For reference, you can have a look at the Debian package.

Alternative zlib implementation

If your distribution ships an alternative zlib library, for example, zlib-ng, some tests will fail:

The following tests FAILED:
        164 - contrib/stream/gz_ostream_test (Failed)
        166 - contrib/stream/bgzf_ostream_test (Failed)
        203 - io/sam_file/sam_file_output_test (Failed)
        210 - io/sequence_file/sequence_file_output_test (Failed)
        224 - io/structure_file/structure_file_output_test (Failed)

This is because we are testing compression separately for some file formats and the expected output refers to (vanilla) zlib's output.
zlib-ng should be automatically detected and causes those checks to be skipped.
If this is not the case, or you are using another zlib alternative, you can manually skip those checks:

cmake <...> -DCMAKE_CXX_FLAGS="-DSEQAN3_TEST_SKIP_ZLIB_DEFLATE=1"

Dependencies

Dependencies are listed in cmake/package-lock.cmake.
We now use CPM for dependency management.

To use locally installed packages, pass -DCPM_USE_LOCAL_PACKAGES=ON to cmake, or set the environment variable CPM_USE_LOCAL_PACKAGES to ON. CPM documentation

If your locally installed packages has an older version, you may need to additionally pass the version to cmake.
The version variables can be found in cmake/package-lock.cmake.
For example, let's assume your googletest version is 1.14.0 instead of 1.15.2 listed in the package-lock.cmake.
CPM (or rather CMake's find_package) would not use your local version because 1.14.0 < 1.15.2.
Passing -DSEQAN3_GOOGLETEST_VERSION=1.14.0 to CMake will result in your local package being used.
If your local package version is newer, it should be used without any additional CMake arguments.

Post install tests

To configure tests with an installed seqan3 version, CPM needs to be available.
However, CPM isn't installed when seqan3 is installed.
To still configure the tests, you have to pass -DSEQAN3_TEST_CPM_DIR=<path> to your CMake command.
For example, -DSEQAN3_TEST_CPM_DIR=${SEQAN3_PACKAGE_SOURCE_DIRECTORY}/cmake ${SEQAN3_PACKAGE_SOURCE_DIRECTORY}/test/unit.
Where SEQAN3_PACKAGE_SOURCE_DIRECTORY is the downloaded source package.
SEQAN3_TEST_CPM_DIR points to the directory containing CPM.cmake.

• [MISC] Bump version by @eseiler in #3187
• [INFRA] Update contrib/std by @eseiler in #3189
• [INFRA] Update contrib by @eseiler in #3194
• [FEATURE] Clang support by @eseiler in #3195
• [FIX] Duplicate symbols by @eseiler in #3196
• [INFRA] Doxygen by @eseiler in #3197
• [FIX] API tests by @eseiler in #3199
• [DOC,INFRA] Doxygen groups by @eseiler in #3200
• [DOC] Fix alignment_result doc by @eseiler in #3204
• [FIX] std::result_of_t by @eseiler in #3208
• [FEATURE] libc++ support by @eseiler in #3209
• [FIX] libc++: header tests by @eseiler in #3210
• [FIX] libc++: performance tests by @eseiler in #3211
• [FIX] Disable SeqAn2 OpenMP benchmark on clang by @eseiler in #3214
• [INFRA] Add macOS libc++ CI by @eseiler in #3213
• [FIX] libc++: snippet tests by @eseiler in #3212
• [DOC] multiple use of section label by @eseiler in #3216
• fix: workaround compiling with debug mode by @SGSSGene in #3222
• [INFRA] Bump minimal CMake version by @eseiler in #3223
• [INFRA] Update documentation directory by @eseiler in #3226
• 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
• [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
• 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] Add CodeQL CI by @eseiler in #3306
• [FIX] CodeQL reports by @eseiler in #3307
• [INFRA] Add CodeChecker by @eseiler in #3310
• [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
• [INFRA] Bump RC by @eseiler in #3317
• [INFRA] Make packaging easier by @eseiler in #3318
• [FIX] cpp26: std::is_trivial_v is deprecated by @eseiler in #3319
• [DOC] Update by @eseiler in #3320
• [INFRA] Sanitizer CI by @eseiler in #3321
• [FIX,TEST] Do not check zlib output for alternative implementations by @eseiler in #3324
• [INFRA] Bump RC version by @eseiler in #3326
• [DOC] Update copyright year by @eseiler in #3327
• [INFRA] Update stl by @eseiler in #3328
• [MISC] Remove workarounds by @eseiler in #3329
• [INFRA,DOC] Update doxygen webtags by @eseiler in #3330
• [FIX] API stability by @eseiler in #3331
• [FIX] CodeQL warnings by @eseiler in #3332
• [INFRA] Debian cron by @eseiler in #3333
• [INFRA] Put SDSL into contrib by @eseiler in #3334
• [TEST] Cleanup header tests by @eseiler in #3336
• [INFRA] Cleanup CI by @eseiler in #3338
• [FIX] Cron sed command by @eseiler in #3339
• [FIX] std::is_trivial is deprecated (sdsl) by @eseiler in #3340
• [INFRA] Buildsystem by @eseiler in #3337
• [INFRA] SeqAn2 release and cache action by @eseiler in #3343
• [INFRA,FIX] latest library sed by @eseiler in #3344
• [FIX] Do not find_package yourself by @eseiler in #3345
• [DOC] Tutorial typos and codeblocks by @eseiler in #3346
• [FIX] compressed stream's overflow by @eseiler in #3349
• [FIX] Bogus warning on gcc-15 with hardened flags by @eseiler in #3350
• [INFRA] Update codechecker by @eseiler in #3351
• patch: Update SDSL to latest master by @SGSSGene in #3353
• [INFRA] Set default SEQAN3_GENERATE_SNIPPETS to OFF by @eseiler in #3356
• Feat/deprecate stuff by @SGSSGene in #3354
• fix: include alignment printer in debug_stream.h by @SGSSGene in #3355
• [MISC] Separate Bloom Filter strong types by @eseiler in #3357
• [MISC] Update sdsl to latest master by @eseiler in #3358
• [FIX,TEST] API by @eseiler in #3359
• [FIX] gcc15: conditionally borrowed_range views by @eseiler in #3360
• [FIX,INFRA] cmake: version variables cannot be forced by @eseiler in #3361
• [INFRA] Update CI by @eseiler in #3367
• [FIX] C++26: std::optional is a view by @eseiler in #3368
• [FIX] missing include by @eseiler in #3369
• [FIX] Unused variable by @eseiler in #3371
• [INFRA] Draft release on tag by @eseiler in #3375
• [DOC] Link check and doxygen-web-tags update by @eseiler in #3376
• [INFRA] Bump version by @eseiler in #3377