Jupyter notebook progress bar

[palakpsheth]

Using dorado, after v0.3.0, the progress bar when duplex basecalling in an interactive jupyter notebook no longer appears. I understand that there was an intentional change made. Any recommendations on how to get the progress bar back when calling dorado commands via subprocess call in python?

thank you!

[GeorgeNikitinNV]

Had the same problem, fixed in #310.

[palakpsheth]

@GeorgeNikitinNV thanks for the fix but looks like the ONT team didnt merge? any feedback there?

[iiSeymour]

@palakpsheth it seems more people are using the progress bar in none tty environments than expected so I think we should enable it by default again?

fyi you can fake it with Python's pty module like so:

import os
import pty
import subprocess

master, slave = pty.openpty()

# Run the subprocess with the slave side of the pty as its stdin, stdout, and stderr
process = subprocess.Popen(['python3', '-c', 'import sys; print(sys.stdout.isatty())'],
                           stdin=slave, stdout=slave, stderr=slave)

os.close(slave)  # Close the slave side in the parent process

# Read output from the master side
output = os.read(master, 1024).decode('utf-8')
print(output)  # This should print "True"

# Clean up
os.close(master)
process.wait()

[palakpsheth]

@iiSeymour Thanks for the python tip! In my experience, a command line flag to control the progress bar visibility would be most robust. Off by default seems fair to me for user experience consistency with previous release.

Appreciate all the hard work!