chore: upgrade deps

[ivan-aksamentov]

Depends on: #168

Upgrade all deps except noodles, which has unreasonable amount of changes and everything becomes broken. We should try and upgrade it too sometimes.

[Copilot]

Pull Request Overview

This PR upgrades various dependencies across the project, except for the noodles dependency which remains unchanged to avoid breaking changes. The upgrade includes updating Rust crates, build dependencies, and related schema generation tooling.

• Upgrades core dependencies like bzip2, flate2, libz-sys, and many others to their latest versions
• Updates the schemars crate from an alpha version to a stable release, requiring method name changes
• Modifies JSON schema generation patterns to use more restrictive pattern-based properties

Reviewed Changes

Copilot reviewed 8 out of 10 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
Cargo.toml	Updates workspace dependencies to latest versions
packages/minimap2-sys/Cargo.toml	Updates build dependencies and removes unnecessary features
packages/pangraph/src/representation/seq_char.rs	Updates method name for schemars compatibility
packages/pangraph/src/representation/seq.rs	Updates method name for schemars compatibility
packages/pangraph/src/io/file.rs	Updates logging format to remove deprecated syntax
packages/pangraph-schemas/Pangraph.schema.json	Adds pattern properties and stricter validation
packages/pangraph-schemas/README.md	Updates output filename in documentation
packages/pangraph-schemas/python/Pangraph_model.py	Regenerated model with updated timestamp and new field

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[mmolari]

Thank you! I tested locally an everything seems to work, and I also launched the benchmarking pipeline to double-test.

I also tried looking into noodles and you're right, it seems like they changed quite some parts of the interface with Cigar strings... Might be a bit of a pain to re-make it compatible but I can give it a try at some point.

[ivan-aksamentov]

I am thinking maybe we don't need changelog? I did not plan to release it, because it's an internal change. Users technically don't even need to know we use Rust - all they get is an opaque binary executable, which works basically the same regardless of Rust version.

I leave it up to you to decide!

[mmolari]

I am thinking maybe we don't need changelog?

Ah maybe you're right. I also wasn't thinking of releasing, it was mostly to keep track of added changes for the next release. But you're right that this is a technical change that probably doesn't need to be reported... Then I'm ok with removing it, sorry for adding it!