Remove `alphabet` parameter from `ScoringMatrix` Python class

lightmotif-py/lightmotif/lib.pyi

@@ -15,7 +15,7 @@ AVX2_SUPPORTED: bool
 FORMAT = Literal["jaspar", "jaspar16", "uniprobe", "transfac"]
 
 class EncodedSequence:
-    def __init__(self, sequence: str, protein: bool = False) -> None: ...
+    def __init__(self, sequence: str, *, protein: bool = False) -> None: ...
     def __str__(self) -> str: ...
     def __len__(self) -> int: ...
     def __copy__(self) -> EncodedSequence: ...
@@ -34,7 +34,7 @@ class StripedSequence:
 
 class CountMatrix:
     def __init__(
-        self, values: Dict[str, Iterable[int]], protein: bool = False
+        self, values: Dict[str, Iterable[int]], *, protein: bool = False
     ) -> None: ...
     def __eq__(self, other: object) -> bool: ...
     def __len__(self) -> int: ...
@@ -57,7 +57,11 @@ class WeightMatrix:
 
 class ScoringMatrix:
     def __init__(
-        self, values: Dict[str, Iterable[float]], protein: bool = False
+        self,
+        values: Dict[str, Iterable[float]],
+        background: Optional[Dict[str, float]] = None,
+        *,
+        protein: bool = False,
     ) -> None: ...
     def __len__(self) -> int: ...
     def __eq__(self, other: object) -> bool: ...
@@ -125,16 +129,24 @@ class Hit:
 M = typing.TypeVar("M", bound=Motif)
 
 class Loader(Generic[M], Iterator[M]):
+    def __init__(
+        self,
+        file: Union[BinaryIO, PathLike[str]],
+        format: Literal["jaspar16"],
+        *,
+        protein: bool = False,
+    ) -> None: ...
     def __iter__(self) -> Loader[M]: ...
     def __next__(self) -> M: ...
 
 def create(
-    sequences: Iterable[str], protein: bool = False, name: Optional[str] = None
+    sequences: Iterable[str], *, protein: bool = False, name: Optional[str] = None
 ) -> Motif: ...
-def stripe(sequence: str, protein: bool = False) -> StripedSequence: ...
+def stripe(sequence: str, *, protein: bool = False) -> StripedSequence: ...
 def scan(
     pssm: ScoringMatrix,
     sequence: StripedSequence,
+    *,
     threshold: float = 0.0,
     block_size: int = 256,
 ) -> Scanner: ...
@@ -143,33 +155,33 @@ def load(
     file: Union[BinaryIO, PathLike[str]],
     format: Literal["jaspar"],
     *,
-    protein: bool = False
+    protein: bool = False,
 ) -> Loader[JasparMotif]: ...
 @typing.overload
 def load(
     file: Union[BinaryIO, PathLike[str]],
     format: Literal["jaspar16"],
     *,
-    protein: bool = False
+    protein: bool = False,
 ) -> Loader[JasparMotif]: ...
 @typing.overload
 def load(
     file: Union[BinaryIO, PathLike[str]],
     format: Literal["uniprobe"],
     *,
-    protein: bool = False
+    protein: bool = False,
 ) -> Loader[UniprobeMotif]: ...
 @typing.overload
 def load(
     file: Union[BinaryIO, PathLike[str]],
     format: Literal["transfac"],
     *,
-    protein: bool = False
+    protein: bool = False,
 ) -> Loader[TransfacMotif]: ...
 @typing.overload
 def load(
     file: Union[BinaryIO, PathLike[str]],
     format: FORMAT = "jaspar",
     *,
-    protein: bool = False
+    protein: bool = False,
 ) -> Loader[Motif]: ...

lightmotif-py/lightmotif/lib.rs

@@ -434,7 +434,7 @@ impl CountMatrix {
     /// Create a new count matrix.
     #[new]
     #[allow(unused_variables)]
-    #[pyo3(signature = (values, protein = false))]
+    #[pyo3(signature = (values, *, protein = false))]
     pub fn __init__<'py>(
         values: Bound<'py, PyDict>,
         protein: bool,
@@ -746,50 +746,63 @@ impl ScoringMatrix {
 impl ScoringMatrix {
     /// Create a new scoring matrix.
     #[new]
-    #[pyo3(signature = (alphabet, values, background = None))]
+    #[pyo3(signature = (values, background = None, *, protein = false))]
     #[allow(unused)]
     pub fn __init__<'py>(
-        alphabet: Bound<'py, PyString>,
         values: Bound<'py, PyDict>,
         background: Option<PyObject>,
+        protein: bool,
     ) -> PyResult<PyClassInitializer<Self>> {
-        // extract the background from the method argument
-        let bg = Python::with_gil(|py| {
-            if let Some(obj) = background {
-                if let Ok(d) = obj.extract::<Bound<PyDict>>(py) {
-                    let p = dict_to_alphabet_array::<Dna>(d)?;
-                    lightmotif::abc::Background::new(p)
-                        .map_err(|_| PyValueError::new_err("Invalid background frequencies"))
-                } else {
-                    Err(PyTypeError::new_err("Invalid type for pseudocount"))
-                }
-            } else {
-                Ok(lightmotif::abc::Background::uniform())
-            }
-        })?;
-
-        // build data
-        let mut data: Option<DenseMatrix<f32, <Dna as Alphabet>::K>> = None;
-        for s in Dna::symbols() {
-            let key = String::from(s.as_char());
-            if let Some(res) = values.get_item(&key)? {
-                let column = res.downcast::<PyList>()?;
-                if data.is_none() {
-                    data = Some(DenseMatrix::new(column.len()));
-                }
-                let matrix = data.as_mut().unwrap();
-                if matrix.rows() != column.len() {
-                    return Err(PyValueError::new_err("Invalid number of rows"));
+        macro_rules! run {
+            ($alphabet:ty) => {{
+                // extract the background from the method argument
+                let bg = Python::with_gil(|py| {
+                    if let Some(obj) = background {
+                        if let Ok(d) = obj.extract::<Bound<PyDict>>(py) {
+                            let p = dict_to_alphabet_array::<$alphabet>(d)?;
+                            lightmotif::abc::Background::<$alphabet>::new(p).map_err(|_| {
+                                PyValueError::new_err("Invalid background frequencies")
+                            })
+                        } else {
+                            Err(PyTypeError::new_err("Invalid type for pseudocount"))
+                        }
+                    } else {
+                        Ok(lightmotif::abc::Background::uniform())
+                    }
+                })?;
+                // build data
+                let mut data: Option<DenseMatrix<f32, <$alphabet as Alphabet>::K>> = None;
+                for s in <$alphabet as Alphabet>::symbols() {
+                    let key = String::from(s.as_char());
+                    if let Some(res) = values.get_item(&key)? {
+                        let column = res.downcast::<PyList>()?;
+                        if data.is_none() {
+                            data = Some(DenseMatrix::new(column.len()));
+                        }
+                        let matrix = data.as_mut().unwrap();
+                        if matrix.rows() != column.len() {
+                            return Err(PyValueError::new_err("Invalid number of rows"));
+                        }
+                        for (i, x) in column.iter().enumerate() {
+                            matrix[i][s.as_index()] = x.extract::<f32>()?;
+                        }
+                    }
                 }
-                for (i, x) in column.iter().enumerate() {
-                    matrix[i][s.as_index()] = x.extract::<f32>()?;
+                // create matrix
+                match data {
+                    None => Err(PyValueError::new_err("Invalid count matrix")),
+                    Some(matrix) => Ok(Self::new(lightmotif::ScoringMatrix::<$alphabet>::new(
+                        bg, matrix,
+                    ))
+                    .into()),
                 }
-            }
+            }};
         }
 
-        match data {
-            None => Err(PyValueError::new_err("Invalid count matrix")),
-            Some(matrix) => Ok(Self::new(lightmotif::ScoringMatrix::<Dna>::new(bg, matrix)).into()),
+        if protein {
+            run!(Protein)
+        } else {
+            run!(Dna)
         }
     }
 
@@ -1272,7 +1285,7 @@ impl From<lightmotif::scan::Hit> for Hit {
 ///         or when the sequence lengths are not consistent.
 ///
 #[pyfunction]
-#[pyo3(signature = (sequences, protein = false, name = None))]
+#[pyo3(signature = (sequences, *, protein = false, name = None))]
 pub fn create(sequences: Bound<PyAny>, protein: bool, name: Option<String>) -> PyResult<Motif> {
     let py = sequences.py();
     macro_rules! run {
@@ -1323,7 +1336,7 @@ pub fn create(sequences: Bound<PyAny>, protein: bool, name: Option<String>) -> P
 ///     `ValueError`: When the sequences contains an invalid character.
 ///
 #[pyfunction]
-#[pyo3(signature = (sequence, protein=false))]
+#[pyo3(signature = (sequence, *, protein=false))]
 pub fn stripe(sequence: Bound<PyString>, protein: bool) -> PyResult<StripedSequence> {
     let py = sequence.py();
     let encoded = EncodedSequence::__init__(sequence, protein).and_then(|e| Py::new(py, e))?;
@@ -1359,7 +1372,7 @@ pub fn stripe(sequence: Bound<PyString>, protein: bool) -> PyResult<StripedSeque
 ///     implementation requirements.  
 ///
 #[pyfunction]
-#[pyo3(signature = (pssm, sequence, threshold = 0.0, block_size = 256))]
+#[pyo3(signature = (pssm, sequence, *, threshold = 0.0, block_size = 256))]
 pub fn scan<'py>(
     pssm: Bound<'py, ScoringMatrix>,
     sequence: Bound<'py, StripedSequence>,