Merge pull request #10 from eseiler/infra/use_sharg

[INFRA] Use sharg includes
seqan · Dec 1, 2021 · c6d164b · c6d164b
2 parents dc47946 + f6f5a6e
commit c6d164b
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Showing 36 changed files with 59 additions and 57 deletions.
diff --git a/include/sharg/all.hpp b/include/sharg/all.hpp
@@ -40,7 +40,7 @@
 
 #pragma once
 
-#include <seqan3/argument_parser/argument_parser.hpp>
-#include <seqan3/argument_parser/auxiliary.hpp>
-#include <seqan3/argument_parser/exceptions.hpp>
-#include <seqan3/argument_parser/validators.hpp>
+#include <sharg/argument_parser.hpp>
+#include <sharg/auxiliary.hpp>
+#include <sharg/exceptions.hpp>
+#include <sharg/validators.hpp>
diff --git a/include/sharg/argument_parser.hpp b/include/sharg/argument_parser.hpp
@@ -21,13 +21,13 @@
 #include <vector>
 #include <regex>
 
-// #include <seqan3/argument_parser/detail/format_ctd.hpp>
-#include <seqan3/argument_parser/detail/format_help.hpp>
-#include <seqan3/argument_parser/detail/format_html.hpp>
-#include <seqan3/argument_parser/detail/format_man.hpp>
-#include <seqan3/argument_parser/detail/format_parse.hpp>
-#include <seqan3/argument_parser/detail/terminal.hpp>
-#include <seqan3/argument_parser/detail/version_check.hpp>
+// #include <sharg/detail/format_ctd.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>
 

diff --git a/include/sharg/detail/format_base.hpp b/include/sharg/detail/format_base.hpp
@@ -19,10 +19,10 @@
 #include <sstream>
 #include <string>
 
-#include <seqan3/argument_parser/auxiliary.hpp>
-#include <seqan3/argument_parser/detail/concept.hpp>
-#include <seqan3/argument_parser/exceptions.hpp>
-#include <seqan3/argument_parser/validators.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>
 

diff --git a/include/sharg/detail/format_help.hpp b/include/sharg/detail/format_help.hpp
@@ -17,8 +17,8 @@
 #include <cassert>
 #include <iostream>
 
-#include <seqan3/argument_parser/detail/format_base.hpp>
-#include <seqan3/argument_parser/detail/terminal.hpp>
+#include <sharg/detail/format_base.hpp>
+#include <sharg/detail/terminal.hpp>
 #include <seqan3/core/detail/test_accessor.hpp>
 
 namespace seqan3::detail
@@ -453,7 +453,7 @@ class format_version : public format_help
  * meta information (e.g. long_copyright) on construction of the parser. Thus the meta information is collected
  * and only evaluated when calling seqan3::detail::format_version::parse.
  *
- * \remark For a complete overview, take a look at \ref argument_parser 
+ * \remark For a complete overview, take a look at \ref argument_parser
  */
 class format_copyright : public format_help
 {

diff --git a/include/sharg/detail/format_html.hpp b/include/sharg/detail/format_html.hpp
@@ -14,8 +14,8 @@
 
 #include <iostream>
 
-#include <seqan3/argument_parser/detail/format_base.hpp>
-#include <seqan3/argument_parser/detail/terminal.hpp>
+#include <sharg/detail/format_base.hpp>
+#include <sharg/detail/terminal.hpp>
 #include <seqan3/version.hpp>
 
 namespace seqan3::detail
@@ -31,7 +31,7 @@ namespace seqan3::detail
  * Thus the calls are stored (parser_set_up_calls and positional_option_calls)
  * and only evaluated when calling format_help::parse().
  *
- * \remark For a complete overview, take a look at \ref argument_parser 
+ * \remark For a complete overview, take a look at \ref argument_parser
  */
 class format_html : public format_help_base<format_html>
 {

diff --git a/include/sharg/detail/format_man.hpp b/include/sharg/detail/format_man.hpp
@@ -14,8 +14,8 @@
 
 #include <iostream>
 
-#include <seqan3/argument_parser/detail/format_base.hpp>
-#include <seqan3/argument_parser/detail/terminal.hpp>
+#include <sharg/detail/format_base.hpp>
+#include <sharg/detail/terminal.hpp>
 #include <seqan3/version.hpp>
 
 namespace seqan3::detail

diff --git a/include/sharg/detail/format_parse.hpp b/include/sharg/detail/format_parse.hpp
@@ -18,7 +18,7 @@
 #include <string>
 #include <vector>
 
-#include <seqan3/argument_parser/detail/format_base.hpp>
+#include <sharg/detail/format_base.hpp>
 #include <seqan3/utility/char_operations/predicate.hpp>
 
 namespace seqan3::detail

diff --git a/include/sharg/detail/version_check.hpp b/include/sharg/detail/version_check.hpp
@@ -21,8 +21,8 @@
 #include <optional>
 #include <regex>
 
-#include <seqan3/argument_parser/auxiliary.hpp>
-#include <seqan3/argument_parser/detail/terminal.hpp>
+#include <sharg/auxiliary.hpp>
+#include <sharg/detail/terminal.hpp>
 #include <seqan3/io/detail/misc.hpp>
 #include <seqan3/io/detail/safe_filesystem_entry.hpp>
 #include <seqan3/std/charconv>

diff --git a/include/sharg/validators.hpp b/include/sharg/validators.hpp
@@ -20,7 +20,7 @@
 #include <regex>
 #include <sstream>
 
-#include <seqan3/argument_parser/exceptions.hpp>
+#include <sharg/exceptions.hpp>
 #include <seqan3/core/debug_stream/detail/to_string.hpp>
 #include <seqan3/core/debug_stream/range.hpp>
 #include <seqan3/io/detail/misc.hpp>

diff --git a/test/snippet/CMakeLists.txt b/test/snippet/CMakeLists.txt
@@ -24,6 +24,7 @@ macro (sharg_snippet test_name_prefix snippet snippet_base_path)
 
     add_executable (${target} "${snippet_base_path}/${snippet}")
     target_link_libraries (${target} PUBLIC snippet_main sharg::sharg)
+    target_include_directories (${target} PUBLIC ${CMAKE_CURRENT_LIST_DIR}/../../include)
     set_target_properties(${target}
         PROPERTIES
         RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/${snippet_target_path}"

diff --git a/test/snippet/argument_parser_1.cpp b/test/snippet/argument_parser_1.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 #include <seqan3/core/debug_stream.hpp>
 
 int main(int argc, char ** argv)

diff --git a/test/snippet/argument_parser_2.cpp b/test/snippet/argument_parser_2.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 #include <seqan3/core/debug_stream.hpp>
 
 int main(int argc, char ** argv)

diff --git a/test/snippet/argument_parser_3.cpp b/test/snippet/argument_parser_3.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 
 int main(int argc, char ** argv)
 {

diff --git a/test/snippet/auxiliary.cpp b/test/snippet/auxiliary.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 
 int main(int argc, const char ** argv)
 {

diff --git a/test/snippet/custom_argument_parsing_enumeration.cpp b/test/snippet/custom_argument_parsing_enumeration.cpp
@@ -1,6 +1,6 @@
 #include <system_error>
 
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 #include <seqan3/std/ranges>
 
 namespace seqan3::custom

diff --git a/test/snippet/custom_enumeration.cpp b/test/snippet/custom_enumeration.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 
 namespace foo
 {

diff --git a/test/snippet/is_option_set.cpp b/test/snippet/is_option_set.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 #include <seqan3/core/debug_stream.hpp>
 
 int main(int argc, char ** argv)

diff --git a/test/snippet/validators_1.cpp b/test/snippet/validators_1.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 #include <seqan3/core/debug_stream.hpp>
 
 int main(int argc, const char ** argv)

diff --git a/test/snippet/validators_2.cpp b/test/snippet/validators_2.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 #include <seqan3/core/debug_stream.hpp>
 
 int main(int argc, const char ** argv)

diff --git a/test/snippet/validators_3.cpp b/test/snippet/validators_3.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/std/filesystem>
 

diff --git a/test/snippet/validators_4.cpp b/test/snippet/validators_4.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 #include <seqan3/core/debug_stream.hpp>
 
 int main(int argc, const char ** argv)

diff --git a/test/snippet/validators_chaining.cpp b/test/snippet/validators_chaining.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 #include <seqan3/std/filesystem>
 
 int main(int argc, const char ** argv)

diff --git a/test/snippet/validators_input_directory.cpp b/test/snippet/validators_input_directory.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/std/filesystem>
 

diff --git a/test/snippet/validators_input_file.cpp b/test/snippet/validators_input_file.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/std/filesystem>
 

diff --git a/test/snippet/validators_input_file_ext_from_file.cpp b/test/snippet/validators_input_file_ext_from_file.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/validators.hpp>
+#include <sharg/validators.hpp>
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/io/sequence_file/input.hpp>
 

diff --git a/test/snippet/validators_output_directory.cpp b/test/snippet/validators_output_directory.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/std/filesystem>
 

diff --git a/test/snippet/validators_output_file.cpp b/test/snippet/validators_output_file.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/all.hpp>
+#include <sharg/all.hpp>
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/std/filesystem>
 

diff --git a/test/snippet/validators_output_file_ext_from_file.cpp b/test/snippet/validators_output_file_ext_from_file.cpp
@@ -1,4 +1,4 @@
-#include <seqan3/argument_parser/validators.hpp>
+#include <sharg/validators.hpp>
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/io/sequence_file/output.hpp>
 

diff --git a/test/unit/CMakeLists.txt b/test/unit/CMakeLists.txt
@@ -29,6 +29,7 @@ macro (sharg_test unit_test_cpp)
 
     add_executable (${target} ${unit_test_cpp})
     target_link_libraries (${target} seqan3::test::unit sharg::sharg)
+    target_include_directories (${target} PUBLIC ${CMAKE_CURRENT_LIST_DIR}/../../include)
     add_include_dependencies (${target} "${SHARG_TEST_CYCLIC_DEPENDING_INCLUDES}")
     collect_used_test (${target})
     if (SHARG_VERBOSE_TESTS)

diff --git a/test/unit/argument_parser_design_error_test.cpp b/test/unit/argument_parser_design_error_test.cpp
@@ -7,7 +7,7 @@
 
 #include <gtest/gtest.h>
 
-#include <seqan3/argument_parser/argument_parser.hpp>
+#include <sharg/argument_parser.hpp>
 
 TEST(design_error, app_name_validation)
 {

diff --git a/test/unit/detail/format_help_test.cpp b/test/unit/detail/format_help_test.cpp
@@ -10,8 +10,8 @@
 
 #include <gtest/gtest.h>
 
-#include <seqan3/argument_parser/argument_parser.hpp>
-#include <seqan3/argument_parser/detail/format_help.hpp>
+#include <sharg/argument_parser.hpp>
+#include <sharg/detail/format_help.hpp>
 
 // reused global variables
 std::string std_cout;

diff --git a/test/unit/detail/format_html_test.cpp b/test/unit/detail/format_html_test.cpp
@@ -7,8 +7,8 @@
 
 #include <gtest/gtest.h>
 
-#include <seqan3/argument_parser/argument_parser.hpp>
-#include <seqan3/argument_parser/detail/format_html.hpp>
+#include <sharg/argument_parser.hpp>
+#include <sharg/detail/format_html.hpp>
 #include <seqan3/utility/char_operations/predicate.hpp>
 
 TEST(html_format, empty_information)

diff --git a/test/unit/detail/format_man_test.cpp b/test/unit/detail/format_man_test.cpp
@@ -10,8 +10,8 @@
 
 #include <gtest/gtest.h>
 
-#include <seqan3/argument_parser/argument_parser.hpp>
-#include <seqan3/argument_parser/detail/format_man.hpp>
+#include <sharg/argument_parser.hpp>
+#include <sharg/detail/format_man.hpp>
 
 // Reused global variables
 struct format_man_test : public ::testing::Test

diff --git a/test/unit/detail/version_check_test.hpp b/test/unit/detail/version_check_test.hpp
@@ -12,7 +12,7 @@
 #include <chrono>
 #include <stdlib.h>
 
-#include <seqan3/argument_parser/argument_parser.hpp>
+#include <sharg/argument_parser.hpp>
 #include <seqan3/test/tmp_filename.hpp>
 
 //------------------------------------------------------------------------------

diff --git a/test/unit/format_parse_test.cpp b/test/unit/format_parse_test.cpp
@@ -7,7 +7,7 @@
 
 #include <gtest/gtest.h>
 
-#include <seqan3/argument_parser/argument_parser.hpp>
+#include <sharg/argument_parser.hpp>
 
 TEST(parse_type_test, add_option_short_id)
 {

diff --git a/test/unit/format_parse_validators_test.cpp b/test/unit/format_parse_validators_test.cpp
@@ -11,7 +11,7 @@
 #include <fstream>
 #include <seqan3/std/ranges>
 
-#include <seqan3/argument_parser/argument_parser.hpp>
+#include <sharg/argument_parser.hpp>
 #include <seqan3/test/file_access.hpp>
 #include <seqan3/test/tmp_filename.hpp>
 
@@ -481,7 +481,7 @@ TEST(validator_test, output_directory)
         seqan3::test::tmp_filename tmp_child_name{"dir/child_dir"};
         std::filesystem::path tmp_child_dir{tmp_child_name.get_path()};
         std::filesystem::path tmp_parent_path{tmp_child_dir.parent_path()};
-        
+
         std::filesystem::create_directory(tmp_parent_path);
 
         EXPECT_TRUE(std::filesystem::exists(tmp_parent_path));
@@ -542,7 +542,7 @@ TEST(validator_test, inputfile_not_regular)
 {
     seqan3::test::tmp_filename tmp{"my_file.test"};
     std::filesystem::path filename = tmp.get_path();
-    mkfifo(filename.c_str(), 0644); 
+    mkfifo(filename.c_str(), 0644);
 
     EXPECT_THROW(seqan3::input_file_validator{}(filename), seqan3::validation_error);
 }