diff --git a/biology/seqan3/Makefile b/biology/seqan3/Makefile index b40ea02c1c63..9c8fc69ba93e 100644 --- a/biology/seqan3/Makefile +++ b/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 diff --git a/biology/seqan3/distinfo b/biology/seqan3/distinfo index d15df1a95c74..8fa5387420f9 100644 --- a/biology/seqan3/distinfo +++ b/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 diff --git a/biology/seqan3/pkg-plist b/biology/seqan3/pkg-plist index 4883e10f6d4b..19d86e63d82e 100644 --- a/biology/seqan3/pkg-plist +++ b/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