[FIX] API Cron

Author: eseiler

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

@@ -1,7 +1,7 @@
-From ca8c640b31970a92080d6c36cc7623de5c6b488b Mon Sep 17 00:00:00 2001
+From 374e3145cb713d6db165727c401ecb6c6d178364 Mon Sep 17 00:00:00 2001
 From: Simon Gene Gottlieb <simon@gottliebtfreitag.de>
 Date: Thu, 5 Oct 2023 13:43:30 +0200
-Subject: [PATCH 1/8] [API] Update TDL
+Subject: [PATCH 1/9] [API] Update TDL
 
 ---
  test/unit/detail/format_ctd_test.cpp |  2 +-
@@ -84,5 +84,5 @@ index d2bb143..5591a88 100644
          "class: CommandLineTool\n"
          "baseCommand:\n"
 -- 
-2.43.2
+2.49.0
 

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

@@ -1,7 +1,7 @@
-From 9ddea5a7db6e7436e157ed25e1cb368c3445bc84 Mon Sep 17 00:00:00 2001
+From fa7be0f2f41cdfa8d8633f50bd847bb9e279f82d Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Mon, 5 Feb 2024 16:02:03 +0100
-Subject: [PATCH 2/8] [API] Quoted strings and paths
+Subject: [PATCH 2/9] [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);
 -- 
-2.43.2
+2.49.0
 

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

@@ -1,7 +1,7 @@
-From 69dfcfa3a693a398200dc7cac0ec6d76b1ecb443 Mon Sep 17 00:00:00 2001
+From e909fcaa7af21040c0a5bdc3a08ad222166bc8af Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Wed, 7 Feb 2024 13:31:22 +0100
-Subject: [PATCH 3/8] [NOAPI] Update copyright
+Subject: [PATCH 3/9] [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), "");
 -- 
-2.43.2
+2.49.0
 

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

@@ -1,7 +1,7 @@
-From 9ec785b9f7761bc020da7972a1c18b61bff53685 Mon Sep 17 00:00:00 2001
+From 51753316a678a0090cf662442f0f5bdff556ec7d Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Fri, 9 Feb 2024 16:17:21 +0100
-Subject: [PATCH 4/8] [INFRA] Update TDL
+Subject: [PATCH 4/9] [INFRA] Update TDL
 
 ---
  test/unit/detail/format_cwl_test.cpp | 28 +++++++++++++++++++++++++++-
@@ -69,5 +69,5 @@ index 1d27cc3..eaf0cad 100644
          "  path04:\n"
          "    type: File?\n"
 -- 
-2.43.2
+2.49.0
 

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

@@ -1,7 +1,7 @@
-From 069d34a5d3997dfdd1b47cac24ef47931b534367 Mon Sep 17 00:00:00 2001
+From 2ef2616e6041875e7ca2c376e134addb902ca588 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Fri, 9 Feb 2024 18:13:36 +0100
-Subject: [PATCH 5/8] [INFRA] Use seqan3 main branch
+Subject: [PATCH 5/9] [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)
 -- 
-2.43.2
+2.49.0
 

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

@@ -1,7 +1,7 @@
-From 94f4ae3d0f188ff9193e05c26b71b5ab8e5398c6 Mon Sep 17 00:00:00 2001
+From f35ebe9a5be9356b54cb4a0307cbf10855717af2 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Wed, 14 Feb 2024 12:34:40 +0100
-Subject: [PATCH 6/8] [API][FIX] positional options in CWL/CTD
+Subject: [PATCH 6/9] [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"
 -- 
-2.43.2
+2.49.0
 

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

@@ -1,7 +1,7 @@
-From 458dd383728e5fbffda9c4f3a1470b321bb75386 Mon Sep 17 00:00:00 2001
+From c4278c4bd49e102046e3709883943e692a949c4f Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Mon, 29 Apr 2024 16:37:15 +0200
-Subject: [PATCH 7/8] [API][MISC] Defer everything to parse()
+Subject: [PATCH 7/9] [API][MISC] Defer everything to parse()
 
 ---
  test/unit/detail/format_help_test.cpp         |  2 +-
@@ -145,5 +145,5 @@ index 4c3406f..4d81119 100644
 
      // no positional/options are allowed
 -- 
-2.43.2
+2.49.0
 

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

@@ -1,7 +1,7 @@
-From 28c35ece0450603abf08bf2705aecbd8365f935a Mon Sep 17 00:00:00 2001
+From c46bff885491340b5306a4a421ae4d199700fa69 Mon Sep 17 00:00:00 2001
 From: Enrico Seiler <enrico.seiler@hotmail.de>
 Date: Mon, 29 Apr 2024 16:37:30 +0200
-Subject: [PATCH 8/8] [API][MISC] Allow options for subcommands
+Subject: [PATCH 8/9] [API][MISC] Allow options for subcommands
 
 ---
  test/unit/parser/format_parse_test.cpp        | 6 +++---
@@ -58,5 +58,5 @@ index 4d81119..e31a2e7 100644
 -    }
  }
 -- 
-2.43.2
+2.49.0
 

test/api_stability/1.1.1/0009-FIX-is_option_set-match-both-long-and-short-ids.patch

@@ -0,0 +1,27 @@
+From 0347f577de59a062fc91e633d171de4acc8517df Mon Sep 17 00:00:00 2001
+From: Enrico Seiler <enrico.seiler@hotmail.de>
+Date: Wed, 2 Apr 2025 18:02:31 +0200
+Subject: [PATCH 9/9] [FIX] is_option_set: match both long and short ids
+
+---
+ test/unit/parser/format_parse_test.cpp | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/test/unit/parser/format_parse_test.cpp b/test/unit/parser/format_parse_test.cpp
+index c2a8f58..8e5b7e2 100644
+--- a/test/unit/parser/format_parse_test.cpp
++++ b/test/unit/parser/format_parse_test.cpp
+@@ -977,8 +977,8 @@ TEST(parse_test, is_option_set)
+     EXPECT_TRUE(parser.is_option_set('l'));
+     EXPECT_TRUE(parser.is_option_set("foobar"));
+ 
+-    EXPECT_FALSE(parser.is_option_set('f'));
+-    EXPECT_FALSE(parser.is_option_set("loo")); // --loo is behind the `--` which signals the end of options!
++    EXPECT_TRUE(parser.is_option_set('f'));
++    EXPECT_TRUE(parser.is_option_set("loo")); // --loo is behind the `--` which signals the end of options!
+ 
+     // errors:
+     EXPECT_THROW(parser.is_option_set("l"), sharg::design_error); // short identifiers are passed as chars not strings
+-- 
+2.49.0
+