diff --git a/test/api_stability/1.0.0/0001-API-FIX-Print-common-options-at-the-end-of-the-help-.patch.license b/test/api_stability/1.0.0/0001-API-FIX-Print-common-options-at-the-end-of-the-help-.patch.license deleted file mode 100644 index 706402f5..00000000 --- a/test/api_stability/1.0.0/0001-API-FIX-Print-common-options-at-the-end-of-the-help-.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/1.0.0/0002-NOAPI-Update-copyright.patch.license b/test/api_stability/1.0.0/0002-NOAPI-Update-copyright.patch.license deleted file mode 100644 index 706402f5..00000000 --- a/test/api_stability/1.0.0/0002-NOAPI-Update-copyright.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/1.0.0/0003-API-FIX-Check-app_name-at-parse.patch.license b/test/api_stability/1.0.0/0003-API-FIX-Check-app_name-at-parse.patch.license deleted file mode 100644 index 706402f5..00000000 --- a/test/api_stability/1.0.0/0003-API-FIX-Check-app_name-at-parse.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/1.0.0/0004-FIX-API-tdl-support.patch.license b/test/api_stability/1.0.0/0004-FIX-API-tdl-support.patch.license deleted file mode 100644 index 706402f5..00000000 --- a/test/api_stability/1.0.0/0004-FIX-API-tdl-support.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/1.1.1/0001-API-Update-TDL.patch b/test/api_stability/1.1.1/0001-API-Update-TDL.patch index 93f57a0f..51bf3a5b 100644 --- a/test/api_stability/1.1.1/0001-API-Update-TDL.patch +++ b/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 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 diff --git a/test/api_stability/1.1.1/0001-API-Update-TDL.patch.license b/test/api_stability/1.1.1/0001-API-Update-TDL.patch.license deleted file mode 100644 index 706402f5..00000000 --- a/test/api_stability/1.1.1/0001-API-Update-TDL.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/1.1.1/0002-API-Quoted-strings-and-paths.patch b/test/api_stability/1.1.1/0002-API-Quoted-strings-and-paths.patch index 453e554d..8681999e 100644 --- a/test/api_stability/1.1.1/0002-API-Quoted-strings-and-paths.patch +++ b/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 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 diff --git a/test/api_stability/1.1.1/0002-API-Quoted-strings-and-paths.patch.license b/test/api_stability/1.1.1/0002-API-Quoted-strings-and-paths.patch.license deleted file mode 100644 index 706402f5..00000000 --- a/test/api_stability/1.1.1/0002-API-Quoted-strings-and-paths.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/1.1.1/0003-NOAPI-Update-copyright.patch b/test/api_stability/1.1.1/0003-NOAPI-Update-copyright.patch index c542291b..63ab9c4a 100644 --- a/test/api_stability/1.1.1/0003-NOAPI-Update-copyright.patch +++ b/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 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 diff --git a/test/api_stability/1.1.1/0003-NOAPI-Update-copyright.patch.license b/test/api_stability/1.1.1/0003-NOAPI-Update-copyright.patch.license deleted file mode 100644 index 706402f5..00000000 --- a/test/api_stability/1.1.1/0003-NOAPI-Update-copyright.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/1.1.1/0004-INFRA-Update-TDL.patch b/test/api_stability/1.1.1/0004-INFRA-Update-TDL.patch index 0fe83cab..c11a4454 100644 --- a/test/api_stability/1.1.1/0004-INFRA-Update-TDL.patch +++ b/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 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 diff --git a/test/api_stability/1.1.1/0004-INFRA-Update-TDL.patch.license b/test/api_stability/1.1.1/0004-INFRA-Update-TDL.patch.license deleted file mode 100644 index 706402f5..00000000 --- a/test/api_stability/1.1.1/0004-INFRA-Update-TDL.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/1.1.1/0005-INFRA-Use-seqan3-main-branch.patch b/test/api_stability/1.1.1/0005-INFRA-Use-seqan3-main-branch.patch index 1b65dd47..116b59c8 100644 --- a/test/api_stability/1.1.1/0005-INFRA-Use-seqan3-main-branch.patch +++ b/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 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 diff --git a/test/api_stability/1.1.1/0005-INFRA-Use-seqan3-main-branch.patch.license b/test/api_stability/1.1.1/0005-INFRA-Use-seqan3-main-branch.patch.license deleted file mode 100644 index 706402f5..00000000 --- a/test/api_stability/1.1.1/0005-INFRA-Use-seqan3-main-branch.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/1.1.1/0006-API-FIX-positional-options-in-CWL-CTD.patch b/test/api_stability/1.1.1/0006-API-FIX-positional-options-in-CWL-CTD.patch index 75763828..ece6eed9 100644 --- a/test/api_stability/1.1.1/0006-API-FIX-positional-options-in-CWL-CTD.patch +++ b/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 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 diff --git a/test/api_stability/1.1.1/0006-API-FIX-positional-options-in-CWL-CTD.patch.license b/test/api_stability/1.1.1/0006-API-FIX-positional-options-in-CWL-CTD.patch.license deleted file mode 100644 index 706402f5..00000000 --- a/test/api_stability/1.1.1/0006-API-FIX-positional-options-in-CWL-CTD.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/1.1.1/0007-API-MISC-Defer-everything-to-parse.patch b/test/api_stability/1.1.1/0007-API-MISC-Defer-everything-to-parse.patch index 79d8c892..572074b8 100644 --- a/test/api_stability/1.1.1/0007-API-MISC-Defer-everything-to-parse.patch +++ b/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 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 diff --git a/test/api_stability/1.1.1/0007-API-MISC-Defer-everything-to-parse.patch.license b/test/api_stability/1.1.1/0007-API-MISC-Defer-everything-to-parse.patch.license deleted file mode 100644 index 706402f5..00000000 --- a/test/api_stability/1.1.1/0007-API-MISC-Defer-everything-to-parse.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/1.1.1/0008-API-MISC-Allow-options-for-subcommands.patch b/test/api_stability/1.1.1/0008-API-MISC-Allow-options-for-subcommands.patch index a40093e5..92b30ebf 100644 --- a/test/api_stability/1.1.1/0008-API-MISC-Allow-options-for-subcommands.patch +++ b/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 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 diff --git a/test/api_stability/1.1.1/0008-API-MISC-Allow-options-for-subcommands.patch.license b/test/api_stability/1.1.1/0008-API-MISC-Allow-options-for-subcommands.patch.license deleted file mode 100644 index 706402f5..00000000 --- a/test/api_stability/1.1.1/0008-API-MISC-Allow-options-for-subcommands.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/1.1.1/0009-FIX-is_option_set-match-both-long-and-short-ids.patch b/test/api_stability/1.1.1/0009-FIX-is_option_set-match-both-long-and-short-ids.patch new file mode 100644 index 00000000..b7bd13e4 --- /dev/null +++ b/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 +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 + diff --git a/test/api_stability/REUSE.toml b/test/api_stability/REUSE.toml new file mode 100644 index 00000000..ab044973 --- /dev/null +++ b/test/api_stability/REUSE.toml @@ -0,0 +1,12 @@ +# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause + +version = 1 + +[[annotations]] +path = "**/*.patch" +precedence = "aggregate" +SPDX-FileCopyrightText = ["2006-2025, Knut Reinert & Freie Universität Berlin", "2016-2025, Knut Reinert & MPI für molekulare Genetik"] +SPDX-License-Identifier = "BSD-3-Clause" +