feos-org · prehner · Apr 22, 2024 · Apr 12, 2024 · Apr 19, 2024 · Apr 19, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,7 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 ### Added
-- Added SAFT-VR Mie equation of state.[#237](https://github.com/feos-org/feos/pull/237)
+- Added SAFT-VR Mie equation of state. [#237](https://github.com/feos-org/feos/pull/237)
 - Added ePC-SAFT equation of state. [#229](https://github.com/feos-org/feos/pull/229)
 
 ### Changed
@@ -20,6 +20,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Removed
 - Removed `VirialOrder` from `uvtheory` module. Orders are now variants of the existing `Perturbation` enum. [#226](https://github.com/feos-org/feos/pull/226)
 
+### Packaging
+- Updated `quantity` dependency to 0.8. [#238](https://github.com/feos-org/feos/pull/238)
+- Updated `num-dual` dependency to 0.9. [#238](https://github.com/feos-org/feos/pull/238)
+- Updated `numpy` and `PyO3` dependencies to 0.21. [#238](https://github.com/feos-org/feos/pull/238)
+
 ## [0.6.1] - 2024-01-11
 - Python only: Release the changes introduced in `feos-core` 0.6.1.
 

diff --git a/Cargo.toml b/Cargo.toml
@@ -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"
@@ -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
 

diff --git a/feos-core/CHANGELOG.md b/feos-core/CHANGELOG.md
@@ -22,7 +22,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 - Added comparison for pressures of both phases in `PyPhaseDiagram.to_dict` to make the method work with `spinodal` constructor. [#224](https://github.com/feos-org/feos/pull/224)
 - Enforce the total moles when providing `State::new` with molefracs that do not add up to 1. [#227](https://github.com/feos-org/feos/pull/227)
-- 
+
+### Packaging
+- Updated `quantity` dependency to 0.8. [#238](https://github.com/feos-org/feos/pull/238)
+- Updated `num-dual` dependency to 0.9. [#238](https://github.com/feos-org/feos/pull/238)
+- Updated `numpy` and `PyO3` dependencies to 0.21. [#238](https://github.com/feos-org/feos/pull/238)
 
 
 ## [0.6.1] 2024-01-11

diff --git a/feos-core/Cargo.toml b/feos-core/Cargo.toml
@@ -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"
@@ -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"

diff --git a/feos-core/src/python/parameter/fragmentation.rs b/feos-core/src/python/parameter/fragmentation.rs
@@ -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>() {
@@ -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>()?;
 
@@ -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>>()?;

diff --git a/feos-core/src/python/parameter/mod.rs b/feos-core/src/python/parameter/mod.rs
@@ -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>() {
@@ -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::<$py_model_record>() {
@@ -558,6 +562,8 @@ macro_rules! impl_parameter {
             impl_parameter!($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 $py_parameter {
             /// Creates parameters from records.
@@ -578,14 +584,14 @@ macro_rules! impl_parameter {
             )]
             fn from_records(
                 pure_records: Vec<PyPureRecord>,
-                binary_records: Option<&PyAny>,
+                binary_records: Option<&Bound<'_, PyAny>>,
                 identifier_option: IdentifierOption,
             ) -> PyResult<Self> {
                 let prs: Vec<_> = pure_records.into_iter().map(|pr| pr.0).collect();
                 let binary_records = binary_records
                     .map(|binary_records| {
                         if let Ok(br) = binary_records.extract::<PyReadonlyArray2<f64>>() {
-                            Ok(Some(br.to_owned_array().mapv(|r| r.try_into().unwrap())))
+                            Ok(Some(br.as_array().mapv(|r| r.try_into().unwrap())))
                         } else if let Ok(br) = binary_records.extract::<Vec<PyBinaryRecord>>() {
                             let brs: Vec<_> = br.into_iter().map(|br| br.0).collect();
                             Ok(<$parameter>::binary_matrix_from_records(
@@ -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
@@ -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(<$parameter>::from_json(
                     substances,
                     pure_path,
@@ -708,13 +715,14 @@ macro_rules! impl_parameter {
                 text_signature = "(input, binary_path=None, identifier_option)"
             )]
             fn from_multiple_json(
-                input: Vec<(Vec<&str>, &str)>,
-                binary_path: Option<&str>,
+                input: Vec<(Vec<PyBackedStr>, PyBackedStr)>,
+                binary_path: Option<PyBackedStr>,
                 identifier_option: Option<IdentifierOption>,
             ) -> Result<Self, ParameterError> {
+                let input: Vec<(Vec<&str>, &str)> = input.iter().map(|(c, f)| (c.iter().map(|c| &**c).collect(), &**f)).collect();
                 Ok(Self(Arc::new(<$parameter>::from_multiple_json(
                     &input,
-                    binary_path,
+                    binary_path.as_deref(),
                     identifier_option.unwrap_or(IdentifierOption::Name),
                 )?)))
             }
@@ -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))
             }
         }
     };
@@ -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 $py_parameter {
             /// Creates parameters from segment records.
@@ -790,12 +800,13 @@ macro_rules! impl_parameter_from_segments {
                 text_signature = "(substances, pure_path, segments_path, binary_path=None, identifier_option)"
             )]
             fn from_json_segments(
-                substances: Vec<&str>,
+                substances: Vec<PyBackedStr>,
                 pure_path: String,
                 segments_path: String,
                 binary_path: Option<String>,
                 identifier_option: IdentifierOption,
             ) -> PyResult<Self> {
+                let substances: Vec<_> = substances.iter().map(|s| &**s).collect();
                 Ok(Self(Arc::new(<$parameter>::from_json_segments(
                     &substances,
                     pure_path,
@@ -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)
             }
@@ -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>,
@@ -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,

diff --git a/feos-core/src/python/phase_equilibria.rs b/feos-core/src/python/phase_equilibria.rs
@@ -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>,
@@ -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>,