,14 +28,14 @@
 class HtmlMaker {
 public:
   std::string html_boilerplate;
-  HtmlMaker();
+  HtmlMaker() : html_boilerplate{FalcoConfig::html_template} {}
   // Fill data from module
   void put_data(const std::string &placeholder, const std::string &data);
 
   // Comment or remove placeholders
   void put_comment(std::string &comment_begin,
                    std::string &comment_end,
-                   bool done);
+                   const bool done);
 
   // Put file details and date
   void put_file_details(const FalcoConfig &falco_config);

src/falco.cpp

@@ -15,20 +15,24 @@
  * General Public License for more details.
  */
 
-#include <chrono>
-#include <filesystem>
-#include <fstream>
-#include <string>
-#include <vector>
 
 #include "FalcoConfig.hpp"
 #include "FastqStats.hpp"
 #include "HtmlMaker.hpp"
 #include "Module.hpp"
+
 #include "OptionParser.hpp"
 #include "StreamReader.hpp"
 #include "smithlab_utils.hpp"
 
+#include "config.h"
+
+#include <chrono>
+#include <filesystem>
+#include <fstream>
+#include <string>
+#include <vector>
+
 // Function to get seconds elapsed in program
 static std::size_t
 get_seconds_since(
@@ -162,7 +166,7 @@ write_results(const FalcoConfig &falco_config, FastqStats &stats,
       log_process("Writing text report to " + qc_data_file);
 
     // put header
-    qc_data_txt << "##Falco\t" + FalcoConfig::FalcoVersion + "\n";
+    qc_data_txt << "##Falco\t" + std::string{VERSION} + "\n";
     if (do_call)
       qc_data_txt << "##Call\t" << falco_config.call << "\n";
   }
@@ -262,17 +266,12 @@ write_results(const FalcoConfig &falco_config, FastqStats &stats,
     html << html_maker.html_boilerplate;
 }
 
-[[nodiscard]] inline bool
-file_exists(const std::string &file_name) {
-  return access(file_name.data(), F_OK) == 0;
-}
-
 int
 main(int argc, char *argv[]) {
 
   try {
     static const std::string FALCO_VERSION =
-      "falco " + FalcoConfig::FalcoVersion;
+      "falco " + std::string{VERSION};
     bool help = false;
     bool version = false;
 
@@ -633,7 +632,7 @@ main(int argc, char *argv[]) {
     // check if all filenames exist
     bool all_files_exist = true;
     for (std::size_t i = 0; i < std::size(all_seq_filenames); ++i) {
-      if (!file_exists(all_seq_filenames[i])) {
+      if (!std::filesystem::exists(all_seq_filenames[i])) {
         std::cerr << "ERROR! File does not exist: " << all_seq_filenames[i]
                   << '\n';
         all_files_exist = false;

src/html_template.hpp

@@ -389,7 +389,7 @@ p {
 
 
 </div>
-<div class="footer">Falco 1.2.5
+<div class="footer">Falco {{version}}
 </div>
 </body>
 <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js"