Bash script to use Anaconda with ROS

.anaconda_with_ros_wrapper.bash

### This script wraps all executables in the anaconda bin folder so that they can be used without adding Anaconda
### to the path which would break some functionality of ROS (Robot Operating System)
###
### The commands e.g. jupyter notebook will cause the script to add anaconda to the path, start jupyter notebook
### and after jupyter notebook terminated remove anaconda from the path again
###
### Notable commands:
### * release-the-snake       Adds conda to the path and removes all aliases defined by this script
###                           Conda will stay in the PATH until the end of the session (terminal is closed) or
###                           until "cage-the-snake" is called
### * cage-the-snake          Removes conda from the path and redefines all aliases for anaconda executables
### * source activate [env]   Works just like with anaconda in the PATH, will activate the environment or (root) and
###                           Anaconda will stay in the PATH for the remaining session or until "source deactivate" is run
### * source deactivate       Deactivates the environment and if Anaconda wasn't released manually using release-the-snake
###                           Anaconda will be removed from the PATH again.

if [ -z ${_ROS_CONDA_ADDED+x} ]
then
  _ROS_CONDA_PATH=~/anaconda3/bin
  _ROS_CONDA_ADDED=0
  _ROS_CONDA_ALIASES=''
  _ROS_CONDA_RELEASED_MANUALLY=0
  _ROS_CONDA_PYTHONPATH_WITHOUT_ROS=$PYTHONPATH
fi

function _ROS_CONDA_addAliases {
  if [[ $_ROS_CONDA_ALIASES != '' ]]
  then
    echo "ROS Conda Wrapper: Error! Aliases already defined!"
    _ROS_CONDA_removeAliases
  fi
  
  for file in $_ROS_CONDA_PATH/*
  do
    local name
    name=${file##*/}
    if ! [ -x "$(command -v $name)" ]
    then
      alias $name='_ROS_CONDA_runWithConda '$name' $@'
      _ROS_CONDA_ALIASES=$_ROS_CONDA_ALIASES" "$name
    fi
  done
}

function _ROS_CONDA_removeAliases {
  for cmd in $_ROS_CONDA_ALIASES
  do
    unalias $cmd
  done
  _ROS_CONDA_ALIASES=''
}

function _ROS_CONDA_runWithConda {
  _ROS_CONDA_ensureCondaInPath
  command $@
  _ROS_CONDA_removeCondaFromPath
}

function _ROS_CONDA_ensureCondaInPath {
  if [ $_ROS_CONDA_ADDED -eq 1 ]
  then
    return 1 # false
  fi
  _ROS_CONDA_ADDED=1

  # Check that the path doesn't start, end or contain the ros conda path
  if [[  $PATH != $_ROS_CONDA_PATH":"* && $PATH != *":"$_ROS_CONDA_PATH && $PATH != *":"$_ROS_CONDA_PATH":"* ]]
  then
    export PATH=$_ROS_CONDA_PATH:$PATH
    # Backup and clear python path to keep ros from checking ros directories for python modules
    _ROS_CONDA_PYTHONPATH_BACKUP=$PYTHONPATH
    export PYTHONPATH=$_ROS_CONDA_PYTHONPATH_WITHOUT_ROS

    # Unalias the stuff
    _ROS_CONDA_removeAliases

    return 0 # true
  fi
  return 1
}

function _ROS_CONDA_removeCondaFromPath {
  if [[ $PATH = $_ROS_CONDA_PATH":"* ]]
  then
    export PATH=${PATH#$_ROS_CONDA_PATH:}
  elif [[ $PATH = *":"$_ROS_CONDA_PATH ]]
  then
    export PATH=${PATH%:$_ROS_CONDA_PATH}
  elif [[ $PATH = *":"$_ROS_CONDA_PATH":"* ]]
  then
    export PATH=${PATH//:$_ROS_CONDA_PATH:/:}
  fi

  if [ $_ROS_CONDA_ADDED -eq 1 ]
  then
    # Restore ROS PYTHONPATH
    export PYTHONPATH=$_ROS_CONDA_PYTHONPATH_BACKUP
    _ROS_CONDA_addAliases
  fi

  _ROS_CONDA_ADDED=0
}

function _ROS_CONDA_sourceWrapper {
  if [ $1 == "activate" ]
  then
    _ROS_CONDA_ensureCondaInPath
    if [ $# == 1 ]
    then
    # If only source activate call source activate root.
    # Otherwise it will fail. Don't know why though
      command source activate
    else
      command source $@
    fi
  elif [ $1 == "deactivate" ]
  then
    command source deactivate
    if [ $_ROS_CONDA_RELEASED_MANUALLY -eq 0 ]
    then
      _ROS_CONDA_removeCondaFromPath
    fi
  else
    command source $@
  fi
}

if [ $_ROS_CONDA_ADDED -eq 0 ]
then
  if [[ $_ROS_CONDA_ALIASES != '' ]]
  then
    _ROS_CONDA_removeAliases
  fi
  _ROS_CONDA_addAliases
fi

alias source='_ROS_CONDA_sourceWrapper'
alias release-the-snake='_ROS_CONDA_RELEASED_MANUALLY=1; if _ROS_CONDA_ensureCondaInPath; then echo "All hail the snake!"; else echo "The snake is in another castle!
Jk, you released it already."; fi'
alias cage-the-snake='_ROS_CONDA_RELEASED_MANUALLY=0; _ROS_CONDA_removeCondaFromPath; echo "The snake has been caged if it wasn'"'"'t already."'

To make Anaconda work with ROS:

1. Remove the line that adds the anaconda bin folder to your PATH in the ~/.bashrc file (if you've let anaconda add itself to the PATH during installation)
2. Download this file and move it to your home folder
3. Change _ROS_CONDA_PATH in line 19 to the path of your Anaconda bin folder (if you didn't install it to ~/anaconda3)
4. Add the following line to your ~/.bashrc file before any ros setup bash files are sourced
   source ~/.anaconda_with_ros_wrapper.bash

This script creates aliases for all executables in the anaconda binary folder that are not already present on the system.
So, basically, it checks for each executable in the binary folder if the system already has an executable with that name in the PATH and only if not it creates an alias that adds Anaconda to the PATH, executes the command and removes Anaconda from the PATH again.
For more info, read the information at the top of the script.

Update 1:

Added functionality to remove ROS from the python path. The issue here being that python looks for packages in the ros paths which may not be compatible with the python version used in the anaconda environment.

IMPORTANT:

To make this functionality as universal as possible, I chose to backup the PYTHONPATH when the script is first sourced. This means it is now necessary to source the .anaconda_with_ros_wrapper.bash before you source any ros setup bash files. The script will backup the PYTHONPATH environment variable when it is loaded and restore the backup when you use any command that activates anaconda. Once you're done with anaconda and deactivate it, the PYTHONPATH is set to whatever it was before the backup was restored.

Hello Stefan,

I appreciate your work here. But I want to use two user accounts for ROS in one account and for Anaconda (Jupyter notebook) for other projects

My question as most of the root installations are global for all users will there be still conflict??

Thanks in advace

Regards
TK

Hey @thejeshk,
thank you! Sorry for the late reply, I only noticed your comment by accident. Unfortunately, GitHub doesn't notify me about new comments here. If anyone reading this has any questions, please don't hesitate to contact me directly.

No, if you use separate accounts for ROS and Anaconda, it shouldn't clash. The installation is global but the conflicts only happen when you source the ros setup.bash and add Anaconda to the PATH environment variable. As long as you don't source ROS on your Anaconda account and don't have Anaconda in your PATH on your ROS account, you shouldn't run into any issues.
I've used that setup for some time but ultimately it was too much of a hassle and a waste of disk space to switch users all the time.

Best,
Stefan

So could we place this bash file in our .bashrc file immediately before sourcing /opt/ros/.../setup.bash and the workspace setup.bash files?

I realize there will be times in which we will use anaconda that we are not using ros. At these times, we could comment out the line in the .bashrc file.

Hey @rojas70,
sorry for the late reply, as already mentioned I don't get notified about comments and again saw it by accident because I'm upgrading to 18.04 today and had to redownload the script.

Regarding your question, I'm not sure what you mean?
As instructed in the first comment, you have to place it before sourcing the ros setup.bash and your workspace setup.bash.
You should also remove whatever anaconda added to the .bashrc.
You could, of course, comment out any ros related setup.bash files at any time but the intention of this script is making this unnecessary.

Hi, I'm a user of your ros with anaconda script,

it used to work but I have found that with more recent versions of anaconda it has stopped.

Anaconda now informs me when I try to activate an env that the shell has not been initialised and I must run conda init bash.

Running conda init bash adds this to .bashrc

# !! Contents within this block are managed by 'conda init' !!           
__conda_setup="$('/home/luke/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then 
    eval "$__conda_setup"
else                                 
    if [ -f "/home/luke/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/home/luke/anaconda3/etc/profile.d/conda.sh"            
    else                                                                   
        export PATH="/home/luke/anaconda3/bin:$PATH"           
    fi                  
fi      
unset __conda_setup  
# <<< conda initialize <<<

and now when I open a shell I get:

bash: eval: line 214: syntax error near unexpected token `('
bash: eval: line 214: `conda() {'

If you have a fix, it would be very much appreciated :)

(I tried sending this on your website but it didn't work)

What version are you using?
With Conda 4.6.14 it should still work. I can't use conda activate [env] but source activate [env] still works.
I've removed the entire initialization code that conda adds to the .bashrc which seems to be required for some newer methods like conda activate env.
I'll have to look into making it compatible with the new initialization code to support the new commands.
It's on my ToDo list but I can't promise that I can look into it before the end of next week.

PS: Thanks for the heads up regarding the contact form on my website. I've fixed it. But the good news is that github finally seems to send me email notifications for new comments. :)

I'm on conda 4.6.14 - ok cool - I'll try source activate [env]
Thankyou!

@StefanFabian I wrote a small installable bash wrapper based on your code. It can be found here.