[MISC] header

doc/cookbook/basic_arg_parse.cpp

@@ -1,11 +1,10 @@
 #include <sharg/all.hpp>
-#include <seqan3/core/debug_stream.hpp>
 
 void run_program(std::filesystem::path const & reference_path,
                  std::filesystem::path const & index_path)
 {
-    seqan3::debug_stream << "reference_file_path: " << reference_path << '\n';
-    seqan3::debug_stream << "index_path           " << index_path << '\n';
+    std::cerr << "reference_file_path: " << reference_path << '\n';
+    std::cerr << "index_path           " << index_path << '\n';
 }
 
 struct cmd_arguments

doc/howto/subcommand_argument_parser/subcommand_arg_parse.cpp

@@ -1,5 +1,4 @@
 #include <sharg/all.hpp>
-#include <seqan3/core/debug_stream.hpp>
 
 // =====================================================================================================================
 // pull
@@ -25,11 +24,11 @@ int run_git_pull(sharg::argument_parser & parser)
     }
     catch (sharg::argument_parser_error const & ext)
     {
-        seqan3::debug_stream << "[Error git pull] " << ext.what() << "\n";
+        std::cerr << "[Error git pull] " << ext.what() << "\n";
         return -1;
     }
 
-    seqan3::debug_stream << "Git pull with repository " << args.repository << " and branch " << args.branch << '\n';
+    std::cerr << "Git pull with repository " << args.repository << " and branch " << args.branch << '\n';
 
     return 0;
 }
@@ -58,11 +57,14 @@ int run_git_push(sharg::argument_parser & parser)
     }
     catch (sharg::argument_parser_error const & ext)
     {
-        seqan3::debug_stream << "[Error git push] " << ext.what() << "\n";
+        std::cerr << "[Error git push] " << ext.what() << "\n";
         return -1;
     }
 
-    seqan3::debug_stream << "Git push with repository " << args.repository << " and branches " << args.branches << '\n';
+    std::cerr << "Git push with repository " << args.repository << " and branches ";
+    for (auto && branch : args.branches)
+        std::cerr << branch << ' ';
+    std::cerr << '\n';
 
     return 0;
 }
@@ -93,7 +95,7 @@ int main(int argc, char const ** argv)
     }
     catch (sharg::argument_parser_error const & ext) // catch user errors
     {
-        seqan3::debug_stream << "[Error] " << ext.what() << "\n"; // customise your error message
+        std::cerr << "[Error] " << ext.what() << "\n"; // customise your error message
         return -1;
     }
 

doc/tutorial/argument_parser/basic_parser_setup.cpp

@@ -1,5 +1,4 @@
 #include <sharg/all.hpp>   // includes all necessary headers
-#include <seqan3/core/debug_stream.hpp>     // our custom output stream
 
 int main(int argc, char ** argv)
 {
@@ -13,7 +12,7 @@ int main(int argc, char ** argv)
     }
     catch (sharg::argument_parser_error const & ext)                     // catch user errors
     {
-        seqan3::debug_stream << "[Winter has come] " << ext.what() << "\n"; // customise your error message
+        std::cerr << "[Winter has come] " << ext.what() << "\n"; // customise your error message
         return -1;
     }
 }

doc/tutorial/argument_parser/small_snippets.cpp

@@ -1,5 +1,4 @@
 #include <sharg/all.hpp>
-#include <filesystem>
 
 //![validator_include]
 #include <sharg/validators.hpp>

doc/tutorial/argument_parser/solution1.cpp

@@ -1,5 +1,4 @@
 #include <sharg/all.hpp> // includes all necessary headers
-#include <seqan3/core/debug_stream.hpp>   // our custom output stream
 
 void initialise_argument_parser(sharg::argument_parser & parser)
 {

doc/tutorial/argument_parser/solution3.cpp

@@ -1,11 +1,5 @@
 //![program]
-#include <seqan3/std/charconv>            // includes std::from_chars
-#include <filesystem>                     // use std::filesystem::path
-#include <fstream>
-#include <numeric>
-
 #include <sharg/all.hpp> // includes all necessary headers
-#include <seqan3/core/debug_stream.hpp>   // our custom output stream
 
 // This is the program!
 // Take a look at it if you are interested in an example of parsing a data file.
@@ -20,7 +14,7 @@ number_type to_number(range_type && range)
 
     if (res.ec != std::errc{})
     {
-        seqan3::debug_stream << "Could not cast '" << range << "' to a valid number\n";
+        std::cerr << "Could not cast '" << str << "' to a valid number\n";
         throw std::invalid_argument{"CAST ERROR"};
     }
     return num;
@@ -48,16 +42,16 @@ void run_program(std::filesystem::path & path, uint32_t yr, std::string & aggr_b
         }
 
         if (aggr_by == "median")
-            seqan3::debug_stream << ([&v] () { std::sort(v.begin(), v.end()); return v[v.size()/2]; })() << '\n';
+            std::cerr << ([&v] () { std::sort(v.begin(), v.end()); return v[v.size()/2]; })() << '\n';
         else if (aggr_by == "mean")
-            seqan3::debug_stream << ([&v] () { double sum{}; for (auto i : v) sum += i; return sum / v.size(); })()
+            std::cerr << ([&v] () { double sum{}; for (auto i : v) sum += i; return sum / v.size(); })()
                                  << '\n';
         else
-            seqan3::debug_stream << "I do not know the aggregation method " << aggr_by << '\n';
+            std::cerr << "I do not know the aggregation method " << aggr_by << '\n';
     }
     else
     {
-        seqan3::debug_stream << "Error: Cannot open file for reading.\n";
+        std::cerr << "Error: Cannot open file for reading.\n";
     }
 }
 // -----------------------------------------------------------------------------
@@ -102,7 +96,7 @@ int main(int argc, char ** argv)
     }
     catch (sharg::argument_parser_error const & ext)                     // catch user errors
     {
-        seqan3::debug_stream << "[Winter has come] " << ext.what() << "\n"; // customise your error message
+        std::cerr << "[Winter has come] " << ext.what() << "\n"; // customise your error message
         return -1;
     }
 

doc/tutorial/argument_parser/solution4.cpp

@@ -1,10 +1,4 @@
-#include <fstream>
-#include <numeric>
-
 #include <sharg/all.hpp> // includes all necessary headers
-#include <seqan3/core/debug_stream.hpp>   // our custom output stream
-#include <seqan3/std/charconv>            // includes std::from_chars
-#include <filesystem>                     // use std::filesystem::path
 
 // This is the program!
 // Take a look at it if you are interested in an example of parsing a data file.
@@ -19,7 +13,7 @@ number_type to_number(range_type && range)
 
     if (res.ec != std::errc{})
     {
-        seqan3::debug_stream << "Could not cast '" << range << "' to a valid number\n";
+        std::cerr << "Could not cast '" << str << "' to a valid number\n";
         throw std::invalid_argument{"CAST ERROR"};
     }
     return num;
@@ -49,16 +43,16 @@ void run_program(std::filesystem::path & path, std::vector<uint8_t> sn, std::str
         //![altered_while]
 
         if (aggr_by == "median")
-            seqan3::debug_stream << ([&v] () { std::sort(v.begin(), v.end()); return v[v.size()/2]; })() << '\n';
+            std::cerr << ([&v] () { std::sort(v.begin(), v.end()); return v[v.size()/2]; })() << '\n';
         else if (aggr_by == "mean")
-            seqan3::debug_stream << ([&v] () { double sum{}; for (auto i : v) sum += i; return sum / v.size(); })()
+            std::cerr << ([&v] () { double sum{}; for (auto i : v) sum += i; return sum / v.size(); })()
                                  << '\n';
         else
-            seqan3::debug_stream << "I do not know the aggregation method " << aggr_by << '\n';
+            std::cerr << "I do not know the aggregation method " << aggr_by << '\n';
     }
     else
     {
-        seqan3::debug_stream << "Error: Cannot open file for reading.\n";
+        std::cerr << "Error: Cannot open file for reading.\n";
     }
 }
 // -----------------------------------------------------------------------------
@@ -102,7 +96,7 @@ int main(int argc, char ** argv)
     }
     catch (sharg::argument_parser_error const & ext)                     // catch user errors
     {
-        seqan3::debug_stream << "[Winter has come] " << ext.what() << "\n"; // customise your error message
+        std::cerr << "[Winter has come] " << ext.what() << "\n"; // customise your error message
         return -1;
     }
 

doc/tutorial/argument_parser/solution5.cpp

@@ -1,10 +1,4 @@
-#include <fstream>
-#include <numeric>
-
 #include <sharg/all.hpp> // includes all necessary headers
-#include <seqan3/core/debug_stream.hpp>   // our custom output stream
-#include <seqan3/std/charconv>            // includes std::from_chars
-#include <filesystem>                     // use std::filesystem::path
 
 // This is the program!
 // Take a look at it if you are interested in an example of parsing a data file.
@@ -19,7 +13,7 @@ number_type to_number(range_type && range)
 
     if (res.ec != std::errc{})
     {
-        seqan3::debug_stream << "Could not cast '" << range << "' to a valid number\n";
+        std::cerr << "Could not cast '" << str << "' to a valid number\n";
         throw std::invalid_argument{"CAST ERROR"};
     }
     return num;
@@ -47,16 +41,16 @@ void run_program(std::filesystem::path & path, std::vector<uint8_t> sn, std::str
         }
 
         if (aggr_by == "median")
-            seqan3::debug_stream << ([&v] () { std::sort(v.begin(), v.end()); return v[v.size()/2]; })() << '\n';
+            std::cerr << ([&v] () { std::sort(v.begin(), v.end()); return v[v.size()/2]; })() << '\n';
         else if (aggr_by == "mean")
-            seqan3::debug_stream << ([&v] () { double sum{}; for (auto i : v) sum += i; return sum / v.size(); })()
+            std::cerr << ([&v] () { double sum{}; for (auto i : v) sum += i; return sum / v.size(); })()
                                  << '\n';
         else
-            seqan3::debug_stream << "I do not know the aggregation method " << aggr_by << '\n';
+            std::cerr << "I do not know the aggregation method " << aggr_by << '\n';
     }
     else
     {
-        seqan3::debug_stream << "Error: Cannot open file for reading.\n";
+        std::cerr << "Error: Cannot open file for reading.\n";
     }
 }
 // -----------------------------------------------------------------------------
@@ -100,7 +94,7 @@ int main(int argc, char ** argv)
     }
     catch (sharg::argument_parser_error const & ext)                     // catch user errors
     {
-        seqan3::debug_stream << "[Winter has come] " << ext.what() << "\n"; // customise your error message
+        std::cerr << "[Winter has come] " << ext.what() << "\n"; // customise your error message
         return -1;
     }
 

doc/tutorial/argument_parser/solution6.cpp

@@ -1,10 +1,4 @@
-#include <fstream>
-#include <numeric>
-
 #include <sharg/all.hpp> // includes all necessary headers
-#include <seqan3/core/debug_stream.hpp>   // our custom output stream
-#include <seqan3/std/charconv>            // includes std::from_chars
-#include <filesystem>                     // use std::filesystem::path
 
 // This is the program!
 // Take a look at it if you are interested in an example of parsing a data file.
@@ -19,7 +13,7 @@ number_type to_number(range_type && range)
 
     if (res.ec != std::errc{})
     {
-        seqan3::debug_stream << "Could not cast '" << range << "' to a valid number\n";
+        std::cerr << "Could not cast '" << str << "' to a valid number\n";
         throw std::invalid_argument{"CAST ERROR"};
     }
     return num;
@@ -47,16 +41,16 @@ void run_program(std::filesystem::path & path, std::vector<uint8_t> sn, std::str
         }
 
         if (aggr_by == "median")
-            seqan3::debug_stream << ([&v] () { std::sort(v.begin(), v.end()); return v[v.size()/2]; })() << '\n';
+            std::cerr << ([&v] () { std::sort(v.begin(), v.end()); return v[v.size()/2]; })() << '\n';
         else if (aggr_by == "mean")
-            seqan3::debug_stream << ([&v] () { double sum{}; for (auto i : v) sum += i; return sum / v.size(); })()
+            std::cerr << ([&v] () { double sum{}; for (auto i : v) sum += i; return sum / v.size(); })()
                                  << '\n';
         else
-            seqan3::debug_stream << "I do not know the aggregation method " << aggr_by << '\n';
+            std::cerr << "I do not know the aggregation method " << aggr_by << '\n';
     }
     else
     {
-        seqan3::debug_stream << "Error: Cannot open file for reading.\n";
+        std::cerr << "Error: Cannot open file for reading.\n";
     }
 }
 // -----------------------------------------------------------------------------
@@ -107,7 +101,7 @@ int main(int argc, char ** argv)
     }
     catch (sharg::argument_parser_error const & ext)                     // catch user errors
     {
-        seqan3::debug_stream << "[Winter has come] " << ext.what() << "\n"; // customise your error message
+        std::cerr << "[Winter has come] " << ext.what() << "\n"; // customise your error message
         return -1;
     }
 

include/sharg/argument_parser.hpp

@@ -12,24 +12,16 @@
 
 #pragma once
 
-#include <future>
-#include <iostream>
 #include <set>
-#include <sstream>
-#include <string>
-#include <variant>
-#include <vector>
-#include <regex>
 
-// #include <sharg/detail/format_ctd.hpp>
+#include <seqan3/core/debug_stream/detail/to_string.hpp>
+
 #include <sharg/detail/format_help.hpp>
 #include <sharg/detail/format_html.hpp>
 #include <sharg/detail/format_man.hpp>
 #include <sharg/detail/format_parse.hpp>
 #include <sharg/detail/terminal.hpp>
 #include <sharg/detail/version_check.hpp>
-#include <seqan3/core/debug_stream/detail/to_string.hpp>
-#include <seqan3/core/detail/test_accessor.hpp>
 
 namespace sharg
 {

include/sharg/auxiliary.hpp

@@ -12,16 +12,15 @@
 
 #pragma once
 
-#include <seqan3/std/concepts>
-#include <sstream>
-#include <seqan3/std/type_traits>
 #include <unordered_map>
 #include <vector>
 
 #include <seqan3/core/debug_stream/debug_stream_type.hpp>
 #include <seqan3/core/detail/customisation_point.hpp>
 #include <seqan3/io/stream/concept.hpp>
 
+#include <sharg/platform.hpp>
+
 namespace sharg::custom
 {
 

include/sharg/detail/concept.hpp

@@ -12,9 +12,7 @@
 
 #pragma once
 
-#include <seqan3/std/concepts>
 #include <string>
-#include <seqan3/std/type_traits>
 
 #include <sharg/platform.hpp>
 

include/sharg/detail/format_base.hpp

@@ -13,18 +13,14 @@
 
 #pragma once
 
-#include <filesystem>
-#include <iostream>
-#include <limits>
-#include <sstream>
-#include <string>
+#include <seqan3/utility/detail/type_name_as_string.hpp>
+#include <seqan3/utility/type_list/traits.hpp>
 
 #include <sharg/auxiliary.hpp>
 #include <sharg/detail/concept.hpp>
 #include <sharg/exceptions.hpp>
 #include <sharg/validators.hpp>
-#include <seqan3/utility/detail/type_name_as_string.hpp>
-#include <seqan3/version.hpp>
+#include <sharg/version.hpp>
 
 namespace sharg::detail
 {

include/sharg/detail/format_help.hpp

@@ -14,12 +14,15 @@
 
 #pragma once
 
-#include <cassert>
-#include <iostream>
-
 #include <sharg/detail/format_base.hpp>
 #include <sharg/detail/terminal.hpp>
-#include <seqan3/core/detail/test_accessor.hpp>
+
+namespace seqan3::detail
+{
+
+struct test_accessor;
+
+} // seqan3::detail
 
 namespace sharg::detail
 {

include/sharg/detail/format_html.hpp

@@ -12,11 +12,9 @@
 
 #pragma once
 
-#include <iostream>
-
 #include <sharg/detail/format_base.hpp>
 #include <sharg/detail/terminal.hpp>
-#include <seqan3/version.hpp>
+#include <sharg/version.hpp>
 
 namespace sharg::detail
 {