chore(deps): bump the dependencies group with 7 updates

Updates the requirements on [thiserror](https://github.com/dtolnay/thiserror), [nalgebra](https://github.com/dimforge/nalgebra), [itertools](https://github.com/rust-itertools/itertools), [reqwest](https://github.com/seanmonstar/reqwest), [criterion](https://github.com/criterion-rs/criterion.rs), [pyo3](https://github.com/pyo3/pyo3) and [numpy](https://github.com/PyO3/rust-numpy) to permit the latest version.

Updates `thiserror` to 2.0.18
- [Release notes](https://github.com/dtolnay/thiserror/releases)
- [Commits](dtolnay/thiserror@1.0.0...2.0.18)

Updates `nalgebra` to 0.34.1
- [Changelog](https://github.com/dimforge/nalgebra/blob/main/CHANGELOG.md)
- [Commits](dimforge/nalgebra@v0.32.0...v0.34.1)

Updates `itertools` to 0.14.0
- [Changelog](https://github.com/rust-itertools/itertools/blob/master/CHANGELOG.md)
- [Commits](rust-itertools/itertools@v0.12.0...v0.14.0)

Updates `reqwest` to 0.13.2
- [Release notes](https://github.com/seanmonstar/reqwest/releases)
- [Changelog](https://github.com/seanmonstar/reqwest/blob/master/CHANGELOG.md)
- [Commits](seanmonstar/reqwest@v0.12.0...v0.13.2)

Updates `criterion` to 0.8.2
- [Release notes](https://github.com/criterion-rs/criterion.rs/releases)
- [Changelog](https://github.com/criterion-rs/criterion.rs/blob/master/CHANGELOG.md)
- [Commits](criterion-rs/criterion.rs@0.5.0...criterion-v0.8.2)

Updates `pyo3` to 0.27.2
- [Release notes](https://github.com/pyo3/pyo3/releases)
- [Changelog](https://github.com/PyO3/pyo3/blob/main/CHANGELOG.md)
- [Commits](PyO3/pyo3@v0.27.0...v0.27.2)

Updates `numpy` to 0.28.0
- [Release notes](https://github.com/PyO3/rust-numpy/releases)
- [Changelog](https://github.com/PyO3/rust-numpy/blob/main/CHANGELOG.md)
- [Commits](PyO3/rust-numpy@v0.27.0...v0.28.0)

---
updated-dependencies:
- dependency-name: thiserror
  dependency-version: 2.0.18
  dependency-type: direct:production
  dependency-group: dependencies
- dependency-name: nalgebra
  dependency-version: 0.34.1
  dependency-type: direct:production
  dependency-group: dependencies
- dependency-name: itertools
  dependency-version: 0.14.0
  dependency-type: direct:production
  dependency-group: dependencies
- dependency-name: reqwest
  dependency-version: 0.13.2
  dependency-type: direct:production
  dependency-group: dependencies
- dependency-name: criterion
  dependency-version: 0.8.2
  dependency-type: direct:production
  dependency-group: dependencies
- dependency-name: pyo3
  dependency-version: 0.27.2
  dependency-type: direct:production
  dependency-group: dependencies
- dependency-name: numpy
  dependency-version: 0.28.0
  dependency-type: direct:production
  dependency-group: dependencies
...

Signed-off-by: dependabot[bot] <support@github.com>

Author: dependabot[bot]

Cargo.toml

@@ -27,19 +27,19 @@ categories = [
 readme = "README.md"
 
 [dependencies]
-thiserror = "1.0"
+thiserror = "2.0"
 rayon = { version = "1.8", optional = true }
-nalgebra = { version = "0.32", optional = true }
-itertools = "0.12"
-reqwest = { version = "0.12", features = ["json", "blocking"], optional = true }
+nalgebra = { version = "0.34", optional = true }
+itertools = "0.14"
+reqwest = { version = "0.13", features = ["json", "blocking"], optional = true }
 serde = { version = "1.0", features = ["derive"], optional = true }
 serde_json = { version = "1.0", optional = true }
 flate2 = { version = "1.0", optional = true }
 tokio = { version = "1.0", features = ["rt-multi-thread", "sync", "time", "fs", "io-util", "macros"], optional = true }
 futures = { version = "0.3", optional = true }
 
 [dev-dependencies]
-criterion = "0.5"
+criterion = "0.8"
 proptest = "1.4"
 tempfile = "3.9"
 codecov = "0.4"

pdbrust-python/Cargo.toml

@@ -16,9 +16,9 @@ name = "_pdbrust"
 crate-type = ["cdylib"]
 
 [dependencies]
-pyo3 = { version = "0.27", features = ["extension-module"] }
+pyo3 = { version = "0.28", features = ["extension-module"] }
 pdbrust = { path = "..", features = ["filter", "descriptors", "quality", "summary", "gzip", "geometry", "dssp", "ligand-quality", "dockq"] }
-numpy = { version = "0.27", optional = true }
+numpy = { version = "0.28", optional = true }
 tokio = { version = "1.0", features = ["rt-multi-thread"], optional = true }
 
 [features]