Migrate xz2 to liblzma (#78)

* Honor individual compression features

* Migrate xz2 dep to liblzma

* Migrated xz2 to liblzma

* Update deps, update PyO3 to use new &Bound syntax

* Update flate2

Cargo.toml

@@ -20,15 +20,16 @@ default = ["compression"]
 compression = ["bzip2", "flate2", "xz2"]
 python = ["pyo3/extension-module"]
 python_test = ["pyo3"]
+xz2 = ["liblzma"]
 
 [dependencies]
 buffer-redux = { version = "1", default_features = false }
 bytecount = { version = "0.6", features = ["runtime-dispatch-simd"] }
 bzip2 = { version = "0.4", optional = true }
-flate2 = { version = "1.0.6", optional = true }
-memchr = "2.2.1"
-pyo3 = { version = "0.18", optional = true }
-xz2 = { version = "0.1.6", optional = true }
+flate2 = { version = "1.0.30", optional = true }
+memchr = "2.7.2"
+pyo3 = { version = "0.21.2", optional = true }
+liblzma = { version = "0.3.1", optional = true }
 
 [dev-dependencies]
 criterion = "0.5"

src/parser/mod.rs

@@ -8,7 +8,7 @@ use bzip2::read::BzDecoder;
 #[cfg(feature = "flate2")]
 use flate2::read::MultiGzDecoder;
 #[cfg(feature = "xz2")]
-use xz2::read::XzDecoder;
+use liblzma::read::XzDecoder;
 
 use crate::errors::ParseError;
 pub use crate::parser::fasta::Reader as FastaReader;

src/python.rs

@@ -128,13 +128,13 @@ pub fn reverse_complement(seq: &str) -> String {
 }
 
 #[pymodule]
-fn needletail(py: Python, m: &PyModule) -> PyResult<()> {
+fn needletail(py: Python, m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_class::<PyFastxReader>()?;
     m.add_wrapped(wrap_pyfunction!(parse_fastx_file))?;
     m.add_wrapped(wrap_pyfunction!(parse_fastx_string))?;
     m.add_wrapped(wrap_pyfunction!(normalize_seq))?;
     m.add_wrapped(wrap_pyfunction!(reverse_complement))?;
-    m.add("NeedletailError", py.get_type::<NeedletailError>())?;
+    m.add("NeedletailError", py.get_type_bound::<NeedletailError>())?;
 
     Ok(())
 }