131 lines
3.6 KiB
Markdown
131 lines
3.6 KiB
Markdown
libBMC
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======
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## Presentation
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A generic Python library to manage bibliography and play with scientific
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papers.
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_Note_: This library is written for Python 3 and may not work with Python 2.
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This is not a major priority for me, but if anyone needed to make it work with
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Python 2 and want to make a PR, I will happily merge it :)
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## Dependencies
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Python dependencies are listed in the `requirements.txt` file at the root of
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this repo, and can be installed with `pip install -r requirements.txt`.
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External dependencies are [OpenDeTeX](https://code.google.com/p/opendetex/)
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(an improved version of DeTeX) and the `pdftotext` and `djvutxt` programs.
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OpenDeTeX is available as a Git submodule in the `libbmc/external` folder. If
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you do not have it installed system-wide, you can use the following steps to
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build it in this repo and the library will use it:
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* `git submodule init; git submodule update` to initialize the Git submodules.
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* `cd libbmc/external/opendetex; make` to build OpenDeTeX (see `INSTALL` file
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in the same folder for more info, you will need `make`, `gcc` and `flex` to
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build it).
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OpenDeTeX is used to get references from a `.bbl` file (or directly from arXiv
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as it uses the same pipeline).
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`pdftotext` and `djvutxt` should be available in the packages of your
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distribution and should be installed systemwide. Both are used to extract
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identifiers from papers PDF files.
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If you plan on using the `libbmc.citations.pdf` functions, you should also
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install the matching software (`CERMINE`, `Grobid` or `pdf-extract`). See the
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docstrings of those functions for more infos on this particular point.
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## Installation
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Either use `pip install libbmc` or download the ZIP archive from this repo and
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install it manually using `python setup.py install`.
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## Running unittests
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Just run
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```
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nosetests --with-doctest
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```
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at the root of the Git repository to run the unittests.
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## Building the doc
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Just run
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```
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cd docs
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make html
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```
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Documentation will be generated in the `docs/build/html` folder.
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## Note on `__valid_identifiers__`
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`libbmc` exposes a `__valid_identifiers__` list, containing the valid
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identifier types. These are those exposing the same function as `doi` or
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`isbn` modules, in particular the extraction from a string and BibTeX
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fetching functions.
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If you write additional modules for others repositories, you can include them
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in the `__valid_identifiers__` list, as long as they provide these functions.
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This list is especially useful for the `libbmc.papers.identifiers` module,
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which is using it to loop through all the available identifier types, to fetch
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for them in the paper and retrieve BibTeX from it.
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You can also write a specific citation extraction module for this repository
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in `libbmc/citations/repositories/{REPOSITORY}.py`.
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## License
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This code is licensed under an MIT license.
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## Acknowledgements
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Thanks a lot to the following authors and programs for helping in building
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this lib:
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* Dominika Tkaczyk, Pawel Szostek, Mateusz Fedoryszak, Piotr Jan Dendek and
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Lukasz Bolikowski.
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CERMINE: automatic extraction of structured metadata from scientific
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literature.
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In International Journal on Document Analysis and Recognition (IJDAR), 2015,
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vol. 18, no. 4, pp. 317-335, doi: 10.1007/s10032-015-0249-8.
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https://github.com/CeON/CERMINE
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* https://github.com/CrossRef/pdfextract
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* https://github.com/kermitt2/grobid
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* https://github.com/sciunto-org/python-bibtexparser
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* http://djvu.sourceforge.net/doc/man/djvutxt.html
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* http://www.foolabs.com/xpdf/home.html
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* https://code.google.com/p/opendetex/
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* https://github.com/nathangrigg/arxiv2bib/
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* https://github.com/xlcnd/isbnlib
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* https://github.com/Anorov/PySocks
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* http://docs.python-requests.org/en/latest/#
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