Allotaxonometer through Python

Allotax icon created by Julia W. Zimmerman

The py-allotax implements a python interface to the allotaxonometer library. This tool provides a way for users to input data and arguments and receive back a saved plot! The tool is designed to be used in a command line or in a python notebook in a few lines of code (see usage instructions at the bottom).

Table of contents:

• Installation
• Usage instructions
• Developer Notes
• Frequent questions or issues
• Repo structure notes
• Resources

Installation

1. Requires python3.11 or greater.

2. If JavaScript tool installs are needed (never used or installed npm, nvm, node):

   1. Install nvm. nvm is a node version manager that streamlines installing the other 2.
   • Otherwise (not recommended): steps to individually install node and npm.

3. Once you have nvm, install the latest of both node and npm with:

   nvm install --lts

4. Install Chrome or Chromium because one package depends on having Chrome (brower) or Chromium (browser driver). If you have Chrome installed, skip this step.

5. Activate your desired python environment.

6. Install package:

   pip3 install py-allotax

Usage instructions

If working in a python notebook or script, you can install the package and use the function directly. Example data must be downloaded from the example_data directory to run the example below and those found in the examples.ipynb. boys 2022 and boys 2023 are the examples used below.

import os
from py_allotax.generate_svg import generate_svg

data_path1 = os.path.join("example_data", "boys_2022.json")
data_path2 = os.path.join("example_data", "boys_2023.json")

generate_svg(data_path1, data_path2, "test.pdf", "0.17", "Boys 2022", "Boys 2023")

If running the example, you can check your result against the example output.

To get help, you can run ?py_allotax.generate_svg.generate_svg in a notebook cell to see argument descriptions.

Note: Your own data must be in the .json format (see json examples in example_data/). If you have a .csv file, you can convert it to .json using utils.convert_csv_data (see examples.ipynb).

Developer Notes

Dependency Manager

pdm is required for the build and testing.

Setup

Once pdm is installed, run:

pdm sync

to install all python dependencies.

Testing

To test the package without building and installing, simply run:

pdm run pytest

This will execute the tests written in the tests dir.

Package Build

Clone this repo and install the requirements:

git clone https://github.com/compstorylab/py-allotax.git &&
cd py-allotax &&
./scripts/build.sh

You should see a .whl file in the newly created dist directory.

Frequent questions or issues

Will any data format work?

• There are specific column/variable names, and the data must be in .json format. The column names and formats vary across a few of the allotaxonometer tools, so there is a data format conversion function in utils.py to go from .csv to .json. See examples.ipynb for how to convert your data from .csv to .json.

I use Google colab or online-based coding environments only.

• Currently, this tool's dependencies may be difficult to install in an online environment. We recommend using Python virtual environments or Anaconda to create and manage Python environments locally. See below some shell instructions to get started with a Python virtual environment.

  Click for Python virtual environment instructions

  • Navigate to ('change directory' with cd) the folder where your coding or related work lives. These instructions will create a folder here containing your environment, env. Inside the folder, python’s virtual environment library, venv, will create files and download libraries. Each time you activate this environment, you have access to its libraries and can manage them.

    cd path-to-create-env
    

  • Generate an env with a name such as allotax_env:

    python3 -m venv <name_of_env>
    

  • Activate (source) the env; unless you automate this step, you will need to do this each time you restart your shell or change env.
    • In the directory where your env is, enter pwd (print working directory) to get its full path. Copy that path and fill in below, leaving the bin/activate at the end:

      source /replace-wth-path-to/name_of_env/bin/activate
      

    • Now you can install the python packages needed or do other library management (type pip help for more commands).
  • You are set up to use a coding application (IDE) or command line to run this tool. If you do not have Anaconda, we recommend VS Code (where you can work with .ipynb files as you might in Jupyter or Colab).

Where do I find the output?

• It is at the path you specified (argument provided) when you ran the generate_svg.

Terminal says there is no nvm after installing it.

• Restart your terminal to activate it.

Terminal says there is no node even after I have already run py-allotax methods.

• This seems to happen when switching environments or changing branches. You can simply re-run the installs. You should already have nvm and be able to start from there.

I am receiving this error: AttributeError: 'ChromiumRemoteConnection' object has no attribute '_url’.

• One of secondary dependencies is selenium, and it seems to break if the version is higher than 4.25.0. Run pip3 install selenium==4.25.0.

I am receiving an npm error regarding canvas, pixman, or other packages I do not recognize.

• You may need canvas and its dependencies. Please follow this guide to installing it based on your OS.

Users accessing these tools is our primary goal, so feel free to contact us by submitting an issue in the repo, emailing, or reaching out in one of our Slack spaces. Include these notes on your issue:

1. What exactly you did and steps leading up to it, and
2. Things you may have tried, and
3. The exact error message(s).

Repo structure notes

• Inside src:
  • generate_svg.py is the main script to generate the pdf. You can run this from command line or in a notebook.
• Outside src: you can download example data and charts and a notebook to run pre-constructed examples that use the library.
• Once you set up your ecosystem, you will see node_modules/, which will contain the npm packages.

Resources

• Allotaxonometer main package
• Allotaxonometer web app
• The work and paper leading to these tools is here.
• See the allo diagram to understand the full tool ecosystem around the allotaxonometer (download and load in draw.io)