2nd miniconda install broken jupyter nb_conda

[nick-youngblut]

My research lab and I use a centralized install of miniconda (not installed via root). We've been using conda <v4.4 due to issues with installing certain software for conda >=4.4. In order to start the transition to >4.4, I created a 2nd centralized install of miniconda. Installing this 2nd version of conda seems to have broken nb_conda for all of our Jupyter notebooks. For creating new notebooks, we now only have two options: "Python 3" or "R". Previously, we could select from ~15 different conda environments. When I click on the "conda" table in Jupyter, I get an error, and this is reported on the command line:

[E 13:43:46.719 NotebookApp] 500 GET /conda/packages/available?_=1519649013685 (127.0.0.1) 44.97ms referer=http://127.0.0.1:9705/tree?
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/exceptions.py", line 640, in conda_exception_handler
    return_value = func(*args, **kwargs)
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/cli/main.py", line 103, in _main
    from ..base.context import context
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/base/context.py", line 771, in <module>
    context = Context(SEARCH_PATH, APP_NAME, None)
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/common/configuration.py", line 727, in __init__
    self._set_search_path(search_path)
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/common/configuration.py", line 745, in _set_search_path
    self._set_raw_data(load_file_configs(search_path))
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/common/configuration.py", line 364, in load_file_configs
    expanded_paths = tuple(expand(path) for path in search_path)
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/common/configuration.py", line 364, in <genexpr>
    expanded_paths = tuple(expand(path) for path in search_path)
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/common/path.py", line 247, in expand
    return abspath(expanduser(expandvars(path)))
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/posixpath.py", line 374, in abspath
    cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/ebio/abt3_projects/software/miniconda3/bin/conda", line 11, in <module>
    sys.exit(main())
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/cli/main.py", line 182, in main
    return conda_exception_handler(_main, *args)
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/exceptions.py", line 644, in conda_exception_handler
    return handle_exception(e)
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/exceptions.py", line 634, in handle_exception
    print_unexpected_error_message(e)
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/exceptions.py", line 579, in print_unexpected_error_message
    from .base.context import context
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/base/context.py", line 771, in <module>
    context = Context(SEARCH_PATH, APP_NAME, None)
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/common/configuration.py", line 727, in __init__
    self._set_search_path(search_path)
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/common/configuration.py", line 745, in _set_search_path
    self._set_raw_data(load_file_configs(search_path))
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/common/configuration.py", line 364, in load_file_configs
    expanded_paths = tuple(expand(path) for path in search_path)
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/common/configuration.py", line 364, in <genexpr>
    expanded_paths = tuple(expand(path) for path in search_path)
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/site-packages/conda/common/path.py", line 247, in expand
    return abspath(expanduser(expandvars(path)))
  File "/ebio/abt3_projects/software/miniconda3/lib/python3.6/posixpath.py", line 374, in abspath
    cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
[E 13:45:08.273 NotebookApp] [nb_conda_kernels] couldn't call conda:

Why did a 2nd conda install affect nb_conda? Isn't everything contained in the conda install directory? Any ideas on how I revert back? Our whole research group of ~20 people now do not have access to the conda environments in Jupyter.

[nick-youngblut]

The simple fix was to restart all of the Jupyter notebook servers. I still don't see why a new conda install (with nb_conda installed in it) would affect Jupyter notebooks servers running from a different conda install. At least it was relatively easy to fix.

[tjd2002]

Maybe related to this bug: anaconda/nb_conda_kernels#73?
(Open pull request with fix at anaconda/nb_conda_kernels#79 )

I say that because of the lines

FileNotFoundError: [Errno 2] No such file or directory
[E 13:45:08.273 NotebookApp] [nb_conda_kernels] couldn't call conda: