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answered 2018-01-09 05:07:32 -0500

StefanFabian gravatar image

Gavran already explained the problem very well.

Here's just another way to solve the issue.
The easiest solutions like using the full path, exporting the path every time it's needed or creating a second user account for Anaconda aren't really convenient which is why I wrote this little script:

https://gist.github.com/StefanFabian/17fa715e783cd2be6a32cd5bbb98acd9

What it does
It basically scans the Anaconda binary folder and for each executable that isn't present on the system already, it creates an alias. Now, when you execute the command e.g. anaconda-navigator, it adds Anaconda to PATH, executes anaconda-navigator (which is now in PATH) and after anaconda-navigator terminated, it removes Anaconda from PATH again.
For more information and how to use it check the top of the script and the comment on GitHub below the script.

Disclaimer
I'm not very good at bash, so, if someone with more experience could take a look at the script, that'd be great.
For now view this script as beta, it works for me but it needs to be tested by more people.
I've tested it on Ubuntu 16.04 with ROS Kinetic but in theory it should work on any bash system.
Don't know about zsh, etc. though.

Here's a copy of the script at the time of writing for the unlikely event that the link goes dead

### 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
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

    # Unalias the stuff
    _ROS_CONDA_removeAliases

    return 0 # true
  fi
  return 1
}

function _ROS_CONDA_removeCondaFromPath {
  _ROS_CONDA_ADDED=0
  if [[ $PATH = $_ROS_CONDA_PATH":"* ]]
  then
    export PATH=${PATH#$_ROS_CONDA_PATH:}
    _ROS_CONDA_addAliases
  elif [[ $PATH = *":"$_ROS_CONDA_PATH ]]
  then
    export PATH=${PATH%:$_ROS_CONDA_PATH}
    _ROS_CONDA_addAliases
  elif [[ $PATH = *":"$_ROS_CONDA_PATH":"* ]]
  then
    export PATH=${PATH//:$_ROS_CONDA_PATH:/:}
    _ROS_CONDA_addAliases
  fi
}

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 wasnt already."'

Gavran already explained the problem very well.

Here's just another way to solve the issue.
The easiest solutions like using the full path, exporting the path every time it's needed or creating a second user account for Anaconda aren't really convenient which is why I wrote this little script:

https://gist.github.com/StefanFabian/17fa715e783cd2be6a32cd5bbb98acd9

What it does
It basically scans the Anaconda binary folder and for each executable that isn't present on the system already, it creates an alias. Now, when you execute the command e.g. anaconda-navigator, it adds Anaconda to PATH, executes anaconda-navigator (which is now in PATH) and after anaconda-navigator terminated, it removes Anaconda from PATH again.
For more information and how to use it check the top of the script and the comment on GitHub below the script.

Disclaimer
I'm not very good at bash, so, if someone with more experience could take a look at the script, that'd be great.
For now view this script as beta, it works for me but it needs to be tested by more people.
I've tested it on Ubuntu 16.04 with ROS Kinetic but in theory it should work on any bash system.
Don't know about zsh, etc. though.

Here's a copy of the script at the time of writing for the unlikely event that the link goes dead

Update 1: The script now removes ROS from the PATH to prevent issues with ROS python stuff that is incompatible with the Anaconda environment python version. To make this functionality as general as possible, the python path is backed up when the script is sourced, therefore, the script has to be source before any ROS setup bash is sourced.

### 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 {
  _ROS_CONDA_ADDED=0
  if [[ $PATH = $_ROS_CONDA_PATH":"* ]]
  then
    export PATH=${PATH#$_ROS_CONDA_PATH:}
    _ROS_CONDA_addAliases
  elif [[ $PATH = *":"$_ROS_CONDA_PATH ]]
  then
    export PATH=${PATH%:$_ROS_CONDA_PATH}
    _ROS_CONDA_addAliases
  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 wasnt wasn'"'"'t already."'
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