├── .github └── workflows │ └── tests.yml ├── .gitignore ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── doc ├── Makefile ├── conf.py ├── index.rst ├── make.bat ├── modules │ ├── index.rst │ └── modules.rst ├── requirements.txt └── tutorials.rst ├── notebooks ├── data │ ├── .gitignore │ ├── example.txt │ └── example_texts.json ├── figures │ └── adeft_gui.png ├── introduction.ipynb └── model_building.ipynb ├── paper ├── paper.bib └── paper.md ├── pyproject.toml ├── setup.py ├── src └── adeft │ ├── __init__.py │ ├── disambiguate.py │ ├── discover.py │ ├── download │ ├── __init__.py │ ├── __main__.py │ └── download.py │ ├── gui │ ├── __init__.py │ └── ground │ │ ├── __init__.py │ │ ├── ground.py │ │ ├── static │ │ ├── ground.css │ │ └── scripts.js │ │ └── templates │ │ └── input.jinja2 │ ├── locations.py │ ├── modeling │ ├── __init__.py │ ├── classify.py │ └── label.py │ ├── nlp │ ├── __init__.py │ ├── nlp.py │ └── stopwords.json │ ├── recognize.py │ ├── score │ ├── __init__.py │ ├── _score.pyx │ ├── permutations.pyx │ └── score.py │ └── util.py └── tests ├── test_classify.py ├── test_corpora.py ├── test_disambiguate.py ├── test_discover.py ├── test_download.py ├── test_ground.py ├── test_nlp.py ├── test_recognize.py ├── test_score.py └── test_util.py /.github/workflows/tests.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/.github/workflows/tests.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/.gitignore -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/README.md -------------------------------------------------------------------------------- /doc/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/doc/Makefile -------------------------------------------------------------------------------- /doc/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/doc/conf.py -------------------------------------------------------------------------------- /doc/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/doc/index.rst -------------------------------------------------------------------------------- /doc/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/doc/make.bat -------------------------------------------------------------------------------- /doc/modules/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/doc/modules/index.rst -------------------------------------------------------------------------------- /doc/modules/modules.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/doc/modules/modules.rst -------------------------------------------------------------------------------- /doc/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/doc/requirements.txt -------------------------------------------------------------------------------- /doc/tutorials.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/doc/tutorials.rst -------------------------------------------------------------------------------- /notebooks/data/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/notebooks/data/.gitignore -------------------------------------------------------------------------------- /notebooks/data/example.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/notebooks/data/example.txt -------------------------------------------------------------------------------- /notebooks/data/example_texts.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/notebooks/data/example_texts.json -------------------------------------------------------------------------------- /notebooks/figures/adeft_gui.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/notebooks/figures/adeft_gui.png -------------------------------------------------------------------------------- /notebooks/introduction.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/notebooks/introduction.ipynb -------------------------------------------------------------------------------- /notebooks/model_building.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/notebooks/model_building.ipynb -------------------------------------------------------------------------------- /paper/paper.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/paper/paper.bib -------------------------------------------------------------------------------- /paper/paper.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/paper/paper.md -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/pyproject.toml -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/setup.py -------------------------------------------------------------------------------- /src/adeft/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/__init__.py -------------------------------------------------------------------------------- /src/adeft/disambiguate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/disambiguate.py -------------------------------------------------------------------------------- /src/adeft/discover.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/discover.py -------------------------------------------------------------------------------- /src/adeft/download/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/download/__init__.py -------------------------------------------------------------------------------- /src/adeft/download/__main__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/download/__main__.py -------------------------------------------------------------------------------- /src/adeft/download/download.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/download/download.py -------------------------------------------------------------------------------- /src/adeft/gui/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/gui/__init__.py -------------------------------------------------------------------------------- /src/adeft/gui/ground/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/gui/ground/__init__.py -------------------------------------------------------------------------------- /src/adeft/gui/ground/ground.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/gui/ground/ground.py -------------------------------------------------------------------------------- /src/adeft/gui/ground/static/ground.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/gui/ground/static/ground.css -------------------------------------------------------------------------------- /src/adeft/gui/ground/static/scripts.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/gui/ground/static/scripts.js -------------------------------------------------------------------------------- /src/adeft/gui/ground/templates/input.jinja2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/gui/ground/templates/input.jinja2 -------------------------------------------------------------------------------- /src/adeft/locations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/locations.py -------------------------------------------------------------------------------- /src/adeft/modeling/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/modeling/__init__.py -------------------------------------------------------------------------------- /src/adeft/modeling/classify.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/modeling/classify.py -------------------------------------------------------------------------------- /src/adeft/modeling/label.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/modeling/label.py -------------------------------------------------------------------------------- /src/adeft/nlp/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/nlp/__init__.py -------------------------------------------------------------------------------- /src/adeft/nlp/nlp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/nlp/nlp.py -------------------------------------------------------------------------------- /src/adeft/nlp/stopwords.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/nlp/stopwords.json -------------------------------------------------------------------------------- /src/adeft/recognize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/recognize.py -------------------------------------------------------------------------------- /src/adeft/score/__init__.py: -------------------------------------------------------------------------------- 1 | from .score import AlignmentBasedScorer 2 | -------------------------------------------------------------------------------- /src/adeft/score/_score.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/score/_score.pyx -------------------------------------------------------------------------------- /src/adeft/score/permutations.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/score/permutations.pyx -------------------------------------------------------------------------------- /src/adeft/score/score.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/score/score.py -------------------------------------------------------------------------------- /src/adeft/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/src/adeft/util.py -------------------------------------------------------------------------------- /tests/test_classify.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/tests/test_classify.py -------------------------------------------------------------------------------- /tests/test_corpora.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/tests/test_corpora.py -------------------------------------------------------------------------------- /tests/test_disambiguate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/tests/test_disambiguate.py -------------------------------------------------------------------------------- /tests/test_discover.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/tests/test_discover.py -------------------------------------------------------------------------------- /tests/test_download.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/tests/test_download.py -------------------------------------------------------------------------------- /tests/test_ground.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/tests/test_ground.py -------------------------------------------------------------------------------- /tests/test_nlp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/tests/test_nlp.py -------------------------------------------------------------------------------- /tests/test_recognize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/tests/test_recognize.py -------------------------------------------------------------------------------- /tests/test_score.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/tests/test_score.py -------------------------------------------------------------------------------- /tests/test_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gyorilab/adeft/HEAD/tests/test_util.py --------------------------------------------------------------------------------