Releases · seqan/seqan3

22 Jan 11:59

eseiler

3.4.0-rc.3

c8e7fdb

SeqAn 3.4.0-rc.3 Pre-release

Pre-release

This is the third release candidate for SeqAn 3.4.0

What's Changed

[INFRA] Bump RC by @eseiler in #3317
[INFRA] Make packaging easier by @eseiler in #3318
[INFRA] Update CPM Packages by @seqan-actions in #3316
[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

Full Changelog: 3.4.0-rc.2...3.4.0-rc.3

Notes for package maintainers

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.

Contributors

eseiler and seqan-actions

Assets 6

13 Dec 17:48

eseiler

3.4.0-rc.2

7ee8398

SeqAn 3.4.0-rc.2 Pre-release

Pre-release

This is the second release candidate for SeqAn 3.4.0

What's Changed

Click to expand

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

Contributors

SGSSGene, rrahn, and 4 other contributors

Assets 6

22 Jan 16:44

eseiler

3.4.0-rc.1

ee718d0

SeqAn 3.4.0-rc.1 Pre-release

Pre-release

This is the first release candidate for SeqAn 3.4.0

SeqAn 3.4.0 offers support for GCC 11/12/13, and new clang 17

Changelog

Assets 6

17 Aug 11:13

eseiler

3.3.0

6b681fb

SeqAn 3.3.0 Latest

Latest

We are glad to announce the SeqAn 3.3.0 release that has a major compiler update:

We dropped GCC 10 and we added GCC 13 support.

While we will present essential changes of the 3.3.0 release in this message, you can also find a comprehensive list of the changes in our changelog.

Get to know SeqAn3 with our tutorials.
Visit our API documentation.
Check out our SeqAn3 Cookbook with all the copy & paste snippets you need.

🎉 New Features

Alignment

The function seqan3::alignment_from_cigar creates an alignment from a CIGAR vector (#3057) or a CIGAR string (#3077).
The function seqan3::cigar_from_alignment creates a CIGAR vector from an alignment (#3057).

Alphabet

Improved performance of vector assignment for alphabets by a factor 2.5 (#3038).
Improved performance of seqan3::dna4::complement() (#3026).
Char literals returning std::vector are now constexpr if supported by the compiler (#3073).

I/O

Made seqan3::sam_file_header::program_info_t easier to copy (#3145).
Reading SAM/BAM files is 2x faster than before (#3106).

Search

The uncompressed seqan3::interleaved_bloom_filter (IBF) can now be constructed from a compressed IBF (#3082).

🐛 Notable bug fixes

Alignment

Resolved an issue resulting in a wrong alignment score (#3098).

I/O

Fixed writing an empty SAM-BAM file resulting in an invalid file (#3081).
seqan3::sequence_file_input_traits now allows char as a sequence alphabet (#3128).

Utility

Fixed spin delay having no effect on the PowerPC platform (#3129).

🛠️ Notable API changes

Alignment

The fields seqan3::field::offset and seqan3::field::alignment have been removed from seqan3::sam_record (#3058, #3089).
For seqan3::field::offset, please check the soft clipping of the CIGAR string (seqan3::sam_record::cigar()).
For seqan3::field::alignment, please use seqan3::alignment_from_cigar.

🔌 External dependencies

Dropped support for GCC 10 (#3148).
Added support for GCC 13 (#3148).
We require at least CMake 3.16 for our test suite. Note that the minimum requirement for using SeqAn3 is unchanged (#3050).
We now use Doxygen version 1.9.6 to build our documentation (#3116).
Updated sdsl-lite to 3.0.3 (#3170, #3174).
Compatibility with SeqAn2: SeqAn2's namespace was changed from seqan to seqan2. For interoperability, an up-to-date checkout of SeqAn2's main branch is required (#3156).

Assets 6

09 Aug 16:59

eseiler

3.3.0-rc.2

05c4347

SeqAn 3.3.0-rc.2 Pre-release

Pre-release

This is the second release candidate for SeqAn 3.3.0

Changelog

Assets 6

17 Jul 10:36

eseiler

3.3.0-rc.1

3423ad5

SeqAn 3.3.0-rc.1 Pre-release

Pre-release

This is the first release candidate for SeqAn 3.3.0

Changelog

Assets 6

20 Jun 14:03

eseiler

3.2.0

84938ed

SeqAn 3.2.0

We are excited to announce the SeqAn 3.2.0 release that has a major compiler update:

We dropped GCC 7, GCC 8, and GCC 9 and we added GCC 12 support.

As a consequence, we also dropped C++17 support and are fully C++20 compatible.

Furthermore, we could drop the range-v3 dependency completely, so be sure to delete the submodule after updating to SeqAn 3.2.0!

While we will present essential changes of the 3.2.0 release in this message, you can also find a comprehensive list of the changes in our changelog.

Get to know SeqAn3 with our tutorials.

Visit our API documentation.
See the porting guide for some help on porting from SeqAn2.
Check out our SeqAn3 Cookbook. It contains a listing of code examples on how to perform particular tasks using the library.

🎉 New Features

We added GCC 12 support!

Alphabet

seqan3::cigar can now be assigned from std::string_view which is much faster (no allocations) than the former assignment from seqan3::small_string.
The new view seqan3::views::char_strictly_to behaves like seqan3::views::char_to, but throws on invalid input.

I/O

The new option seqan3::sequence_file_option::fasta_ignore_blanks_before_id lets you keep blanks before IDs when reading FASTA files.
This ensures a "perfekt roundtrip" when reading and writing FASTA files.
E.g., fasta_ignore_blanks_before_id = true (default): > some_id will only store "some_id" as ID.
E.g., fasta_ignore_blanks_before_id = false: > some_id will store " some_id" as ID.

Search

Improved performance of seqan3::counting_vector::operator+= by 25%.

Utility

Added seqan3::list_traits::repeat.

🛠️ Notable API changes

seqan3::views::to is no view anymore but C++23 conform

We replaced seqan3::views::to (implemented via range-v3) with seqan3::ranges::to (implemented in SeqAn3). seqan3::ranges::to provides a subset of C++23's std::ranges::to and will be replaced with the STL-equivalent in a future version.
Since it is not a view anymore, it cannot be properly deprecated. Please keep this in mind if you encounter errors with seqan3::views::to.

Example:

auto vec = std::views::iota(0, 10) | seqan3::views::to<std::vector>; // Before
auto vec = std::views::iota(0, 10) | seqan3::ranges::to<std::vector>(); // After

Removed several headers in seqan3/std/

All headers in seqan3/std/ except charconv and new have been deprecated, since their STL-equivalents are available in GCC >= 10. Please use the equivalent std includes.

Example:

// Before
#include <seqan3/std/bit>
#include <seqan3/std/charconv>
// After
#include <bit>
#include <seqan3/std/charconv>

Removed namespace std::cpp20

The namespace std::cpp20 has been deprecated, since, e.g., the implementation of the std::back_inserter among others are now C++20-conform with GCC >= 10. Please use the std:: namespace.

Example:

std::ranges::copy(range, std::cpp20::back_inserter(other_range)); // Before
std::ranges::copy(range, std::back_inserter(other_range)); // After

🐛 Notable bug fixes

Core

Added missing implementations for AVX512 .

IO

FASTA files containing IDs starting with >, e.g., > >MyID, are now parsed correctly.

Search

Relaxed kmer_hash_view::iterator difference requirement .
Relaxed seqan3::views::minimiser requirements to be C++20-compatible.
Relaxed seqan3::views::kmer_hash requirements to be C++20-compatible.

Utility

seqan3::views::single_pass_input cannot propagate the std::ranges::output_range property because it cannot satisfy the following requirement:
```
*it++ = value;
// must be the same as
*it = value; ++it;
// but it actually would be the same as
++it; *it = value;
```
Fixed signature of seqan3::detail::store_sse4. This might have affected some public API.
Relaxed seqan3::views::to_simd requirements to be C++20-compatible.

🔌 External dependencies

GCC 7, 8, and 9 have been removed.
SeqAn 3.2.0 is known to compile with GCC 10.3, 11.3, and 12.1. Future versions might work, but were not yet available at the time of this release.
Other compilers, e.g., clang, and MSVC, are known to not be compatible with SeqAn 3.2.0.
We removed range-v3, and now require cereal 1.3.2 as well as sdsl-lite 3.0.1.
We use doxygen 1.9.4 to build our documentation.

Assets 6

15 Jun 18:11

eseiler

3.2.0-rc.1

1148ce1

SeqAn 3.2.0-rc.1 Pre-release

Pre-release

This is the first release candidate for SeqAn 3.2.0

You can find a list of changes in our changelog.

Notable API-changes (not final)

We removed the std::cpp20 namespace. We use std instead, since all supported compilers provide the C++20 versions of the entities we used with std::cpp20.
We replaced seqan3::views::to with seqan3::range::to. As planned for C++23, it is no longer a view, but a function object. seqan3::views::to<std::vector> changes to seqan3::range::to<std::vector>().

Dependencies

cereal bumped to 1.3.2
sdsl-lite bumped to 3.0.1
range-v3 removed
For documentation: doxygen bumped to 1.9.4

Assets 6

11 Nov 08:45

eseiler

3.1.0

4668203

SeqAn 3.1.0

We are thrilled to announce the SeqAn 3.1.0 release with the first stable SeqAn module: Alphabet

The Alphabet module is the foundation of SeqAn, thoroughly used and tested in other modules as well as external projects (e.g. raptor). We are confident to release the code with few exceptions as the first stable module of SeqAn3.
Check out notes about our API stability or the API documentation for more details.

In the upcoming future we strive to let the other modules follow suit.

While we will present essential changes of the 3.1.0 in this message, you can also find a comprehensive list of the changes in our changelog.

Get to know SeqAn3 with our tutorials.

Visit our API documentation.
See the porting guide for some help on porting from SeqAn2.
Check out our SeqAn3 Cookbook. It contains a listing of code examples on how to perform particular tasks using the library.

🔒 API Stability

With few exceptions, the Alphabet module of SeqAn3 is now stable. Additionally, the following entities are marked stable in this release:

seqan3::kmer_hash - A view to compute all k-mers of a sequence
seqan3::minimiser - A view to compute minimisers of a sequence

While 3.0.3 only deprecated entities, the affected items are removed in 3.1.0!

If you are upgrading from an older version than 3.0.3, we strongly recommend first upgrading to 3.0.3, and afterwards to 3.1.0. The version 3.0.3 contains deprecation notices that will help you to transition with ease.

🛠️ Notable API changes

There are no API changes upgrading from 3.0.3. See the 3.0.3 release message for an overview of previous changes.

🐛 Notable bug fixes

The seqan3::fm_index/seqan3::bi_fm_index correctly index large texts like the human genome.

🔌 External dependencies

SeqAn 3.1.0 is known to compile with GCC 7.5, 8.4, 9.4, 10.3, and 11.2. Future versions might work, but were not yet available at the time of this release.
Other compilers, e.g. GCC 12 (currently in development), clang, and MSVC, are known to not be compatible with SeqAn 3.1.0.
We support ranges-v3 versions ≥ 0.11.0 and < 0.12.0, sdsl-lite 3.0.0, and cereal 1.3.0.
We use doxygen 1.9.2 to build our documentation.

Assets 6

09 Aug 10:53

eseiler

3.1.0-rc.1

4604f1b

SeqAn 3.1.0-rc.1 Pre-release

Pre-release

This is the first release candidate for SeqAn 3.1.0

You can find a list of changes in our changelog.

Assets 6

Releases: seqan/seqan3

SeqAn 3.4.0-rc.3

What's Changed

Notes for package maintainers

Alternative zlib implementation

Dependencies

Post install tests

Contributors

SeqAn 3.4.0-rc.2

What's Changed

Contributors

SeqAn 3.4.0-rc.1

SeqAn 3.3.0

🎉 New Features

Alignment

Alphabet

I/O

Search

🐛 Notable bug fixes

Alignment

I/O

Utility

🛠️ Notable API changes

Alignment

🔌 External dependencies

SeqAn 3.3.0-rc.2

SeqAn 3.3.0-rc.1

SeqAn 3.2.0

🎉 New Features

Alphabet

I/O

Search

Utility

🛠️ Notable API changes

seqan3::views::to is no view anymore but C++23 conform

Removed several headers in seqan3/std/

Removed namespace std::cpp20

🐛 Notable bug fixes

Core

IO

Search

Utility

🔌 External dependencies

SeqAn 3.2.0-rc.1

Notable API-changes (not final)

Dependencies

SeqAn 3.1.0

🔒 API Stability

🛠️ Notable API changes

🐛 Notable bug fixes

🔌 External dependencies

SeqAn 3.1.0-rc.1