submission

“The Submission”

Overview

Class 11

Homework from previous class

• Work on the presentation of your paper.

Agenda

• Share the work you have done on your presentation (10 mins ea.)
  • Focus on Conclusion
  • Show us the structure of your paper
• Brief example of how to set up workflows in PaperPile
• Discuss reproducibility.
  • Results need to be generated within your notebook
    • (or as a consequence of executing your notebook).
  • Single script should reproduce all outputs: reproduce.sh
  • "It works on my computer!" → reproducibility with binder.
    • There different version of python
    • different versions of packages we use (pandas, etc.)
    • mybinder is a tool that we can specify the specific versions of these things and generate a link that some one can click on and open a notebook with these things installed.
  • Create a file of YOUR environment:
    • In your paper directory
    • Create a folder: binder

      mkdir binder
      cd binder
      

    • create the environment file: This will create a file with all installed packages including versions

      conda env export -f environment.yml
      

  • Create a reproduce.sh file:
    • copy and paste the file from AMonninger
    • Replace jupyter notebook names with the file names of your paper
    • give the script permission to be executable using your terminal
      • ls -las (shows if it is executable)
      • chmod u+x reproduce.sh
      • ls -las(reproduce.sh file should be green now)
    • run the file using /bin/bash reproduce.sh
    • NOTE: I build the paper using myst and save it as a pdf. To specify options here, adjust your myst.yml file
  • Sync your GitHub fork to assure that binder can access all information
• In class work time.
  • Bring your questions.
  • Receive help with Python, Jupyter, build-jb, myst-start LitMaps, Paperpile, … anything!
• Q&A About the final draft.

Homework

• Work on your Final Draft

• Revisit your PaperPile

  • denote with a tag the citations that you actually reference in your draft
  • Set up a workflow that will automatically update your bibfile when you change the papers you are referencing

• Please create a final Litmap with all the papers you used(should be > 10 and < 100). Make sure to have tagging done right(a solid number of tags + show which papers address multiple tags in a single paper)