Skip to content

Bump pyo3 verison #81

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
treynr wants to merge 1 commit into
base: master
Choose a base branch
from
+47 −35
Open

Bump pyo3 verison #81

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion Cargo.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ edition = "2021"

[dependencies]
memchr = "2.2.1"
pyo3 = { version = "0.18", optional = true }
pyo3 = { version = "0.29", optional = true }
quick-xml = "0.27"
serde = { version = "1.0.104", features = ["derive"] }
serde_json = "1.0.44"
Expand Down
80 changes: 46 additions & 34 deletions src/python.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,8 @@ use pyo3::basic::CompareOp;
use pyo3::create_exception;
use pyo3::exceptions::PyKeyError;
use pyo3::prelude::*;
use pyo3::types::{PyBytes, PyDict, PyList, PyType};
use pyo3::types::{PyAny, PyBytes, PyDict, PyList, PyType};
use pyo3::IntoPyObjectExt;
use serde_json::Value;

use crate::base::InternalIndex;
Expand All @@ -30,25 +31,25 @@ macro_rules! py_try {
};
}

fn json_value_to_pyobject(val: &Value) -> PyObject {
Python::with_gil(|py| match val {
fn json_value_to_pyobject(val: &Value) -> Py<PyAny> {
Python::attach(|py| match val {
Value::Null => py.None(),
Value::Bool(b) => b.to_object(py),
Value::Bool(b) => b.into_py_any(py).unwrap(),
Value::Number(n) => {
if let Some(n1) = n.as_i64() {
return n1.to_object(py);
return n1.into_py_any(py).unwrap();
}
n.as_f64().unwrap().to_object(py)
n.as_f64().unwrap().into_py_any(py).unwrap()
}
Value::String(s) => s.to_object(py),
Value::String(s) => s.into_py_any(py).unwrap(),
Value::Array(arr) => {
let pylist = PyList::empty(py);
for v in arr {
pylist
.append(json_value_to_pyobject(v))
.expect("can add items to list");
}
pylist.to_object(py)
pylist.into_any().unbind()
}
Value::Object(obj) => {
let pydict = PyDict::new(py);
Expand All @@ -57,7 +58,7 @@ fn json_value_to_pyobject(val: &Value) -> PyObject {
.set_item(key, json_value_to_pyobject(val))
.expect("can add items to dict");
}
pydict.to_object(py)
pydict.into_any().unbind()
}
})
}
Expand Down Expand Up @@ -92,22 +93,22 @@ impl TaxonomyNode {
hasher.finish()
}

fn __richcmp__(&self, other: PyRef<TaxonomyNode>, op: CompareOp) -> Py<PyAny> {
fn __richcmp__(&self, other: PyRef<TaxonomyNode>, op: CompareOp) -> PyResult<Py<PyAny>> {
let py = other.py();
match op {
CompareOp::Eq => (self == other.deref()).into_py(py),
CompareOp::Ne => (self != other.deref()).into_py(py),
_ => py.NotImplemented(),
CompareOp::Eq => (self == other.deref()).into_py_any(py),
CompareOp::Ne => (self != other.deref()).into_py_any(py),
_ => Ok(py.NotImplemented()),
}
}

fn __getitem__(&self, obj: &PyAny, py: Python<'_>) -> PyResult<PyObject> {
fn __getitem__(&self, obj: &Bound<'_, PyAny>, py: Python<'_>) -> PyResult<Py<PyAny>> {
let key: &str = obj.extract()?;
match key {
"id" => Ok(self.id.to_object(py)),
"name" => Ok(self.name.to_object(py)),
"parent" => Ok(self.parent.to_object(py)),
"rank" => Ok(self.rank.to_object(py)),
"id" => self.id.as_str().into_py_any(py),
"name" => self.name.as_str().into_py_any(py),
"parent" => self.parent.as_deref().into_py_any(py),
"rank" => self.rank.as_str().into_py_any(py),
_ => {
if self.extra.contains_key(key) {
Ok(json_value_to_pyobject(self.extra.get(key).unwrap()))
Expand Down Expand Up @@ -170,7 +171,7 @@ impl Taxonomy {
///
/// Load a Taxonomy from a GTDB-encoded string.
#[classmethod]
fn from_gtdb(_cls: &PyType, value: &str) -> PyResult<Taxonomy> {
fn from_gtdb(_cls: &Bound<'_, PyType>, value: &str) -> PyResult<Taxonomy> {
let mut c = Cursor::new(value);
let tax = py_try!(gtdb::load(&mut c));
Ok(Taxonomy { tax })
Expand All @@ -184,7 +185,12 @@ impl Taxonomy {
/// If `path` is specified, the JSON will be traversed to that sub-object
/// before being parsed as a taxonomy. `path` has to be a valid JSON path string.
#[classmethod]
fn from_json(_cls: &PyType, value: &str, json_pointer: Option<&str>) -> PyResult<Taxonomy> {
#[pyo3(signature = (value, json_pointer=None))]
fn from_json(
_cls: &Bound<'_, PyType>,
value: &str,
json_pointer: Option<&str>,
) -> PyResult<Taxonomy> {
let mut c = Cursor::new(value);
let tax = py_try!(json::load(&mut c, json_pointer));
Ok(Taxonomy { tax })
Expand All @@ -195,7 +201,7 @@ impl Taxonomy {
///
/// Load a Taxonomy from a Newick-encoded string.
#[classmethod]
fn from_newick(_cls: &PyType, value: &str) -> PyResult<Taxonomy> {
fn from_newick(_cls: &Bound<'_, PyType>, value: &str) -> PyResult<Taxonomy> {
let mut c = Cursor::new(value);
let tax = py_try!(newick::load(&mut c));
Ok(Taxonomy { tax })
Expand All @@ -207,7 +213,7 @@ impl Taxonomy {
/// Load a Taxonomy from a directory.
/// The directory must contain the `nodes.dmp` and `names.dmp` files.
#[classmethod]
fn from_ncbi(_cls: &PyType, dump_dir: &str) -> PyResult<Taxonomy> {
fn from_ncbi(_cls: &Bound<'_, PyType>, dump_dir: &str) -> PyResult<Taxonomy> {
let tax = py_try!(ncbi::load(dump_dir));
Ok(Taxonomy { tax })
}
Expand All @@ -219,7 +225,7 @@ impl Taxonomy {
///
/// Experimental.
#[classmethod]
fn from_phyloxml(_cls: &PyType, value: &str) -> PyResult<Taxonomy> {
fn from_phyloxml(_cls: &Bound<'_, PyType>, value: &str) -> PyResult<Taxonomy> {
let mut c = Cursor::new(value);
let tax = py_try!(phyloxml::load(&mut c));
Ok(Taxonomy { tax })
Expand All @@ -237,30 +243,30 @@ impl Taxonomy {
/// --
///
/// Export a Taxonomy as a JSON-encoded byte string in a tree format
fn to_json_tree(&self, py: Python<'_>) -> PyResult<PyObject> {
fn to_json_tree(&self, py: Python<'_>) -> PyResult<Py<PyAny>> {
let mut bytes = Vec::new();
py_try!(json::save::<_, &str, _>(
&mut bytes,
&self.tax,
JsonFormat::Tree,
None
));
Ok(PyBytes::new(py, &bytes).into())
Ok(PyBytes::new(py, &bytes).into_any().unbind())
}

/// to_json_node_links(self)
/// --
///
/// Export a Taxonomy as a JSON-encoded byte string in a node link format
fn to_json_node_links(&self, py: Python<'_>) -> PyResult<PyObject> {
fn to_json_node_links(&self, py: Python<'_>) -> PyResult<Py<PyAny>> {
let mut bytes = Vec::new();
py_try!(json::save::<_, &str, _>(
&mut bytes,
&self.tax,
JsonFormat::NodeLink,
None
));
Ok(PyBytes::new(py, &bytes).into())
Ok(PyBytes::new(py, &bytes).into_any().unbind())
}

/// to_ncbi(self, output_dir: str)
Expand All @@ -280,14 +286,14 @@ impl Taxonomy {
/// --
///
/// Export a Taxonomy as a Newick-encoded byte string.
fn to_newick(&self, py: Python<'_>) -> PyResult<PyObject> {
fn to_newick(&self, py: Python<'_>) -> PyResult<Py<PyAny>> {
let mut bytes = Vec::new();
py_try!(newick::save(
&mut bytes,
&self.tax,
Some(TaxonomyTrait::<&str>::root(&self.tax))
));
Ok(PyBytes::new(py, &bytes).into())
Ok(PyBytes::new(py, &bytes).into_any().unbind())
}

/// node(self, tax_id: str) -> Optional[TaxonomyNode]
Expand Down Expand Up @@ -319,6 +325,7 @@ impl Taxonomy {
///
/// If `at_rank` is provided, scan all the nodes in the node's lineage and return
/// the parent id at that rank.
#[pyo3(signature = (tax_id, at_rank=None))]
fn parent_with_distance(
&self,
tax_id: &str,
Expand Down Expand Up @@ -351,6 +358,7 @@ impl Taxonomy {
///
/// If `at_rank` is provided, scan all the nodes in the node's lineage and return
/// the parent id at that rank.
#[pyo3(signature = (tax_id, at_rank=None))]
fn parent(&self, tax_id: &str, at_rank: Option<&str>) -> PyResult<Option<TaxonomyNode>> {
let (node, _) = self.parent_with_distance(tax_id, at_rank)?;
Ok(node)
Expand Down Expand Up @@ -428,12 +436,15 @@ impl Taxonomy {
/// Return a copy of the taxonomy containing:
/// - only the nodes in `keep` and their parents if provided
/// - all of the nodes except those in remove and their children if provided
fn prune(&self, keep: Option<Vec<&str>>, remove: Option<Vec<&str>>) -> PyResult<Taxonomy> {
#[pyo3(signature = (keep=None, remove=None))]
fn prune(&self, keep: Option<Vec<String>>, remove: Option<Vec<String>>) -> PyResult<Taxonomy> {
let mut tax = self.tax.clone();
if let Some(k) = keep {
let k: Vec<&str> = k.iter().map(|s| s.as_str()).collect();
tax = py_try!(prune_to(&tax, &k, false));
}
if let Some(r) = remove {
let r: Vec<&str> = r.iter().map(|s| s.as_str()).collect();
tax = py_try!(prune_away(&tax, &r));
}
Ok(Taxonomy { tax })
Expand Down Expand Up @@ -468,6 +479,7 @@ impl Taxonomy {
/// --
///
/// Edit properties on a taxonomy node.
#[pyo3(signature = (tax_id, name=None, rank=None, parent_id=None, parent_distance=None))]
fn edit_node(
&mut self,
tax_id: &str,
Expand Down Expand Up @@ -560,7 +572,7 @@ impl Taxonomy {
let root = slf.tax.root();
let root_idx = slf.tax.to_internal_index(root).unwrap();
Ok(TaxonomyIterator {
t: slf.into_py(py),
t: slf.into_py_any(py)?,
nodes_left: vec![root_idx],
visited_nodes: Vec::new(),
})
Expand All @@ -569,7 +581,7 @@ impl Taxonomy {

#[pyclass]
pub struct TaxonomyIterator {
t: PyObject,
t: Py<PyAny>,
visited_nodes: Vec<usize>,
nodes_left: Vec<usize>,
}
Expand Down Expand Up @@ -629,10 +641,10 @@ impl TaxonomyIterator {

/// The taxonomy module
#[pymodule]
fn taxonomy(py: Python, m: &PyModule) -> PyResult<()> {
fn taxonomy(m: &Bound<'_, PyModule>) -> PyResult<()> {
m.add_class::<Taxonomy>()?;
m.add_class::<TaxonomyNode>()?;
m.add("TaxonomyError", py.get_type::<TaxonomyError>())?;
m.add("TaxonomyError", m.py().get_type::<TaxonomyError>())?;

Ok(())
}
Loading