P.A.P.E.R.

P.A.P.E.R. (Pablo's Artifacts and Papers Environment plus Repository) helps keep track of metadata about what you read, breadcrumbs to find it again. It helps with known-item search.

It contains:

• Data model: a hierarchical attribute-value pair DAG, completely contained in a YAML file. BibTeX file + Mind Map You can define your own relations. It can be opened with any text editor, search inside of it, carry it in your phone, etc. It can be committed to version control.

• File repository: a digital assets manager that copies PDFs and other source paper files into a unified folder-balanced hash-based space in your file system.

• Search engine: for files in the paper file repository, the text is extracted and stored in an index that allows queries, including query-by-example, to find similar papers to existing ones.

Features

• Exports to a static website.
• Imports BibTeX files.
• BibTeX generation.
• Imports from plain text files annotated with custom codes.
• Custom Jupyter widgets for editing and adding papers.
• Easy to hack, only 10 python files and 2000+ loc.

Learning more

Take a look at the sample_notebooks folder for examples and the tests folder. The sample notebooks are rendered as HTML in https://drdub.github.io/PAPER/sample_notebooks/

There is also a docs folder containing known issues, a detailed model explanation and slides from talks about the tool. The following talks are in YouTube:

• Vancouver Learn Data Science Lighting talk, 2020/09/30.
• Montreal Python talk, 2021/09/21.

Install

virtualenv -p python3 /path/to/virtualenv/paperapp
source /path/to/virtualenv/paperapp/bin/activate
pip install -r requirements.txt

To use the development version then issue (from the root of this repository):

pip install -e .

To use Jupyter notebooks inside this virtual environment, you need to register before launching it:

python -m ipykernel install --user --name=paperapp
jupyter notebook

Alternatively, it can be installed from pip (test PyPI):

python3 -m pip install --index-url https://test.pypi.org/simple/ --no-deps paperapp_DrDub
pip install paperapp_DrDub[widgets]
pip install paperapp_DrDub[fulltext]

Acknowledgements

This tool got started at Les Laboratoires Foulab, Montreal's hackerspace. It came up to speed for the writing of The Art of Feature Engineering, where it handled hundreds of references.