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e07c809767..0000000000 --- a/test/api_stability/3.0.3/0009-NOAPI-fix-snippet-generation.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.1.0/0001-API-BREAKAGE-views-to-ranges-to.patch.license b/test/api_stability/3.1.0/0001-API-BREAKAGE-views-to-ranges-to.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.1.0/0001-API-BREAKAGE-views-to-ranges-to.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.1.0/0002-NOAPI-DETAIL-Remove-STL-tests.patch.license 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a/test/api_stability/3.1.0/0004-NOAPI-DETAIL-Concept-definitions.patch.license b/test/api_stability/3.1.0/0004-NOAPI-DETAIL-Concept-definitions.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.1.0/0004-NOAPI-DETAIL-Concept-definitions.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.1.0/0005-NOAPI-DETAIL-Unused-variables.patch.license b/test/api_stability/3.1.0/0005-NOAPI-DETAIL-Unused-variables.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.1.0/0005-NOAPI-DETAIL-Unused-variables.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin -SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik 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2006-2025 Knut Reinert & Freie Universität Berlin -SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik -SPDX-License-Identifier: BSD-3-Clause diff --git a/test/api_stability/3.1.0/0010-API-BREAKGE-FASTA-ID-parsing.patch.license b/test/api_stability/3.1.0/0010-API-BREAKGE-FASTA-ID-parsing.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.1.0/0010-API-BREAKGE-FASTA-ID-parsing.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.1.0/0011-API-FIX-single_pass_input-output_range.patch.license b/test/api_stability/3.1.0/0011-API-FIX-single_pass_input-output_range.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.1.0/0011-API-FIX-single_pass_input-output_range.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.1.0/0012-NOAPI-DETAIL-Disable-warning-about-ABI.patch.license b/test/api_stability/3.1.0/0012-NOAPI-DETAIL-Disable-warning-about-ABI.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.1.0/0012-NOAPI-DETAIL-Disable-warning-about-ABI.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.2.0/0001-NOAPI-DETAIL-Remove-seqan3-detail-persist.patch.license b/test/api_stability/3.2.0/0001-NOAPI-DETAIL-Remove-seqan3-detail-persist.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.2.0/0001-NOAPI-DETAIL-Remove-seqan3-detail-persist.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.2.0/0002-NOAPI-Fix-wrong-alignment-score.patch.license b/test/api_stability/3.2.0/0002-NOAPI-Fix-wrong-alignment-score.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.2.0/0002-NOAPI-Fix-wrong-alignment-score.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.2.0/0003-API-BREAKAGE-Remove-field-alignment-offset-and-impro.patch.license b/test/api_stability/3.2.0/0003-API-BREAKAGE-Remove-field-alignment-offset-and-impro.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.2.0/0003-API-BREAKAGE-Remove-field-alignment-offset-and-impro.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.2.0/0004-API-FIX-Use-namespace-seqan2.patch.license b/test/api_stability/3.2.0/0004-API-FIX-Use-namespace-seqan2.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.2.0/0004-API-FIX-Use-namespace-seqan2.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.2.0/0005-API-FIX-views-zip-is-no-range-adaptor.patch.license b/test/api_stability/3.2.0/0005-API-FIX-views-zip-is-no-range-adaptor.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.2.0/0005-API-FIX-views-zip-is-no-range-adaptor.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.2.0/0006-API-FIX-views-chunk-preserves-common_range.patch.license b/test/api_stability/3.2.0/0006-API-FIX-views-chunk-preserves-common_range.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.2.0/0006-API-FIX-views-chunk-preserves-common_range.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.2.0/0007-NOAPI-DETAIL-Update-copyright.patch.license b/test/api_stability/3.2.0/0007-NOAPI-DETAIL-Update-copyright.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.2.0/0007-NOAPI-DETAIL-Update-copyright.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.3.0/0001-FIX-take_until_view_test.patch b/test/api_stability/3.3.0/0001-FIX-take_until_view_test.patch index 455a94e279..7adcc80935 100644 --- a/test/api_stability/3.3.0/0001-FIX-take_until_view_test.patch +++ b/test/api_stability/3.3.0/0001-FIX-take_until_view_test.patch @@ -1,7 +1,7 @@ -From 91551c67f266dd87da101b27a46e63a678c01ad8 Mon Sep 17 00:00:00 2001 +From 04d9216d36505d9368ee84f969ccd5ed656820e9 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Thu, 28 Sep 2023 21:28:37 +0200 -Subject: [PATCH 1/8] [FIX] take_until_view_test +Subject: [PATCH 1/9] [FIX] take_until_view_test mutable refers to the capture --- @@ -27,5 +27,5 @@ index 970a3a1b1..8f34f7014 100644 }); do_concepts(adapt2, false); -- -2.47.2 +2.49.0 diff --git a/test/api_stability/3.3.0/0001-FIX-take_until_view_test.patch.license b/test/api_stability/3.3.0/0001-FIX-take_until_view_test.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.3.0/0001-FIX-take_until_view_test.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.3.0/0002-FIX-Change-constexpr-test.patch b/test/api_stability/3.3.0/0002-FIX-Change-constexpr-test.patch index 1375cf0e1c..aeb4503504 100644 --- a/test/api_stability/3.3.0/0002-FIX-Change-constexpr-test.patch +++ b/test/api_stability/3.3.0/0002-FIX-Change-constexpr-test.patch @@ -1,7 +1,7 @@ -From 760b8f7d5d3222a786dff1d8f0c2d3fe4fcead47 Mon Sep 17 00:00:00 2001 +From a897db06e12dbf172b6158d9e763e59ddf29f373 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Thu, 28 Sep 2023 19:35:57 +0200 -Subject: [PATCH 2/8] [FIX] Change constexpr test +Subject: [PATCH 2/9] [FIX] Change constexpr test gcc11 complains suddenly --- @@ -21,5 +21,5 @@ index 54bcb640c..460fab223 100644 + [[maybe_unused]] static constinit auto combined = adaptor1 | adaptor2; } -- -2.47.2 +2.49.0 diff --git a/test/api_stability/3.3.0/0002-FIX-Change-constexpr-test.patch.license b/test/api_stability/3.3.0/0002-FIX-Change-constexpr-test.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.3.0/0002-FIX-Change-constexpr-test.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.3.0/0003-API-hamming-scoring-scheme.patch b/test/api_stability/3.3.0/0003-API-hamming-scoring-scheme.patch index 01b351430c..8a61d2e373 100644 --- a/test/api_stability/3.3.0/0003-API-hamming-scoring-scheme.patch +++ b/test/api_stability/3.3.0/0003-API-hamming-scoring-scheme.patch @@ -1,7 +1,7 @@ -From 19f492b5e22fad6c94ce617af2c979072627e856 Mon Sep 17 00:00:00 2001 +From 4aca2fefe2bd6a7c20bd257d1e016cea4cd435c8 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Sun, 28 Jul 2024 15:17:28 +0200 -Subject: [PATCH 3/8] [API] hamming scoring scheme +Subject: [PATCH 3/9] [API] hamming scoring scheme --- .../08_pairwise_alignment/pa_assignment_3_solution.cpp | 6 ++++-- @@ -77,5 +77,5 @@ index 7ec211537..ee2e501a8 100644 if (i == j) EXPECT_EQ((scheme.score(seqan3::assign_rank_to(i, seqan3::dna15{}), -- -2.47.2 +2.49.0 diff --git a/test/api_stability/3.3.0/0003-API-hamming-scoring-scheme.patch.license b/test/api_stability/3.3.0/0003-API-hamming-scoring-scheme.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.3.0/0003-API-hamming-scoring-scheme.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.3.0/0004-API-seqan3-sam_file_program_info_t-user_tags.patch b/test/api_stability/3.3.0/0004-API-seqan3-sam_file_program_info_t-user_tags.patch index 693b8e6537..af52d8b357 100644 --- a/test/api_stability/3.3.0/0004-API-seqan3-sam_file_program_info_t-user_tags.patch +++ b/test/api_stability/3.3.0/0004-API-seqan3-sam_file_program_info_t-user_tags.patch @@ -1,7 +1,7 @@ -From 0e7614bad80a7271b0161e52b2239b27ac390555 Mon Sep 17 00:00:00 2001 +From 644d03ff0e7b85ac1fd71f47dd479dd1562f4788 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Mon, 19 Aug 2024 14:13:08 +0200 -Subject: [PATCH 4/8] [API] seqan3::sam_file_program_info_t::user_tags +Subject: [PATCH 4/9] [API] seqan3::sam_file_program_info_t::user_tags --- test/unit/io/sam_file/format_sam_test.cpp | 13 ++----------- @@ -51,5 +51,5 @@ index 8cd712ddb..599a04bbc 100644 header.comments.push_back("This is a comment."); -- -2.47.2 +2.49.0 diff --git a/test/api_stability/3.3.0/0004-API-seqan3-sam_file_program_info_t-user_tags.patch.license b/test/api_stability/3.3.0/0004-API-seqan3-sam_file_program_info_t-user_tags.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.3.0/0004-API-seqan3-sam_file_program_info_t-user_tags.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.3.0/0005-NOAPI-DETAIL-Update-copyright.patch b/test/api_stability/3.3.0/0005-NOAPI-DETAIL-Update-copyright.patch index dbbc062375..d424687cdc 100644 --- a/test/api_stability/3.3.0/0005-NOAPI-DETAIL-Update-copyright.patch +++ b/test/api_stability/3.3.0/0005-NOAPI-DETAIL-Update-copyright.patch @@ -1,7 +1,7 @@ -From ddaa2f283f1e7c6ec3ec8ef5b36b78a89ed94a2b Mon Sep 17 00:00:00 2001 +From 8ebc91358cec390e00b9e6acfa277ce5a19747f1 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Wed, 22 Jan 2025 14:55:53 +0100 -Subject: [PATCH 5/8] [NOAPI][DETAIL] Update copyright +Subject: [PATCH 5/9] [NOAPI][DETAIL] Update copyright --- test/unit/argument_parser/detail/format_help_test.cpp | 10 +++++----- @@ -121,5 +121,5 @@ index 5cdd9cdea..ee0c810a5 100644 testing::internal::CaptureStdout(); EXPECT_EXIT(parser.parse(), ::testing::ExitedWithCode(EXIT_SUCCESS), ""); -- -2.47.2 +2.49.0 diff --git a/test/api_stability/3.3.0/0005-NOAPI-DETAIL-Update-copyright.patch.license b/test/api_stability/3.3.0/0005-NOAPI-DETAIL-Update-copyright.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.3.0/0005-NOAPI-DETAIL-Update-copyright.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.3.0/0006-NOAPI-DETAIL-Use-std-ranges-all.patch b/test/api_stability/3.3.0/0006-NOAPI-DETAIL-Use-std-ranges-all.patch index 4dcd25ac33..de5aba24d9 100644 --- a/test/api_stability/3.3.0/0006-NOAPI-DETAIL-Use-std-ranges-all.patch +++ b/test/api_stability/3.3.0/0006-NOAPI-DETAIL-Use-std-ranges-all.patch @@ -1,7 +1,7 @@ -From e963f7c17989824777d2ee7a7a71bc7bf7d88365 Mon Sep 17 00:00:00 2001 +From 73550abadb9469d88ef49d6dd9ad9ead974f8a09 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Wed, 22 Jan 2025 17:11:10 +0100 -Subject: [PATCH 6/8] [NOAPI][DETAIL] Use std::ranges::all +Subject: [PATCH 6/9] [NOAPI][DETAIL] Use std::ranges::all --- test/performance/search/search_benchmark.cpp | 5 ++--- @@ -241,5 +241,5 @@ index 1567d93ed..a800b317c 100644 using sentinel_type = std::ranges::sentinel_t; -- -2.47.2 +2.49.0 diff --git a/test/api_stability/3.3.0/0006-NOAPI-DETAIL-Use-std-ranges-all.patch.license b/test/api_stability/3.3.0/0006-NOAPI-DETAIL-Use-std-ranges-all.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.3.0/0006-NOAPI-DETAIL-Use-std-ranges-all.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.3.0/0007-NOAPI-DETAIL-Remove-copyable_wrapper.patch b/test/api_stability/3.3.0/0007-NOAPI-DETAIL-Remove-copyable_wrapper.patch index 5d2333e0d6..2efcf6c88d 100644 --- a/test/api_stability/3.3.0/0007-NOAPI-DETAIL-Remove-copyable_wrapper.patch +++ b/test/api_stability/3.3.0/0007-NOAPI-DETAIL-Remove-copyable_wrapper.patch @@ -1,7 +1,7 @@ -From 6f15e1a5a5224fc29fabd183f7edcc85415224c0 Mon Sep 17 00:00:00 2001 +From 949aaedee9428bd4eb57bb7899230622a34322ab Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Wed, 22 Jan 2025 17:16:19 +0100 -Subject: [PATCH 7/8] [NOAPI][DETAIL] Remove copyable_wrapper +Subject: [PATCH 7/9] [NOAPI][DETAIL] Remove copyable_wrapper --- test/snippet/core/detail/copyable_wrapper.cpp | 16 ---------------- @@ -41,5 +41,5 @@ index 2b24e3127..000000000 -2 -6 -- -2.47.2 +2.49.0 diff --git a/test/api_stability/3.3.0/0007-NOAPI-DETAIL-Remove-copyable_wrapper.patch.license b/test/api_stability/3.3.0/0007-NOAPI-DETAIL-Remove-copyable_wrapper.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.3.0/0007-NOAPI-DETAIL-Remove-copyable_wrapper.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.3.0/0008-NOAPI-DETAIL-Put-SDSL-into-contrib.patch b/test/api_stability/3.3.0/0008-NOAPI-DETAIL-Put-SDSL-into-contrib.patch index 45f2d781d6..362e417952 100644 --- a/test/api_stability/3.3.0/0008-NOAPI-DETAIL-Put-SDSL-into-contrib.patch +++ b/test/api_stability/3.3.0/0008-NOAPI-DETAIL-Put-SDSL-into-contrib.patch @@ -1,7 +1,7 @@ -From 8d7406dfdaf1e084cc7df970d1a88918b5be3aa9 Mon Sep 17 00:00:00 2001 +From 91f686e20165f0d884eb04ca2f4649db16aa4e29 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Wed, 12 Feb 2025 14:39:21 +0100 -Subject: [PATCH 8/8] [NOAPI][DETAIL] Put SDSL into contrib +Subject: [PATCH 8/9] [NOAPI][DETAIL] Put SDSL into contrib --- .../range/container_push_back_benchmark.cpp | 5 ++--- @@ -252,5 +252,5 @@ index 612683cf3..2133abd37 100644 TYPED_TEST(bloom_filter_test, serialisation) -- -2.47.2 +2.49.0 diff --git a/test/api_stability/3.3.0/0008-NOAPI-DETAIL-Put-SDSL-into-contrib.patch.license b/test/api_stability/3.3.0/0008-NOAPI-DETAIL-Put-SDSL-into-contrib.patch.license deleted file mode 100644 index e07c809767..0000000000 --- a/test/api_stability/3.3.0/0008-NOAPI-DETAIL-Put-SDSL-into-contrib.patch.license +++ /dev/null @@ -1,3 +0,0 @@ -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 diff --git a/test/api_stability/3.3.0/0009-FIX-include-alignment_printer-in-debug_stream.patch b/test/api_stability/3.3.0/0009-FIX-include-alignment_printer-in-debug_stream.patch new file mode 100644 index 0000000000..a4c61d607f --- /dev/null +++ b/test/api_stability/3.3.0/0009-FIX-include-alignment_printer-in-debug_stream.patch @@ -0,0 +1,108 @@ +From e59dbf474f3bc714a6ef53e101bc4f0e65a1bf82 Mon Sep 17 00:00:00 2001 +From: Simon Gene Gottlieb +Date: Tue, 1 Apr 2025 15:24:33 +0200 +Subject: [PATCH 9/9] [FIX] include alignment_printer in debug_stream + +--- + .../pairwise_alignment_solution_4.err | 6 +++++- + .../pairwise_alignment_solution_5.err | 6 +++++- + .../cigar_conversion/alignment_from_cigar.err | 6 +++++- + .../alignment_from_cigar_io.err | 18 +++++++++++++++--- + .../align_cfg_output_examples.err | 18 +++++++++++++++--- + 5 files changed, 45 insertions(+), 9 deletions(-) + +diff --git a/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_4.err b/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_4.err +index 1889cdb7a..4aa696a7e 100644 +--- a/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_4.err ++++ b/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_4.err +@@ -2,4 +2,8 @@ Score: 62 + Begin: (4,0) + End: (34,31) + Alignment: +-(GTACGGAC-T-AGCTACAACATTACGGACTAC,GGAC-GACATGACGTACGACTTTACGTACGAC) ++ 0 . : . : . : ++ GTACGGAC-T-AGCTACAACATTACGGACTAC ++ | || ||| | | ||| || ||||| || || ++ GGAC-GACATGACGTACGACTTTACGTACGAC ++ +diff --git a/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_5.err b/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_5.err +index 1889cdb7a..4aa696a7e 100644 +--- a/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_5.err ++++ b/doc/tutorial/08_pairwise_alignment/pairwise_alignment_solution_5.err +@@ -2,4 +2,8 @@ Score: 62 + Begin: (4,0) + End: (34,31) + Alignment: +-(GTACGGAC-T-AGCTACAACATTACGGACTAC,GGAC-GACATGACGTACGACTTTACGTACGAC) ++ 0 . : . : . : ++ GTACGGAC-T-AGCTACAACATTACGGACTAC ++ | || ||| | | ||| || ||||| || || ++ GGAC-GACATGACGTACGACTTTACGTACGAC ++ +diff --git a/test/snippet/alignment/cigar_conversion/alignment_from_cigar.err b/test/snippet/alignment/cigar_conversion/alignment_from_cigar.err +index 269fcf4f8..c771bf5a9 100644 +--- a/test/snippet/alignment/cigar_conversion/alignment_from_cigar.err ++++ b/test/snippet/alignment/cigar_conversion/alignment_from_cigar.err +@@ -1 +1,5 @@ +-(ACTGA,AC-GA) ++ 0 . ++ ACTGA ++ || || ++ AC-GA ++ +diff --git a/test/snippet/alignment/cigar_conversion/alignment_from_cigar_io.err b/test/snippet/alignment/cigar_conversion/alignment_from_cigar_io.err +index 65e809957..43d4207db 100644 +--- a/test/snippet/alignment/cigar_conversion/alignment_from_cigar_io.err ++++ b/test/snippet/alignment/cigar_conversion/alignment_from_cigar_io.err +@@ -1,3 +1,15 @@ +-(ACT-,C-GT) +-(CTGATCGAG,AGGCTGN-A) +-(T-G-A-TC,G-AGTA-T) ++ 0 ++ ACT- ++ ++ C-GT ++ ++ 0 . ++ CTGATCGAG ++ | | ++ AGGCTGN-A ++ ++ 0 . ++ T-G-A-TC ++ | ++ G-AGTA-T ++ +diff --git a/test/snippet/alignment/configuration/align_cfg_output_examples.err b/test/snippet/alignment/configuration/align_cfg_output_examples.err +index 43207860d..9dfe1222c 100644 +--- a/test/snippet/alignment/configuration/align_cfg_output_examples.err ++++ b/test/snippet/alignment/configuration/align_cfg_output_examples.err +@@ -1,10 +1,22 @@ + {score: -4} + { + alignment: +-(ACGTA-G-C-,A-GTACGACG)} ++ 0 . : ++ ACGTA-G-C- ++ | ||| | | ++ A-GTACGACG ++} + {score: -4, + alignment: +-(ACGTA-G-C-,A-GTACGACG)} ++ 0 . : ++ ACGTA-G-C- ++ | ||| | | ++ A-GTACGACG ++} + {sequence1 id: 0, sequence2 id: 0, score: -4, begin: (0,0), end: (7,9), + alignment: +-(ACGTA-G-C-,A-GTACGACG)} ++ 0 . : ++ ACGTA-G-C- ++ | ||| | | ++ A-GTACGACG ++} +-- +2.49.0 + diff --git a/test/api_stability/REUSE.toml b/test/api_stability/REUSE.toml new file mode 100644 index 0000000000..ab044973a8 --- /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" +