Merge pull request #44 from Irallia/MISC/Remove_depencency_of_seqan3_IO

[MISC] Remove depencency of seqan3 io
seqan · Jan 20, 2022 · 1506aa8 · 1506aa8 · vercel · Jan 20, 2022
2 parents f1104c8 + ec6060f
commit 1506aa8
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Showing 8 changed files with 54 additions and 159 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -23,3 +23,14 @@ The following API changes should be documented as such:
 
 If possible, provide tooling that performs the changes, e.g. a shell-script.
 -->
+
+## API changes
+
+#### I/O
+
+* In order to avoid using the seqan3 I/O module, you now have to give a list of file extensions explicitly to
+`sharg::input_file_validator` and `sharg::output_file_validator`:
+For example `sharg::input_file_validator validator{std::vector<std::string>{{"exe"}, {"fasta"}}};`. Please follow
+https://github.com/seqan/seqan3/issues/2927 to see how the list of file extensions can be extracted from seqan3 files.
+We also removed the `default_extensions()` function, as we now can construct `output_file_validator` with just a given
+mode: `output_file_validator(output_file_open_options const mode)`. The extensions will be an empty array in this case.
diff --git a/include/sharg/argument_parser.hpp b/include/sharg/argument_parser.hpp
@@ -13,6 +13,7 @@
 #pragma once
 
 #include <set>
+#include <variant>
 
 #include <sharg/detail/format_help.hpp>
 #include <sharg/detail/format_html.hpp>

diff --git a/include/sharg/validators.hpp b/include/sharg/validators.hpp
@@ -12,12 +12,12 @@
 
 #pragma once
 
+#include <seqan3/std/algorithm>
 #include <fstream>
 #include <regex>
 
 #include <seqan3/core/debug_stream/detail/to_string.hpp>
 #include <seqan3/core/debug_stream/range.hpp>
-#include <seqan3/io/detail/misc.hpp>
 
 #include <sharg/detail/safe_filesystem_entry.hpp>
 #include <sharg/exceptions.hpp>
@@ -262,7 +262,6 @@ value_list_validator(range_type && rng) -> value_list_validator<std::ranges::ran
 
 /*!\brief An abstract base class for the file and directory validators.
  * \ingroup argument_parser
- * \tparam file_t The type of the file to get the valid extensions for; `void` on default.
  *
  * \details
  *
@@ -458,7 +457,6 @@ class file_validator_base
 /*!\brief A validator that checks if a given path is a valid input file.
  * \ingroup argument_parser
  * \implements sharg::validator
- * \tparam file_t The type of the file to get the valid extensions for; `void` on default.
  *
  * \details
  *
@@ -469,47 +467,26 @@ class file_validator_base
  *
  * \include test/snippet/argument_parser/validators_input_file.cpp
  *
- * The valid extensions can also be obtained from a seqan3 formatted file type, e.g. sharg::sequence_input_file, if
- * it is given as template argument to this class. The following snippet demonstrates the different ways to instantiate
- * the sharg::input_file_validator.
+ * The following snippet demonstrates the different ways to instantiate the sharg::input_file_validator.
  *
  * \include test/snippet/argument_parser/validators_input_file_ext_from_file.cpp
  *
  * \note The validator works on every type that can be implicitly converted to std::filesystem::path.
  *
  * \remark For a complete overview, take a look at \ref argument_parser
  */
-template <typename file_t = void>
 class input_file_validator : public file_validator_base
 {
 public:
 
-    static_assert(std::same_as<file_t, void> || seqan3::detail::has_type_valid_formats<file_t>,
-                  "Expected either a template type with a static member called valid_formats (a file type) or void.");
-
     // Import from base class.
     using typename file_validator_base::option_value_type;
 
     /*!\name Constructors, destructor and assignment
      * \{
      */
 
-    /*!\brief Default constructor.
-     *
-     * \details
-     *
-     * If the class' template argument `file_t` names a valid seqan3 file type that contains a
-     * static member `valid_formats`, e.g. seqan3::sequence_input_file::valid_formats, then it generates the
-     * list of valid extensions from this file. Otherwise the extensions list is empty.
-     */
-    input_file_validator()
-    {
-        if constexpr (!std::same_as<file_t, void>)
-            file_validator_base::extensions = seqan3::detail::valid_file_extensions<typename file_t::valid_formats>();
-
-        file_validator_base::extensions_str = create_extensions_str();
-    }
-
+    input_file_validator() = default;                                         //!< Defaulted.
     input_file_validator(input_file_validator const &) = default;             //!< Defaulted.
     input_file_validator(input_file_validator &&) = default;                  //!< Defaulted.
     input_file_validator & operator=(input_file_validator const &) = default; //!< Defaulted.
@@ -518,17 +495,8 @@ class input_file_validator : public file_validator_base
 
     /*!\brief Constructs from a given collection of valid extensions.
      * \param[in] extensions The valid extensions to validate for.
-     *
-     * \details
-     *
-     * This constructor is only available if `file_t` does not name a valid seqan3 file type that contains a
-     * static member `valid_formats`.
      */
-    explicit input_file_validator(std::vector<std::string> extensions)
-    //!\cond
-        requires std::same_as<file_t, void>
-    //!\endcond
-        : file_validator_base{}
+    explicit input_file_validator(std::vector<std::string> extensions) : file_validator_base{}
     {
         file_validator_base::extensions = std::move(extensions);
         file_validator_base::extensions_str = create_extensions_str();
@@ -592,7 +560,6 @@ enum class output_file_open_options
 /*!\brief A validator that checks if a given path is a valid output file.
  * \ingroup argument_parser
  * \implements sharg::validator
- * \tparam file_t The type of the file to get the valid extensions for; `void` on default.
  *
  * \details
  *
@@ -607,22 +574,17 @@ enum class output_file_open_options
  *
  * \include test/snippet/argument_parser/validators_output_file.cpp
  *
- * The valid extensions can also be obtained from a seqan3 formatted file type, e.g. sharg::sequence_input_file, if
- * it is given as template argument to this class. The following snippet demonstrates the different ways to instantiate
- * the sharg::output_file_validator.
+ * The following snippet demonstrates the different ways to instantiate the sharg::output_file_validator.
  *
  * \include test/snippet/argument_parser/validators_output_file_ext_from_file.cpp
  *
  * \note The validator works on every type that can be implicitly converted to std::filesystem::path.
  *
  * \remark For a complete overview, take a look at \ref argument_parser
  */
-template <typename file_t = void>
 class output_file_validator : public file_validator_base
 {
 public:
-    static_assert(std::same_as<file_t, void> || seqan3::detail::has_type_valid_formats<file_t>,
-                "Expected either a template type with a static member called valid_formats (a file type) or void.");
 
     // Import from base class.
     using typename file_validator_base::option_value_type;
@@ -632,23 +594,20 @@ class output_file_validator : public file_validator_base
      */
 
     //!\copydoc sharg::input_file_validator::input_file_validator()
-    output_file_validator() : output_file_validator{output_file_open_options::create_new}
-    {}
+    output_file_validator() : output_file_validator{output_file_open_options::create_new} {}
 
-    output_file_validator(output_file_validator const &) = default; //!< Defaulted.
-    output_file_validator(output_file_validator &&) = default; //!< Defaulted.
+    output_file_validator(output_file_validator const &) = default;             //!< Defaulted.
+    output_file_validator(output_file_validator &&) = default;                  //!< Defaulted.
     output_file_validator & operator=(output_file_validator const &) = default; //!< Defaulted.
-    output_file_validator & operator=(output_file_validator &&) = default; //!< Defaulted.
+    output_file_validator & operator=(output_file_validator &&) = default;      //!< Defaulted.
     virtual ~output_file_validator() = default; //!< Virtual Destructor.
 
     /*!\brief Constructs from a given overwrite mode and a list of valid extensions.
      * \param[in] mode A sharg::output_file_open_options indicating whether the validator throws if a file already
                        exists.
-     * \param[in] extensions The valid extensions to validate for. Defaults to
-     *                       sharg::output_file_validator::default_extensions.
+     * \param[in] extensions The valid extensions to validate for.
      */
-    explicit output_file_validator(output_file_open_options const mode,
-                                   std::vector<std::string> extensions = default_extensions())
+    explicit output_file_validator(output_file_open_options const mode, std::vector<std::string> extensions = {})
         : file_validator_base{}, mode{mode}
     {
         file_validator_base::extensions = std::move(extensions);
@@ -659,21 +618,6 @@ class output_file_validator : public file_validator_base
     using file_validator_base::file_validator_base;
     //!\}
 
-    /*!\brief The default extensions of `file_t`.
-     * \returns A list of default extensions for `file_t`, will be empty if `file_t` is `void`.
-     *
-     * \details
-     *
-     * If `file_t` does name a valid seqan3 file type that contains a static member `valid_formats` returns the
-     * extensions of that `file_t` type. Otherwise returns an empty list.
-     */
-    static std::vector<std::string> default_extensions()
-    {
-        if constexpr (!std::same_as<file_t, void>)
-            return seqan3::detail::valid_file_extensions<typename file_t::valid_formats>();
-        return {};
-    }
-
     // Import the base::operator()
     using file_validator_base::operator();
 

diff --git a/test/snippet/validators_input_file_ext_from_file.cpp b/test/snippet/validators_input_file_ext_from_file.cpp
@@ -1,5 +1,3 @@
-#include <seqan3/io/sequence_file/input.hpp>
-
 #include <sharg/validators.hpp>
 
 int main()
@@ -12,9 +10,5 @@ int main()
     sharg::input_file_validator validator2{std::vector{std::string{"exe"}, std::string{"fasta"}}};
     std::cerr << validator2.get_help_page_message() << '\n';
 
-    // Give the seqan3 file type as a template argument to get all valid extensions for this file.
-    sharg::input_file_validator<seqan3::sequence_file_input<>> validator3{};
-    std::cerr << validator3.get_help_page_message() << '\n';
-
     return 0;
 }
diff --git a/test/snippet/validators_input_file_ext_from_file.err b/test/snippet/validators_input_file_ext_from_file.err
@@ -1,3 +1,2 @@
 The input file must exist and read permissions must be granted.
 The input file must exist and read permissions must be granted. Valid file extensions are: [exe, fasta].
-The input file must exist and read permissions must be granted. Valid file extensions are: [embl, fasta, fa, fna, ffn, faa, frn, fas, fastq, fq, genbank, gb, gbk, sam].
diff --git a/test/snippet/validators_output_file_ext_from_file.cpp b/test/snippet/validators_output_file_ext_from_file.cpp
@@ -1,5 +1,3 @@
-#include <seqan3/io/sequence_file/output.hpp>
-
 #include <sharg/validators.hpp>
 
 int main()
@@ -10,15 +8,8 @@ int main()
 
     // Specify your own extensions for the output file.
     sharg::output_file_validator validator2{sharg::output_file_open_options::create_new,
-                                             std::vector{std::string{"exe"}, std::string{"fasta"}}};
+                                            std::vector{std::string{"exe"}, std::string{"fasta"}}};
     std::cerr << validator2.get_help_page_message() << '\n';
 
-    // Give the seqan3 file type as a template argument to get all valid extensions for this file.
-    sharg::output_file_validator<seqan3::sequence_file_output<>> validator3
-    {
-        sharg::output_file_open_options::create_new
-    };
-    std::cerr << validator3.get_help_page_message() << '\n';
-
     return 0;
 }
diff --git a/test/snippet/validators_output_file_ext_from_file.err b/test/snippet/validators_output_file_ext_from_file.err
@@ -1,3 +1,2 @@
 The output file must not exist already and write permissions must be granted.
 The output file must not exist already and write permissions must be granted. Valid file extensions are: [exe, fasta].
-The output file must not exist already and write permissions must be granted. Valid file extensions are: [embl, fasta, fa, fna, ffn, faa, frn, fas, fastq, fq, genbank, gb, gbk, sam].