AttributeError: module 'time' has no attribute 'clock'

[ARW-UBT]

AttributeError: module 'time' has no attribute 'clock'

[transcript]

Ah, it looks like time.clock() was removed in Python 3.8. I'll probably update these to time.time() instead; you could make the swap yourself if you don't want to wait for me to push the changes.

[transcript]

Okay, see commit baa352c - time.clock() is now replaced by time.time(). I don't have Python 3.8 locally, but test this and reopen if there are still issues.

[ARW-UBT]

I have changed time.clock to time.time also in lines 87, 98, 112, and 185 in addition to line 53. Restarted the master script again, but it seems that the entire analyses are repeated from the very beginning, although the checkpoints file existed in the input dir. I will see if this applies only to the trimmomatic step or to all other steps, too.
Unfortunately, the script failed after 7 days.
Are there other py scripts which should be edited for time.time?

[ARW-UBT]

Sorry, I have overlooked that you did change this also in other scripts (#61). I assume the easiest way is to replace the local files with yours from python_scripts, right? Those modified a few hours ago.
Thanks for your help!

[transcript]

Hi, yes, I went ahead and pushed a new commit with time.clock() replaced in all Python files. The easiest solution is to pull the new files and relaunch.

For the master_script.sh, you can always comment out the already-completed steps, or create an edited version of the file and delete the steps that have already been run. There is some limited step-checking, but especially if you are re-pulling the repo, it makes sense to manually cut the steps that have already been completed.