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Add api patch
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-21
lines changed

‎test/api_stability/3.3.0/0001-FIX-take_until_view_test.patch‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
1-
From b83e281578b8ead4fccdaeee6b924cc34bdfd222 Mon Sep 17 00:00:00 2001
1+
From 9a1de3d5e83f3b290658d8ad2e62949646d1074e Mon Sep 17 00:00:00 2001
22
From: Enrico Seiler <[email protected]>
33
Date: Thu, 28 Sep 2023 21:28:37 +0200
4-
Subject: [PATCH 1/7] [FIX] take_until_view_test
4+
Subject: [PATCH 1/8] [FIX] take_until_view_test
55

66
mutable refers to the capture
77
---
@@ -27,5 +27,5 @@ index 970a3a1b1..8f34f7014 100644
2727
});
2828
do_concepts(adapt2, false);
2929
--
30-
2.45.2
30+
2.47.2
3131

‎test/api_stability/3.3.0/0002-FIX-Change-constexpr-test.patch‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
1-
From c734afc727852e3318ebc940fce7244689b81ae3 Mon Sep 17 00:00:00 2001
1+
From c7a2ba19e997df634f141584b5d325fe6ed2c9cb Mon Sep 17 00:00:00 2001
22
From: Enrico Seiler <[email protected]>
33
Date: Thu, 28 Sep 2023 19:35:57 +0200
4-
Subject: [PATCH 2/7] [FIX] Change constexpr test
4+
Subject: [PATCH 2/8] [FIX] Change constexpr test
55

66
gcc11 complains suddenly
77
---
@@ -21,5 +21,5 @@ index 54bcb640c..460fab223 100644
2121
+ [[maybe_unused]] static constinit auto combined = adaptor1 | adaptor2;
2222
}
2323
--
24-
2.45.2
24+
2.47.2
2525

‎test/api_stability/3.3.0/0003-API-hamming-scoring-scheme.patch‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
1-
From abeb5d0c40c71c16a8b04f98f0bbc8810929ca30 Mon Sep 17 00:00:00 2001
1+
From 19fd7c04654c70d70201ed468e5a64cac424769e Mon Sep 17 00:00:00 2001
22
From: Enrico Seiler <[email protected]>
33
Date: Sun, 28 Jul 2024 15:17:28 +0200
4-
Subject: [PATCH 3/7] [API] hamming scoring scheme
4+
Subject: [PATCH 3/8] [API] hamming scoring scheme
55

66
---
77
.../08_pairwise_alignment/pa_assignment_3_solution.cpp | 6 ++++--
@@ -77,5 +77,5 @@ index 7ec211537..ee2e501a8 100644
7777
if (i == j)
7878
EXPECT_EQ((scheme.score(seqan3::assign_rank_to(i, seqan3::dna15{}),
7979
--
80-
2.45.2
80+
2.47.2
8181

‎test/api_stability/3.3.0/0004-API-seqan3-sam_file_program_info_t-user_tags.patch‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
1-
From 02fe12c864222def7762b28197b6bd72c013640a Mon Sep 17 00:00:00 2001
1+
From 5bccf5c2aaebd483689262b0e5e0d8d393acb059 Mon Sep 17 00:00:00 2001
22
From: Enrico Seiler <[email protected]>
33
Date: Mon, 19 Aug 2024 14:13:08 +0200
4-
Subject: [PATCH 4/7] [API] seqan3::sam_file_program_info_t::user_tags
4+
Subject: [PATCH 4/8] [API] seqan3::sam_file_program_info_t::user_tags
55

66
---
77
test/unit/io/sam_file/format_sam_test.cpp | 13 ++-----------
@@ -51,5 +51,5 @@ index 8cd712ddb..599a04bbc 100644
5151
header.comments.push_back("This is a comment.");
5252

5353
--
54-
2.45.2
54+
2.47.2
5555

‎test/api_stability/3.3.0/0005-NOAPI-DETAIL-Update-copyright.patch‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
1-
From 2fffc406b2126b41b3933f43cba50710806dd53b Mon Sep 17 00:00:00 2001
1+
From aa6a35024ef988921146d98862a620b752f3514d Mon Sep 17 00:00:00 2001
22
From: Enrico Seiler <[email protected]>
33
Date: Wed, 22 Jan 2025 14:55:53 +0100
4-
Subject: [PATCH 5/7] [NOAPI][DETAIL] Update copyright
4+
Subject: [PATCH 5/8] [NOAPI][DETAIL] Update copyright
55

66
---
77
test/unit/argument_parser/detail/format_help_test.cpp | 10 +++++-----
@@ -121,5 +121,5 @@ index 5cdd9cdea..ee0c810a5 100644
121121
testing::internal::CaptureStdout();
122122
EXPECT_EXIT(parser.parse(), ::testing::ExitedWithCode(EXIT_SUCCESS), "");
123123
--
124-
2.45.2
124+
2.47.2
125125

‎test/api_stability/3.3.0/0006-NOAPI-DETAIL-Use-std-ranges-all.patch‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
1-
From ca5604875b712292c3f1a64b745830ebec3e29ab Mon Sep 17 00:00:00 2001
1+
From 011776734fcdc33a369c68cfcc0c940adf8bea84 Mon Sep 17 00:00:00 2001
22
From: Enrico Seiler <[email protected]>
33
Date: Wed, 22 Jan 2025 17:11:10 +0100
4-
Subject: [PATCH 6/7] [NOAPI][DETAIL] Use std::ranges::all
4+
Subject: [PATCH 6/8] [NOAPI][DETAIL] Use std::ranges::all
55

66
---
77
test/performance/search/search_benchmark.cpp | 5 ++---
@@ -241,5 +241,5 @@ index 1567d93ed..a800b317c 100644
241241
using sentinel_type = std::ranges::sentinel_t<view_type>;
242242

243243
--
244-
2.45.2
244+
2.47.2
245245

‎test/api_stability/3.3.0/0007-NOAPI-DETAIL-Remove-copyable_wrapper.patch‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
1-
From 636d021ac6750454ddcad34e5dee160d2d0c0751 Mon Sep 17 00:00:00 2001
1+
From 80085aed5b5c7c98fe22d27101cda54c8ed07be7 Mon Sep 17 00:00:00 2001
22
From: Enrico Seiler <[email protected]>
33
Date: Wed, 22 Jan 2025 17:16:19 +0100
4-
Subject: [PATCH 7/7] [NOAPI][DETAIL] Remove copyable_wrapper
4+
Subject: [PATCH 7/8] [NOAPI][DETAIL] Remove copyable_wrapper
55

66
---
77
test/snippet/core/detail/copyable_wrapper.cpp | 16 ----------------
@@ -41,5 +41,5 @@ index 2b24e3127..000000000
4141
-2
4242
-6
4343
--
44-
2.45.2
44+
2.47.2
4545

‎test/api_stability/3.3.0/0008-NOAPI-DETAIL-Put-SDSL-into-contrib.patch‎

Lines changed: 242 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,242 @@
1+
From 0f4d6caf3c4e4ecf4f3ebc2651bb5a952a40b3fc Mon Sep 17 00:00:00 2001
2+
From: Enrico Seiler <[email protected]>
3+
Date: Wed, 12 Feb 2025 14:39:21 +0100
4+
Subject: [PATCH 8/8] [NOAPI][DETAIL] Put SDSL into contrib
5+
6+
---
7+
.../range/container_push_back_benchmark.cpp | 5 ++---
8+
.../range/container_seq_read_benchmark.cpp | 5 ++---
9+
.../range/container_seq_write_benchmark.cpp | 5 ++---
10+
.../core/detail/template_inspection_usage.cpp | 2 ++
11+
test/snippet/utility/tuple_utility.cpp | 2 ++
12+
.../container/container_concept_test.cpp | 11 +++++------
13+
.../interleaved_bloom_filter_test.cpp | 2 +-
14+
...fm_index_cursor_collection_test_template.hpp | 17 ++++++++++-------
15+
.../fm_index_cursor_test_template.hpp | 17 ++++++++++-------
16+
test/unit/search/sdsl_index_test.cpp | 2 +-
17+
.../utility/bloom_filter/bloom_filter_test.cpp | 2 +-
18+
11 files changed, 38 insertions(+), 32 deletions(-)
19+
20+
diff --git a/test/performance/range/container_push_back_benchmark.cpp b/test/performance/range/container_push_back_benchmark.cpp
21+
index 32470ac9b..59860b0c7 100644
22+
--- a/test/performance/range/container_push_back_benchmark.cpp
23+
+++ b/test/performance/range/container_push_back_benchmark.cpp
24+
@@ -11,16 +11,15 @@
25+
#include <list>
26+
#include <vector>
27+
28+
-#include <sdsl/int_vector.hpp>
29+
-
30+
#include <seqan3/alignment/decorator/gap_decorator.hpp>
31+
#include <seqan3/alphabet/all.hpp>
32+
#include <seqan3/alphabet/container/bitpacked_sequence.hpp>
33+
+#include <seqan3/contrib/sdsl-lite.hpp>
34+
#include <seqan3/test/seqan2.hpp>
35+
#include <seqan3/utility/container/small_vector.hpp>
36+
37+
template <typename t>
38+
-using sdsl_int_vec = sdsl::int_vector<sizeof(t) * 8>;
39+
+using sdsl_int_vec = seqan3::contrib::sdsl::int_vector<sizeof(t) * 8>;
40+
41+
template <typename t>
42+
using small_vec = seqan3::small_vector<t, 10'000>;
43+
diff --git a/test/performance/range/container_seq_read_benchmark.cpp b/test/performance/range/container_seq_read_benchmark.cpp
44+
index 6a3e41fc5..e460a29f3 100644
45+
--- a/test/performance/range/container_seq_read_benchmark.cpp
46+
+++ b/test/performance/range/container_seq_read_benchmark.cpp
47+
@@ -11,17 +11,16 @@
48+
#include <list>
49+
#include <vector>
50+
51+
-#include <sdsl/int_vector.hpp>
52+
-
53+
#include <seqan3/alignment/decorator/gap_decorator.hpp>
54+
#include <seqan3/alphabet/all.hpp>
55+
#include <seqan3/alphabet/container/bitpacked_sequence.hpp>
56+
+#include <seqan3/contrib/sdsl-lite.hpp>
57+
#include <seqan3/test/performance/sequence_generator.hpp>
58+
#include <seqan3/test/seqan2.hpp>
59+
#include <seqan3/utility/container/small_vector.hpp>
60+
61+
template <typename t>
62+
-using sdsl_int_vec = sdsl::int_vector<sizeof(t) * 8>;
63+
+using sdsl_int_vec = seqan3::contrib::sdsl::int_vector<sizeof(t) * 8>;
64+
65+
template <typename t>
66+
using small_vec = seqan3::small_vector<t, 10'000>;
67+
diff --git a/test/performance/range/container_seq_write_benchmark.cpp b/test/performance/range/container_seq_write_benchmark.cpp
68+
index 193ab6965..a990d0abe 100644
69+
--- a/test/performance/range/container_seq_write_benchmark.cpp
70+
+++ b/test/performance/range/container_seq_write_benchmark.cpp
71+
@@ -11,17 +11,16 @@
72+
#include <list>
73+
#include <vector>
74+
75+
-#include <sdsl/int_vector.hpp>
76+
-
77+
#include <seqan3/alignment/decorator/gap_decorator.hpp>
78+
#include <seqan3/alphabet/all.hpp>
79+
#include <seqan3/alphabet/container/bitpacked_sequence.hpp>
80+
+#include <seqan3/contrib/sdsl-lite.hpp>
81+
#include <seqan3/test/performance/sequence_generator.hpp>
82+
#include <seqan3/test/seqan2.hpp>
83+
#include <seqan3/utility/container/small_vector.hpp>
84+
85+
template <typename t>
86+
-using sdsl_int_vec = sdsl::int_vector<sizeof(t) * 8>;
87+
+using sdsl_int_vec = seqan3::contrib::sdsl::int_vector<sizeof(t) * 8>;
88+
89+
template <typename t>
90+
using small_vec = seqan3::small_vector<t, 10'000>;
91+
diff --git a/test/snippet/core/detail/template_inspection_usage.cpp b/test/snippet/core/detail/template_inspection_usage.cpp
92+
index 74b798cea..fd0070cab 100644
93+
--- a/test/snippet/core/detail/template_inspection_usage.cpp
94+
+++ b/test/snippet/core/detail/template_inspection_usage.cpp
95+
@@ -1,3 +1,5 @@
96+
+#include <tuple>
97+
+
98+
#include <seqan3/core/detail/template_inspection.hpp>
99+
#include <seqan3/utility/type_list/type_list.hpp>
100+
101+
diff --git a/test/snippet/utility/tuple_utility.cpp b/test/snippet/utility/tuple_utility.cpp
102+
index 91dbe8f0c..211c57557 100644
103+
--- a/test/snippet/utility/tuple_utility.cpp
104+
+++ b/test/snippet/utility/tuple_utility.cpp
105+
@@ -1,3 +1,5 @@
106+
+#include <string>
107+
+
108+
#include <seqan3/utility/tuple/split.hpp>
109+
110+
int main()
111+
diff --git a/test/unit/alphabet/container/container_concept_test.cpp b/test/unit/alphabet/container/container_concept_test.cpp
112+
index f6dd0d60f..e62982fb0 100644
113+
--- a/test/unit/alphabet/container/container_concept_test.cpp
114+
+++ b/test/unit/alphabet/container/container_concept_test.cpp
115+
@@ -14,13 +14,12 @@
116+
#include <string>
117+
#include <vector>
118+
119+
-#include <sdsl/int_vector.hpp>
120+
-
121+
#include <seqan3/alphabet/container/bitpacked_sequence.hpp>
122+
#include <seqan3/alphabet/container/concatenated_sequences.hpp>
123+
#include <seqan3/alphabet/nucleotide/dna4.hpp>
124+
#include <seqan3/alphabet/quality/phred42.hpp>
125+
#include <seqan3/alphabet/quality/qualified.hpp>
126+
+#include <seqan3/contrib/sdsl-lite.hpp>
127+
#include <seqan3/utility/container/concept.hpp>
128+
129+
TEST(range_concept, forward_range)
130+
@@ -179,10 +178,10 @@ TEST(container, reservible_container)
131+
EXPECT_TRUE((seqan3::reservible_container<seqan3::concatenated_sequences<std::string>>));
132+
EXPECT_TRUE((seqan3::reservible_container<seqan3::concatenated_sequences<std::vector<char>>>));
133+
134+
- EXPECT_TRUE((seqan3::reservible_container<sdsl::bit_vector>));
135+
- EXPECT_TRUE((seqan3::reservible_container<sdsl::int_vector<>>));
136+
- EXPECT_TRUE((seqan3::reservible_container<sdsl::int_vector<13>>));
137+
- EXPECT_TRUE((seqan3::reservible_container<sdsl::int_vector<64>>));
138+
+ EXPECT_TRUE((seqan3::reservible_container<seqan3::contrib::sdsl::bit_vector>));
139+
+ EXPECT_TRUE((seqan3::reservible_container<seqan3::contrib::sdsl::int_vector<>>));
140+
+ EXPECT_TRUE((seqan3::reservible_container<seqan3::contrib::sdsl::int_vector<13>>));
141+
+ EXPECT_TRUE((seqan3::reservible_container<seqan3::contrib::sdsl::int_vector<64>>));
142+
EXPECT_TRUE((seqan3::reservible_container<seqan3::bitpacked_sequence<seqan3::dna4>>));
143+
EXPECT_TRUE(
144+
(seqan3::reservible_container<seqan3::bitpacked_sequence<seqan3::qualified<seqan3::dna4, seqan3::phred42>>>));
145+
diff --git a/test/unit/search/dream_index/interleaved_bloom_filter_test.cpp b/test/unit/search/dream_index/interleaved_bloom_filter_test.cpp
146+
index 71ba36238..a6c608ec6 100644
147+
--- a/test/unit/search/dream_index/interleaved_bloom_filter_test.cpp
148+
+++ b/test/unit/search/dream_index/interleaved_bloom_filter_test.cpp
149+
@@ -350,7 +350,7 @@ TYPED_TEST(interleaved_bloom_filter_test, data_access)
150+
{
151+
seqan3::interleaved_bloom_filter ibf{seqan3::bin_count{1024u}, seqan3::bin_size{1024u}};
152+
153+
- EXPECT_LE(sdsl::size_in_mega_bytes(ibf.raw_data()), 1.0f);
154+
+ EXPECT_LE(seqan3::contrib::sdsl::size_in_mega_bytes(ibf.raw_data()), 1.0f);
155+
}
156+
157+
TYPED_TEST(interleaved_bloom_filter_test, serialisation)
158+
diff --git a/test/unit/search/fm_index_cursor/fm_index_cursor_collection_test_template.hpp b/test/unit/search/fm_index_cursor/fm_index_cursor_collection_test_template.hpp
159+
index 5b80df314..4ef040186 100644
160+
--- a/test/unit/search/fm_index_cursor/fm_index_cursor_collection_test_template.hpp
161+
+++ b/test/unit/search/fm_index_cursor/fm_index_cursor_collection_test_template.hpp
162+
@@ -17,13 +17,16 @@
163+
164+
#include "../helper.hpp"
165+
166+
-using sdsl_byte_index_type = sdsl::csa_wt<
167+
- sdsl::wt_blcd<sdsl::bit_vector, sdsl::rank_support_v<>, sdsl::select_support_scan<>, sdsl::select_support_scan<0>>,
168+
- 16,
169+
- 10000000,
170+
- sdsl::sa_order_sa_sampling<>,
171+
- sdsl::isa_sampling<>,
172+
- sdsl::byte_alphabet>;
173+
+using sdsl_byte_index_type =
174+
+ seqan3::contrib::sdsl::csa_wt<seqan3::contrib::sdsl::wt_blcd<seqan3::contrib::sdsl::bit_vector,
175+
+ seqan3::contrib::sdsl::rank_support_v<>,
176+
+ seqan3::contrib::sdsl::select_support_scan<>,
177+
+ seqan3::contrib::sdsl::select_support_scan<0>>,
178+
+ 16,
179+
+ 10'000'000,
180+
+ seqan3::contrib::sdsl::sa_order_sa_sampling<>,
181+
+ seqan3::contrib::sdsl::isa_sampling<>,
182+
+ seqan3::contrib::sdsl::byte_alphabet>;
183+
184+
template <typename T>
185+
struct fm_index_cursor_collection_test;
186+
diff --git a/test/unit/search/fm_index_cursor/fm_index_cursor_test_template.hpp b/test/unit/search/fm_index_cursor/fm_index_cursor_test_template.hpp
187+
index 8564b1df6..b11b1c985 100644
188+
--- a/test/unit/search/fm_index_cursor/fm_index_cursor_test_template.hpp
189+
+++ b/test/unit/search/fm_index_cursor/fm_index_cursor_test_template.hpp
190+
@@ -16,13 +16,16 @@
191+
192+
#include "../helper.hpp"
193+
194+
-using sdsl_byte_index_type = sdsl::csa_wt<
195+
- sdsl::wt_blcd<sdsl::bit_vector, sdsl::rank_support_v<>, sdsl::select_support_scan<>, sdsl::select_support_scan<0>>,
196+
- 16,
197+
- 10000000,
198+
- sdsl::sa_order_sa_sampling<>,
199+
- sdsl::isa_sampling<>,
200+
- sdsl::byte_alphabet>;
201+
+using sdsl_byte_index_type =
202+
+ seqan3::contrib::sdsl::csa_wt<seqan3::contrib::sdsl::wt_blcd<seqan3::contrib::sdsl::bit_vector,
203+
+ seqan3::contrib::sdsl::rank_support_v<>,
204+
+ seqan3::contrib::sdsl::select_support_scan<>,
205+
+ seqan3::contrib::sdsl::select_support_scan<0>>,
206+
+ 16,
207+
+ 10'000'000,
208+
+ seqan3::contrib::sdsl::sa_order_sa_sampling<>,
209+
+ seqan3::contrib::sdsl::isa_sampling<>,
210+
+ seqan3::contrib::sdsl::byte_alphabet>;
211+
212+
using locate_result_t = std::vector<std::pair<uint64_t, uint64_t>>;
213+
214+
diff --git a/test/unit/search/sdsl_index_test.cpp b/test/unit/search/sdsl_index_test.cpp
215+
index 29042c51b..2277cd624 100644
216+
--- a/test/unit/search/sdsl_index_test.cpp
217+
+++ b/test/unit/search/sdsl_index_test.cpp
218+
@@ -9,7 +9,7 @@
219+
220+
#include <seqan3/search/fm_index/concept.hpp>
221+
222+
-using namespace sdsl;
223+
+using namespace seqan3::contrib::sdsl;
224+
225+
template <typename T>
226+
class sdsl_index_test : public ::testing::Test
227+
diff --git a/test/unit/utility/bloom_filter/bloom_filter_test.cpp b/test/unit/utility/bloom_filter/bloom_filter_test.cpp
228+
index 612683cf3..2133abd37 100644
229+
--- a/test/unit/utility/bloom_filter/bloom_filter_test.cpp
230+
+++ b/test/unit/utility/bloom_filter/bloom_filter_test.cpp
231+
@@ -125,7 +125,7 @@ TYPED_TEST(bloom_filter_test, reset)
232+
TYPED_TEST(bloom_filter_test, data_access)
233+
{
234+
seqan3::bloom_filter bf{seqan3::bin_size{1024u}};
235+
- EXPECT_LE(sdsl::size_in_mega_bytes(bf.raw_data()), 0.001f);
236+
+ EXPECT_LE(seqan3::contrib::sdsl::size_in_mega_bytes(bf.raw_data()), 0.001f);
237+
}
238+
239+
TYPED_TEST(bloom_filter_test, serialisation)
240+
--
241+
2.47.2
242+

‎test/api_stability/3.3.0/0008-NOAPI-DETAIL-Put-SDSL-into-contrib.patch.license‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
2+
SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
3+
SPDX-License-Identifier: BSD-3-Clause

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