biology/seqan3: update 3.2.0 → 3.3.0

PR:		273670
Reported by:	 Lorenzo Salvadore <salvadore@freebsd.org>

biology/seqan3/Makefile

@@ -1,6 +1,5 @@
 PORTNAME=	seqan3
-DISTVERSION=	3.2.0
-PORTREVISION=	2
+DISTVERSION=	3.3.0
 CATEGORIES=	biology devel math
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -20,9 +19,10 @@ USES=		cmake localbase
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	seqan
-GH_TUPLE=	xxsds:sdsl-lite:cf9ff4a:sdsl_lite/submodules/sdsl-lite
+GH_TUPLE=	xxsds:sdsl-lite:d54d389:sdsl_lite/submodules/sdsl-lite
 
 USE_GCC=	yes # tests only pass with gcc, see https://github.com/seqan/seqan3/issues/2643, otherwise gcc isn't needed because this is a header-only library
+# tests fail to compile, see https://github.com/seqan/seqan3/issues/3191
 
 TEST_WRKSRC=	${WRKSRC}/.test
 

biology/seqan3/distinfo

@@ -1,5 +1,5 @@
-TIMESTAMP = 1656041922
-SHA256 (seqan-seqan3-3.2.0_GH0.tar.gz) = 80d41dd035407cfec83eb3a4466d0421adc27129af684290c0c4da31421e7276
-SIZE (seqan-seqan3-3.2.0_GH0.tar.gz) = 1522246
-SHA256 (xxsds-sdsl-lite-cf9ff4a_GH0.tar.gz) = 9e328d00c3bdead09cfa35e75e20ace0e668d6dac0436ce9256f2156088f22e8
-SIZE (xxsds-sdsl-lite-cf9ff4a_GH0.tar.gz) = 1166065
+TIMESTAMP = 1694368553
+SHA256 (seqan-seqan3-3.3.0_GH0.tar.gz) = 96975406445c8a5974803eefa146ee2f85206f6d2c2bccf45171ee0b1a653fb8
+SIZE (seqan-seqan3-3.3.0_GH0.tar.gz) = 1564852
+SHA256 (xxsds-sdsl-lite-d54d389_GH0.tar.gz) = eaac28144b34a833afb8c03139abbe427d4b95a827bf5b9b6532353f9cff9ec1
+SIZE (xxsds-sdsl-lite-d54d389_GH0.tar.gz) = 1183835

biology/seqan3/pkg-plist

@@ -2,6 +2,9 @@ include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp
 include/seqan3/alignment/aligned_sequence/all.hpp
 include/seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp
 include/seqan3/alignment/all.hpp
+include/seqan3/alignment/cigar_conversion/alignment_from_cigar.hpp
+include/seqan3/alignment/cigar_conversion/all.hpp
+include/seqan3/alignment/cigar_conversion/cigar_from_alignment.hpp
 include/seqan3/alignment/configuration/align_config_band.hpp
 include/seqan3/alignment/configuration/align_config_debug.hpp
 include/seqan3/alignment/configuration/align_config_edit.hpp
@@ -184,9 +187,29 @@ include/seqan3/argument_parser/detail/terminal.hpp
 include/seqan3/argument_parser/detail/version_check.hpp
 include/seqan3/argument_parser/exceptions.hpp
 include/seqan3/argument_parser/validators.hpp
+include/seqan3/contrib/README.md
 include/seqan3/contrib/parallel/buffer_queue.hpp
 include/seqan3/contrib/parallel/serialised_resource_pool.hpp
 include/seqan3/contrib/parallel/suspendable_queue.hpp
+include/seqan3/contrib/std/.clang-format
+include/seqan3/contrib/std/.gitignore
+include/seqan3/contrib/std/LICENSE
+include/seqan3/contrib/std/README.md
+include/seqan3/contrib/std/all_view.hpp
+include/seqan3/contrib/std/chunk_view.hpp
+include/seqan3/contrib/std/concepts.hpp
+include/seqan3/contrib/std/detail/adaptor_base.hpp
+include/seqan3/contrib/std/detail/adaptor_for_view_without_args.hpp
+include/seqan3/contrib/std/detail/adaptor_from_functor.hpp
+include/seqan3/contrib/std/detail/compiler_definitions.hpp
+include/seqan3/contrib/std/detail/exposition_only.hpp
+include/seqan3/contrib/std/detail/non_propagating_cache.hpp
+include/seqan3/contrib/std/join_with_view.hpp
+include/seqan3/contrib/std/pair.hpp
+include/seqan3/contrib/std/to.hpp
+include/seqan3/contrib/std/tuple.hpp
+include/seqan3/contrib/std/zip_view.hpp
+include/seqan3/contrib/stream/bgzf.hpp
 include/seqan3/contrib/stream/bgzf_istream.hpp
 include/seqan3/contrib/stream/bgzf_ostream.hpp
 include/seqan3/contrib/stream/bgzf_stream_util.hpp
@@ -229,7 +252,6 @@ include/seqan3/core/detail/deferred_crtp_base.hpp
 include/seqan3/core/detail/empty_type.hpp
 include/seqan3/core/detail/is_class_template_declarable.hpp
 include/seqan3/core/detail/iterator_traits.hpp
-include/seqan3/core/detail/persist_view.hpp
 include/seqan3/core/detail/strong_type.hpp
 include/seqan3/core/detail/template_inspection.hpp
 include/seqan3/core/detail/test_accessor.hpp
@@ -243,7 +265,6 @@ include/seqan3/core/range/detail/inherited_iterator_base.hpp
 include/seqan3/core/range/detail/misc.hpp
 include/seqan3/core/range/detail/random_access_iterator.hpp
 include/seqan3/core/range/type_traits.hpp
-include/seqan3/core/semiregular_box.hpp
 include/seqan3/io/all.hpp
 include/seqan3/io/detail/ignore_output_iterator.hpp
 include/seqan3/io/detail/in_file_iterator.hpp
@@ -341,17 +362,8 @@ include/seqan3/search/views/all.hpp
 include/seqan3/search/views/kmer_hash.hpp
 include/seqan3/search/views/minimiser.hpp
 include/seqan3/search/views/minimiser_hash.hpp
-include/seqan3/std/algorithm
-include/seqan3/std/bit
 include/seqan3/std/charconv
-include/seqan3/std/concepts
-include/seqan3/std/filesystem
-include/seqan3/std/iterator
-include/seqan3/std/memory
 include/seqan3/std/new
-include/seqan3/std/ranges
-include/seqan3/std/span
-include/seqan3/std/type_traits
 include/seqan3/submodules/sdsl-lite/include/sdsl/.gitignore
 include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vector_il.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vectors.hpp
@@ -421,6 +433,9 @@ include/seqan3/submodules/sdsl-lite/include/sdsl/qsufsort.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/ram_filebuf.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/ram_fs.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support.hpp
+include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_int.hpp
+include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_int_scan.hpp
+include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_int_v.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_scan.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_v.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_v5.hpp
@@ -441,7 +456,6 @@ include/seqan3/submodules/sdsl-lite/include/sdsl/sorted_int_stack.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/sorted_multi_stack_support.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/sorted_stack_support.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/structure_tree.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/structure_tree.hpp.cmake
 include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_array_algorithm.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_array_helper.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_arrays.hpp
@@ -460,6 +474,7 @@ include/seqan3/submodules/sdsl-lite/include/sdsl/wm_int.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/wt_algorithm.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/wt_ap.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/wt_blcd.hpp
+include/seqan3/submodules/sdsl-lite/include/sdsl/wt_epr.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/wt_gmr.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/wt_helper.hpp
 include/seqan3/submodules/sdsl-lite/include/sdsl/wt_huff.hpp
@@ -476,8 +491,6 @@ include/seqan3/utility/char_operations/predicate_detail.hpp
 include/seqan3/utility/char_operations/pretty_print.hpp
 include/seqan3/utility/char_operations/transform.hpp
 include/seqan3/utility/concept.hpp
-include/seqan3/utility/concept/all.hpp
-include/seqan3/utility/concept/exposition_only/core_language.hpp
 include/seqan3/utility/container/aligned_allocator.hpp
 include/seqan3/utility/container/all.hpp
 include/seqan3/utility/container/concept.hpp
@@ -549,7 +562,6 @@ include/seqan3/utility/views/repeat.hpp
 include/seqan3/utility/views/repeat_n.hpp
 include/seqan3/utility/views/single_pass_input.hpp
 include/seqan3/utility/views/slice.hpp
-include/seqan3/utility/views/to.hpp
 include/seqan3/utility/views/type_reduce.hpp
 include/seqan3/utility/views/zip.hpp
 include/seqan3/version.hpp