From nobody Mon Nov 15 05:19:00 2021 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id D9EE91869A39; Mon, 15 Nov 2021 05:19:00 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4HsyCm3XNpz4rwf; Mon, 15 Nov 2021 05:19:00 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 32D9313CC1; Mon, 15 Nov 2021 05:19:00 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 1AF5J0dc001979; Mon, 15 Nov 2021 05:19:00 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 1AF5J0JC001978; Mon, 15 Nov 2021 05:19:00 GMT (envelope-from git) Date: Mon, 15 Nov 2021 05:19:00 GMT Message-Id: <202111150519.1AF5J0JC001978@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: e8e22bb84f36 - main - biology/seqan3: Update 3.0.3 -> 3.1.0 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: e8e22bb84f36ed63f09ae40872e260238bfdd317 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=e8e22bb84f36ed63f09ae40872e260238bfdd317 commit e8e22bb84f36ed63f09ae40872e260238bfdd317 Author: Yuri Victorovich AuthorDate: 2021-11-15 05:13:10 +0000 Commit: Yuri Victorovich CommitDate: 2021-11-15 05:18:53 +0000 biology/seqan3: Update 3.0.3 -> 3.1.0 Reported by: portscout --- biology/seqan3/Makefile | 8 +- biology/seqan3/distinfo | 10 +-- biology/seqan3/pkg-plist | 187 +++++++---------------------------------------- 3 files changed, 36 insertions(+), 169 deletions(-) diff --git a/biology/seqan3/Makefile b/biology/seqan3/Makefile index c4a9e6453274..b465d96ca305 100644 --- a/biology/seqan3/Makefile +++ b/biology/seqan3/Makefile @@ -1,5 +1,5 @@ PORTNAME= seqan3 -DISTVERSION= 3.0.3 +DISTVERSION= 3.1.0 CATEGORIES= biology devel math MAINTAINER= yuri@FreeBSD.org @@ -18,7 +18,9 @@ USES= cmake localbase USE_GITHUB= yes GH_ACCOUNT= seqan -GH_TUPLE= xxsds:sdsl-lite:9a0d567:sdsl_lite/submodules/sdsl-lite +GH_TUPLE= xxsds:sdsl-lite:cf9ff4a: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 TEST_WRKSRC= ${WRKSRC}/.test @@ -27,7 +29,7 @@ NO_ARCH= yes post-install: @${RM} -r ${STAGEDIR}${DOCSDIR} -do-test: # fail: https://github.com/seqan/seqan3/issues/2643 +do-test: @${MKDIR} ${TEST_WRKSRC} && cd ${TEST_WRKSRC} && \ ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} ${WRKSRC}/test/unit && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ diff --git a/biology/seqan3/distinfo b/biology/seqan3/distinfo index 252bac55dbe3..3aaf97f0a829 100644 --- a/biology/seqan3/distinfo +++ b/biology/seqan3/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1622351721 -SHA256 (seqan-seqan3-3.0.3_GH0.tar.gz) = 736d7c07759f51b1d6f4ca806dafd219a2a35b0250e018eb038010063d23eecd -SIZE (seqan-seqan3-3.0.3_GH0.tar.gz) = 1478459 -SHA256 (xxsds-sdsl-lite-9a0d567_GH0.tar.gz) = 1727ec6897535a493b99ff36a6d19d8205964be2b2a027ba547fc77ab7dbd74e -SIZE (xxsds-sdsl-lite-9a0d567_GH0.tar.gz) = 1156974 +TIMESTAMP = 1636950170 +SHA256 (seqan-seqan3-3.1.0_GH0.tar.gz) = 5dc87c5da064a7d1a5afec96c6c1da79a6d1ec6a045e1fe100166c88f559ce51 +SIZE (seqan-seqan3-3.1.0_GH0.tar.gz) = 1447998 +SHA256 (xxsds-sdsl-lite-cf9ff4a_GH0.tar.gz) = 9e328d00c3bdead09cfa35e75e20ace0e668d6dac0436ce9256f2156088f22e8 +SIZE (xxsds-sdsl-lite-cf9ff4a_GH0.tar.gz) = 1166065 diff --git a/biology/seqan3/pkg-plist b/biology/seqan3/pkg-plist index 835bf6eba19c..dc4dab769c9a 100644 --- a/biology/seqan3/pkg-plist +++ b/biology/seqan3/pkg-plist @@ -2,8 +2,6 @@ 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/band/all.hpp -include/seqan3/alignment/band/static_band.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 @@ -19,17 +17,16 @@ include/seqan3/alignment/configuration/align_config_scoring_scheme.hpp include/seqan3/alignment/configuration/align_config_vectorised.hpp include/seqan3/alignment/configuration/all.hpp include/seqan3/alignment/configuration/detail.hpp +include/seqan3/alignment/decorator/all.hpp include/seqan3/alignment/decorator/gap_decorator.hpp include/seqan3/alignment/detail/pairwise_alignment_concept.hpp include/seqan3/alignment/exception.hpp -include/seqan3/alignment/matrix/alignment_coordinate.hpp -include/seqan3/alignment/matrix/alignment_optimum.hpp include/seqan3/alignment/matrix/all.hpp -include/seqan3/alignment/matrix/debug_matrix.hpp include/seqan3/alignment/matrix/detail/advanceable_alignment_coordinate.hpp include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp include/seqan3/alignment/matrix/detail/aligned_sequence_builder.hpp include/seqan3/alignment/matrix/detail/alignment_matrix_column_major_range_base.hpp +include/seqan3/alignment/matrix/detail/alignment_optimum.hpp include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column.hpp include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_banded.hpp include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_base.hpp @@ -41,8 +38,14 @@ include/seqan3/alignment/matrix/detail/alignment_trace_matrix_proxy.hpp include/seqan3/alignment/matrix/detail/all.hpp include/seqan3/alignment/matrix/detail/combined_score_and_trace_matrix.hpp include/seqan3/alignment/matrix/detail/coordinate_matrix.hpp +include/seqan3/alignment/matrix/detail/debug_matrix.hpp +include/seqan3/alignment/matrix/detail/edit_distance_score_matrix_full.hpp +include/seqan3/alignment/matrix/detail/edit_distance_trace_matrix_full.hpp +include/seqan3/alignment/matrix/detail/matrix_concept.hpp include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp +include/seqan3/alignment/matrix/detail/row_wise_matrix.hpp include/seqan3/alignment/matrix/detail/score_matrix_single_column.hpp +include/seqan3/alignment/matrix/detail/trace_directions.hpp include/seqan3/alignment/matrix/detail/trace_iterator.hpp include/seqan3/alignment/matrix/detail/trace_iterator_banded.hpp include/seqan3/alignment/matrix/detail/trace_iterator_base.hpp @@ -50,11 +53,6 @@ include/seqan3/alignment/matrix/detail/trace_matrix_full.hpp include/seqan3/alignment/matrix/detail/two_dimensional_matrix.hpp include/seqan3/alignment/matrix/detail/two_dimensional_matrix_iterator_base.hpp include/seqan3/alignment/matrix/detail/two_dimensional_matrix_iterator_concept.hpp -include/seqan3/alignment/matrix/edit_distance_score_matrix_full.hpp -include/seqan3/alignment/matrix/edit_distance_trace_matrix_full.hpp -include/seqan3/alignment/matrix/matrix_concept.hpp -include/seqan3/alignment/matrix/row_wise_matrix.hpp -include/seqan3/alignment/matrix/trace_directions.hpp include/seqan3/alignment/pairwise/align_pairwise.hpp include/seqan3/alignment/pairwise/align_result_selector.hpp include/seqan3/alignment/pairwise/alignment_algorithm.hpp @@ -90,7 +88,6 @@ include/seqan3/alignment/scoring/all.hpp include/seqan3/alignment/scoring/aminoacid_scoring_scheme.hpp include/seqan3/alignment/scoring/detail/simd_match_mismatch_scoring_scheme.hpp include/seqan3/alignment/scoring/detail/simd_matrix_scoring_scheme.hpp -include/seqan3/alignment/scoring/gap_scheme.hpp include/seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp include/seqan3/alignment/scoring/scoring_scheme_base.hpp include/seqan3/alignment/scoring/scoring_scheme_concept.hpp @@ -111,7 +108,6 @@ include/seqan3/alphabet/aminoacid/translation_details.hpp include/seqan3/alphabet/aminoacid/translation_genetic_code.hpp include/seqan3/alphabet/cigar/all.hpp include/seqan3/alphabet/cigar/cigar.hpp -include/seqan3/alphabet/cigar/cigar_op.hpp include/seqan3/alphabet/cigar/exposition_only/cigar_operation.hpp include/seqan3/alphabet/composite/all.hpp include/seqan3/alphabet/composite/alphabet_tuple_base.hpp @@ -119,6 +115,7 @@ include/seqan3/alphabet/composite/alphabet_variant.hpp include/seqan3/alphabet/composite/detail.hpp include/seqan3/alphabet/composite/semialphabet_any.hpp include/seqan3/alphabet/concept.hpp +include/seqan3/alphabet/container/all.hpp include/seqan3/alphabet/container/bitpacked_sequence.hpp include/seqan3/alphabet/container/concatenated_sequences.hpp include/seqan3/alphabet/detail/alphabet_proxy.hpp @@ -143,18 +140,16 @@ include/seqan3/alphabet/nucleotide/nucleotide_base.hpp include/seqan3/alphabet/nucleotide/rna15.hpp include/seqan3/alphabet/nucleotide/rna4.hpp include/seqan3/alphabet/nucleotide/rna5.hpp -include/seqan3/alphabet/nucleotide/sam_dna16.hpp include/seqan3/alphabet/quality/aliases.hpp include/seqan3/alphabet/quality/all.hpp include/seqan3/alphabet/quality/concept.hpp include/seqan3/alphabet/quality/phred42.hpp include/seqan3/alphabet/quality/phred63.hpp -include/seqan3/alphabet/quality/phred68legacy.hpp include/seqan3/alphabet/quality/phred68solexa.hpp include/seqan3/alphabet/quality/phred94.hpp include/seqan3/alphabet/quality/phred_base.hpp include/seqan3/alphabet/quality/qualified.hpp -include/seqan3/alphabet/quality/quality_base.hpp +include/seqan3/alphabet/range/all.hpp include/seqan3/alphabet/range/hash.hpp include/seqan3/alphabet/range/sequence.hpp include/seqan3/alphabet/structure/all.hpp @@ -203,29 +198,13 @@ include/seqan3/contrib/stream/gz_ostream.hpp include/seqan3/core/add_enum_bitwise_operators.hpp include/seqan3/core/algorithm/algorithm_result_generator_range.hpp include/seqan3/core/algorithm/all.hpp -include/seqan3/core/algorithm/bound.hpp -include/seqan3/core/algorithm/concept.hpp -include/seqan3/core/algorithm/configuration.hpp -include/seqan3/core/algorithm/configuration_element_debug_mode.hpp -include/seqan3/core/algorithm/configuration_element_parallel_mode.hpp -include/seqan3/core/algorithm/configuration_utility.hpp include/seqan3/core/algorithm/detail/algorithm_executor_blocking.hpp include/seqan3/core/algorithm/detail/all.hpp include/seqan3/core/algorithm/detail/execution_handler_parallel.hpp include/seqan3/core/algorithm/detail/execution_handler_sequential.hpp -include/seqan3/core/algorithm/pipeable_config_element.hpp include/seqan3/core/all.hpp -include/seqan3/core/bit_manipulation.hpp -include/seqan3/core/char_operations/all.hpp -include/seqan3/core/char_operations/predicate.hpp -include/seqan3/core/char_operations/predicate_detail.hpp -include/seqan3/core/char_operations/pretty_print.hpp -include/seqan3/core/char_operations/transform.hpp -include/seqan3/core/common_tuple.hpp include/seqan3/core/concept/all.hpp include/seqan3/core/concept/cereal.hpp -include/seqan3/core/concept/core_language.hpp -include/seqan3/core/concept/tuple.hpp include/seqan3/core/configuration/all.hpp include/seqan3/core/configuration/configuration.hpp include/seqan3/core/configuration/detail/all.hpp @@ -235,6 +214,7 @@ include/seqan3/core/configuration/detail/configuration_element_parallel_mode.hpp include/seqan3/core/configuration/detail/configuration_utility.hpp include/seqan3/core/configuration/pipeable_config_element.hpp include/seqan3/core/debug_stream.hpp +include/seqan3/core/debug_stream/all.hpp include/seqan3/core/debug_stream/byte.hpp include/seqan3/core/debug_stream/debug_stream_type.hpp include/seqan3/core/debug_stream/detail/to_string.hpp @@ -244,35 +224,17 @@ include/seqan3/core/debug_stream/tuple.hpp include/seqan3/core/debug_stream/variant.hpp include/seqan3/core/detail/all.hpp include/seqan3/core/detail/customisation_point.hpp -include/seqan3/core/detail/debug_stream_alphabet.hpp -include/seqan3/core/detail/debug_stream_byte.hpp -include/seqan3/core/detail/debug_stream_optional.hpp -include/seqan3/core/detail/debug_stream_range.hpp -include/seqan3/core/detail/debug_stream_tuple.hpp -include/seqan3/core/detail/debug_stream_type.hpp -include/seqan3/core/detail/debug_stream_variant.hpp include/seqan3/core/detail/deferred_crtp_base.hpp include/seqan3/core/detail/empty_type.hpp -include/seqan3/core/detail/endian.hpp -include/seqan3/core/detail/int_types.hpp include/seqan3/core/detail/is_class_template_declarable.hpp include/seqan3/core/detail/iterator_traits.hpp -include/seqan3/core/detail/pack_algorithm.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 -include/seqan3/core/detail/to_string.hpp include/seqan3/core/detail/transfer_type_modifier_onto.hpp -include/seqan3/core/detail/type_inspection.hpp -include/seqan3/core/math.hpp -include/seqan3/core/parallel/all.hpp -include/seqan3/core/parallel/detail/latch.hpp -include/seqan3/core/parallel/detail/reader_writer_manager.hpp -include/seqan3/core/parallel/detail/spin_delay.hpp -include/seqan3/core/parallel/execution.hpp include/seqan3/core/platform.hpp -include/seqan3/core/pod_tuple.hpp +include/seqan3/core/range/all.hpp include/seqan3/core/range/detail/adaptor_base.hpp include/seqan3/core/range/detail/adaptor_for_view_without_args.hpp include/seqan3/core/range/detail/adaptor_from_functor.hpp @@ -281,55 +243,9 @@ 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/core/simd/all.hpp -include/seqan3/core/simd/concept.hpp -include/seqan3/core/simd/debug_stream_simd.hpp -include/seqan3/core/simd/detail/builtin_simd.hpp -include/seqan3/core/simd/detail/builtin_simd_intrinsics.hpp -include/seqan3/core/simd/detail/default_simd_backend.hpp -include/seqan3/core/simd/detail/default_simd_length.hpp -include/seqan3/core/simd/detail/simd_algorithm_avx2.hpp -include/seqan3/core/simd/detail/simd_algorithm_avx512.hpp -include/seqan3/core/simd/detail/simd_algorithm_sse4.hpp -include/seqan3/core/simd/simd.hpp -include/seqan3/core/simd/simd_algorithm.hpp -include/seqan3/core/simd/simd_traits.hpp -include/seqan3/core/simd/view_iota_simd.hpp -include/seqan3/core/simd/view_to_simd.hpp -include/seqan3/core/tuple_utility.hpp -include/seqan3/core/type_list/all.hpp -include/seqan3/core/type_list/traits.hpp -include/seqan3/core/type_list/type_list.hpp -include/seqan3/core/type_traits/all.hpp -include/seqan3/core/type_traits/basic.hpp -include/seqan3/core/type_traits/concept.hpp -include/seqan3/core/type_traits/deferred_crtp_base.hpp -include/seqan3/core/type_traits/function.hpp -include/seqan3/core/type_traits/iterator.hpp -include/seqan3/core/type_traits/lazy.hpp -include/seqan3/core/type_traits/pack.hpp -include/seqan3/core/type_traits/pre.hpp -include/seqan3/core/type_traits/range.hpp -include/seqan3/core/type_traits/template_inspection.hpp -include/seqan3/core/type_traits/transformation_trait_or.hpp -include/seqan3/io/alignment_file/all.hpp -include/seqan3/io/alignment_file/detail.hpp -include/seqan3/io/alignment_file/format_bam.hpp -include/seqan3/io/alignment_file/format_sam.hpp -include/seqan3/io/alignment_file/format_sam_base.hpp -include/seqan3/io/alignment_file/header.hpp -include/seqan3/io/alignment_file/input.hpp -include/seqan3/io/alignment_file/input_format_concept.hpp -include/seqan3/io/alignment_file/input_options.hpp -include/seqan3/io/alignment_file/misc.hpp -include/seqan3/io/alignment_file/output.hpp -include/seqan3/io/alignment_file/output_format_concept.hpp -include/seqan3/io/alignment_file/output_options.hpp -include/seqan3/io/alignment_file/sam_tag_dictionary.hpp include/seqan3/io/all.hpp include/seqan3/io/detail/ignore_output_iterator.hpp include/seqan3/io/detail/in_file_iterator.hpp -include/seqan3/io/detail/istreambuf_view.hpp include/seqan3/io/detail/magic_header.hpp include/seqan3/io/detail/misc.hpp include/seqan3/io/detail/misc_input.hpp @@ -338,10 +254,6 @@ include/seqan3/io/detail/out_file_iterator.hpp include/seqan3/io/detail/record.hpp include/seqan3/io/detail/record_like.hpp include/seqan3/io/detail/safe_filesystem_entry.hpp -include/seqan3/io/detail/take_exactly_view.hpp -include/seqan3/io/detail/take_line_view.hpp -include/seqan3/io/detail/take_until_view.hpp -include/seqan3/io/detail/take_view.hpp include/seqan3/io/exception.hpp include/seqan3/io/record.hpp include/seqan3/io/sam_file/all.hpp @@ -376,7 +288,6 @@ include/seqan3/io/stream/concept.hpp include/seqan3/io/stream/detail/fast_istreambuf_iterator.hpp include/seqan3/io/stream/detail/fast_ostreambuf_iterator.hpp include/seqan3/io/stream/detail/stream_buffer_exposer.hpp -include/seqan3/io/stream/iterator.hpp include/seqan3/io/structure_file/all.hpp include/seqan3/io/structure_file/detail.hpp include/seqan3/io/structure_file/format_vienna.hpp @@ -387,64 +298,12 @@ include/seqan3/io/structure_file/output.hpp include/seqan3/io/structure_file/output_format_concept.hpp include/seqan3/io/structure_file/output_options.hpp include/seqan3/io/structure_file/record.hpp +include/seqan3/io/views/all.hpp include/seqan3/io/views/async_input_buffer.hpp -include/seqan3/range/all.hpp -include/seqan3/range/concept.hpp -include/seqan3/range/container/aligned_allocator.hpp -include/seqan3/range/container/all.hpp -include/seqan3/range/container/bitcompressed_vector.hpp -include/seqan3/range/container/concatenated_sequences.hpp -include/seqan3/range/container/concept.hpp -include/seqan3/range/container/dynamic_bitset.hpp -include/seqan3/range/container/small_string.hpp -include/seqan3/range/container/small_vector.hpp -include/seqan3/range/decorator/all.hpp -include/seqan3/range/decorator/gap_decorator.hpp -include/seqan3/range/detail/inherited_iterator_base.hpp -include/seqan3/range/detail/misc.hpp -include/seqan3/range/detail/random_access_iterator.hpp -include/seqan3/range/hash.hpp -include/seqan3/range/shortcuts.hpp -include/seqan3/range/views/all.hpp -include/seqan3/range/views/as_const.hpp -include/seqan3/range/views/async_input_buffer.hpp -include/seqan3/range/views/char_to.hpp -include/seqan3/range/views/chunk.hpp -include/seqan3/range/views/complement.hpp -include/seqan3/range/views/convert.hpp -include/seqan3/range/views/deep.hpp -include/seqan3/range/views/detail.hpp -include/seqan3/range/views/drop.hpp -include/seqan3/range/views/enforce_random_access.hpp -include/seqan3/range/views/get.hpp -include/seqan3/range/views/interleave.hpp -include/seqan3/range/views/istreambuf.hpp -include/seqan3/range/views/join.hpp -include/seqan3/range/views/kmer_hash.hpp -include/seqan3/range/views/minimiser.hpp -include/seqan3/range/views/minimiser_hash.hpp -include/seqan3/range/views/move.hpp -include/seqan3/range/views/pairwise_combine.hpp -include/seqan3/range/views/persist.hpp -include/seqan3/range/views/rank_to.hpp -include/seqan3/range/views/repeat.hpp -include/seqan3/range/views/repeat_n.hpp -include/seqan3/range/views/single_pass_input.hpp -include/seqan3/range/views/slice.hpp -include/seqan3/range/views/take.hpp -include/seqan3/range/views/take_exactly.hpp -include/seqan3/range/views/take_line.hpp -include/seqan3/range/views/take_until.hpp -include/seqan3/range/views/to.hpp -include/seqan3/range/views/to_char.hpp -include/seqan3/range/views/to_lower.hpp -include/seqan3/range/views/to_rank.hpp -include/seqan3/range/views/to_upper.hpp -include/seqan3/range/views/translate.hpp -include/seqan3/range/views/translate_join.hpp -include/seqan3/range/views/trim_quality.hpp -include/seqan3/range/views/type_reduce.hpp -include/seqan3/range/views/zip.hpp +include/seqan3/io/views/detail/istreambuf_view.hpp +include/seqan3/io/views/detail/take_exactly_view.hpp +include/seqan3/io/views/detail/take_line_view.hpp +include/seqan3/io/views/detail/take_until_view.hpp include/seqan3/search/all.hpp include/seqan3/search/configuration/all.hpp include/seqan3/search/configuration/default_configuration.hpp @@ -477,6 +336,7 @@ include/seqan3/search/kmer_index/all.hpp include/seqan3/search/kmer_index/shape.hpp include/seqan3/search/search.hpp include/seqan3/search/search_result.hpp +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 @@ -492,7 +352,6 @@ 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/CMakeLists.txt include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vector_il.hpp include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vectors.hpp include/seqan3/submodules/sdsl-lite/include/sdsl/bits.hpp @@ -613,13 +472,15 @@ include/seqan3/utility/char_operations/predicate.hpp 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/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 include/seqan3/utility/container/dynamic_bitset.hpp include/seqan3/utility/container/small_string.hpp include/seqan3/utility/container/small_vector.hpp include/seqan3/utility/detail/bits_of.hpp -include/seqan3/utility/detail/exposition_only_concept.hpp include/seqan3/utility/detail/integer_traits.hpp include/seqan3/utility/detail/multi_invocable.hpp include/seqan3/utility/detail/to_little_endian.hpp @@ -630,6 +491,7 @@ include/seqan3/utility/parallel/detail/all.hpp include/seqan3/utility/parallel/detail/latch.hpp include/seqan3/utility/parallel/detail/reader_writer_manager.hpp include/seqan3/utility/parallel/detail/spin_delay.hpp +include/seqan3/utility/range/all.hpp include/seqan3/utility/range/concept.hpp include/seqan3/utility/simd/algorithm.hpp include/seqan3/utility/simd/all.hpp @@ -644,6 +506,7 @@ include/seqan3/utility/simd/detail/simd_algorithm_avx512.hpp include/seqan3/utility/simd/detail/simd_algorithm_sse4.hpp include/seqan3/utility/simd/simd.hpp include/seqan3/utility/simd/simd_traits.hpp +include/seqan3/utility/simd/views/all.hpp include/seqan3/utility/simd/views/iota_simd.hpp include/seqan3/utility/simd/views/to_simd.hpp include/seqan3/utility/tuple/all.hpp @@ -653,9 +516,11 @@ include/seqan3/utility/tuple/pod_tuple.hpp include/seqan3/utility/tuple/pop_front.hpp include/seqan3/utility/tuple/split.hpp include/seqan3/utility/type_list/all.hpp +include/seqan3/utility/type_list/detail/type_list_algorithm.hpp include/seqan3/utility/type_list/traits.hpp include/seqan3/utility/type_list/type_list.hpp include/seqan3/utility/type_pack/all.hpp +include/seqan3/utility/type_pack/detail/type_pack_algorithm.hpp include/seqan3/utility/type_pack/traits.hpp include/seqan3/utility/type_traits/all.hpp include/seqan3/utility/type_traits/basic.hpp @@ -663,7 +528,7 @@ include/seqan3/utility/type_traits/concept.hpp include/seqan3/utility/type_traits/detail/transformation_trait_or.hpp include/seqan3/utility/type_traits/function_traits.hpp include/seqan3/utility/type_traits/lazy_conditional.hpp -include/seqan3/utility/type_traits/pre.hpp +include/seqan3/utility/views/all.hpp include/seqan3/utility/views/chunk.hpp include/seqan3/utility/views/convert.hpp include/seqan3/utility/views/deep.hpp