CODEWITHSUNDEEP
pythonbashshellpathautocomplete
zweiHuehner
zweiHuehner

Reputation: 113

How to autocomplete my python functions in bash?

I am working on a HPC-Linux-cluster and need to conduct a lot of Post Processing of data with python functions and scripts. My current workflow looks like the following:

  1. cd to folder where my data is. The intended python function/script is also saved in this folder
  2. Do: python myfunction arg1 arg2
  3. Review results

Since this doesn't allow me to store my python functions in one location it can get quite annoying sometimes when debugging.

So I was wondering if it is possible to store my functions at one location and autocomplete them after the python command without declaring their entire paths?

Ideally it would look like this:

python myfunction arg1 arg2

and not

python path-to-function/myfunction arg1 arg2

I have already managed to do so in the python interactive via the $PYTHONPATH and then import my functions, but frankly I don't like this solution since it is just a couple of more lines to type.

I also set a global variable to proceed as following: python $MYFUNCTIONS_PATH/myfunction arg1 arg2 but autocomplete won't work and it is also extra typing.

This is my first post here, I hope the question is nicely understood.

Upvotes: 4

Views: 358

Answers (2)

zweiHuehner
zweiHuehner

Reputation: 113

I found a solution that fits my problem and is even more comfortable.

  1. In the first line of your python scripts (the Shebang) add python as an executor with its path:

    #!/usr/bin/python

    If you are unsure about your pyhton path do: ẁhich python

  2. Store all your wished python scripts at a fitting location and add this location to your PATH (e.g. in you .bashrc):

    PATH=$PATH:/path/to/your/python/scripts

  3. Make all your scripts in this location executable with:

    chmod +x

After a new login or sourcing your .bashrc you should now be able to run the scripts from everywhere with autocomplete and you don't even have to type "python" before the script name:

yourscript.py arg1 arg2

Also see here.

Upvotes: 1

Synthaze
Synthaze

Reputation: 6090

Well not sure but I was doing that to chain process on HPC:

ls your/paths/of/interests/*/ > list.dat

Then:

#You process each of the element in your list
cat list.dat | while read -r line; do
    #You cd to it
    cd ${line}/gromacs/
    #You use EOF to pass arguments
    gmx distance -f step7_all.xtc -oall DIST_D103_K81_${line}.xvg -n index.ndx - 
    select 'cog of group "r_103_&_OD1_OD2" plus cog of group "r_81_&_NZ"' <<EOF
    20
    EOF
    #You take your stuff away and cd back
    cp DIST*xvg ../../
    cd ../../

Upvotes: 0

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