====== Python on a lab bench ======

[[https://github.com/btel/aspp_munich_2015|Github repository]] with code, slides and data




===== Lecture =====

[[http://btel.github.io/aspp_munich_2015|Slides]]

[[https://github.com/btel/aspp_munich_2015/blob/master/docs/lecture_notes.md|Lecture notes]]


===== Exercises =====


=== Data exploration ===

  * clone repository to your home directory

        git clone yourusername@python.g-node.org:/home/bartosz/lab_bench

  * copy data to ''data'' subdir:

        cp ~/lab-bench-data/* ~/lab_bench/data

  * set path for extra libaries:

        echo "export PYTHONPATH=/home/student/lab_bench/libs" >> ~/.bashrc
        source ~/.bashrc

  * create a new branch (use unique names for your team):

        cd lab_bench
        git checkout -b MYTEAM_pairwise_correlations

  * in the script we worked on during the lecture, calculate all pairwise correlations between all neurons (use nested for loops and plot the histogram)

  * commit and push your branch back to ''origin'' (replace MYTEAM with ...):

        git push origin --set-upstream MYTEAM_pairwise_correlations

=== Workflow ===

  * update your master branch

        git checkout master
        git pull

  * create a new branch:

        git checkout -b MYTEAM_first_workflow

  * add new command line argument (''-​-bin-size'' of type ''float'' and default value of 10) and pass it to ''calc_corr_coef'' function. 

  * write script ''plot_correlations_histogram.py'' which reads correlation files (given in the first command line argument), plots a histogram and saves it in a file given by ''-​-save-fig'' argument (use ''plt.savefig'') . 

  * Test the script on files generated with ''open_data.py'' script. 

  * Don't forget to add ''plot_correlations_histogram.py'' to you repository

        git add plot_correlations_histogram.py

  * commit and push your branch back to ''origin'':

        git push origin MYTEAM_first_workflow

=== Automation/batch processing ===

  * update your master branch

        git checkout master
        git pull

  * create a new branch:

        git checkout -b MYTEAM_automation

  * add ''task_merge_correlations.py'' to ''dodo.py'' (located in ''workflows'' directory), which merges correlations from all files generated by ''task_open_data'' (dependencies)  and saves them in new npz file (target).

  * update ''task_plot_correlations_histogram'' to plot histogram of merged correlations

  * run doit -- change to workflows directory and run ''doit''

  * try what happens when a single file from ''results'' is deleted.

  * commit and push your branch back to ''origin'':

        git push origin MYTEAM_automation
        
=== .bashrc ===

In case you accidentally overwrote your ''.bashrc'', here is a copy:
{{:bashrc.txt|}}. Download it, move it to your home directory and rename it to ''.bashrc''