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Merged
prehner merged 4 commits into from
Apr 22, 2024
Merged

Update PyO3 to 0.21 #238

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f19f74d
Update PyO3 to 0.21
prehner Apr 12, 2024
c95b05a
rebase
prehner Apr 19, 2024
3b9edc4
remove unused python tokens
prehner Apr 19, 2024
1d94de9
update changelogs
prehner Apr 22, 2024
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Update PyO3 to 0.21
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@prehner
prehner committed Apr 19, 2024
commit f19f74d1269c70b69299c0f88d99cd537b964edc
8 changes: 4 additions & 4 deletions Cargo.toml
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Expand Up @@ -22,12 +22,12 @@ members = ["feos-core", "feos-dft", "feos-derive"]
crate-type = ["rlib", "cdylib"]

[dependencies]
quantity = { version = "0.7", optional = true }
num-dual = "0.8"
quantity = { version = "0.8", optional = true }
num-dual = "0.9"
feos-core = { version = "0.6", path = "feos-core" }
feos-dft = { version = "0.6", path = "feos-dft", optional = true }
feos-derive = { version = "0.4", path = "feos-derive" }
numpy = { version = "0.20", optional = true }
numpy = { version = "0.21", optional = true }
ndarray = { version = "0.15", features = ["approx"] }
petgraph = { version = "0.6", optional = true }
thiserror = "1.0"
Expand All @@ -42,7 +42,7 @@ itertools = "0.12"
typenum = "1.16"

[dependencies.pyo3]
version = "0.20"
version = "0.21"
features = ["extension-module", "abi3", "abi3-py37"]
optional = true

Expand Down
8 changes: 4 additions & 4 deletions feos-core/Cargo.toml
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Expand Up @@ -18,8 +18,8 @@ rustdoc-args = [ "--html-in-header", "./docs-header.html" ]
features = [ "rayon" ]

[dependencies]
quantity = { version = "0.7", optional = true }
num-dual = { version = "0.8", features = ["linalg"] }
quantity = { version = "0.8", optional = true }
num-dual = { version = "0.9", features = ["linalg"] }
ndarray = { version = "0.15", features = ["serde", "approx-0_5"] }
nalgebra = "0.32"
num-traits = "0.2"
Expand All @@ -28,8 +28,8 @@ serde = { version = "1.0", features = ["derive"] }
serde_json = "1.0"
indexmap = "2.0"
conv = "0.3"
numpy = { version = "0.20", optional = true }
pyo3 = { version = "0.20", optional = true }
numpy = { version = "0.21", optional = true }
pyo3 = { version = "0.21", optional = true }
rayon = { version = "1.5", optional = true }
typenum = "1.16"
approx = "0.5"
Expand Down
8 changes: 4 additions & 4 deletions feos-core/src/python/parameter/fragmentation.rs
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Expand Up @@ -85,10 +85,10 @@ impl_json_handling!(PySmartsRecord);
impl PyChemicalRecord {
#[staticmethod]
pub fn from_smiles(
py: Python<'_>,
identifier: &PyAny,
identifier: &Bound<'_, PyAny>,
smarts: Vec<PySmartsRecord>,
) -> PyResult<Self> {
let py = identifier.py();
let identifier = if let Ok(smiles) = identifier.extract::<String>() {
Identifier::new(None, None, None, Some(&smiles), None, None)
} else if let Ok(identifier) = identifier.extract::<PyIdentifier>() {
Expand All @@ -113,7 +113,7 @@ fn fragment_molecule(
smiles: &str,
smarts: Vec<PySmartsRecord>,
) -> PyResult<(Vec<String>, Vec<[usize; 2]>)> {
let chem = py.import("rdkit.Chem")?;
let chem = py.import_bound("rdkit.Chem")?;
let mol = chem.call_method1("MolFromSmiles", (smiles,))?;
let atoms = mol.call_method0("GetNumHeavyAtoms")?.extract::<usize>()?;

Expand Down Expand Up @@ -155,7 +155,7 @@ fn fragment_molecule(
.for_each(|(_, m)| m.retain(|m| !(m.len() == 1 && large_segments.contains(&m[0]))));

let bonds = mol.call_method0("GetBonds")?;
let builtins = py.import("builtins")?;
let builtins = py.import_bound("builtins")?;
let bonds = builtins
.call_method1("list", (bonds,))?
.extract::<Vec<&PyAny>>()?;
Expand Down
54 changes: 31 additions & 23 deletions feos-core/src/python/parameter/mod.rs
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Expand Up @@ -212,7 +212,11 @@ macro_rules! impl_binary_record {
#[pymethods]
impl PyBinaryRecord {
#[new]
fn new(id1: PyIdentifier, id2: PyIdentifier, model_record: &PyAny) -> PyResult<Self> {
fn new(
id1: PyIdentifier,
id2: PyIdentifier,
model_record: &Bound<'_, PyAny>,
) -> PyResult<Self> {
if let Ok(mr) = model_record.extract::<f64>() {
Ok(Self(BinaryRecord::new(id1.0, id2.0, mr.try_into()?)))
} else if let Ok(mr) = model_record.extract::<$py_model_record>() {
Expand Down Expand Up @@ -264,16 +268,16 @@ macro_rules! impl_binary_record {
}

#[getter]
fn get_model_record(&self, py: Python) -> PyObject {
if let Ok(mr) = f64::try_from(self.0.model_record.clone()) {
mr.to_object(py)
fn get_model_record<'py>(&self, py: Python<'py>) -> PyResult<Bound<'py, PyAny>> {
Ok(if let Ok(mr) = f64::try_from(self.0.model_record.clone()) {
pyo3::types::PyFloat::new_bound(py, mr).into_any()
} else {
$py_model_record(self.0.model_record.clone()).into_py(py)
}
Bound::new(py, $py_model_record(self.0.model_record.clone()))?.into_any()
})
}

#[setter]
fn set_model_record(&mut self, model_record: &PyAny) -> PyResult<()> {
fn set_model_record(&mut self, model_record: &Bound<'_, PyAny>) -> PyResult<()> {
if let Ok(mr) = model_record.extract::<f64>() {
self.0.model_record = mr.try_into()?;
} else if let Ok(mr) = model_record.extract::<$py_model_record>() {
Expand Down Expand Up @@ -558,6 +562,8 @@ macro_rules! impl_parameter {
impl_parameter!($parameter, $py_parameter, $py_model_record, PyNoBinaryModelRecord);
};
($parameter:ty, $py_parameter:ty, $py_model_record:ty, $py_binary_model_record:ty) => {
use pyo3::pybacked::*;

#[pymethods]
impl $py_parameter {
/// Creates parameters from records.
Expand All @@ -578,14 +584,14 @@ macro_rules! impl_parameter {
)]
fn from_records(
pure_records: Vec<PyPureRecord>,
binary_records: Option<&PyAny>,
binary_records: Option<&Bound<'_, PyAny>>,
identifier_option: IdentifierOption,
) -> PyResult<Self> {
let prs: Vec<_> = pure_records.into_iter().map(|pr| pr.0).collect();
let binary_records = binary_records
.map(|binary_records| {
if let Ok(br) = binary_records.extract::<PyReadonlyArray2<f64>>() {
Ok(Some(br.to_owned_array().mapv(|r| r.try_into().unwrap())))
Ok(Some(br.as_array().mapv(|r| r.try_into().unwrap())))
} else if let Ok(br) = binary_records.extract::<Vec<PyBinaryRecord>>() {
let brs: Vec<_> = br.into_iter().map(|br| br.0).collect();
Ok(<$parameter>::binary_matrix_from_records(
Expand Down Expand Up @@ -628,7 +634,7 @@ macro_rules! impl_parameter {
#[pyo3(text_signature = "(pure_records, binary_record=None)")]
fn new_binary(
pure_records: Vec<PyPureRecord>,
binary_record: Option<&PyAny>,
binary_record: Option<&Bound<'_, PyAny>>,
) -> PyResult<Self> {
let prs = pure_records.into_iter().map(|pr| pr.0).collect();
let br = binary_record
Expand Down Expand Up @@ -678,11 +684,12 @@ macro_rules! impl_parameter {
text_signature = "(substances, pure_path, binary_path=None, identifier_option)"
)]
fn from_json(
substances: Vec<&str>,
substances: Vec<PyBackedStr>,
pure_path: String,
binary_path: Option<String>,
identifier_option: IdentifierOption,
) -> Result<Self, ParameterError> {
let substances = substances.iter().map(|s| &**s).collect();
Ok(Self(Arc::new(<$parameter>::from_json(
substances,
pure_path,
Expand All @@ -708,13 +715,14 @@ macro_rules! impl_parameter {
text_signature = "(input, binary_path=None, identifier_option)"
)]
fn from_multiple_json(
input: Vec<(Vec<&str>, &str)>,
binary_path: Option<&str>,
input: Vec<(Vec<PyBackedStr>, PyBackedStr)>,
binary_path: Option<PyBackedStr>,
identifier_option: Option<IdentifierOption>,
) -> Result<Self, ParameterError> {
let input: Vec<(Vec<&str>, &str)> = input.iter().map(|(c, f)| (c.iter().map(|c| &**c).collect(), &**f)).collect();
Ok(Self(Arc::new(<$parameter>::from_multiple_json(
&input,
binary_path,
binary_path.as_deref(),
identifier_option.unwrap_or(IdentifierOption::Name),
)?)))
}
Expand All @@ -730,11 +738,11 @@ macro_rules! impl_parameter {
}

#[getter]
fn get_binary_records<'py>(&self, py: Python<'py>) -> Option<&'py PyArray2<f64>> {
fn get_binary_records<'py>(&self, py: Python<'py>) -> Option<Bound<'py, PyArray2<f64>>> {
self.0
.records()
.1
.map(|r| r.mapv(|r| f64::try_from(r).unwrap()).view().to_pyarray(py))
.map(|r| r.mapv(|r| f64::try_from(r).unwrap()).view().to_pyarray_bound(py))
}
}
};
Expand All @@ -743,6 +751,8 @@ macro_rules! impl_parameter {
#[macro_export]
macro_rules! impl_parameter_from_segments {
($parameter:ty, $py_parameter:ty) => {
use pyo3::pybacked::*;

#[pymethods]
impl $py_parameter {
/// Creates parameters from segment records.
Expand Down Expand Up @@ -790,12 +800,13 @@ macro_rules! impl_parameter_from_segments {
text_signature = "(substances, pure_path, segments_path, binary_path=None, identifier_option)"
)]
fn from_json_segments(
substances: Vec<&str>,
substances: Vec<PyBackedStr>,
pure_path: String,
segments_path: String,
binary_path: Option<String>,
identifier_option: IdentifierOption,
) -> PyResult<Self> {
let substances: Vec<_> = substances.iter().map(|s| &**s).collect();
Ok(Self(Arc::new(<$parameter>::from_json_segments(
&substances,
pure_path,
Expand Down Expand Up @@ -824,15 +835,14 @@ macro_rules! impl_parameter_from_segments {
#[staticmethod]
#[pyo3(text_signature = "(identifier, smarts_records, segment_records, binary_segment_records=None)")]
fn from_smiles(
py: Python<'_>,
identifier: Vec<&PyAny>,
identifier: Vec<Bound<'_,PyAny>>,
smarts_records: Vec<PySmartsRecord>,
segment_records: Vec<PySegmentRecord>,
binary_segment_records: Option<Vec<PyBinarySegmentRecord>>,
) -> PyResult<Self> {
let chemical_records: Vec<_> = identifier
.into_iter()
.map(|i| PyChemicalRecord::from_smiles(py, i, smarts_records.clone()))
.map(|i| PyChemicalRecord::from_smiles(&i, smarts_records.clone()))
.collect::<PyResult<_>>()?;
Self::from_segments(chemical_records, segment_records, binary_segment_records)
}
Expand All @@ -857,8 +867,7 @@ macro_rules! impl_parameter_from_segments {
text_signature = "(identifier, smarts_path, segments_path, binary_path=None)"
)]
fn from_json_smiles(
py: Python<'_>,
identifier: Vec<&PyAny>,
identifier: Vec<Bound<'_,PyAny>>,
smarts_path: String,
segments_path: String,
binary_path: Option<String>,
Expand All @@ -867,7 +876,6 @@ macro_rules! impl_parameter_from_segments {
let segment_records = PySegmentRecord::from_json(&segments_path)?;
let binary_segment_records = binary_path.map(|p| PyBinarySegmentRecord::from_json(&p)).transpose()?;
Self::from_smiles(
py,
identifier,
smarts_records,
segment_records,
Expand Down
12 changes: 6 additions & 6 deletions feos-core/src/python/phase_equilibria.rs
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Expand Up @@ -155,12 +155,12 @@ macro_rules! impl_phase_equilibrium {
/// PhaseEquilibrium
#[staticmethod]
#[pyo3(text_signature = "(eos, temperature_or_pressure, liquid_molefracs, tp_init=None, vapor_molefracs=None, max_iter_inner=None, max_iter_outer=None, tol_inner=None, tol_outer=None, verbosity=None)")]
pub fn bubble_point(
pub fn bubble_point<'py>(
eos: $py_eos,
temperature_or_pressure: PySINumber,
liquid_molefracs: &PyArray1<f64>,
liquid_molefracs: &Bound<'py, PyArray1<f64>>,
tp_init: Option<PySINumber>,
vapor_molefracs: Option<&PyArray1<f64>>,
vapor_molefracs: Option<&Bound<'py, PyArray1<f64>>>,
max_iter_inner: Option<usize>,
max_iter_outer: Option<usize>,
tol_inner: Option<f64>,
Expand Down Expand Up @@ -232,12 +232,12 @@ macro_rules! impl_phase_equilibrium {
/// PhaseEquilibrium
#[staticmethod]
#[pyo3(text_signature = "(eos, temperature_or_pressure, vapor_molefracs, tp_init=None, liquid_molefracs=None, max_iter_inner=None, max_iter_outer=None, tol_inner=None, tol_outer=None, verbosity=None)")]
pub fn dew_point(
pub fn dew_point<'py>(
eos: $py_eos,
temperature_or_pressure: PySINumber,
vapor_molefracs: &PyArray1<f64>,
vapor_molefracs: &Bound<'py, PyArray1<f64>>,
tp_init: Option<PySINumber>,
liquid_molefracs: Option<&PyArray1<f64>>,
liquid_molefracs: Option<&Bound<'py, PyArray1<f64>>>,
max_iter_inner: Option<usize>,
max_iter_outer: Option<usize>,
tol_inner: Option<f64>,
Expand Down
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