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expose IdentifierOption enum to Python and use it instead of a string… #58

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prehner merged 2 commits into from
Jun 10, 2022
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expose IdentifierOption enum to Python and use it instead of a string… #58

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f658ab7
expose IdentifierOption enum to Python and use it instead of a string…
g-bauer Jun 8, 2022
fa12323
remove TryFrom and update CHANGELOG
prehner Jun 10, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Made `cas` field of `Identifier` optional. [#56](https://github.com/feos-org/feos-core/pull/56)
- Added type parameter to `FromSegments` and made its `from_segments` function fallible for more control over model limitations. [#56](https://github.com/feos-org/feos-core/pull/56)
- Reverted `ChemicalRecord` back to a struct that only contains the structural information (and not segment and bond counts). [#56](https://github.com/feos-org/feos-core/pull/56)
- Made `IdentifierOption` directly usable in Python using `PyO3`'s new `#[pyclass]` for fieldless enums feature. [#58](https://github.com/feos-org/feos-core/pull/58)

## [0.2.0] - 2022-04-12
### Added
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2 changes: 2 additions & 0 deletions build_wheel/src/lib.rs
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@@ -1,6 +1,7 @@
use feos_core::python::joback::PyJobackRecord;
use feos_core::python::parameter::*;
use feos_core::{Contributions, Verbosity};
use feos_core::parameter::IdentifierOption;
use pyo3::prelude::*;
use pyo3::wrap_pymodule;
use quantity::python::__PYO3_PYMODULE_DEF_QUANTITY;
Expand All @@ -17,6 +18,7 @@ pub fn feos_core(py: Python<'_>, m: &PyModule) -> PyResult<()> {
m.add_class::<Contributions>()?;
m.add_class::<PyChemicalRecord>()?;
m.add_class::<PyJobackRecord>()?;
m.add_class::<IdentifierOption>()?;

m.add_wrapped(wrap_pymodule!(user_defined))?;
m.add_wrapped(wrap_pymodule!(cubic))?;
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21 changes: 1 addition & 20 deletions src/parameter/identifier.rs
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@@ -1,11 +1,9 @@
use super::ParameterError;
use serde::{Deserialize, Serialize};
use std::convert::TryFrom;
use std::hash::{Hash, Hasher};

/// Possible variants to identify a substance.
#[repr(C)]
#[derive(Serialize, Deserialize, Debug, Clone, Copy)]
#[cfg_attr(feature = "python", pyo3::pyclass)]
pub enum IdentifierOption {
Cas,
Name,
Expand All @@ -15,23 +13,6 @@ pub enum IdentifierOption {
Formula,
}

impl TryFrom<&str> for IdentifierOption {
type Error = ParameterError;

fn try_from(s: &str) -> Result<Self, Self::Error> {
let lower = s.to_lowercase();
match lower.as_str() {
"cas" => Ok(Self::Cas),
"name" => Ok(Self::Name),
"iupacname" => Ok(Self::IupacName),
"smiles" => Ok(Self::Smiles),
"inchi" => Ok(Self::Inchi),
"formula" => Ok(Self::Formula),
_ => Err(ParameterError::IdentifierNotFound(s.to_owned())),
}
}
}

/// A collection of identifiers for a chemical structure or substance.
#[derive(Serialize, Deserialize, Debug, Clone, Default)]
pub struct Identifier {
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59 changes: 20 additions & 39 deletions src/python/parameter.rs
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Expand Up @@ -545,27 +545,25 @@ macro_rules! impl_parameter {
/// binary_records : numpy.ndarray[float] or List[BinaryRecord]
/// A matrix of binary interaction parameters or a list
/// containing records for binary interactions.
/// search_option : str, optional, defaults to "Name"
/// Identifier that is used to search substance if binary_records is
/// passed as a list.
/// One of 'Name', 'Cas', 'Inchi', 'IupacName', 'Formula', 'Smiles'
/// search_option : IdentifierOption, optional, defaults to IdentifierOption.Name
/// Identifier that is used to search binary records.
#[staticmethod]
#[pyo3(text_signature = "(pure_records, binary_records, search_option='Name')")]
#[pyo3(text_signature = "(pure_records, binary_records, search_option)")]
fn from_records(
pure_records: Vec<PyPureRecord>,
binary_records: &PyAny,
search_option: Option<&str>,
search_option: Option<IdentifierOption>,
) -> PyResult<Self> {
let prs = pure_records.into_iter().map(|pr| pr.0).collect();
let brs = if let Ok(br) = binary_records.extract::<PyReadonlyArray2<f64>>() {
Ok(br.to_owned_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();
let io = match search_option {
Some(o) => IdentifierOption::try_from(o)?,
None => IdentifierOption::Name,
};
Ok(<$parameter>::binary_matrix_from_records(&prs, &brs, io))
Ok(<$parameter>::binary_matrix_from_records(
&prs,
&brs,
search_option.unwrap_or(IdentifierOption::Name),
))
} else {
Err(PyErr::new::<PyTypeError, _>(format!(
"Could not parse binary input!"
Expand Down Expand Up @@ -628,28 +626,21 @@ macro_rules! impl_parameter {
/// Path to file containing pure substance parameters.
/// binary_path : str, optional
/// Path to file containing binary substance parameters.
/// search_option : str, optional, defaults to "Name"
/// search_option : IdentifierOption, optional, defaults to IdentifierOption.Name
/// Identifier that is used to search substance.
/// One of 'Name', 'Cas', 'Inchi', 'IupacName', 'Formula', 'Smiles'
#[staticmethod]
#[pyo3(
text_signature = "(substances, pure_path, binary_path=None, search_option='Name')"
)]
#[pyo3(text_signature = "(substances, pure_path, binary_path, search_option)")]
fn from_json(
substances: Vec<&str>,
pure_path: String,
binary_path: Option<String>,
search_option: Option<&str>,
search_option: Option<IdentifierOption>,
) -> Result<Self, ParameterError> {
let io = match search_option {
Some(o) => IdentifierOption::try_from(o)?,
None => IdentifierOption::Name,
};
Ok(Self(Rc::new(<$parameter>::from_json(
substances,
pure_path,
binary_path,
io,
search_option.unwrap_or(IdentifierOption::Name),
)?)))
}

Expand All @@ -662,24 +653,19 @@ macro_rules! impl_parameter {
/// E.g. [(["methane", "propane"], "parameters/alkanes.json"), (["methanol"], "parameters/alcohols.json")]
/// binary_path : str, optional
/// Path to file containing binary substance parameters.
/// search_option : str, optional, defaults to "Name"
/// search_option : IdentifierOption, optional, defaults to IdentifierOption.Name
/// Identifier that is used to search substance.
/// One of 'Name', 'Cas', 'Inchi', 'IupacName', 'Formula', 'Smiles'
#[staticmethod]
#[pyo3(text_signature = "(input, binary_path=None, search_option='Name')")]
fn from_multiple_json(
input: Vec<(Vec<&str>, &str)>,
binary_path: Option<&str>,
search_option: Option<&str>,
search_option: Option<IdentifierOption>,
) -> Result<Self, ParameterError> {
let io = match search_option {
Some(o) => IdentifierOption::try_from(o)?,
None => IdentifierOption::Name,
};
Ok(Self(Rc::new(<$parameter>::from_multiple_json(
&input,
binary_path,
io,
search_option.unwrap_or(IdentifierOption::Name),
)?)))
}

Expand Down Expand Up @@ -738,30 +724,25 @@ macro_rules! impl_parameter_from_segments {
/// Path to file containing segment parameters.
/// binary_path : str, optional
/// Path to file containing binary segment-segment parameters.
/// search_option : str, optional, defaults to "Name"
/// search_option : IdentifierOption, optional, defaults to IdentifierOption.Name
/// Identifier that is used to search substance.
/// One of 'Name', 'Cas', 'Inchi', 'IupacName', 'Formula', 'Smiles'
#[staticmethod]
#[pyo3(
text_signature = "(substances, pure_path, segments_path, binary_path=None, search_option='Name')"
text_signature = "(substances, pure_path, segments_path, binary_path, search_option)"
)]
fn from_json_segments(
substances: Vec<&str>,
pure_path: String,
segments_path: String,
binary_path: Option<String>,
search_option: Option<&str>,
search_option: Option<IdentifierOption>,
) -> Result<Self, ParameterError> {
let io = match search_option {
Some(o) => IdentifierOption::try_from(o)?,
None => IdentifierOption::Name,
};
Ok(Self(Rc::new(<$parameter>::from_json_segments(
&substances,
pure_path,
segments_path,
binary_path,
io,
search_option.unwrap_or(IdentifierOption::Name),
)?)))
}
}
Expand Down