only base environment being detected/displayed

[fperez]

I have two environments, base and rtc, and in fact this version of JupyterLab was started from the rtc one. From a terminal in Lab I can see conda env list correctly showing both, but gator only shows base:

Any thoughts on what could be happening?

Context

• Python package version:

# Name                    Version                   Build  Channel
mamba_gator               5.1.1              pyhd8ed1ab_0    conda-forge

• Extension version:

(rtc) blanca[~]> jupyter labextension list
JupyterLab v3.1.0a10
/Users/fperez/local/conda/envs/rtc/copip/share/jupyter/labextensions
        spreadsheet-editor v0.5.1 enabled OK (python, jupyterlab-spreadsheet-editor)

/Users/fperez/local/conda/envs/rtc/share/jupyter/labextensions
        jupyterlab-link-share v0.2.0 enabled OK (python, jupyterlab-link-share)
        @mamba-org/gator-lab v3.0.1 enabled OK (python, mamba_gator)
        @retrolab/lab-extension v0.2.1 enabled OK

conda info output

(rtc) blanca[~]> conda info

     active environment : rtc
    active env location : /Users/fperez/local/conda/envs/rtc
            shell level : 2
       user config file : /Users/fperez/.condarc
 populated config files : /Users/fperez/.condarc
          conda version : 4.10.1
    conda-build version : not installed
         python version : 3.9.4.final.0
       virtual packages : __osx=11.4=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /Users/fperez/local/conda  (writable)
      conda av data dir : /Users/fperez/local/conda/etc/conda
  conda av metadata url : https://repo.anaconda.com/pkgs/main
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/fperez/local/conda/pkgs
                          /Users/fperez/.conda/pkgs
       envs directories : /Users/fperez/local/conda/envs
                          /Users/fperez/.conda/envs
               platform : osx-64
             user-agent : conda/4.10.1 requests/2.25.1 CPython/3.9.4 Darwin/20.5.0 OSX/11.4
                UID:GID : 33212:20665
             netrc file : None
           offline mode : False

[fcollonval]

Thanks for reporting the issue @fperez

Could you run JupyterLab in debug mode and report the here the output log?

You should see the executed command and their results.

One source of trouble I have seen previously is due to conda or mamba being installed in the environment itself - although from the result of conda info it does not seems to be the case here.

[hackeye]

[D 2021-06-09 14:12:59.148 ServerApp.mamba_gator] output: [
      {
        "base_url": "https://conda.anaconda.org/pypi",
        "build_number": 0,
        "build_string": "pypi_0",
        "channel": "pypi",
        "dist_name": "aiohttp-3.7.4.post0-pypi_0",
        "name": "aiohttp",
        "platform": "pypi",
        "version": "3.7.4.post0"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 1,
        "build_string": "py38hecd8cb5_1",
        "channel": "pkgs/main",
        "dist_name": "anyio-2.2.0-py38hecd8cb5_1",
        "name": "anyio",
        "platform": "osx-64",
        "version": "2.2.0"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 1001,
        "build_string": "py38hecd8cb5_1001",
        "channel": "pkgs/main",
        "dist_name": "appnope-0.1.2-py38hecd8cb5_1001",
        "name": "appnope",
        "platform": "osx-64",
        "version": "0.1.2"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 1,
        "build_string": "py38h9ed2024_1",
        "channel": "pkgs/main",
        "dist_name": "argon2-cffi-20.1.0-py38h9ed2024_1",
        "name": "argon2-cffi",
        "platform": "osx-64",
        "version": "20.1.0"
      },
      {
        "base_url": "https://conda.anaconda.org/pypi",
        "build_number": 0,
        "build_string": "pypi_0",
        "channel": "pypi",
        "dist_name": "async-timeout-3.0.1-pypi_0",
        "name": "async-timeout",
        "platform": "pypi",
        "version": "3.0.1"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 0,
        "build_string": "pyhd3eb1b0_0",
        "channel": "pkgs/main",
        "dist_name": "async_generator-1.10-pyhd3eb1b0_0",
        "name": "async_generator",
        "platform": "noarch",
        "version": "1.10"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 0,
        "build_string": "pyhd3eb1b0_0",
        "channel": "pkgs/main",
        "dist_name": "attrs-21.2.0-pyhd3eb1b0_0",
        "name": "attrs",
        "platform": "noarch",
        "version": "21.2.0"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 0,
        "build_string": "pyhd3eb1b0_0",
        "channel": "pkgs/main",
        "dist_name": "babel-2.9.1-pyhd3eb1b0_0",
        "name": "babel",
        "platform": "noarch",
        "version": "2.9.1"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 0,
        "build_string": "pyhd3eb1b0_0",
        "channel": "pkgs/main",
        "dist_name": "backcall-0.2.0-pyhd3eb1b0_0",
        "name": "backcall",
        "platform": "noarch",
        "version": "0.2.0"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 1,
        "build_string": "mkl",
        "channel": "pkgs/main",
        "dist_name": "blas-1.0-mkl",
        "name": "blas",
        "platform": "osx-64",
        "version": "1.0"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 0,
        "build_string": "pyhd3eb1b0_0",
        "channel": "pkgs/main",
        "dist_name": "bleach-3.3.0-pyhd3eb1b0_0",
        "name": "bleach",
        "platform": "noarch",
        "version": "3.3.0"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 0,
        "build_string": "py38hecd8cb5_0",
        "channel": "pkgs/main",
        "dist_name": "bokeh-2.3.2-py38hecd8cb5_0",
        "name": "bokeh",
        "platform": "osx-64",
        "version": "2.3.2"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 1003,
        "build_string": "py38h9ed2024_1003",
        "channel": "pkgs/main",
        "dist_name": "brotlipy-0.7.0-py38h9ed2024_1003",
        "name": "brotlipy",
        "platform": "osx-64",
        "version": "0.7.0"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 0,
        "build_string": "h1de35cc_0",
        "channel": "pkgs/main",
        "dist_name": "bzip2-1.0.8-h1de35cc_0",
        "name": "bzip2",
        "platform": "osx-64",
        "version": "1.0.8"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 0,
        "build_string": "h9ed2024_0",
        "channel": "pkgs/main",
        "dist_name": "c-ares-1.17.1-h9ed2024_0",
        "name": "c-ares",
        "platform": "osx-64",
        "version": "1.17.1"
      },
      {
        "base_url": "https://conda.anaconda.org/conda-forge",
        "build_number": 0,
        "build_string": "h033912b_0",
        "channel": "conda-forge",
        "dist_name": "ca-certificates-2021.5.30-h033912b_0",
        "name": "ca-certificates",
        "platform": "osx-64",
        "version": "2021.5.30"
      },
      {
        "base_url": "https://conda.anaconda.org/conda-forge",
        "build_number": 0,
        "build_string": "py38h50d1736_0",
        "channel": "conda-forge",
        "dist_name": "certifi-2021.5.30-py38h50d1736_0",
        "name": "certifi",
        "platform": "osx-64",
        "version": "2021.5.30"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 0,
        "build_string": "py38h2125817_0",
        "channel": "pkgs/main",
        "dist_name": "cffi-1.14.5-py38h2125817_0",
        "name": "cffi",
        "platform": "osx-64",
        "version": "1.14.5"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 1003,
        "build_string": "py38hecd8cb5_1003",
        "channel": "pkgs/main",
        "dist_name": "chardet-4.0.0-py38hecd8cb5_1003",
        "name": "chardet",
        "platform": "osx-64",
        "version": "4.0.0"
      },
      {
        "base_url": "https://conda.anaconda.org/pypi",
        "build_number": 0,
        "build_string": "pypi_0",
        "channel": "pypi",
        "dist_name": "click-8.0.1-pypi_0",
        "name": "click",
        "platform": "pypi",
        "version": "8.0.1"
      },
      {
        "base_url": "https://conda.anaconda.org/pypi",
        "build_number": 0,
        "build_string": "pypi_0",
        "channel": "pypi",
        "dist_name": "cloudpickle-1.6.0-pypi_0",
        "name": "cloudpickle",
        "platform": "pypi",
        "version": "1.6.0"
      },
      {
        "base_url": "https://repo.anaconda.com/pkgs/main",
        "build_number": 0,
        "build_string": "pyhd3eb1b0_0",
        "channel": "pkgs/main",
        "dist_name": "colorama-0.4.4-pyhd3eb1b0_0",
        "name": "colorama",
        "platform": "noarch",
        "version": "0.4.4"
      },
      {
        "base_url": "https://conda.anaconda.org/conda-f
[D 2021-06-09 14:12:59.149 ServerApp.mamba_gator] ...
[D 2021-06-09 14:12:59.150 ServerApp.mamba_gator] 200 GET /conda/environments/base?1623219178377 (::1) 770.83ms

[fcollonval]

Thanks @hackeye

But this is the request to list the package of the base environment. You should see a request GET /conda/environments prior to that one. That is the one listing the environments.

[jamestwebber]

I have a (maybe?) related issue. I just set up a new JupyterLab 3 environment and installed gator to manage conda envs (I previously used nb_conda_kernels but it doesn't look like it works anymore?).

The gator tab shows all my existing kernels but I can't start a notebook in anything but the base environment. Is there some
additional step I need to take to make them discoverable?

edit: I guess my issue is different and just required ipython kernel install --user --name=<name>. Somehow in the past that wasn't necessary for me to see new kernels.