Final renaming

Signed-off-by: Lydia Buntrock <[email protected]>

CHANGELOG.md

@@ -52,7 +52,7 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele
   * `seqan3::argument_parser::add_line`
   * `seqan3::argument_parser::add_list_item`
   Note that other `seqan3::argument_parser::option_spec`s like `REQUIRED` are ignored.
-* We expanded the `seqan3::output_file_validator`, with a parameter `seqan3::output_file_open_mode` to allow overwriting
+* We expanded the `seqan3::output_file_validator`, with a parameter `seqan3::output_file_open_options` to allow overwriting
   output files ([\#2009](https://github.com/seqan/seqan3/pull/2009)).
 
 #### I/O

doc/tutorial/argument_parser/index.md

@@ -390,7 +390,7 @@ of the parsed option value.
 The validator throws a seqan3::validation_error exception whenever a given filename's extension is not in the
 given list of valid extensions. In addition, the seqan3::input_file_validator checks if the file exists, is a regular
 file and is readable.
-Moreover, you have to add an additional flag seqan3::output_file_open_mode to the seqan3::output_file_validator,
+Moreover, you have to add an additional flag seqan3::output_file_open_options to the seqan3::output_file_validator,
 which you can use to indicate whether you want to allow the output files to be overwritten.
 
 \note If you want to allow any extension just use a default constructed file validator.

doc/tutorial/read_mapper/read_mapper_indexer_step1.cpp

@@ -24,7 +24,7 @@ void initialise_argument_parser(seqan3::argument_parser & parser, cmd_arguments
                       seqan3::input_file_validator{{"fa","fasta"}});
     parser.add_option(args.index_path, 'o', "output", "The output index file path.",
                       seqan3::option_spec::DEFAULT,
-                      seqan3::output_file_validator{seqan3::output_file_open_mode::exclusive, {"index"}});
+                      seqan3::output_file_validator{seqan3::output_file_open_options::create_new, {"index"}});
 }
 
 //![main]

doc/tutorial/read_mapper/read_mapper_indexer_step2.cpp

@@ -51,7 +51,7 @@ void initialise_argument_parser(seqan3::argument_parser & parser, cmd_arguments
                       seqan3::input_file_validator{{"fa","fasta"}});
     parser.add_option(args.index_path, 'o', "output", "The output index file path.",
                       seqan3::option_spec::DEFAULT,
-                      seqan3::output_file_validator{seqan3::output_file_open_mode::exclusive, {"index"}});
+                      seqan3::output_file_validator{seqan3::output_file_open_options::create_new, {"index"}});
 }
 
 int main(int argc, char const ** argv)

doc/tutorial/read_mapper/read_mapper_indexer_step3.cpp

@@ -66,7 +66,7 @@ void initialise_argument_parser(seqan3::argument_parser & parser, cmd_arguments
                       seqan3::input_file_validator{{"fa","fasta"}});
     parser.add_option(args.index_path, 'o', "output", "The output index file path.",
                       seqan3::option_spec::DEFAULT,
-                      seqan3::output_file_validator{seqan3::output_file_open_mode::exclusive, {"index"}});
+                      seqan3::output_file_validator{seqan3::output_file_open_options::create_new, {"index"}});
 }
 
 int main(int argc, char const ** argv)

doc/tutorial/read_mapper/read_mapper_step1.cpp

@@ -39,7 +39,7 @@ void initialise_argument_parser(seqan3::argument_parser & parser, cmd_arguments
                       seqan3::input_file_validator{{"index"}});
     parser.add_option(args.sam_path, 'o', "output", "The output SAM file path.",
                       seqan3::option_spec::DEFAULT,
-                      seqan3::output_file_validator{seqan3::output_file_open_mode::exclusive, {"sam"}});
+                      seqan3::output_file_validator{seqan3::output_file_open_options::create_new, {"sam"}});
     parser.add_option(args.errors, 'e', "error", "Maximum allowed errors.",
                       seqan3::option_spec::DEFAULT,
                       seqan3::arithmetic_range_validator{0, 4});

doc/tutorial/read_mapper/read_mapper_step2.cpp

@@ -103,7 +103,7 @@ void initialise_argument_parser(seqan3::argument_parser & parser, cmd_arguments
                       seqan3::input_file_validator{{"index"}});
     parser.add_option(args.sam_path, 'o', "output", "The output SAM file path.",
                       seqan3::option_spec::DEFAULT,
-                      seqan3::output_file_validator{seqan3::output_file_open_mode::exclusive, {"sam"}});
+                      seqan3::output_file_validator{seqan3::output_file_open_options::create_new, {"sam"}});
     parser.add_option(args.errors, 'e', "error", "Maximum allowed errors.",
                       seqan3::option_spec::DEFAULT,
                       seqan3::arithmetic_range_validator{0, 4});

doc/tutorial/read_mapper/read_mapper_step3.cpp

@@ -126,7 +126,7 @@ void initialise_argument_parser(seqan3::argument_parser & parser, cmd_arguments
                       seqan3::input_file_validator{{"index"}});
     parser.add_option(args.sam_path, 'o', "output", "The output SAM file path.",
                       seqan3::option_spec::DEFAULT,
-                      seqan3::output_file_validator{seqan3::output_file_open_mode::exclusive, {"sam"}});
+                      seqan3::output_file_validator{seqan3::output_file_open_options::create_new, {"sam"}});
     parser.add_option(args.errors, 'e', "error", "Maximum allowed errors.",
                       seqan3::option_spec::DEFAULT,
                       seqan3::arithmetic_range_validator{0, 4});

doc/tutorial/read_mapper/read_mapper_step4.cpp

@@ -134,7 +134,7 @@ void initialise_argument_parser(seqan3::argument_parser & parser, cmd_arguments
                       seqan3::input_file_validator{{"index"}});
     parser.add_option(args.sam_path, 'o', "output", "The output SAM file path.",
                       seqan3::option_spec::DEFAULT,
-                      seqan3::output_file_validator{seqan3::output_file_open_mode::exclusive, {"sam"}});
+                      seqan3::output_file_validator{seqan3::output_file_open_options::create_new, {"sam"}});
     parser.add_option(args.errors, 'e', "error", "Maximum allowed errors.",
                       seqan3::option_spec::DEFAULT,
                       seqan3::arithmetic_range_validator{0, 4});

include/seqan3/argument_parser/validators.hpp

@@ -575,12 +575,12 @@ class input_file_validator : public file_validator_base
 };
 
 //!\brief Mode of an output file: Determines whether an existing file is accepted for writing.
-enum output_file_open_mode
+enum output_file_open_options
 {
     //!\brief Allow to overwrite the output file
-    overwritable,
+    open_or_create,
     //!\brief Forbid overwriting the output file
-    exclusive
+    create_new
 };
 
 /*!\brief A validator that checks if a given path is a valid output file.
@@ -611,7 +611,7 @@ class output_file_validator : public file_validator_base
 {
 private:
     //!\brief Stores the current mode of whether it is valid to overwrite the output file.
-    output_file_open_mode mode;
+    output_file_open_options mode;
 
 public:
     static_assert(std::same_as<file_t, void> || detail::has_type_valid_formats<file_t>,
@@ -639,7 +639,7 @@ class output_file_validator : public file_validator_base
      * This constructor is only available if `file_t` does not name a valid seqan3 file type that contains a
      * static member `valid_formats`.
      */
-    explicit output_file_validator(output_file_open_mode const mode) : file_validator_base{}, mode{mode}
+    explicit output_file_validator(output_file_open_options const mode) : file_validator_base{}, mode{mode}
     {
         if constexpr (!std::same_as<file_t, void>)
             file_validator_base::extensions = detail::valid_file_extensions<typename file_t::valid_formats>();
@@ -654,7 +654,7 @@ class output_file_validator : public file_validator_base
      * This constructor is only available if `file_t` does not name a valid seqan3 file type that contains a
      * static member `valid_formats`.
      */
-    explicit output_file_validator(output_file_open_mode const mode, std::vector<std::string> extensions)
+    explicit output_file_validator(output_file_open_options const mode, std::vector<std::string> extensions)
     //!\cond
         requires std::same_as<file_t, void>
     //!\endcond
@@ -679,7 +679,7 @@ class output_file_validator : public file_validator_base
     {
         try
         {
-            if ((mode == exclusive) && std::filesystem::exists(file))
+            if ((mode == create_new) && std::filesystem::exists(file))
                 throw validation_error{detail::to_string("The file ", file, " already exists!")};
 
             // Check if file has any write permissions.
@@ -700,9 +700,9 @@ class output_file_validator : public file_validator_base
     //!\brief Returns a message that can be appended to the (positional) options help page info.
     std::string get_help_page_message() const
     {
-        if (mode == overwritable)
+        if (mode == open_or_create)
             return "Write permissions must be granted." + valid_extensions_help_page_message();
-        else // mode == exclusive
+        else // mode == create_new
             return "The output file must not exist already and write permissions must be granted." +
                    valid_extensions_help_page_message();
     }

test/snippet/argument_parser/validators_output_directory.cpp

@@ -11,7 +11,7 @@ int main(int argc, const char ** argv)
 
     myparser.add_option(mydir, 'd', "dir", "The output directory for storing the files.",
                         seqan3::option_spec::DEFAULT,
-                        seqan3::output_file_validator{seqan3::output_file_open_mode::exclusive});
+                        seqan3::output_file_validator{seqan3::output_file_open_options::create_new});
     //! [validator_call]
 
     // an exception will be thrown if the user specifies a directory that cannot be created by the filesystem either

test/snippet/argument_parser/validators_output_file.cpp

@@ -9,12 +9,12 @@ int main(int argc, const char ** argv)
     //! [validator_call]
     std::filesystem::path myfile{};
 
-                        // Add the output_file_open_mode, to allow overwriting existing files, or to avoid this.
+                        // Add the output_file_open_options, to allow overwriting existing files, or to avoid this.
     myparser.add_option(myfile,'f',"file","Output file containing the processed sequences.",
                         seqan3::option_spec::DEFAULT,
-                        seqan3::output_file_validator{seqan3::output_file_open_mode::overwritable, {"fa","fasta"}});
+                        seqan3::output_file_validator{seqan3::output_file_open_options::open_or_create, {"fa","fasta"}});
                         // or
-                        // seqan3::output_file_validator{seqan3::output_file_open_mode::exclusive, {"fa","fasta"}});
+                        // seqan3::output_file_validator{seqan3::output_file_open_options::create_new, {"fa","fasta"}});
     //! [validator_call]
 
     // an exception will be thrown if the user specifies a filename

test/snippet/argument_parser/validators_output_file_ext_from_file.cpp

@@ -5,16 +5,18 @@
 int main(int argc, const char ** argv)
 {
     // Default constructed validator has an empty extension list.
-    seqan3::output_file_validator validator1{seqan3::output_file_open_mode::exclusive};
+    seqan3::output_file_validator validator1{seqan3::output_file_open_options::create_new};
     seqan3::debug_stream << validator1.get_help_page_message() << "\n";
 
     // Specify your own extensions for the output file.
-    seqan3::output_file_validator validator2{seqan3::output_file_open_mode::exclusive,
+    seqan3::output_file_validator validator2{seqan3::output_file_open_options::create_new,
                                              std::vector{std::string{"exe"}, std::string{"fasta"}}};
     seqan3::debug_stream << validator2.get_help_page_message() << "\n";
 
     // Give the seqan3 file type as a template argument to get all valid extensions for this file.
-    seqan3::output_file_validator<seqan3::sequence_file_output<>> validator3{seqan3::output_file_open_mode::exclusive};
+    seqan3::output_file_validator<seqan3::sequence_file_output<>> validator3{
+                                                                        seqan3::output_file_open_options::create_new
+                                                                  };
     seqan3::debug_stream << validator3.get_help_page_message() << "\n";
 
     return 0;