py-allotax 1.0.0

Python implementation of allotaxonometer to produce static graphs.

Allotaxonometer through Python

The py-allotax implements a python interface to the allotaxonometer library. The tool here 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. Here are the recommended steps to 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. One package depends on having Chrome (brower) or Chromium (browser driver) installed. If you have Chrome installed, you can skip this step. Otherwise, install Chrome or Chromium.

5. Activate your desired python environment then

   pip3 install py-allotax
   

Usage instructions

Package

If working in a python notebook or script, you can install the package and use the function directly. Example data can 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.

CLI

1. Clone the GitHub repository.
2. Verify your data is in the required format (.json) by seeing json examples in example_data/.
   • See helper functions in utils to convert among csv, json, and js formats.
   • The method utils.convert_csv_data exists to convert your data from .csv to .json if needed--see examples.ipynb.
3. Add your 2 system's files. You need 2 data.json files, one for each system.

Verify this test against example_charts/test.pdf.

To get help, you can run the following python src/py_allotax/generate_svg.py --help. It will show the following:

usage: generate_svg.py [-h] [--desired_format {pdf,html}] json_file_1 json_file_2 output_file alpha title1 title2

Generate allotaxonometer plot.

positional arguments:
  json_file_1           Path to the first json data file.
  json_file_2           Path to the second json data file.
  output_file           Path to save the output pdf file.
  alpha                 Alpha value.
  title1                Title of system 1
  title2                Title of system 2.

options:
  -h, --help            show this help message and exit
  --desired_format {pdf,html}
                        Desired output format (default: pdf).

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 is a repo (not yet a package) and its 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):

      pip3 install pandas pyhtml2pdf selenium==4.25.0
      

  • 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.

Other packages are erring out or not installing.

• We will eventually package this repo and streamline installation.

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.