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Research Software Encyclopedia Analysis

We ultimately want to be able to group the different software into categories. E.g., if I'm an astronomy researcher I want to quickly see what other libraries are being developed.

Background

Version 1

To do this, I originally started with word2vec on text from the repos to derive a set of embeddings that represent each code repository. This meant that each repository is going to be represented as a vector of numbers. I then could take the label data (where we have topics on the repo) and train a model to derive the probability of each embedding (without labels) of having the labels. We can try a "separate label" model, or a multiple label model. In practie, this worked well up until the data got large, and then I couldn't run it on my computer. I also then realized I couldn't automate it on GitHub.

I took a few weeks break, went off and learned about online machine learning with river, developer some of my own Django plugins to allow making a server and ran it again. This worked great to generate the clustering, but I realized this wasn't super useful.

For the current version, I stepped back and decided to do something more simple - instead of parsing the code repos I would just use the repository metadata that the RSEpedia already provides, and then do some extra parsing of dependencies from the repository with citelang. This reflects the current state of the repository, and the content in the root here.

Analysis Steps

  1. Compile all the metadata into a single file, including descriptions and topics
  2. Clean up text, etc., to prepare a vector of words for our model (combining topics and description)
  3. Cluster
  4. Then try training some probabilistic model to predict software topics based on cluster!

If this basic idea works (has signal), we could explore looking for more robust sources of text for each repository.

Usage

0. Install

Install dependencies (ideally in a virtual environment)

$ python -m venv env
$ source env/bin/activate
$ pip install -r requirements.txt
$ python -m nltk.downloader popular

This will install the research software encyclopedia, and nltk and data we need.

1. Data from Repositories

This next step will derive text from each repo, and a master lookup of topics to use later. If you haven't yet, clone the software repository (or use your own) somewhere else. E.g.,:

$ cd ../
$ git clone https://github.com/rseng/software
$ cd rsepedia-analysis

Then run the analysis script, targeting the correct rse.ini settings file for the software respository we just cloned. This will download the main data (or updated data):

$ mkdir -p _repos/ _data/ docs/
$ python 1.download.py --settings-file ../software/rse.ini -o ./_repos

This generates, for each repository that we find a requirements file for:

  • a badge that shows the dependencies
  • a data export of the same
  • and a saved requirments file.

2. Analysis

Then run a short analysis that mostly generates summary data and tables.

$ python 2.analysis.py --settings-file ../software/rse.ini -o ./_repos

For all repos we generate high level metadata and a summary of all dependencies.

3 Parse One / Redo

If you need to update one parsing (e.g., look for new deps, etc.):

$ python 3.parse_one.py --settings-file ../software/rse.ini -o ./_repos github/sylabs/singularity

Or to re-run for an entire language (or more than one). Below we would re-parse python repos:

$ python 4.redo_language.py  --settings-file ../software/rse.ini -o ./_repos --language-file setup.py --language-file requirements.txt

Or for just repos with package.json files or Go files:

$ python 4.redo_language.py  --settings-file ../software/rse.ini -o ./_repos  --language-file package.json
$ python 4.redo_language.py  --settings-file ../software/rse.ini -o ./_repos  --language-file go.mod

And then you might update the summary data, etc.

$ python 2.analysis.py --settings-file ../software/rse.ini -o ./_repos

Diary

I first did steps 1-3 (download through vectors) just using markdown files. The result looked like lips - there was distinction between Python and R but only slightly.

docs/img/md-only-lips.png

It looked a little bit like lips? I figured this happens because it's probably impossible to remove the language terms for README and other markdown files - e.g., "this is a Python project..." or similar. So then I decided to run steps 1-3 again, but this time include markdown, Rmd, Rd, and rst files. There is now more of a distinction between Python and R repositories.

docs/img/md-plus-others-brain.png

And this one looks a little bit like a brain? I'm worried that the distinction might be due to using Rmd documentation files that tend to have more code in them, and the greatest distinction reflecting common documentation practices over anything else. But we will see!