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biology/seqan3: update 3.3.0 → 3.4.0 

Reported by:	portscout
This commit is contained in:
Yuri Victorovich 2025-08-28 12:26:31 -07:00
parent c669bf1c7a
commit 2bf6663f53
4 changed files with 40 additions and 132 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

17
biology/seqan3/Makefile
View File

@ -1,10 +1,16 @@
PORTNAME= seqan3
DISTVERSION= 3.3.0
DISTVERSION= 3.4.0
CATEGORIES= biology devel math
MASTER_SITES= https://github.com/cpm-cmake/CPM.cmake/releases/download/v0.42.0/:cpm
DISTFILES= CPM.cmake:cpm
DIST_SUBDIR= ${PORTNAME}-${DISTVERSION}
EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} \
xxsds-sdsl-lite-d54d389_GH0${EXTRACT_SUFX}
MAINTAINER= yuri@FreeBSD.org
COMMENT= C++ header-only library for biological sequence analysis
WWW= https://github.com/seqan/seqan3
WWW= https://www.seqan.de/ \
https://github.com/seqan/seqan3
LICENSE= BSD3CLAUSE
LICENSE_FILE= ${WRKSRC}/LICENSE.md
@ -15,14 +21,13 @@ BUILD_DEPENDS= ${HPP_DEPENDS}
RUN_DEPENDS= ${HPP_DEPENDS} \
coin-or-lemon>0:math/lemon
USES= cmake localbase
USES= cmake compiler:c++23-lang localbase
USE_GITHUB= yes
GH_ACCOUNT= seqan
GH_TUPLE= xxsds:sdsl-lite:d54d389:sdsl_lite/submodules/sdsl-lite
USE_GCC= yes # tests only pass with gcc, see https://github.com/seqan/seqan3/issues/2643, otherwise gcc isn't needed because this is a header-only library
# tests fail to compile, see https://github.com/seqan/seqan3/issues/3191
CMAKE_ARGS= -DCPM_LOCATION=${DISTDIR}/${DIST_SUBDIR}
TEST_WRKSRC= ${WRKSRC}/.test
@ -33,7 +38,7 @@ post-install:
do-test:
@${MKDIR} ${TEST_WRKSRC} && cd ${TEST_WRKSRC} && \
${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} ${WRKSRC}/test/unit && \
${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DFETCHCONTENT_FULLY_DISCONNECTED=OFF ${WRKSRC}/test/unit && \
${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \
ctest

12
biology/seqan3/distinfo
View File

@ -1,5 +1,7 @@
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
TIMESTAMP = 1756395731
SHA256 (seqan3-3.4.0/CPM.cmake) = 2020b4fc42dba44817983e06342e682ecfc3d2f484a581f11cc5731fbe4dce8a
SIZE (seqan3-3.4.0/CPM.cmake) = 44969
SHA256 (seqan3-3.4.0/seqan-seqan3-3.4.0_GH0.tar.gz) = 8e000e6788f1e2ada071b36f64231d56f18e2d687ab4122d86cd3aefc6c87743
SIZE (seqan3-3.4.0/seqan-seqan3-3.4.0_GH0.tar.gz) = 1749810
SHA256 (seqan3-3.4.0/xxsds-sdsl-lite-d54d389_GH0.tar.gz) = eaac28144b34a833afb8c03139abbe427d4b95a827bf5b9b6532353f9cff9ec1
SIZE (seqan3-3.4.0/xxsds-sdsl-lite-d54d389_GH0.tar.gz) = 1183835

11
biology/seqan3/files/patch-cmake_CPM.cmake Normal file
View File

@ -0,0 +1,11 @@
--- cmake/CPM.cmake.orig 2025-08-28 15:36:29 UTC
+++ cmake/CPM.cmake
@@ -16,7 +16,7 @@ get_filename_component (CPM_DOWNLOAD_LOCATION ${CPM_DO
# Expand relative path. This is important if the provided path contains a tilde (~)
get_filename_component (CPM_DOWNLOAD_LOCATION ${CPM_DOWNLOAD_LOCATION} ABSOLUTE)
-file (DOWNLOAD https://github.com/cpm-cmake/CPM.cmake/releases/download/v${CPM_DOWNLOAD_VERSION}/CPM.cmake
+file (DOWNLOAD file://${CPM_LOCATION}/CPM.cmake
${CPM_DOWNLOAD_LOCATION} EXPECTED_HASH SHA256=${CPM_HASH_SUM})
include (${CPM_DOWNLOAD_LOCATION})

132
biology/seqan3/pkg-plist
View File

@ -91,6 +91,7 @@ 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/hamming_scoring_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
@ -191,11 +192,16 @@ 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/sdsl-lite.hpp
include/seqan3/contrib/std/.clang-format
include/seqan3/contrib/std/.gitignore
include/seqan3/contrib/std/LICENSE
include/seqan3/contrib/std/LICENSE.md
include/seqan3/contrib/std/LICENSES/BSD-3-Clause.txt
include/seqan3/contrib/std/LICENSES/CC-BY-4.0.txt
include/seqan3/contrib/std/LICENSES/CC0-1.0.txt
include/seqan3/contrib/std/README.md
include/seqan3/contrib/std/all_view.hpp
include/seqan3/contrib/std/chunk_by_view.hpp
include/seqan3/contrib/std/chunk_view.hpp
include/seqan3/contrib/std/concepts.hpp
include/seqan3/contrib/std/detail/adaptor_base.hpp
@ -203,7 +209,9 @@ 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/movable_box.hpp
include/seqan3/contrib/std/detail/non_propagating_cache.hpp
include/seqan3/contrib/std/enumerate_view.hpp
include/seqan3/contrib/std/join_with_view.hpp
include/seqan3/contrib/std/pair.hpp
include/seqan3/contrib/std/to.hpp
@ -239,14 +247,13 @@ 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/default_printer.hpp
include/seqan3/core/debug_stream/detail/to_string.hpp
include/seqan3/core/debug_stream/optional.hpp
include/seqan3/core/debug_stream/range.hpp
include/seqan3/core/debug_stream/tuple.hpp
include/seqan3/core/debug_stream/variant.hpp
include/seqan3/core/detail/all.hpp
include/seqan3/core/detail/all_view.hpp
include/seqan3/core/detail/copyable_wrapper.hpp
include/seqan3/core/detail/customisation_point.hpp
include/seqan3/core/detail/deferred_crtp_base.hpp
include/seqan3/core/detail/empty_type.hpp
@ -364,127 +371,10 @@ include/seqan3/search/views/minimiser.hpp
include/seqan3/search/views/minimiser_hash.hpp
include/seqan3/std/charconv
include/seqan3/std/new
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
include/seqan3/submodules/sdsl-lite/include/sdsl/bits.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_algorithm.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_g.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_gg.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_sada.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/cereal.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/coder.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/coder_comma.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/coder_elias_delta.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/coder_elias_gamma.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/coder_fibonacci.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/config.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/construct.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/construct_bwt.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/construct_config.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/construct_isa.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/construct_lcp.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/construct_lcp_helper.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/construct_sa.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/construct_sa_se.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/csa_alphabet_strategy.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/csa_bitcompressed.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/csa_sada.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/csa_sampling_strategy.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/csa_wt.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/cst_fully.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/cst_iterators.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/cst_sada.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/cst_sct3.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/dac_vector.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/divsufsort.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/enc_vector.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/fast_cache.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/hyb_vector.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector_buffer.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector_mapper.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/inv_perm_support.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/io.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/iterators.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/k2_treap.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/k2_treap_algorithm.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/k2_treap_helper.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/k2_tree.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/k2_tree_helper.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/lcp.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_bitcompressed.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_byte.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_dac.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_support_sada.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_support_tree.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_support_tree2.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_vlc.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_wt.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/louds_tree.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/memory_management.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/memory_tracking.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/nearest_neighbour_dictionary.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/nn_dict_dynamic.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/platform.hpp
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
include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_succinct_sada.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_succinct_sct.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_support.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_support_sparse_table.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/rrr_helper.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/rrr_vector.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/rrr_vector_15.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/sd_vector.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/sdsl_concepts.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/select_support.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/select_support_mcl.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/select_support_scan.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/sfstream.hpp
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/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
include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_tree_algorithm.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_tree_helper.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_trees.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/uint128_t.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/uint256_t.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/uintx_t.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/util.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/vectors.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/vlc_vector.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/wavelet_trees.hpp
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
include/seqan3/submodules/sdsl-lite/include/sdsl/wt_hutu.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/wt_int.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/wt_pc.hpp
include/seqan3/submodules/sdsl-lite/include/sdsl/wt_rlmn.hpp
include/seqan3/utility/all.hpp
include/seqan3/utility/bloom_filter/all.hpp
include/seqan3/utility/bloom_filter/bloom_filter.hpp
include/seqan3/utility/bloom_filter/bloom_filter_strong_types.hpp
include/seqan3/utility/char_operations/all.hpp
include/seqan3/utility/char_operations/predicate.hpp
include/seqan3/utility/char_operations/predicate_detail.hpp