JupyterLab fails looking for old Anaconda installation, not new (Homebrew) location

[bobtodd]

Howdy y'all,

I used to have Anaconda installed via the Mac OS installer in my home folder in the default location ($HOME/anaconda). Referring to this thread, which itself refers to the official Anaconda instructions, I uninstalled Anaconda.

I reinstalled Anaconda from the Homebrew Cask (placing export PATH=/usr/local/anaconda3/bin:"$PATH" in my .bashrc). Now when I

• run jupyter-lab,
• create a new notebook, and
• select a Python 3 kernel,

the process fails with the following output:

Traceback (most recent call last):
  File "/usr/local/anaconda3/lib/python3.6/site-packages/tornado/web.py", line 1543, in _execute
    result = yield result
  File "/usr/local/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 1099, in run
    value = future.result()
  File "/usr/local/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 1107, in run
    yielded = self.gen.throw(*exc_info)
  File "/usr/local/anaconda3/lib/python3.6/site-packages/notebook/services/sessions/handlers.py", line 73, in post
    type=mtype))
  File "/usr/local/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 1099, in run
    value = future.result()
  File "/usr/local/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 1107, in run
    yielded = self.gen.throw(*exc_info)
  File "/usr/local/anaconda3/lib/python3.6/site-packages/notebook/services/sessions/sessionmanager.py", line 79, in create_session
    kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name)
  File "/usr/local/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 1099, in run
    value = future.result()
  File "/usr/local/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 1107, in run
    yielded = self.gen.throw(*exc_info)
  File "/usr/local/anaconda3/lib/python3.6/site-packages/notebook/services/sessions/sessionmanager.py", line 92, in start_kernel_for_session
    self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name)
  File "/usr/local/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 1099, in run
    value = future.result()
  File "/usr/local/anaconda3/lib/python3.6/site-packages/tornado/gen.py", line 315, in wrapper
    yielded = next(result)
  File "/usr/local/anaconda3/lib/python3.6/site-packages/notebook/services/kernels/kernelmanager.py", line 148, in start_kernel
    super(MappingKernelManager, self).start_kernel(**kwargs)
  File "/usr/local/anaconda3/lib/python3.6/site-packages/jupyter_client/multikernelmanager.py", line 110, in start_kernel
    km.start_kernel(**kwargs)
  File "/usr/local/anaconda3/lib/python3.6/site-packages/jupyter_client/manager.py", line 259, in start_kernel
    **kw)
  File "/usr/local/anaconda3/lib/python3.6/site-packages/jupyter_client/manager.py", line 204, in _launch_kernel
    return launch_kernel(kernel_cmd, **kw)
  File "/usr/local/anaconda3/lib/python3.6/site-packages/jupyter_client/launcher.py", line 128, in launch_kernel
    proc = Popen(cmd, **kwargs)
  File "/usr/local/anaconda3/lib/python3.6/subprocess.py", line 709, in __init__
    restore_signals, start_new_session)
  File "/usr/local/anaconda3/lib/python3.6/subprocess.py", line 1344, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '~/anaconda/bin/python': '~/anaconda/bin/python'

I'm not sure why this error is occurring: I specifically removed all of the $HOME/anaconda references from my path. Does anyone happen to know why the program would be searching $HOME/anaconda (my old install location), when Homebrew installed (without error) into /usr/local/anaconda3? I'm not clear on where JupyterLab could be looking, such that it finds a reference to that old path, when I've removed it from my user setup. Everything else in the traceback is correctly looking in /usr/local/anaconda3/.

I've tried using grep to find what file might have that old path stored in it, and all I find is Library/Caches/com.apple.Safari/WebKitCache/Version 12/Records/. Presumably that's because JupyterLab opened with my default browser as Safari. But when I try to run in Chrome, I get the same error.

I tried seeking help with the folks at Homebrew, but it seems this is not quite in their purview.

Any suggestions would be greatly appreciated.

Peace out,
Todd

[bobtodd]

It was suggested that I post the question to StackOverflow, so as not to take up project bandwidth here. I've asked the question here. Closing the issue.

[jasongrout]

Perhaps it is a kernel config file pointing there? Try doing jupyter kernelspec list to see where your kernels are defined, and look at those to see if one references the old path.

[bobtodd]

Super. Thanks for pointing out that command. My output is

> jupyter kernelspec list
Available kernels:
  python3    ~/Library/Jupyter/kernels/python3

Looking in that directory, there's a file kernel.json (which is roughly a year old, so older than my new install) with the following contents:

{
 "display_name": "Python 3",
 "argv": [
  "~/anaconda/bin/python",
  "-m",
  "ipykernel_launcher",
  "-f",
  "{connection_file}"
 ],
 "language": "python"
}

It looks like you're right that that's (at least one of the places) where JupyterLab is picking up that path from.

How do you suggest I fix this? Should I edit the file directly inserting the output of which

> which python3
/usr/local/anaconda3/bin/python3

which is what I'd be expecting given the setup with Anaconda installed via Homebrew? Or should I remove the file... and perhaps let the system rebuild it (if it does that)?

Thanks very much for the help.

[jasongrout]

If I were you, I'd just delete that directory. Then check to see if jupyter kernelspec list gives another kernel.

[bobtodd]

Great suggestion. I removed the directory and re-ran jupyter kernelspec list. That yielded

> jupyter kernelspec list
Available kernels:
  python3    /usr/local/anaconda3/share/jupyter/kernels/python3

as hoped. Things seem to be working now. Thanks for the help.

[tzuhsuancheng]

Thanks for the help!!!!

[jasongrout]

No problem!