[#83] Introduce abstractions for signals and fast5 files (#84)

* [#83] Introduce abstractions for signals and fast5 files

* Removed class method from FractionalizedSignal

* Architecting signal and fast5 data organization

Co-authored-by: Jessica Dunstan <[email protected]>
Co-authored-by: Katie Doroschak <[email protected]>

Author: 3 people

poretitioner/fast5s.py

@@ -6,7 +6,6 @@
 Classes for reading, writing and validating fast5 files.
 """
 
-from dataclasses import dataclass
 from os import PathLike
 from pathlib import Path, PurePosixPath
 from typing import List, NewType, Optional, Union
@@ -21,14 +20,14 @@
     RawSignal,
     VoltageSignal,
 )
+
 from .utils.classify import (
     NULL_CLASSIFICATION_RESULT,
     ClassificationResult,
     ClassifierConfiguration,
     ClassifierDetails,
     NullClassificationResult,
 )
-from .utils.core import NumpyArrayLike
 
 __all__ = ["BulkFile", "CaptureFile", "channel_path_for_read_id", "signal_path_for_read_id"]
 
@@ -348,7 +347,7 @@ def get_voltage(self, start=None, end=None) -> VoltageSignal:
 
         Returns
         -------
-        NumpyArrayLike[int]
+        VoltageSignal[int]
             Voltage(s) in millivolts (mV).
         """
         bias_voltage_multiplier = 5  # Signal changes in increments of 5 mV.

tests/test_signals.py

@@ -180,6 +180,12 @@ def can_serialize_test(self):
 class TestPicoampereSignal:
     def signal_converts_to_fractionalized_test(self):
         pico = PicoampereSignal(PICO_SIGNAL, CHANNEL_NUMBER, CALIBRATION)
+        median = np.median(pico)
+
+        expected = compute_fractional_blockage(pico, median)
+        frac = raw.to_fractionalized()
+        assert np.isclose(frac, expected), "Fractionalized current should match expected."
+
 
 class PicoampereSignalTest:
     def __init__(self):