:checkhealth shows Python3 Provider `unable to load neovim Python Module` - typical solutions not working

Healthcheck fails. Python3 can’t find neovim Python3 module. Python 2 provider can.

Scroll to bottom for attempts at solving based on googling, stackoverflowing, and searching this repo’s issues.

Expected result of checkhealth : All passed

System information:

lsb_release -a

Distributor ID:	Ubuntu
Description:	Ubuntu 18.04.2 LTS
Release:	18.04
Codename:	bionic

nvim --version

NVIM v0.3.4
Build type: RelWithDebInfo
LuaJIT 2.0.5
Compilation: /usr/bin/cc -Wconversion -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -O2 -g -DMIN_LOG_LEVEL=3 -Og -g -Wall -Wextra -pedantic -Wno-unused-parameter -Wstrict-prototypes -std=gnu99 -Wimplicit-fallthrough -Wvla -fstack-protector-strong -fdiagnostics-color=auto -Wno-array-bounds -DINCLUDE_GENERATED_DECLARATIONS -D_GNU_SOURCE -DNVIM_MSGPACK_HAS_FLOAT32 -DNVIM_UNIBI_HAS_VAR_FROM -I/home/caleb/Downloads/neovim-0.3.4/build/config -I/home/caleb/Downloads/neovim-0.3.4/src -I/home/caleb/Downloads/neovim-0.3.4/.deps/usr/include -I/usr/include -I/home/caleb/Downloads/neovim-0.3.4/build/src/nvim/auto -I/home/caleb/Downloads/neovim-0.3.4/build/include
Compiled by caleb@caleb-Potatop

Features: +acl +iconv +jemalloc +tui 
See ":help feature-compile"

   system vimrc file: "$VIM/sysinit.vim"
  fall-back for $VIM: "/usr/local/share/nvim"

Run :checkhealth for more info

:checkhealth

health#nvim#check
========================================================================
## Configuration
  - OK: no issues found

## Performance
  - OK: Build type: RelWithDebInfo

## Remote Plugins
  - OK: Up to date

## terminal
  - INFO: key_backspace (kbs) terminfo entry: key_backspace=\177
  - INFO: key_dc (kdch1) terminfo entry: key_dc=\E[3~
  - INFO: $VTE_VERSION='5202'
  - INFO: $COLORTERM='truecolor'

health#provider#check
========================================================================
## Clipboard (optional)
  - OK: Clipboard tool found: xclip

## Python 2 provider (optional)
  - INFO: Using: g:python_host_prog = "/home/caleb/.cache/vim/venv/neovim2/bin/python"
  - INFO: Executable: /home/caleb/.cache/vim/venv/neovim2/bin/python
  - INFO: Python version: 2.7.15
  - INFO: pynvim version: 0.3.2
  - OK: Latest pynvim is installed.

## Python 3 provider (optional)
  - INFO: Using: g:python3_host_prog = "/home/caleb/.cache/vim/venv/neovim3/bin/python3"
  - INFO: Executable: /home/caleb/.cache/vim/venv/neovim3/bin/python3
  - ERROR: Command error (job=9, exit code 1): `'/home/caleb/.cache/vim/venv/neovim3/bin/python3' -c 'import sys; sys.path.remove(""); import neovim; print(neovim.__file__)'` (in '/home/caleb/.cache/vim/venv/neovim3/bin')
    Output: Traceback (most recent call last):  File "<string>", line 1, in <module>ModuleNotFoundError: No module named 'neovim'
    Stderr: Traceback (most recent call last):  File "<string>", line 1, in <module>ModuleNotFoundError: No module named 'neovim'
  - INFO: Python version: 3.6.7
  - INFO: pynvim version: unable to load neovim Python module
  - ERROR: pynvim is not installed.
    Error: unable to load neovim Python module
    - ADVICE:
      - Run in shell: pip3 install pynvim

## Ruby provider (optional)
  - INFO: Disabled. g:loaded_ruby_provider=1

## Node.js provider (optional)
  - INFO: Node.js: v11.10.1
  - WARNING: Missing "neovim" npm (or yarn) package.
    - ADVICE:
      - Run in shell: npm install -g neovim
      - Run in shell (if you use yarn): yarn global add neovim

Attempts to Solve:

pip3 uninstall neovim
pip3 uninstall pynvim
pip3 install pynvim

pip2 uninstall neovim
pip2 uninstall pynvim
pip2 install pynvim

pip uninstall neovim
pip uninstall pynvim
pip install pynvim

No other pip is installed on this system.

I suspect this has something to do with the large number of python runtimes installed on this system, though I’ve pointed g:python_host_prog all over the place to no joy.

python[tab]

python             python2.7          python2-config     python3.6          python3.6m         python3-config     python3m-config    
python2            python2.7-config   python3            python3.6-config   python3.6m-config  python3m           python-config  

[komali2]

I couldn’t do bin/python -m pip because the pip module wasn’t installed for uh, these pythons in here. Not sure. Anyway this solved it.

cd /home/caleb/.cache/vim/venv/neovim3/bin/

Use the get-pip script from this directory:

curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py

./python3 get-pip.py

./python3 -m pip uninstall neovim

./python3 -m pip uninstall pynvim

./python3 -m pip install pynvim

It’s messy, but it works now. Cheers for the help.

[justinmk]

g:python3_host_prog points to a venv, but it’s not clear which commands were executed in the context of the venv. E.g. when you say pip3 uninstall neovim, is that with the venv activated? Alternatively:

/home/caleb/.cache/vim/venv/neovim3/bin/pip uninstall neovim
/home/caleb/.cache/vim/venv/neovim3/bin/pip uninstall pynvim
/home/caleb/.cache/vim/venv/neovim3/bin/pip install pynvim