[INFRA,TEST] API patches

test/api_stability/1.1.1/0001-API-Update-TDL.patch

@@ -1,7 +1,7 @@
-From 769620513bcc59d257119aacfa06020df7ca45a6 Mon Sep 17 00:00:00 2001
+From ca8c640b31970a92080d6c36cc7623de5c6b488b Mon Sep 17 00:00:00 2001
 From: Simon Gene Gottlieb <[email protected]>
 Date: Thu, 5 Oct 2023 13:43:30 +0200
-Subject: [PATCH 1/6] [API] Update TDL
+Subject: [PATCH 1/8] [API] Update TDL
 
 ---
  test/unit/detail/format_ctd_test.cpp |  2 +-
@@ -84,5 +84,5 @@ index d2bb143..5591a88 100644
          "class: CommandLineTool\n"
          "baseCommand:\n"
 -- 
-2.43.0
+2.43.2
 

test/api_stability/1.1.1/0002-API-Quoted-strings-and-paths.patch

@@ -1,7 +1,7 @@
-From 9d8035baa8b0ff4accd6ba2e60a22f779986483d Mon Sep 17 00:00:00 2001
+From 9ddea5a7db6e7436e157ed25e1cb368c3445bc84 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <[email protected]>
 Date: Mon, 5 Feb 2024 16:02:03 +0100
-Subject: [PATCH 2/6] [API] Quoted strings and paths
+Subject: [PATCH 2/8] [API] Quoted strings and paths
 
 ---
  test/snippet/readme_sneak_peek.out            |  6 ++---
@@ -341,5 +341,5 @@ index cade0f9..ba1694d 100644
              + basic_options_str + "\n" + basic_version_str;
          EXPECT_EQ(my_stdout, expected);
 -- 
-2.43.0
+2.43.2
 

test/api_stability/1.1.1/0003-NOAPI-Update-copyright.patch

@@ -1,7 +1,7 @@
-From a4fffdf64380b018822b13a9ad72586f0564385f Mon Sep 17 00:00:00 2001
+From 69dfcfa3a693a398200dc7cac0ec6d76b1ecb443 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <[email protected]>
 Date: Wed, 7 Feb 2024 13:31:22 +0100
-Subject: [PATCH 3/6] [NOAPI] Update copyright
+Subject: [PATCH 3/8] [NOAPI] Update copyright
 
 ---
  test/unit/detail/format_help_test.cpp | 10 +++++-----
@@ -121,5 +121,5 @@ index 307b58b..eefffd6 100644
      testing::internal::CaptureStdout();
      EXPECT_EXIT(parser.parse(), ::testing::ExitedWithCode(EXIT_SUCCESS), "");
 -- 
-2.43.0
+2.43.2
 

test/api_stability/1.1.1/0004-INFRA-Update-TDL.patch

@@ -1,7 +1,7 @@
-From 1481f5dfdc68d2d5e04cb5abbec45fab7f15fbcd Mon Sep 17 00:00:00 2001
+From 9ec785b9f7761bc020da7972a1c18b61bff53685 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <[email protected]>
 Date: Fri, 9 Feb 2024 16:17:21 +0100
-Subject: [PATCH 4/6] [INFRA] Update TDL
+Subject: [PATCH 4/8] [INFRA] Update TDL
 
 ---
  test/unit/detail/format_cwl_test.cpp | 28 +++++++++++++++++++++++++++-
@@ -69,5 +69,5 @@ index 1d27cc3..eaf0cad 100644
          "  path04:\n"
          "    type: File?\n"
 -- 
-2.43.0
+2.43.2
 

test/api_stability/1.1.1/0005-INFRA-Use-seqan3-main-branch.patch

@@ -1,7 +1,7 @@
-From 085bc1fd63f3c48999610e0a9a916895a7cf9207 Mon Sep 17 00:00:00 2001
+From 069d34a5d3997dfdd1b47cac24ef47931b534367 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <[email protected]>
 Date: Fri, 9 Feb 2024 18:13:36 +0100
-Subject: [PATCH 5/6] [INFRA] Use seqan3 main branch
+Subject: [PATCH 5/8] [INFRA] Use seqan3 main branch
 
 ---
  test/unit/detail/CMakeLists.txt | 2 +-
@@ -21,5 +21,5 @@ index 392f878..1f9a8e0 100644
  sharg_test (seqan3_test.cpp)
  target_include_directories (seqan3_test SYSTEM PUBLIC ${CMAKE_BINARY_DIR}/include)
 -- 
-2.43.0
+2.43.2
 

test/api_stability/1.1.1/0006-API-FIX-positional-options-in-CWL-CTD.patch

@@ -1,7 +1,7 @@
-From c84f8aeeba0895677c64d9740f4df908674cd0be Mon Sep 17 00:00:00 2001
+From 94f4ae3d0f188ff9193e05c26b71b5ab8e5398c6 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <[email protected]>
 Date: Wed, 14 Feb 2024 12:34:40 +0100
-Subject: [PATCH 6/6] [API][FIX] positional options in CWL/CTD
+Subject: [PATCH 6/8] [API][FIX] positional options in CWL/CTD
 
 ---
  test/unit/detail/format_ctd_test.cpp | 4 ++--
@@ -55,5 +55,5 @@ index eaf0cad..52079db 100644
          "    doc: \"this is a int option. Default: 5\"\n"
          "    type: long?\n"
 -- 
-2.43.0
+2.43.2
 

test/api_stability/1.1.1/0007-API-MISC-Defer-everything-to-parse.patch

@@ -0,0 +1,149 @@
+From 458dd383728e5fbffda9c4f3a1470b321bb75386 Mon Sep 17 00:00:00 2001
+From: Enrico Seiler <[email protected]>
+Date: Mon, 29 Apr 2024 16:37:15 +0200
+Subject: [PATCH 7/8] [API][MISC] Defer everything to parse()
+
+---
+ test/unit/detail/format_help_test.cpp         |  2 +-
+ test/unit/detail/format_html_test.cpp         | 10 ++++--
+ test/unit/parser/format_parse_test.cpp        | 34 ++++++++++++-------
+ test/unit/parser/parser_design_error_test.cpp |  4 +--
+ 4 files changed, 31 insertions(+), 19 deletions(-)
+
+diff --git a/test/unit/detail/format_help_test.cpp b/test/unit/detail/format_help_test.cpp
+index be31399..20f4c39 100644
+--- a/test/unit/detail/format_help_test.cpp
++++ b/test/unit/detail/format_help_test.cpp
+@@ -575,7 +575,7 @@ TEST(parse_test, subcommand_parser)
+                            "    See the respective help page for further details (e.g. by calling\n"
+                            "    test_parser sub1 -h).\n"
+                            "\n"
+-                           "    The following options below belong to the top-level parser and need to be\n"
++                           "    The following options belong to the top-level parser and need to be\n"
+                            "    specified before the subcommand key word. Every argument after the\n"
+                            "    subcommand key word is passed on to the corresponding sub-parser.\n"
+                            "\nOPTIONS\n"
+diff --git a/test/unit/detail/format_html_test.cpp b/test/unit/detail/format_html_test.cpp
+index 6fd41d1..6f485cc 100644
+--- a/test/unit/detail/format_html_test.cpp
++++ b/test/unit/detail/format_html_test.cpp
+@@ -217,11 +217,15 @@ TEST(export_help, parse_error)
+     std::array const argv3{"./help_add_test", "--version-check", "false", "--export-help", "atml"};
+
+     // no value after --export-help
+-    EXPECT_THROW((sharg::parser{"test_parser", argv.size(), argv.data()}), sharg::parser_error);
++    auto parser = sharg::parser{"test_parser", argv.size(), argv.data()};
++    EXPECT_THROW(parser.parse(), sharg::parser_error);
+
+     // wrong value after --export-help
+-    EXPECT_THROW((sharg::parser{"test_parser", argv2.size(), argv2.data()}), sharg::validation_error);
++    parser = sharg::parser{"test_parser", argv2.size(), argv2.data()};
++    EXPECT_THROW(parser.parse(), sharg::validation_error);
+
+     // wrong value after --export-help
+-    EXPECT_THROW((sharg::parser{"test_parser", argv3.size(), argv3.data()}), sharg::validation_error);
++    parser = sharg::parser{"test_parser", argv3.size(), argv3.data()};
++    EXPECT_THROW(parser.parse(), sharg::validation_error);
++
+ }
+diff --git a/test/unit/parser/format_parse_test.cpp b/test/unit/parser/format_parse_test.cpp
+index 8e5a286..f63fa61 100644
+--- a/test/unit/parser/format_parse_test.cpp
++++ b/test/unit/parser/format_parse_test.cpp
+@@ -815,12 +815,14 @@ TEST(parse_test, version_check_option_error)
+ {
+     { // version-check must be followed by a value
+         char const * argv[] = {"./parser_test", "--version-check"};
+-        EXPECT_THROW((sharg::parser{"test_parser", 2, argv}), sharg::parser_error);
++        auto parser = sharg::parser{"test_parser", 2, argv};
++        EXPECT_THROW(parser.parse(), sharg::parser_error);
+     }
+
+     { // version-check value must be 0 or 1
+         char const * argv[] = {"./parser_test", "--version-check", "foo"};
+-        EXPECT_THROW((sharg::parser{"test_parser", 3, argv}), sharg::parser_error);
++        auto parser = sharg::parser{"test_parser", 3, argv};
++        EXPECT_THROW(parser.parse(), sharg::parser_error);
+     }
+ }
+
+@@ -1107,44 +1109,50 @@ TEST(parse_test, container_default)
+
+ TEST(parse_test, executable_name)
+ {
+-    testing::internal::CaptureStdout();
+     {
+-        std::array argv{"parser_test"};
++        bool flag{false};
++        std::array argv{"parser_test", "-t"};
+         sharg::parser parser{"test_parser", argv.size(), argv.data(), sharg::update_notifications::off};
+-        EXPECT_EXIT(parser.parse(), ::testing::ExitedWithCode(EXIT_SUCCESS), "");
++        parser.add_flag(flag, sharg::config{.short_id = 't'});
++        EXPECT_NO_THROW(parser.parse());
+         auto & executable_name = sharg::detail::test_accessor::executable_name(parser);
+         ASSERT_EQ(executable_name.size(), 1);
+         EXPECT_EQ(executable_name[0], "parser_test");
+     }
+
+     {
+-        std::array argv{"./parser_test"};
++        bool flag{false};
++        std::array argv{"./parser_test", "-t"};
+         sharg::parser parser{"test_parser", argv.size(), argv.data(), sharg::update_notifications::off};
+-        EXPECT_EXIT(parser.parse(), ::testing::ExitedWithCode(EXIT_SUCCESS), "");
++        parser.add_flag(flag, sharg::config{.short_id = 't'});
++        EXPECT_NO_THROW(parser.parse());
+         auto & executable_name = sharg::detail::test_accessor::executable_name(parser);
+         ASSERT_EQ(executable_name.size(), 1);
+         EXPECT_EQ(executable_name[0], "./parser_test");
+     }
+
+     {
+-        std::array argv{"./bin/parser_test"};
++        bool flag{false};
++        std::array argv{"./bin/parser_test", "-t"};
+         sharg::parser parser{"test_parser", argv.size(), argv.data(), sharg::update_notifications::off};
+-        EXPECT_EXIT(parser.parse(), ::testing::ExitedWithCode(EXIT_SUCCESS), "");
++        parser.add_flag(flag, sharg::config{.short_id = 't'});
++        EXPECT_NO_THROW(parser.parse());
+         auto & executable_name = sharg::detail::test_accessor::executable_name(parser);
+         ASSERT_EQ(executable_name.size(), 1);
+         EXPECT_EQ(executable_name[0], "./bin/parser_test");
+     }
+
+     {
+-        std::array argv{"./bin/parser_test", "build"};
++        bool flag{false};
++        std::array argv{"./bin/parser_test", "build", "-t"};
+         sharg::parser parser{"test_parser", argv.size(), argv.data(), sharg::update_notifications::off, {"build"}};
+-        parser.parse();
++        EXPECT_NO_THROW(parser.parse());
+         auto & sub_parser = parser.get_sub_parser();
+-        EXPECT_EXIT(sub_parser.parse(), ::testing::ExitedWithCode(EXIT_SUCCESS), "");
++        sub_parser.add_flag(flag, sharg::config{.short_id = 't'});
++        EXPECT_NO_THROW(sub_parser.parse());
+         auto & executable_name = sharg::detail::test_accessor::executable_name(sub_parser);
+         ASSERT_EQ(executable_name.size(), 2);
+         EXPECT_EQ(executable_name[0], "./bin/parser_test");
+         EXPECT_EQ(executable_name[1], "build");
+     }
+-    testing::internal::GetCapturedStdout();
+ }
+diff --git a/test/unit/parser/parser_design_error_test.cpp b/test/unit/parser/parser_design_error_test.cpp
+index 4c3406f..4d81119 100644
+--- a/test/unit/parser/parser_design_error_test.cpp
++++ b/test/unit/parser/parser_design_error_test.cpp
+@@ -272,8 +272,8 @@ TEST(parse_test, subcommand_parser_error)
+     // subcommand key word must only contain alpha numeric characters
+     {
+         char const * argv[]{"./top_level", "-f"};
+-        EXPECT_THROW((sharg::parser{"top_level", 2, argv, sharg::update_notifications::off, {"with space"}}),
+-                     sharg::design_error);
++        auto parser = sharg::parser{"top_level", 2, argv, sharg::update_notifications::off, {"with space"}};
++        EXPECT_THROW(parser.parse(), sharg::design_error);
+     }
+
+     // no positional/options are allowed
+-- 
+2.43.2
+

test/api_stability/1.1.1/0007-API-MISC-Defer-everything-to-parse.patch.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
+SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+SPDX-License-Identifier: BSD-3-Clause

test/api_stability/1.1.1/0008-API-MISC-Allow-options-for-subcommands.patch

@@ -0,0 +1,62 @@
+From 28c35ece0450603abf08bf2705aecbd8365f935a Mon Sep 17 00:00:00 2001
+From: Enrico Seiler <[email protected]>
+Date: Mon, 29 Apr 2024 16:37:30 +0200
+Subject: [PATCH 8/8] [API][MISC] Allow options for subcommands
+
+---
+ test/unit/parser/format_parse_test.cpp        | 6 +++---
+ test/unit/parser/parser_design_error_test.cpp | 9 ---------
+ 2 files changed, 3 insertions(+), 12 deletions(-)
+
+diff --git a/test/unit/parser/format_parse_test.cpp b/test/unit/parser/format_parse_test.cpp
+index f63fa61..c2a8f58 100644
+--- a/test/unit/parser/format_parse_test.cpp
++++ b/test/unit/parser/format_parse_test.cpp
+@@ -899,7 +899,7 @@ TEST(parse_test, subcommand_parser_error)
+         std::array argv{"./top_level", "subiddysub", "-f"};
+         sharg::parser top_level_parser{"top", argv.size(), argv.data(), sharg::update_notifications::off, {"sub1"}};
+
+-        EXPECT_THROW(top_level_parser.parse(), sharg::parser_error);
++        EXPECT_THROW(top_level_parser.parse(), sharg::user_input_error);
+     }
+
+     // incorrect sub command with no other arguments
+@@ -907,7 +907,7 @@ TEST(parse_test, subcommand_parser_error)
+         std::array argv{"./top_level", "subiddysub"};
+         sharg::parser top_level_parser{"top", argv.size(), argv.data(), sharg::update_notifications::off, {"sub1"}};
+
+-        EXPECT_THROW(top_level_parser.parse(), sharg::parser_error);
++        EXPECT_THROW(top_level_parser.parse(), sharg::user_input_error);
+     }
+
+     // incorrect sub command with trailing special option
+@@ -915,7 +915,7 @@ TEST(parse_test, subcommand_parser_error)
+         std::array argv{"./top_level", "subiddysub", "-h"};
+         sharg::parser top_level_parser{"top", argv.size(), argv.data(), sharg::update_notifications::off, {"sub1"}};
+
+-        EXPECT_THROW(top_level_parser.parse(), sharg::parser_error);
++        EXPECT_THROW(top_level_parser.parse(), sharg::user_input_error);
+     }
+ }
+
+diff --git a/test/unit/parser/parser_design_error_test.cpp b/test/unit/parser/parser_design_error_test.cpp
+index 4d81119..e31a2e7 100644
+--- a/test/unit/parser/parser_design_error_test.cpp
++++ b/test/unit/parser/parser_design_error_test.cpp
+@@ -275,13 +275,4 @@ TEST(parse_test, subcommand_parser_error)
+         auto parser = sharg::parser{"top_level", 2, argv, sharg::update_notifications::off, {"with space"}};
+         EXPECT_THROW(parser.parse(), sharg::design_error);
+     }
+-
+-    // no positional/options are allowed
+-    {
+-        char const * argv[]{"./top_level", "foo"};
+-        sharg::parser top_level_parser{"top_level", 2, argv, sharg::update_notifications::off, {"foo"}};
+-
+-        EXPECT_THROW((top_level_parser.add_option(flag_value, sharg::config{.short_id = 'f'})), sharg::design_error);
+-        EXPECT_THROW((top_level_parser.add_positional_option(flag_value, sharg::config{})), sharg::design_error);
+-    }
+ }
+-- 
+2.43.2
+

test/api_stability/1.1.1/0008-API-MISC-Allow-options-for-subcommands.patch.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
+SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+SPDX-License-Identifier: BSD-3-Clause