Fix all typing errors and run mypy in pre-commit

.pre-commit-config.yaml

@@ -19,3 +19,7 @@ repos:
   rev: 22.3.0
   hooks:
     - id: black
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v1.3.0
+  hooks:
+  -   id: mypy

bletl/core.py

@@ -8,7 +8,7 @@
 import urllib.request
 import warnings
 from collections.abc import Iterable
-from typing import Optional, Union
+from typing import Optional, Sequence, Union
 
 import numpy
 import pandas
@@ -92,14 +92,14 @@ def get_parser(filepath: Union[str, pathlib.Path]) -> BLDParser:
 def _parse(
     filepath: str,
     drop_incomplete_cycles: bool,
-    lot_number: int,
-    temp: int,
-    cal_0: float = None,
-    cal_100: float = None,
-    phi_min: float = None,
-    phi_max: float = None,
-    pH_0: float = None,
-    dpH: float = None,
+    lot_number: Optional[int],
+    temp: Optional[int],
+    cal_0: Optional[float] = None,
+    cal_100: Optional[float] = None,
+    phi_min: Optional[float] = None,
+    phi_max: Optional[float] = None,
+    pH_0: Optional[float] = None,
+    dpH: Optional[float] = None,
 ) -> BLData:
     """Parses a raw BioLector CSV file into a BLData object.
 
@@ -138,29 +138,39 @@ def _parse(
         When the file contents do not match with a known BioLector result file format.
     """
     parser = get_parser(filepath)
-    data = parser.parse(filepath, lot_number, temp, cal_0, cal_100, phi_min, phi_max, pH_0, dpH)
+    data = parser.parse(
+        filepath,
+        lot_number=lot_number,
+        temp=temp,
+        cal_0=cal_0,
+        cal_100=cal_100,
+        phi_min=phi_min,
+        phi_max=phi_max,
+        pH_0=pH_0,
+        dpH=dpH,
+    )
 
     if (not data.measurements.empty) and drop_incomplete_cycles:
         index_names, measurements = utils._unindex(data.measurements)
         latest_full_cycle = utils._last_full_cycle(measurements)
         measurements = measurements[measurements.cycle <= latest_full_cycle]
-        data._measurements = utils._reindex(measurements, index_names)
+        data._measurements = utils._reindex(measurements, index_names)  # type: ignore
 
     return data
 
 
 def parse(
-    filepaths,
+    filepaths: Union[str, Sequence[str]],
     *,
     drop_incomplete_cycles: bool = True,
-    lot_number: int = None,
-    temp: int = None,
-    cal_0: float = None,
-    cal_100: float = None,
-    phi_min: float = None,
-    phi_max: float = None,
-    pH_0: float = None,
-    dpH: float = None,
+    lot_number: Optional[int] = None,
+    temp: Optional[int] = None,
+    cal_0: Optional[float] = None,
+    cal_100: Optional[float] = None,
+    phi_min: Optional[float] = None,
+    phi_max: Optional[float] = None,
+    pH_0: Optional[float] = None,
+    dpH: Optional[float] = None,
 ) -> BLData:
     """Parses a raw BioLector CSV file into a BLData object and applies calibration.
 

bletl/growth.py

@@ -1,5 +1,6 @@
 import logging
 import typing
+from typing import Dict, Optional, Sequence, Tuple, Union
 
 import arviz
 import calibr8
@@ -10,7 +11,7 @@
 try:
     import pytensor.tensor as pt
 except ModuleNotFoundError:
-    import aesara.tensor as pt
+    import aesara.tensor as pt  # type: ignore
 
 
 _log = logging.getLogger(__file__)
@@ -22,13 +23,13 @@ class GrowthRateResult:
     def __init__(
         self,
         *,
-        t_data: numpy.ndarray,
-        t_segments: numpy.ndarray,
-        y: numpy.ndarray,
+        t_data: Union[Sequence[float], numpy.ndarray],
+        t_segments: Union[Sequence[float], numpy.ndarray],
+        y: Union[Sequence[float], numpy.ndarray],
         calibration_model: calibr8.CalibrationModel,
-        switchpoints: typing.Dict[float, str],
+        switchpoints: Dict[float, str],
         pmodel: pm.Model,
-        theta_map: dict,
+        theta_map: Dict[str, numpy.ndarray],
     ):
         """Creates a result object of a growth rate analysis.
 
@@ -47,9 +48,9 @@ def __init__(
         theta_map : dict
             the PyMC MAP estimate
         """
-        self._t_data = t_data
-        self._t_segments = t_segments
-        self._y = y
+        self._t_data = numpy.asarray(t_data)
+        self._t_segments = numpy.asarray(t_segments)
+        self._y = numpy.asarray(y)
         self._switchpoints = switchpoints
         self.calibration_model = calibration_model
         self._pmodel = pmodel
@@ -73,17 +74,17 @@ def y(self) -> numpy.ndarray:
         return self._y
 
     @property
-    def switchpoints(self) -> typing.Dict[float, str]:
+    def switchpoints(self) -> Dict[float, str]:
         """Dictionary (by time) of known and detected switchpoints."""
         return self._switchpoints
 
     @property
-    def known_switchpoints(self) -> typing.Tuple[float]:
+    def known_switchpoints(self) -> Tuple[float, ...]:
         """Time values of previously known switchpoints in the model."""
         return tuple(t for t, label in self.switchpoints.items() if label != "detected")
 
     @property
-    def detected_switchpoints(self) -> typing.Tuple[float]:
+    def detected_switchpoints(self) -> Tuple[float, ...]:
         """Time values of switchpoints that were autodetected from the fit."""
         return tuple(t for t, label in self.switchpoints.items() if label == "detected")
 
@@ -93,12 +94,12 @@ def pmodel(self) -> pm.Model:
         return self._pmodel
 
     @property
-    def theta_map(self) -> dict:
+    def theta_map(self) -> Dict[str, numpy.ndarray]:
         """MAP estimate of the model parameters."""
         return self._theta_map
 
     @property
-    def idata(self) -> typing.Optional[arviz.InferenceData]:
+    def idata(self) -> Optional[arviz.InferenceData]:
         """ArviZ InferenceData object of the MCMC trace."""
         return self._idata
 
@@ -113,18 +114,20 @@ def x_map(self) -> numpy.ndarray:
         return self.theta_map["X"]
 
     @property
-    def mu_mcmc(self) -> typing.Optional[numpy.ndarray]:
+    def mu_mcmc(self) -> Optional[numpy.ndarray]:
         """Posterior samples of growth rates in segments between data points."""
         if not self.idata:
             return None
+        assert hasattr(self.idata, "posterior")
         return self.idata.posterior.mu_t.stack(sample=("chain", "draw")).values.T
 
     @property
-    def x_mcmc(self) -> typing.Optional[numpy.ndarray]:
+    def x_mcmc(self) -> Optional[numpy.ndarray]:
         """Posterior samples of biomass curve."""
-        if not self.idata:
+        if self.idata is None:
             return None
-        return self._idata.posterior["X"].stack(sample=("chain", "draw")).T
+        assert hasattr(self.idata, "posterior")
+        return self.idata.posterior["X"].stack(sample=("chain", "draw")).T
 
     def sample(self, **kwargs) -> None:
         """Runs MCMC sampling with default settings on the growth model.
@@ -157,8 +160,8 @@ def _make_random_walk(
     nu: float = 1,
     length: int,
     student_t: bool,
-    initval: numpy.ndarray = None,
-    dims: typing.Optional[str] = None,
+    initval: Optional[numpy.ndarray] = None,
+    dims: Optional[str] = None,
 ):
     """Create a random walk with either a Normal or Student-t distribution.
 
@@ -215,7 +218,11 @@ def _make_random_walk(
 
 
 def _get_smoothed_mu(
-    t: numpy.ndarray, y: numpy.ndarray, cm_cdw: calibr8.CalibrationModel, *, clip=0.5
+    t: Sequence[float],
+    y: Sequence[float],
+    cm_cdw: calibr8.CalibrationModel,
+    *,
+    clip: float = 0.5,
 ) -> numpy.ndarray:
     """Calculate a rough estimate of the specific growth rate from smoothed observations.
 
@@ -236,10 +243,10 @@ def _get_smoothed_mu(
         A vector of specific growth rates.
     """
     # apply moving average to reduce backscatter noise
-    y = numpy.convolve(y, numpy.ones(5) / 5, "same")
+    yarr = numpy.convolve(y, numpy.ones(5) / 5, "same")
 
     # convert to biomass
-    X = cm_cdw.predict_independent(y)
+    X = cm_cdw.predict_independent(yarr)
 
     # calculate growth rate
     dX = numpy.diff(X)
@@ -259,17 +266,17 @@ def _get_smoothed_mu(
 
 
 def fit_mu_t(
-    t: typing.Sequence[float],
-    y: typing.Sequence[float],
+    t: Sequence[float],
+    y: Sequence[float],
     calibration_model: calibr8.CalibrationModel,
     *,
-    switchpoints: typing.Optional[typing.Union[typing.Sequence[float], typing.Dict[float, str]]] = None,
+    switchpoints: Optional[Union[Sequence[float], Dict[float, str]]] = None,
     mcmc_samples: int = 0,
     mu_prior: float = 0,
     drift_scale: float,
     nu: float = 5,
     x0_prior: float = 0.25,
-    student_t: typing.Optional[bool] = None,
+    student_t: Optional[bool] = None,
     switchpoint_prob: float = 0.01,
     replicate_id: str = "unnamed",
 ):
@@ -357,7 +364,7 @@ def fit_mu_t(
             mu_segments = []
             i_from = 0
             for i, t_switch in enumerate(t_switchpoints_known):
-                i_to = numpy.argmax(t > t_switch)
+                i_to = int(numpy.argmax(t > t_switch))
                 i_len = len(t[i_from:i_to])
                 name = f"mu_phase_{i}"
                 slc = slice(i_from, i_to)
@@ -460,10 +467,10 @@ def fit_mu_t(
 
 def detect_switchpoints(
     switchpoint_prob: float,
-    t_data: typing.Sequence[float],
+    t_data: Sequence[float],
     pmodel: pm.Model,
-    theta_map: typing.Dict[str, numpy.ndarray],
-) -> typing.Dict[float, str]:
+    theta_map: Dict[str, numpy.ndarray],
+) -> Dict[float, str]:
     """Helper function to detect switchpoints from a fitted random walk.
 
     Parameters
@@ -509,15 +516,15 @@ def detect_switchpoints(
             # To get our <number of segments> length vector to align with the <number of points>,
             # we prepend a 0.5 as a placeholder for the CDF of the initial point of the random walk.
             cdf_evals += [0.5, *numpy.exp(logcdfs)]
-    cdf_evals = numpy.array(cdf_evals)
-    if len(cdf_evals) != len(t_data) - 1:
+    cdf_evals_arr = numpy.array(cdf_evals)
+    if len(cdf_evals_arr) != len(t_data) - 1:
         raise Exception(
-            f"Failed to find all random walk segments. Found {len(cdf_evals)}, expected {len(t_data) - 1}."
+            f"Failed to find all random walk segments. Found {len(cdf_evals_arr)}, expected {len(t_data) - 1}."
         )
     # Filter for the elements that lie outside of the [0.005, 0.995] interval (if switchpoint_prob=0.01).
     significance_mask = numpy.logical_or(
-        cdf_evals < (switchpoint_prob / 2),
-        cdf_evals > (1 - switchpoint_prob / 2),
+        cdf_evals_arr < (switchpoint_prob / 2),
+        cdf_evals_arr > (1 - switchpoint_prob / 2),
     )
     # Collect switchpoint information from points with significant CDF values.
     # Here we don't need to filter known switchpoints, because these correspond to the first

bletl/parsing/bl1.py

@@ -92,12 +92,12 @@ def calibrate_with_lot(self, data: BLData, lot_number: Optional[int] = None, tem
     def calibrate_with_parameters(
         self,
         data: BLData,
-        cal_0: float = None,
-        cal_100: float = None,
-        phi_min: float = None,
-        phi_max: float = None,
-        pH_0: float = None,
-        dpH: float = None,
+        cal_0: Optional[float] = None,
+        cal_100: Optional[float] = None,
+        phi_min: Optional[float] = None,
+        phi_max: Optional[float] = None,
+        pH_0: Optional[float] = None,
+        dpH: Optional[float] = None,
     ):
         def process_backscatter(raw_data_df, cycle_ref_df, global_ref):
             """
@@ -182,14 +182,14 @@ def process_DO(raw_data_df, cal_0, cal_100):
     def parse(
         self,
         filepath,
-        lot_number: int = None,
-        temp: int = None,
-        cal_0: float = None,
-        cal_100: float = None,
-        phi_min: float = None,
-        phi_max: float = None,
-        pH_0: float = None,
-        dpH: float = None,
+        lot_number: Optional[int] = None,
+        temp: Optional[int] = None,
+        cal_0: Optional[float] = None,
+        cal_100: Optional[float] = None,
+        phi_min: Optional[float] = None,
+        phi_max: Optional[float] = None,
+        pH_0: Optional[float] = None,
+        dpH: Optional[float] = None,
     ):
         headerlines, data = split_header_data(filepath)
 
@@ -476,6 +476,8 @@ def fetch_calibration_data(lot_number: int, temp: int):
         Dictionary containing calibration data.
         Can be readily used in calibration function.
     """
+    assert utils.__spec__ is not None
+    assert utils.__spec__.origin is not None
     module_path = pathlib.Path(utils.__spec__.origin).parents[0]
     calibration_file = pathlib.Path(module_path, "cache", "CalibrationLot.ini")