├── .github └── workflows │ └── python-publish.yml ├── .gitignore ├── .python-version ├── .travis.yml ├── CODE_OF_CONDUCT.md ├── HISTORY.txt ├── LICENSE ├── PKG-INFO ├── Pipfile ├── Pipfile.lock ├── README.md ├── README.rst ├── allofplos ├── .gitignore ├── __init__.py ├── allofplos_basics.ipynb ├── article.py ├── citation_utilities.py ├── corpus │ ├── __init__.py │ ├── corpus.py │ └── plos_corpus.py ├── dbtoorm.py ├── dois.txt ├── elements │ ├── __init__.py │ ├── article_elements.py │ ├── journal.py │ └── license.py ├── jupyter_nbconvert_config.py ├── makedb.py ├── plos_regex.py ├── samples │ ├── __init__.py │ └── corpus_analysis.py ├── starter.db ├── starter_corpus │ ├── __init__.py │ ├── journal.pbio.0020188.xml │ ├── journal.pbio.0020334.xml │ ├── journal.pbio.0030408.xml │ ├── journal.pbio.0040088.xml │ ├── journal.pbio.1000359.xml │ ├── journal.pbio.1001044.xml │ ├── journal.pbio.1001199.xml │ ├── journal.pbio.1001289.xml │ ├── journal.pbio.1001315.xml │ ├── journal.pbio.1001473.xml │ ├── journal.pbio.1001636.xml │ ├── journal.pcbi.0030158.xml │ ├── journal.pcbi.1000112.xml │ ├── journal.pcbi.1000204.xml │ ├── journal.pcbi.1000589.xml │ ├── journal.pcbi.1001051.xml │ ├── journal.pcbi.1001083.xml │ ├── journal.pcbi.1002484.xml │ ├── journal.pcbi.1003292.xml │ ├── journal.pcbi.1004079.xml │ ├── journal.pcbi.1004082.xml │ ├── journal.pcbi.1004089.xml │ ├── journal.pcbi.1004113.xml │ ├── journal.pcbi.1004141.xml │ ├── journal.pcbi.1004152.xml │ ├── journal.pcbi.1004156.xml │ ├── journal.pcbi.1004453.xml │ ├── journal.pcbi.1004692.xml │ ├── journal.pgen.1000052.xml │ ├── journal.pgen.1002912.xml │ ├── journal.pgen.1003316.xml │ ├── journal.pmed.0020007.xml │ ├── journal.pmed.0020124.xml │ ├── journal.pmed.0020171.xml │ ├── journal.pmed.0020402.xml │ ├── journal.pmed.0030132.xml │ ├── journal.pmed.0030205.xml │ ├── journal.pmed.0030445.xml │ ├── journal.pmed.0030520.xml │ ├── journal.pmed.0040303.xml │ ├── journal.pmed.1000097.xml │ ├── journal.pmed.1000431.xml │ ├── journal.pmed.1001080.xml │ ├── journal.pmed.1001186.xml │ ├── journal.pmed.1001300.xml │ ├── journal.pmed.1001418.xml │ ├── journal.pmed.1001473.xml │ ├── journal.pmed.1001518.xml │ ├── journal.pmed.1001786.xml │ ├── journal.pntd.0000149.xml │ ├── journal.pntd.0001041.xml │ ├── journal.pntd.0001969.xml │ ├── journal.pntd.0002570.xml │ ├── journal.pone.0002554.xml │ ├── journal.pone.0005723.xml │ ├── journal.pone.0008519.xml │ ├── journal.pone.0008915.xml │ ├── journal.pone.0010685.xml │ ├── journal.pone.0012262.xml │ ├── journal.pone.0016329.xml │ ├── journal.pone.0016976.xml │ ├── journal.pone.0026358.xml │ ├── journal.pone.0028031.xml │ ├── journal.pone.0036880.xml │ ├── journal.pone.0040259.xml │ ├── journal.pone.0042593.xml │ ├── journal.pone.0046041.xml │ ├── journal.pone.0047391.xml │ ├── journal.pone.0050698.xml │ ├── journal.pone.0052690.xml │ ├── journal.pone.0055490.xml │ ├── journal.pone.0058242.xml │ ├── journal.pone.0066742.xml │ ├── journal.pone.0067179.xml │ ├── journal.pone.0067227.xml │ ├── journal.pone.0067380.xml │ ├── journal.pone.0068090.xml │ ├── journal.pone.0069640.xml │ ├── journal.pone.0070598.xml │ ├── journal.pone.0074790.xml │ ├── journal.pone.0078761.xml │ ├── journal.pone.0078921.xml │ ├── journal.pone.0080518.xml │ ├── journal.pone.0081648.xml │ ├── journal.pone.0087236.xml │ ├── journal.pone.0097541.xml │ ├── journal.pone.0100977.xml │ ├── journal.pone.0108198.xml │ ├── journal.pone.0111971.xml │ ├── journal.pone.0114370.xml │ ├── journal.pone.0115067.xml │ ├── journal.pone.0116201.xml │ ├── journal.pone.0116586.xml │ ├── journal.pone.0116752.xml │ ├── journal.pone.0117014.xml │ ├── journal.pone.0117688.xml │ ├── journal.pone.0117949.xml │ ├── journal.pone.0118238.xml │ ├── journal.pone.0118342.xml │ ├── journal.pone.0119074.xml │ ├── journal.pone.0119705.xml │ ├── journal.pone.0120049.xml │ ├── journal.pone.0120924.xml │ ├── journal.pone.0121226.xml │ ├── journal.pone.0126470.xml │ ├── journal.pone.0138823.xml │ ├── journal.pone.0146913.xml │ ├── journal.pone.0147124.xml │ ├── journal.pone.0152025.xml │ ├── journal.pone.0152459.xml │ ├── journal.pone.0153152.xml │ ├── journal.pone.0153170.xml │ ├── journal.pone.0160653.xml │ ├── journal.ppat.0020025.xml │ ├── journal.ppat.0040045.xml │ ├── journal.ppat.1000105.xml │ ├── journal.ppat.1000166.xml │ ├── journal.ppat.1002247.xml │ ├── journal.ppat.1002735.xml │ ├── journal.ppat.1002769.xml │ ├── journal.ppat.1003133.xml │ └── journal.ppat.1005207.xml ├── starter_data.py ├── transformations.py ├── update.py └── utils.py ├── contributing.rst ├── docs └── source │ └── Basic_Corpus_Tutorial.ipynb ├── pyproject.toml ├── setup.cfg └── tests ├── __init__.py ├── test_corpus.py ├── test_unittests.py └── testdata ├── journal.pbio.2001413.xml ├── journal.pbio.2002354.xml ├── journal.pbio.2002399.xml ├── journal.pone.0185809.xml └── plos.correction.3155a3e9-5fbe-435c-a07a-e9a4846ec0b6.xml /.github/workflows/python-publish.yml: 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