SeqAn 3.4.0-rc.2

This is the second release candidate for SeqAn 3.4.0

What's Changed

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• Bump actions/cache from 3 to 4 by @dependabot in #3224
• [INFRA] Update documentation directory by @eseiler in #3226
• Bump peter-evans/create-or-update-comment from 3 to 4 by @dependabot in #3228
• Patch/copyrightyear update by @SGSSGene in #3229
• [INFRA] Add IntelLLVM CI by @eseiler in #3225
• [INFRA] Rename master to main by @eseiler in #3230
• [FIX] Documentation by @eseiler in #3231
• [INFRA] Check markdown files for doxygen by @eseiler in #3233
• [DOC] Improve version selector by @eseiler in #3234
• doc,fix: variable bgzf_thread_count is no longer static by @SGSSGene in #3238
• [FIX] CPP23 by @eseiler in #3240
• [MISC] gcc 14 workaorund by @eseiler in #3241
• fix,doc: condition of the max number of 1s inside a shape. by @SGSSGene in #3243
• [MISC] Remove gcc14 workaround by @eseiler in #3245
• [MISC] Improve error message when using kmer_hash_view with invalid shapes by @eseiler in #3244
• [FEATURE] Allow setting warning stream for sam file by @eseiler in #3246
• [DOC] unknown tags will not throw by @eseiler in #3247
• Bump fsfe/reuse-action from 2 to 3 by @dependabot in #3249
• [FIX] Missing include by @eseiler in #3252
• Refactor selection of Myers' bitparallel edit distance algorithm. by @rrahn in #3254
• [MISC] Refine unknown tag handling (HD/PG) by @eseiler in #3248
• [FIX] clang-18 by @eseiler in #3257
• [INFRA] Update SDSL by @eseiler in #3260
• [INFRA] Update contrib/std by @eseiler in #3261
• [FIX] Correctly propagate the constness of the inner range type. by @rrahn in #3262
• Bump fsfe/reuse-action from 3 to 4 by @dependabot in #3263
• Fixes #3266: Incorrect begin/end of alignment for banded alignment by @rrahn in #3269
• Fix/issue_3264 by @rrahn in #3268
• [INFRA] CI and Compilers by @eseiler in #3270
• [FIX] Codecov by @eseiler in #3274
• [INFRA] Documentation preview by @eseiler in #3273
• [DOC] Remove vercel by @eseiler in #3275
• [MISC] clang-format-18 by @eseiler in #3276
• [INFRA] Nightly fixes by @eseiler in #3277
• [FIX] gcc-15: Better bogus memcpy fix by @eseiler in #3278
• Adds missing char8_t type to list of viable char types for which char adaption works. by @rrahn in #3279
• [INFRA] API Stability by @eseiler in #3281
• Updated PR for the printer design proposal by @rrahn in #3259
• [FEATURE] Accept user-defined tags by @eseiler in #3256
• [FIX] API tests by @eseiler in #3284
• Use explicit _MM_PERM_ENUM type for intrinsics. by @rrahn in #3285
• [INFRA] Use macos-14 by @eseiler in #3287
• [INFRA] Fail CI if ctest finds no tests by @eseiler in #3290
• [MISC] Add -Wnrvo warning by @eseiler in #3289
• [INFRA] Acknowledge CMake 3.30 policies by @eseiler in #3291
• [INFRA] Use CPM by @eseiler in #3288
• [INFRA] Rename build_system to cmake by @eseiler in #3292
• [FIX] CI by @eseiler in #3293
• [FIX,INFRA] Cron: Always create comment body by @eseiler in #3294
• [INFRA] Remove GIT_TAG for URL download by @eseiler in #3295
• [INFRA] CPM find_package and package update cron by @eseiler in #3296
• [INFRA] Add clang-19 by @eseiler in #3298
• [INFRA] Extend SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY by @eseiler in #3297
• [FIX] sam_file_output by @eseiler in #3300
• [FIX] ciso646 is deprecated by @eseiler in #3302
• fix, doc: we don't have to talk about submodules anymore by @SGSSGene in #3301
• [TEST] Skip parallel tests on machines having a single CPU by @sanvila in #3303
• [INFRA] Update CPM Packages by @seqan-actions in #3304
• Bump fsfe/reuse-action from 4 to 5 by @dependabot in #3305
• [INFRA] Add CodeQL CI by @eseiler in #3306
• [FIX] CodeQL reports by @eseiler in #3307
• [INFRA] Update CPM Packages by @seqan-actions in #3308
• [INFRA] Add CodeChecker by @eseiler in #3310
• [INFRA] Update CPM Packages by @seqan-actions in #3311
• [FIX] version check URL, default for prompt by @eseiler in #3312
• [INFRA] Bump CMake by @eseiler in #3314
• [MISC] Use cpp23 by @eseiler in #3313
• [INFRA] Bump RC by @eseiler in #3315

Full Changelog: 3.4.0-rc.1...3.4.0-rc.2