Python on a lab bench

Github repository with code, slides and data

Lecture

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