jedi-vim: Some modules not found

Issue

Trying to use jedi-vim with a python3 conda environment, I find that some modules are found but others are not, and result in "Omni completion (^O^N^P) Pattern not found. Some modules that are not working are scipy numpy sympy pandas

Examples of modules that are working matplotlib jsonschema markupsafe

Steps to reproduce

With the following minimal vim setup:

• set nocompatible " be iMproved, required
• filetype off " required
• let g:pymode_python = ‘python3’
• let &pythonthreedll = ‘/panfs/pfs.local/software/7/install/anaconda/4.7/lib/libpython3.7m.so.1.0’
• color elflord
• syntax on
• filetype plugin on
• set nu

Running “:python3 import numpy; print(np.arange(10))” returns the expected array. " :python3 import sys; print(sys.path) " includes the path to my conda environment.

Not sure what else to try.

Output of “:verbose JediDebugInfo”

• jedi-vim git version: Unknown option: -C usage: git [–version] [–help] [-c name=value] [–exec-path[=<path>]] [–html-path] [–man-path] [–info-path] [-p|–paginate|–no-pager] [–no-replace-objects] [–bare] [–git-dir=<path>] [–work-tree=<path>] [–namespace=<name>] <command> [<args>]
• jedi git submodule status: Unknown option: -C usage: git [–version] [–help] [-c name=value] [–exec-path[=<path>]] [–html-path] [–man-path] [–info-path] [-p|–paginate|–no-pager] [–no-replace-objects] [–bare] [–git-dir=<path>] [–work-tree=<path>] [–namespace=<name>] <command> [<args>]
• parso git submodule status: Unknown option: -C usage: git [–version] [–help] [-c name=value] [–exec-path[=<path>]] [–html-path] [–man-path] [–info-path] [-p|–paginate|–no-pager] [–no-replace-objects] [–bare] [–git-dir=<path>] [–work-tree=<path>] [–namespace=<name>] <command> [<args>]

Global Python

Using Python version 3 to access Jedi.

• global sys.executable: /home/sether35/.conda/envs/notebook/bin/python3
• global sys.version: 3.7.3 (default, Mar 27 2019, 22:15:47), [GCC 7.3.0]
• global site module: /home/sether35/.conda/envs/notebook/lib/python3.7/site.py

Jedi

• path: /panfs/pfs.local/home/sether35/.vim/pack/plugins/start/jedi-vim/pythonx/jedi/jedi/__init__.py
• version: 0.15.1

Jedi environment: <SameEnvironment: 3.7.3 in /home/sether35/.conda/envs/notebook>

• executable: /home/sether35/.conda/envs/notebook/bin/python3
• sys_path:
  • /panfs/pfs.local/work/laird/sether35/hoomd-blue
  • /panfs/pfs.local/home/sether35
  • /home/sether35/.conda/envs/notebook/lib/python37.zip
  • /home/sether35/.conda/envs/notebook/lib/python3.7
  • /home/sether35/.conda/envs/notebook/lib/python3.7/lib-dynload
  • /home/sether35/.conda/envs/notebook/lib/python3.7/site-packages

Known environments

• <Environment: 3.7.3 in /home/sether35/.conda/envs/notebook> (/home/sether35/.conda/envs/notebook/bin/python3.7)

• <Environment: 2.7.5 in /usr> (/usr/bin/python2.7)

Settings

  omnifunc=jedi#completions
	Last set from ~/.vim/bundle/jedi-vim/autoload/jedi.vim line 620
  completeopt=menuone,longest,preview
	Last set from ~/.vim/bundle/jedi-vim/plugin/jedi.vim line 36

:version

VIM - Vi IMproved 8.1 (2018 May 18, compiled Sep 18 2019 16:07:18)
Included patches: 1-2052
Compiled by r557e636@login1
Huge version without GUI.  Features included (+) or not (-):
+acl               +cindent           +cursorshape       +file_in_path      +jumplist          +mksession         +mouse_xterm       +printer           -sound             +terminal          +virtualedit       -xim
+arabic            +clientserver      +dialog_con        +find_in_path      +keymap            +modify_fname      +multi_byte        +profile           +spell             +terminfo          +visual            -xpm
+autocmd           +clipboard         +diff              +float             +lambda            +mouse             +multi_lang        +python/dyn        +startuptime       +termresponse      +visualextra       +xsmp_interact
+autochdir         +cmdline_compl     +digraphs          +folding           +langmap           -mouseshape        -mzscheme          +python3/dyn       +statusline        +textobjects       +viminfo           +xterm_clipboard
-autoservername    +cmdline_hist      -dnd               -footer            +libcall           +mouse_dec         +netbeans_intg     +quickfix          -sun_workshop      +textprop          +vreplace          -xterm_save
-balloon_eval      +cmdline_info      -ebcdic            +fork()            +linebreak         -mouse_gpm         +num64             +reltime           +syntax            +timers            +wildignore        
+balloon_eval_term +comments          +emacs_tags        +gettext           +lispindent        -mouse_jsbterm     +packages          +rightleft         +tag_binary        +title             +wildmenu          
-browse            +conceal           +eval              -hangul_input      +listcmds          +mouse_netterm     +path_extra        -ruby              -tag_old_static    -toolbar           +windows           
++builtin_terms    +cryptv            +ex_extra          +iconv             +localmap          +mouse_sgr         +perl              +scrollbind        -tag_any_white     +user_commands     +writebackup       
+byte_offset       +cscope            +extra_search      +insert_expand     +lua               -mouse_sysmouse    +persistent_undo   +signs             -tcl               +vartabs           +X11               
+channel           +cursorbind        -farsi             +job               +menu              +mouse_urxvt       +postscript        +smartindent       +termguicolors     +vertsplit         +xfontset          
   system vimrc file: "$VIM/vimrc"
     user vimrc file: "$HOME/.vimrc"
 2nd user vimrc file: "~/.vim/vimrc"
      user exrc file: "$HOME/.exrc"
       defaults file: "$VIMRUNTIME/defaults.vim"
  fall-back for $VIM: "/panfs/pfs.local/work/laird/sether35/sw/vim/share/vim"
Compilation: gcc -std=gnu99 -c -I. -Iproto -DHAVE_CONFIG_H     -g -O2 -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1       
Linking: gcc -std=gnu99   -Wl,--enable-new-dtags -Wl,-rpath,/usr/lib64/perl5/CORE   -L/usr/local/lib -Wl,--as-needed -o vim    -lSM -lICE -lXpm -lXt -lX11 -lSM -lICE  -lm -ltinfo -lnsl    -ldl  -L/usr/lib -llua -Wl,--enable-new-dtags -Wl,-rpath,/usr/lib64/perl5/CORE  -fstack-protector  -L/usr/lib64/perl5/CORE -lperl -lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc        

:messages

Messages maintainer: Bram Moolenaar <Bram@vim.org>
"test.py" 14L, 183C
VIM - Vi IMproved 8.1 (2018 May 18, compiled Sep 18 2019 16:07:18)
  1: ~/.vimrc
  2: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/ftoff.vim
  3: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/colors/elflord.vim
  4: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/syntax/syntax.vim
  5: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/syntax/synload.vim
  6: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/syntax/syncolor.vim
  7: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/filetype.vim
  8: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/ftplugin.vim
  9: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/plugin/getscriptPlugin.vim
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 12: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/plugin/manpager.vim
 13: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/plugin/matchparen.vim
 14: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/plugin/netrwPlugin.vim
 15: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/plugin/rrhelper.vim
 16: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/plugin/spellfile.vim
 17: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/plugin/tarPlugin.vim

  1: ~/.vimrc
  2: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/ftoff.vim
  3: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/colors/elflord.vim
  4: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/syntax/syntax.vim
  5: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/syntax/synload.vim
  6: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/syntax/syncolor.vim
  7: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/filetype.vim
  8: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/ftplugin.vim
  9: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/plugin/getscriptPlugin.vim
 10: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/plugin/gzip.vim
 11: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/plugin/logiPat.vim
 12: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/plugin/manpager.vim
 13: /panfs/pfs.local/work/laird/sether35/sw/vim/share/vim/vim81/plugin/matchparen.vim
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 21: ~/.vim/bundle/jedi-vim/plugin/jedi.vim
 22: ~/.vim/bundle/nerdtree/plugin/NERD_tree.vim
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