handle datetime with sub seconds

Author: iiSeymour

bonito/fast5.py

@@ -14,6 +14,7 @@
 import torch
 import numpy as np
 from tqdm import tqdm
+from dateutil import parser
 from scipy.signal import find_peaks
 from ont_fast5_api.fast5_interface import get_fast5_file
 
@@ -67,7 +68,7 @@ def __init__(self, read, filename, meta=False):
         self.start = read_attrs['start_time'] / self.sampling_rate
         self.duration = read_attrs['duration'] / self.sampling_rate
 
-        exp_start_dt = datetime.strptime(self.exp_start_time, "%Y-%m-%dT%H:%M:%S")
+        exp_start_dt = parser.parse(self.exp_start_time)
         start_time = exp_start_dt + timedelta(seconds=self.start)
         self.start_time = start_time.replace(microsecond=0).isoformat()
 

requirements-cuda111.txt

@@ -11,6 +11,7 @@ requests==2.25.1
 ont-remora==0.1.1
 ont-fast5-api==3.3.0
 fast-ctc-decode==0.3.0
+python-dateutil==2.8.2
 # cuda requirements
 torch==1.10.0+cu111
 koi-cuda111==0.0.5

requirements-cuda113.txt

@@ -11,6 +11,7 @@ requests==2.25.1
 ont-remora==0.1.1
 ont-fast5-api==3.3.0
 fast-ctc-decode==0.3.0
+python-dateutil==2.8.2
 # cuda requirements
 torch==1.10.0+cu113
 koi-cuda113==0.0.5

requirements.txt

@@ -11,6 +11,7 @@ requests==2.25.1
 ont-remora==0.1.1
 ont-fast5-api==3.3.0
 fast-ctc-decode==0.3.0
+python-dateutil==2.8.2
 # cuda requirements
 torch~=1.10.0
 koi-cuda102==0.0.5