A python library to deal with scientific papers.
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README.md

libBMC

Presentation

A generic Python library to manage bibliography and play with scientific papers.

Note: This library is written for Python 3 and may not work with Python 2. This is not a major priority for me, but if anyone needed to make it work with Python 2 and want to make a PR, I will happily merge it :)

Dependencies

Python dependencies are listed in the requirements.txt file at the root of this repo, and can be installed with pip install -r requirements.txt.

External dependencies are OpenDeTeX (an improved version of DeTeX) and the pdftotext and djvutxt programs.

OpenDeTeX is available as a Git submodule in the libbmc/external folder. If you do not have it installed system-wide, you can use the following steps to build it in this repo and the library will use it:

  • git submodule init; git submodule update to initialize the Git submodules.
  • cd libbmc/external/opendetex; make to build OpenDeTeX (see INSTALL file in the same folder for more info, you will need make, gcc and flex to build it).

OpenDeTeX is used to get references from a .bbl file (or directly from arXiv as it uses the same pipeline).

pdftotext and djvutxt should be available in the packages of your distribution and should be installed systemwide. Both are used to extract identifiers from papers PDF files.

If you plan on using the libbmc.citations.pdf functions, you should also install the matching software (CERMINE, Grobid or pdf-extract). See the docstrings of those functions for more infos on this particular point.

Installation

Either use pip install libbmc or download the ZIP archive from this repo and install it manually using python setup.py install.

Running unittests

Just run

nosetests --with-doctest

at the root of the Git repository to run the unittests.

Building the doc

Just run

cd docs
make html

Documentation will be generated in the docs/build/html folder.

Note on __valid_identifiers__

libbmc exposes a __valid_identifiers__ list, containing the valid identifier types. These are those exposing the same function as doi or isbn modules, in particular the extraction from a string and BibTeX fetching functions.

If you write additional modules for others repositories, you can include them in the __valid_identifiers__ list, as long as they provide these functions.

This list is especially useful for the libbmc.papers.identifiers module, which is using it to loop through all the available identifier types, to fetch for them in the paper and retrieve BibTeX from it.

You can also write a specific citation extraction module for this repository in libbmc/citations/repositories/{REPOSITORY}.py.

License

This code is licensed under an MIT license.

Acknowledgements

Thanks a lot to the following authors and programs for helping in building this lib: