3.0.3 Release #2334
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SeqAn's RPM Package page in the Fedora Project is https://src.fedoraproject.org/rpms/seqan3 |
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draft release note: https://hackmd.io/DAj-lfXkQYOqbPoZZfTtEg?both see prior release: #2001 |
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create header list with: |
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Es gibt mit dem performance test noch ein paar bugs in die ich hinein gucken werde. ich hab mal alle sachen mir ausgeben lassen die ±20% schneller/langsamer sind. Vergleich 3.0.2 zu master (cca92c4) branch. click meSignifikant langsamer: click me |
This was referenced May 10, 2021
Merged
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I created a release-3.0.3 branch |
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Some CHANGELOG.md changes that were misplaced: Click me@@ -34,6 +300,13 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele
* SeqAn 3.0.2 is known to compile with GCC 7.5, 8.4, 9.3 and 10.2. Future versions (e.g. GCC 10.3 and 11) might work,
but weren’t yet available at the time of this release.
+## Notable Bug-fixes
+
+#### I/O
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+* The SAM/BAM format reads the quality field (or any other text field) that starts with an asterisk (`*`) but is not
+ empty correctly now ([\#2184](https://github.com/seqan/seqan3/pull/2184)).
+
## New features
#### Alignment
@@ -73,7 +346,7 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele
* The `seqan3::views::minimiser` has been added. This is a view that computes the minimum in a window shifted over a
range of comparable values ([\#1654](https://github.com/seqan/seqan3/pull/1654)).
* The `seqan3::views::minimiser_hash` has been added. This is a view that computes the minimisers of a range of type
- `seqan3::semialphabet` ([\#1721](https://https://github.com/seqan/seqan3/pull/1721)).
+ `seqan3::semialphabet` ([\#1721](https://github.com/seqan/seqan3/pull/1721)).
#### Search
@@ -83,6 +356,8 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele
([\#1853](https://github.com/seqan/seqan3/pull/1853)).
* Added `seqan3::search_cfg::on_result`, which allows providing a custom callback for the search algorithm
([\#2019](https://github.com/seqan/seqan3/pull/2019)).
+* The `seqan3::fm_index_cursor` and `seqan3::bi_fm_index_cursor` can be serialised
+ ([\#2048](https://github.com/seqan/seqan3/pull/2019)).
## API changes
@@ -152,7 +427,7 @@ Header Changes:
* The `seqan3::forward_range` has been removed. Use `std::ranges::borrowed_range` instead
([\#2038](https://github.com/seqan/seqan3/pull/2038)).
* The `seqan3::views:trim` has been renamed to `seqan3::views:trim_quality`
- ([\#2025](https://https://github.com/seqan/seqan3/pull/2025)).
+ ([\#2025](https://github.com/seqan/seqan3/pull/2025)).
Header Changes:
via cli: |
Merged
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In the above I was using gcc10 with Release. I retried it with "powersave" governour, so the cpu is running at a constant rate. (I checked it and it wasn't changing). But very similar results. I also tried it with gcc9 with "RelWithDbgInfo" with fixed cpu speed. Increase of Runtimes (Bad!) (factors) Click meBenchmarkfile Benchmark Time CPU
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For the Edit: How do you read the increase? Is it a factor/percentag/seconds? |
This was referenced May 20, 2021
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+1.13 means that the old benchmark needed 1s and the new one needs 2.13s. |
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Can someone tag a release candidate? I can then make experimental builds on Debian |
We're about to (in the course of the day, after https://github.com/seqan/seqan3/actions/runs/863386619 finished successfully) |
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There's a tag now https://github.com/seqan/seqan3/tree/3.0.3-rc.1 Edit: https://github.com/seqan/seqan3/releases/tag/3.0.3-rc.1 |
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seqan3-3.0.3-rc.1 tests are correctly built/ran in Fedora 34+ |
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On Debian, I've got two failing tests, probably due to being run as |
Can you run ctest with |
That worked, thanks! |
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I've uploaded Seqan3 3.0.3 to Debian's experimental archive at https://buildd.debian.org/status/package.php?p=seqan3&suite=experimental Once the next version of Debian is released I'll bump this to the development distribution where it will flow to the next testing distribution. Please let me know if there are any Seqan3 using applications ready for packaging! |
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release-[VERSION], and enable branch protection in the repository settings.platform.hpp. Are they still valid, or can they be limited to specific compiler versions?seqan3-[VERSION]-{Linux,Source}.tar.xz{,.sha265}. (Instructions)seqan3-[VERSION]-{Linux,Source}.tar.xz{,.sha265}to the release. (Instructions)[email protected].Instructions
Creating a pre-release
GitHub is not able to create annotated releases (seqan/product_backlog#159), so we have to manually sign the release.
Make sure you have set up signed commits.
git checkout release-[VERSION] git tag -s [VERSION]-rc.[RC] # e.g. 3.1.0-rc.1 git push upstream [VERSION]-rc.[RC]You will need to provide a tag message. Since this is a pre-release, it can be as simple as
Tag 3.1.0-rc.1.Now follow the packaging instructions to create
seqan3-[VERSION]-rc.[RC]-{Linux,Source}.tar.xz{,.sha265}.Go to https://github.com/seqan/seqan3/releases and create a new release using the created tag and attach the source packages.
Once again, the release message can be simply something along the lines of:
Afterwards, bump the succeeding release candidate number in the release branch: include/seqan3/version.hpp.
Updating cppreference index
Check for new releases and update the link and hash in test/documentation/seqan3-doxygen.cmake.
You can compute the hash via
wget -O- <link to html book> | sha256sum.Freezing the release branch
SEQAN3_RELEASE_CANDIDATEto0include/seqan3/version.hpp.Creating versioned documentation
/web/docs.seqan.de/htdocs/seqan/doc_usr/html/*) into the directory./web/docs.seqan.de/htdocs/seqan3.htmlwith a link to the new documentation build.Creating source packages
Use a new clone of the repository.
Note: Do not use
git clone --recurse-submodules https://github.com/seqan/seqan3.gitbecause it will recursively pull sub-submodules!Checking the changelog
[\#2540](https://github.com/seqan/seqan3/pull/2538):(\[\\#)(\d+)(\]\(.+?)(\d+)(\))and replace$1$2$3$2$5(i.e., replace link issue-id by the displayed id).Creating a release
GitHub is not able to create annotated releases (seqan/product_backlog#159), so we have to manually sign the release.
Make sure you have set up signed commits.
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)
Bumping the version
SEQAN3_RELEASE_CANDIDATEmust be set to1as0indicates a stable release.The text was updated successfully, but these errors were encountered: