3.0.2 Release

[marehr]

• Create a release branch, e.g. release-3.0.3

• Check for critical performance regressions. Use https://github.com/wvandertoorn/cmp_benchmarks

• Check Nightlies for critical build failures. Change nightlies to build on release branch.

• Check workarounds in platform.hpp. Are they still valid or can they be limited to specific compiler versions.

• Check the Changelog.md for completeness (including changed headers).

• Update the index from cppreference.com so that up-to-date documentation links are generated.

  Click for detailed steps

  
  

  Check for new releases and update the link and hash
  in the code base.

  For the hash do

  wget -O- <link to html book> | sha256sum
  

• Add versioned documentation build on docs.seqan.de.

  Click for detailed steps

  1. Build the documentation locally

  2. Create a #.#.# directory for the release in /web/docs.seqan.de/htdocs/seqan/

  3. Copy everything from the local build (doc_usr/html/*) into the directory.

  4. Alter the file /web/docs.seqan.de/htdocs/seqan3.html with a link to the new documentation build.

• Prepare seqan3-[VERSION]-{Linux,Source}.tar.xz{,.sha265}.

  Click for detailed steps

  
  

  Make a fresh clone of the repository and recursively delete the .git directories.

  mkdir package-build
  
  git clone https://github.com/seqan/seqan3.git
  cd seqan3
  
  git checkout 3.0.2 # version to pack
  
  git submodule init
  git submodule update
  
  cd ../package-build
  
  cmake ../seqan3 # configure
  
  cpack # builds binary package, e.g. seqan3-3.0.2-Linux.tar.xz{,.sha265}
  
  cmake --build . --target package_source # builds source package, e.g. seqan3-3.0.2-Source.tar.xz{,.sha265}
  

  Note: Do not do git clone -recurse-submodules https://github.com/seqan/seqan3.git because it will recursively
  pull sub-submodules which we do not want!

• Prepare a release note with notable features, API changes, bugs, and external dependency updates.

---

• Tag release on Github and attach seqan3-[VERSION]-{Linux,Source}.tar.xz{,.sha265} to the release.

  Click for detailed steps

  
  

  Github is not able to create annotated releases (Btw, next time you tag a release please add the -a flag. Otherwise git describe uses 3.0.0 as reference. product_backlog#159), so we have to manually sign the release.

  git checkout release-3.x.y
  git tag -s 3.x.y
  git push upstream 3.x.y

  You will need to provide a tag message. We use the first sentences of the release note:

  E.g. (see https://github.com/seqan/seqan3/tags)

  SeqAn 3.0.2 Release
  
  
  Despite all circumstances, we are excited to present a new update of our SeqAn library.
  We present some great new features and also a lot of usability improvements.
  Among others, this release will fully comply with the final C++-20 standard.
  
  :warning: In this release we harmonised the algorithm configurations for a better user experience.
  This, much like 2020, will break a lot of code. But rest assured that the changes are easy to apply and are worth every bit. :smile:
  
  You can find a comprehensive list of the changes in our [changelog](http://docs.seqan.de/seqan/3.0.2/about_changelog.html).
  

---

• Merge release branch into master.
• Bump succeeding version number in master. (include/seqan3/version.hpp)
• Update the SeqAn version here to ensure
  that the server in Tübingen, which takes care of the argument parser update notifications, is aware of it
  (@smehringer).
• Delete release branch.
• Announce release on twitter (https://twitter.com/seqanlib).
• Announce release on www.seqan.de.
• Announce release on mailing list seqan-dev@lists.fu-berlin.de.
• Announce release on public Gitter channel .
• Notify upstream package maintainers
  • brew (@rrahn) PR: seqan3 3.0.2 brewsci/homebrew-bio#1165
  • macports (@rrahn) PR: seqan3: new port macports/macports-ports#8769
  • conda (@eseiler)
  • debian (@mr-c)
  • fedora (@sagitter)
• add seqan3 to https://github.com/rigtorp/awesome-modern-cpp.
• update release template with the current release tasks 🍻 .
• Celebrate 🎉 🍺

[mr-c]

I would like to test a pre-release for Debian. Should I take a snapshot now, or should I wait a little longer?

[mr-c]

gcc 10.2 compatibility should be added to the Changelong

[marehr]

I would like to test a pre-release for Debian. Should I take a snapshot now, or should I wait a little longer?

I think you can do a snapshot, because of the vacation time and the current low output, there shouldn't be anything game-changing until the release.

I thought about adding a step for a (temporary) feature freeze branch, maybe called release-3.0.x, to avoid conflicting last minute changes / to allow a smooth transition between the current and the next release.

But we actually need to discuss what (final) changes we want in release 3.0.2, I guess gcc-10.2 was one of them :)

[marehr]

Hi @seqan/team,
/cc: @mr-c, @sagitter

we are in our final sprint before the next release. 🎊

We created a new branch release-3.0.2, which will act as release-candidate branch. Every PR which fixes one of our open tasks of the sprint should be created against this release-3.0.2 branch. Everything unrelated to the release should use the master branch.

This means if you work on any of those tasks you should first checkout the release-3.0.2 branch, create a new branch and then do your changes.

The workflow would be like this:

# within the seqan3 repository
git fetch upstream
git checkout upstream/release-3.0.2 # switch to the current release branch
git checkout -b <my_new_branch_name>

# ... work on my stuff, commit and push
git commit
git push origin <my_new_branch_name>

When creating a new PR make sure to select release-3.0.2 as base. (Try to avoid pulling the current master into that branch).

A short Rational:

• This will ensure that we only pull in changes that are needed for the release.
• We don't have any last-minute (unrelated) changes within our next release / merge-conflicts will be lesser.
• We have a release candidate branch that our volunteering package maintainer can use (to test their set-up)
• You can work on new things / create patches during our release (by creating PR against master).
• We'll regularly pull in the changes from the release-3.0.2 into the master.

[marehr]

• Check if all moved headers are listed in the CHANGELOG

My use case:

-#include <seqan3/alignment/configuration/align_config_scoring.hpp>
+#include <seqan3/alignment/configuration/align_config_scoring_scheme.hpp>

[joergi-w]

The list of changed header files since 3.0.1 release:

Alignment

include/seqan3/alignment/configuration/{align_config_max_error.hpp => align_config_min_score.hpp}
include/seqan3/alignment/configuration/{align_config_scoring.hpp => align_config_scoring_scheme.hpp}
include/seqan3/alignment/configuration/{align_config_vectorise.hpp => align_config_vectorised.hpp}
include/seqan3/alignment/configuration/{align_config_gap.hpp => align_config_gap_cost_affine.hpp}
include/seqan3/alignment/configuration/{align_config_mode.hpp => align_config_method.hpp}
include/seqan3/alignment/configuration/{align_config_result.hpp => align_config_score_type.hpp}

include/seqan3/alignment/configuration/align_config_aligned_ends.hpp [deleted without replacement]
include/seqan3/alignment/configuration/align_config_result_type.hpp [added as align_config_alignment_result_capture.hpp and then renamed]
include/seqan3/alignment/configuration/align_config_on_result.hpp [added]

include/seqan3/{alignment/pairwise => core/algorithm}/alignment_range.hpp
include/seqan3/{alignment/pairwise/execution => core/algorithm/detail}/alignment_executor_two_way.hpp
include/seqan3/{alignment/pairwise/execution => core/algorithm/detail}/all.hpp
include/seqan3/{alignment/pairwise/execution => core/algorithm/detail}/execution_handler_parallel.hpp
include/seqan3/{alignment/pairwise/execution => core/algorithm/detail}/execution_handler_sequential.hpp

include/seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp [added]

Argument Parser

include/seqan3/{core => argument_parser}/detail/terminal.hpp

Core

include/seqan3/core/math.hpp [added]
include/seqan3/core/semiregular_box.hpp [added]
include/seqan3/core/simd/view_iota_simd.hpp [added]

Range

include/seqan3/range/views/{trim.hpp => trim_quality.hpp}
include/seqan3/range/detail/enable_view.hpp [deleted without replacement]
include/seqan3/range/views/minimiser.hpp [added]
include/seqan3/range/views/minimiser_hash.hpp [added]

Search

include/seqan3/search/algorithm/detail/search.hpp [deleted as include/seqan3/search/detail/search.hpp]
include/seqan3/search/{algorithm => }/detail/search_common.hpp
include/seqan3/search/{algorithm => }/detail/search_scheme_algorithm.hpp
include/seqan3/search/{algorithm => }/detail/search_scheme_precomputed.hpp
include/seqan3/search/{algorithm => }/detail/search_traits.hpp
include/seqan3/search/{algorithm/detail/search_trivial.hpp => detail/unidirectional_search_algorithm.hpp}
include/seqan3/search/{algorithm => }/search.hpp
include/seqan3/search/search_result.hpp [added]
include/seqan3/{search/search_result_range.hpp => core/algorithm/algorithm_result_generator_range.hpp}

include/seqan3/search/configuration/{mode.hpp => hit.hpp}
include/seqan3/search/configuration/{max_error_rate.hpp => max_error.hpp AND max_error_common.hpp}
include/seqan3/search/configuration/on_result.hpp [added]
include/seqan3/search/configuration/result_type.hpp [added]

include/seqan3/search/dream_index/interleaved_bloom_filter.hpp [added]
include/seqan3/search/fm_index/detail/csa_alphabet_strategy.hpp [deleted, content moved to SDSL]

[mr-c]

70dff0c builds fine in Debian !

[rrahn]

Changelog TODOS:

• add missing pr links
• describe the change to invoke configuration elements without constructor arguments with a {}
• highlight seqan3::align_cfg::mode configuration
• align_cfg::on_result has beend added
• core: std::remove_cvref_t
• highlight seqan3::semialphabet
• move Change the align_cfg::max_error to align_cfg::min_score and thus prepare it for non-edit scoring schemes in the future as well (#2021) to API

Typos:

• The seqan3::format_fasta accepts the file extenstion

Important points for release note

• The seqan3::search_result_range returns now a seqan3::search_result which unifies the interface for all search instances, e.g. using an index over a single text or a text collection ([FEATURE] search result struct #1706).
• alignment configurations -> on_result
• Added seqan3::interleaved_bloom_filter, a data structure that efficiently answers set-membership queries for multiple bins ([FEATURE] binning_directory #920).
• minimiser_hash view?

[marehr]

Packaging seqan3:

• use cpack for a source package, i.e. seqan3-3.0.2-Source.tar.xz (cmake --build . --target package_source)
• use cpack for a binary package, i.e. seqan3-3.0.2-Linux.tar.xz (cpack)
• sign package:
  • see https://wiki.debian.org/Creating%20signed%20GitHub%20releases
  • https://narfation.org/2013/06/23/signed-upstream-tarballs-in-debian

[marehr]

I think most of this is done, so we can close this ticket.