diff --git a/mypy.ini b/mypy.ini index 38010937..f7bc0335 100644 --- a/mypy.ini +++ b/mypy.ini @@ -1,4 +1,11 @@ [mypy] +plugins = pydantic.mypy ignore_missing_imports = True python_version = 3.8 + +[pydantic-mypy] +init_typed = true + +init_forbid_extra = True +warn_untyped_fields = True diff --git a/src/ramanchada2/io/experimental/read_txt.py b/src/ramanchada2/io/experimental/read_txt.py index bb2e6740..7a85a970 100644 --- a/src/ramanchada2/io/experimental/read_txt.py +++ b/src/ramanchada2/io/experimental/read_txt.py @@ -21,9 +21,9 @@ def read_txt(data_in: TextIO) -> Tuple[NDArray, NDArray, Dict]: lines = data_in.readlines() if lines[0].startswith('File Version;BW'): data, meta = bw_format(lines) - positions = data['RamanShift'] - intensities = data['DarkSubtracted#1'] + positions = data['RamanShift'].to_numpy() + intensities = data['DarkSubtracted#1'].to_numpy() else: # assume two column spectrum positions, intensities = two_column_spe(lines) meta = dict() - return positions.to_numpy(), intensities.to_numpy(), meta + return positions, intensities, meta diff --git a/src/ramanchada2/spectrum/peaks/find_peaks.py b/src/ramanchada2/spectrum/peaks/find_peaks.py index 1b9e8ac8..5b66c7aa 100644 --- a/src/ramanchada2/spectrum/peaks/find_peaks.py +++ b/src/ramanchada2/spectrum/peaks/find_peaks.py @@ -2,7 +2,7 @@ from typing import Union, Tuple, List from scipy import signal -from pydantic import validate_arguments, Field +from pydantic import validate_arguments, PositiveFloat from ..spectrum import Spectrum from ramanchada2.misc.spectrum_deco import (add_spectrum_method, @@ -44,7 +44,7 @@ def find_peak_groups( prominence: float = 1e-2, wlen=None, width: Union[int, Tuple[int, int]] = 1, - n_sigma_group: float = Field(5, ge=0) + n_sigma_group: PositiveFloat = 5. ) -> List[PeakCandidatesListModel]: res = signal.find_peaks(spe.y, prominence=prominence, width=width, wlen=wlen) return PeakCandidatesListModel.from_find_peaks(res).group_neighbours(n_sigma=n_sigma_group)