bdpedigo/talks

Catalog of slides for talks

talks

Abstract

Coming soon

Repo structure

• .github: Files specifying how the repo behaves on GitHub.
• data: Directory to store the raw data.
• docs: Files to build the documentation website (in the form of a Jupyter Book), talks, and posters.
• overleaf: Link to an Overleaf document as a git submodule.
• pkg: A local Python package used for analysis in the Jupyter Notebooks/Python scripts.
• results: Place to store intermediate outputs, figures, and saved variables.
• sandbox: Junk scripts not part of the final paper/project.
• scripts: Python scripts used to do all analyses
• shell: Shell scripts used to run the entire project, copy results, etc.

Guide to using the repository

Getting the code and setting up an environment

Prerequisites: git, working knowledge of Python and command line tools.

Using Poetry

I recommend using Poetry to create and manage a reproducible environment for running the code for this project.

• If you don't have it already, install Poetry following their linked instructions.

• Navigate to a directory where you want to store the project, and clone this repo:

  git clone https://github.com/neurodata/talks
  

• (TEMPORARY) Clone the sister repository, giskard:

  git clone https://github.com/bdpedigo/giskard.git
  

  • Note: once the code is stable, this will be replaced by an install from PyPI

• Enter the newly cloned directory:

  cd talks
  

• Create a Poetry environment:

  • Note: this requires that you have a Python 3.9 installation on your machine. It is possible that the code for this project will run with other versions of Python, but I haven't tested it. To check if you have Python 3.9, you can do:

    which python3.9
    

    If the result says python3.9 not found then you'll need to get a 3.9 interpreter on your machine. Common ways to install an interpreter are via python.org, brew, or conda.
  • After you have ensured you have a Python 3.9 installation, do:

    poetry env use python3.9
    

  • For me, the output looks like

    Creating virtualenv talks in /Users/bpedigo/bilateral-test/talks/.venv
    Using virtualenv: /Users/bpedigo/bilateral-test/talks/.venv
    

  • To install dependencies, do

    poetry install --with dev-dependencies
    

• To activate the new environment, do

  source .venv/bin/activate
  

  • If you need to deactivate this environment, just type deactivate

Using pip

Coming soon

Getting the data

Coming soon

Running the code

• Make sure your virtual environment from the last section is active.
• Now you should be able to run any individual python files like normal, for example:

  python ./talks/scripts/er_unmatched_test.py
  

• Instead of running as a Python file, you can also easily convert a Python file to a notebook, execute it, and have it included in the documentation folder for rendering as a Jupyter Book. To do so, use the make_notebook.sh script and pass in the name of the python file (without the .py file extension):

  sh ./talks/shell/make_notebook er_unmatched_test
  

  If you'd like to build that individual notebook and then rebuild the documentation, just add the -b argument to the same script:

  sh ./talks/shell/make_notebook -b er_unmatched_test
  

• You can also build and run all notebooks which are essential to the final paper via the make_project.sh script:

  sh ./talks/shell/make_project.sh
  

Building the documentation Jupyter Book

The notebooks associated with this project are assembled into a Jupyter Book.

• To build the documentation, do:

  jb build ./talks/docs
  

• You can then view the locally built HTML by pasting the produced link into your browser. For me, the built index is stored at ./talks/docs/_build/html/index.html

Questions about the code or paper

Please get in touch! You are welcome to make an issue or email me at [email protected].