build(deps): update pyo3 requirement from 0.21.2 to 0.22.2

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ggetrs"
-version = "0.1.81"
+version = "0.1.82"
 edition = "2021"
 license = "MIT"
 description = "Efficient querying of biological databases from the command line"
@@ -30,7 +30,7 @@ futures = "0.3.24"
 indicatif = "0.17.5"
 mysql = "25.0.1"
 polars = { version = "0.42.0", default-features = false, features = ["json"] }
-pyo3 = { version = "0.21.2", features = ["extension-module", "anyhow"] }
+pyo3 = { version = "0.22.2", features = ["extension-module", "anyhow"] }
 regex = "1.6.0"
 reqwest = { version = "0.12.5", features = [
     "json",

src/blast/python.rs

@@ -12,9 +12,10 @@ use pyo3::{
 
 #[pyfunction(name = "blast")]
 #[pyo3(
-    text_signature = "(query, program = None, database = None, limit = 50, expect = 10.0, low_comp_filter = False, megablast = True)"
+    signature = (query, program = None, database = None, limit = None, expect = None, low_comp_filter = None, megablast = None)
 )]
 #[allow(clippy::too_many_arguments)]
+
 pub fn python_blast<'py>(
     py: Python<'py>,
     query: &str,

src/ensembl/python.rs

@@ -9,6 +9,7 @@ use pyo3::{
 
 #[pyfunction(name = "search")]
 #[allow(clippy::needless_pass_by_value)]
+#[pyo3(signature = (search_terms, database = None, species = None, db_type = None, release = None, assembly = None))]
 pub fn python_ensembl_search<'py>(
     py: Python<'py>,
     search_terms: Vec<String>,
@@ -39,6 +40,7 @@ pub fn python_ensembl_search<'py>(
 #[pyfunction(name = "database")]
 #[must_use]
 #[allow(clippy::needless_pass_by_value)]
+#[pyo3(signature = (filter = None))]
 pub fn python_ensembl_database(_py: Python, filter: Option<String>) -> Vec<String> {
     let results = database(&filter).expect("Could not query ensembl SQL");
     results.as_vec()
@@ -50,6 +52,7 @@ pub fn python_ensembl_release(_py: Python) -> usize {
 }
 
 #[pyfunction(name = "reference")]
+#[pyo3(signature = (species = None, release = None, datatype = None))]
 pub fn python_ensembl_reference<'py>(
     py: Python<'py>,
     species: Option<&str>,
@@ -87,6 +90,7 @@ pub fn python_ensembl_reference<'py>(
 }
 
 #[pyfunction(name = "species")]
+#[pyo3(signature = (release = None, datatype = None))]
 pub fn python_ensembl_species(
     _py: Python,
     release: Option<usize>,

src/info/python.rs

@@ -7,7 +7,7 @@ use pyo3::{
 };
 
 #[pyfunction(name = "info")]
-#[pyo3(text_signature = "(search_terms, species = 'homo_sapiens', taxon_id = 9606)")]
+#[pyo3(signature = (search_terms, species = None, taxon_id = None))]
 #[allow(clippy::needless_pass_by_value)]
 pub fn python_info(
     py: Python<'_>,

src/lib.rs

@@ -1,4 +1,8 @@
-use pyo3::{pymodule, types::PyModule, wrap_pyfunction, Bound, PyResult, Python};
+use pyo3::{
+    pymodule,
+    types::{PyModule, PyModuleMethods},
+    wrap_pyfunction, Bound, PyResult, Python,
+};
 
 /// `Enrichr` submodule
 pub mod enrichr;

src/seq/python.rs

@@ -4,7 +4,7 @@ use anyhow::{bail, Result};
 use pyo3::{pyfunction, types::PyList, Bound, Python};
 
 #[pyfunction(name = "seq")]
-#[pyo3(text_signature = "(search_terms, translate = False, db_name = 'homo_sapiens')")]
+#[pyo3(signature = (search_terms, translate = None, species = None))]
 #[allow(clippy::needless_pass_by_value)]
 pub fn python_seq(
     py: Python<'_>,

src/ucsc/python.rs

@@ -8,7 +8,7 @@ use pyo3::{
 };
 
 #[pyfunction(name = "blat")]
-#[pyo3(text_signature = "(sequence, seqtype = 'dna', db_name = 'hg38')")]
+#[pyo3(signature = (sequence, seqtype = None,  db_name = None))]
 pub fn python_ucsc_blat<'py>(
     py: Python<'py>,
     sequence: &str,