chore: upgrade rust to 1.90.0

[ivan-aksamentov]

Haven't updated in a while. Should probably semi-automate this (new lints will still require manual intervention).

What attracted my attention in 1.90.0 is that lld linker is now used by default on Linux. Which also reminds me that we should play with cross-language LTO sometimes - we use rather heavy C dependency, so it could help squeezing some more perf juice out of it. Not even mentioning how cool is that to be able to link C and Rust code like it's the same thing! Need to update LLVM in the container to version 20 first though.

[Copilot]

Pull Request Overview

Upgrade Rust toolchain to 1.90.0 and adopt newly stabilized std features, removing external dependencies and modernizing syntax.

• Replace lazy_static with std::sync::LazyLock and const slices
• Introduce newer standard library conveniences (&raw mut, isize::midpoint, std::io::Error::other) and adjust formatting/error messages
• Remove unused dependency (lazy_static) and tweak lint configuration

Reviewed Changes

Copilot reviewed 20 out of 21 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
rust-toolchain.toml	Bumps toolchain to Rust 1.90.0
packages/pangraph/src/utils/lock.rs	Removes must_use on Clone impl
packages/pangraph/src/utils/float_fmt.rs	Replaces lazy_static with LazyLock
packages/pangraph/src/utils/error.rs	Simplifies iterator filter logic
packages/pangraph/src/pangraph/reweave.rs	Cleans stray semicolons after if blocks
packages/pangraph/src/pangraph/detach_unaligned.rs	Uses inline format string capture
packages/pangraph/src/io/yaml.rs	Adjusts error message path formatting
packages/pangraph/src/io/json.rs	Adjusts error message path formatting
packages/pangraph/src/io/gfa.rs	Adjusts error message path formatting
packages/pangraph/src/io/fs.rs	Adjusts directory and file error message formatting
packages/pangraph/src/io/file.rs	Adjusts file open/create error message formatting
packages/pangraph/src/io/compression.rs	Uses Error::other and removes ErrorKind import
packages/pangraph/src/commands/root_args.rs	Replaces lazy_static vector with const slice
packages/pangraph/src/circularize/merge_blocks.rs	Modern inline formatting in logs
packages/pangraph/src/align/nextclade/align_with_nextclade.rs	Replaces lazy_static with LazyLock in tests
packages/pangraph/src/align/nextclade/align/seed_alignment.rs	Uses isize::midpoint for safer average
packages/pangraph/Cargo.toml	Removes lazy_static dependency
packages/minimap2/src/options.rs	Uses &raw mut for raw pointer creation
packages/minimap2/src/map.rs	Uses &raw mut for FFI call argument
Cargo.toml	Removes lazy_static and adds new lint allowance

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[mmolari]

Very nice! Thank you for taking care of the upgrade. Everything looks good to me.
I didn't know about cross-language LTO, that is very cool!
Given that calls to minimap2 might be the most time-consuming part of the process it might be worth looking into, especially if it's a matter of just a few changes...