From 08af45eda33f0dabe07f13802d548344e20000cb Mon Sep 17 00:00:00 2001
From: Jake Bradford <jake.bradford@qut.edu.au>
Date: Thu, 11 Jan 2024 13:50:21 +1000
Subject: [PATCH] github-issue-10

fixed timestamp issues
---
 src/crackling/Crackling.py | 18 +++++++++---------
 src/crackling/Helpers.py   | 13 ++++++++++++-
 2 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/src/crackling/Crackling.py b/src/crackling/Crackling.py
index 3cdd376..ed646cf 100644
--- a/src/crackling/Crackling.py
+++ b/src/crackling/Crackling.py
@@ -7,7 +7,7 @@
     - See config.ini
 '''
 
-import ast, csv, joblib, os, re, sys, time, tempfile
+import ast, csv, joblib, os, re, sys, time, tempfile, shutil
 
 from crackling.Paginator import Paginator
 from crackling.Batchinator import Batchinator
@@ -875,17 +875,17 @@ def processSequence(sequence):
 
         printer(f'{len(candidateGuides)} guides evaluated.')
 
-        printer('This batch ran in {} (dd hh:mm:ss) or {} seconds'.format(
-            time.strftime('%d %H:%M:%S', time.gmtime((time.time() - batchStartTime))),
-            (time.time() - batchStartTime)
-        ))
+        batchEndTime = time.time()
+        timeDelta = batchEndTime - batchStartTime
+
+        printer(f'This batch ran in {elapsedTimeString(batchStartTime, batchEndTime)} (dd hh:mm:ss) or {timeDelta:.3} seconds')
 
         batchFileId += 1
 
-    printer('Total run time (dd hh:mm:ss) or {} seconds'.format(
-        time.strftime('%d %H:%M:%S', time.gmtime((time.time() - startTime))),
-        (time.time() - startTime)
-    ))
+    endTime = time.time()
+    timeDelta = endTime - startTime
+
+    printer(f'Total run time {elapsedTimeString(startTime, endTime)} (dd hh:mm:ss) or {timeDelta:.3} seconds')
 
     sys.stdout.log.close()
     sys.stderr.log.close()
diff --git a/src/crackling/Helpers.py b/src/crackling/Helpers.py
index 6424f9a..a6d7b60 100644
--- a/src/crackling/Helpers.py
+++ b/src/crackling/Helpers.py
@@ -1,7 +1,7 @@
 from subprocess import run
 from datetime import datetime
 
-__all__ = ['rc','transToDNA','AT_percentage','printer','runner']
+__all__ = ['rc','transToDNA','AT_percentage','printer','runner','elapsedTimeString']
 
 # Function that returns the reverse-complement of a given sequence
 def rc(dna):
@@ -40,3 +40,14 @@ def runner(*args, **kwargs):
     printer(f"| Calling: {args}")
     run(*args, **kwargs)
     printer(f"| Finished")
+
+
+# Function that generates a string representing elapsed time
+def elapsedTimeString(start_time, end_time):
+    elapsed_seconds = end_time - start_time
+
+    days, remainder = divmod(elapsed_seconds, 86400)
+    hours, remainder = divmod(remainder, 3600)
+    minutes, seconds = divmod(remainder, 60)
+
+    return f"{int(days)} {int(hours):02d}:{int(minutes):02d}:{int(seconds):02d}"