sourmash-bio / sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.
http://sourmash.readthedocs.io/en/latest/
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upgrade rocksdb to 0.22.0 #3383

Closed mr-c closed 1 week ago

mr-c commented 2 weeks ago

Seeing if we can upgrade to the latest rocksdb safely.

codspeed-hq[bot] commented 2 weeks ago

CodSpeed Performance Report

Merging #3383 will not alter performance

Comparing mr-c:rocksdb_0.22.0 (399776a) with latest (de1a597)

Summary

✅ 21 untouched benchmarks

mr-c commented 2 weeks ago

Ah, it would require bumping the minimum rustc version to 1.66

codecov[bot] commented 2 weeks ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 86.46%. Comparing base (de1a597) to head (399776a). Report is 2 commits behind head on latest.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## latest #3383 +/- ## ========================================== - Coverage 86.47% 86.46% -0.01% ========================================== Files 137 137 Lines 16092 16092 Branches 2219 2219 ========================================== - Hits 13915 13914 -1 - Misses 1870 1871 +1 Partials 307 307 ``` | [Flag](https://app.codecov.io/gh/sourmash-bio/sourmash/pull/3383/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=sourmash-bio) | Coverage Δ | | |---|---|---| | [hypothesis-py](https://app.codecov.io/gh/sourmash-bio/sourmash/pull/3383/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=sourmash-bio) | `25.43% <ø> (ø)` | | | [python](https://app.codecov.io/gh/sourmash-bio/sourmash/pull/3383/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=sourmash-bio) | `92.40% <ø> (ø)` | | | [rust](https://app.codecov.io/gh/sourmash-bio/sourmash/pull/3383/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=sourmash-bio) | `62.23% <ø> (-0.04%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=sourmash-bio#carryforward-flags-in-the-pull-request-comment) to find out more.

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luizirber commented 2 weeks ago

Ah, it would require bumping the minimum rustc version to 1.66

This is OK for us, we try to keep the MSRV compatible with what is available in Debian. What is the current Rust available in Debian? I usually check https://packages.debian.org/search?keywords=rustc but it is 503 now, repology says 1.63 for bookworm and up to 1.82 for trixie?

mr-c commented 2 weeks ago

Ah, it would require bumping the minimum rustc version to 1.66

This is OK for us, we try to keep the MSRV compatible with what is available in Debian. What is the current Rust available in Debian? I usually check https://packages.debian.org/search?keywords=rustc but it is 503 now,

On a Debian system, you can run rmadison rustc (or any Debian package name) to see which versions are in the official archive.

repology says 1.63 for bookworm and up to 1.82 for trixie?

And repology is also a decent source, yes 👍🏻

https://packages.ubuntu.com/rustc

Okay, shall I bump the MSRV and retry this PR?

In Debian we are getting a weird error with the older rocksdb crate, so I wanted to see if the newer version broke anything for sourmash.

https://paste.debian.net/1334814/

thread 'test_column_family_with_transactiondb' panicked at core/src/panicking.rs:221:5: unsafe precondition(s) violated: ptr::copy_nonoverlapping requires that both pointer arguments are aligned and non-null and the specified memory ranges do not overlap