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Slides

Lecture notes

• 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

• 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

• 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
      

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