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‎Paper.ipynb

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‎README.md

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# HaPy-Bug - Human Annotated Python Bug Resolution Dataset
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Data and code package is available on https://figshare.com/s/9cbc129a95a8fc3a9640
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Structure (missing data directories are on figshare):
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* 'annotated_data' and 'collective' contain manual annotations extracted from label studio instance
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* 'code' contains scripts used to gather data and prepare dataset
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* 'label-studio' contains copy of label studio sources used for manual annotations
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* 'label-studio-frontend' contains modified copy of label studio frontend used for manual annotation
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* 'raw_data' contains gathered data before manual annotation
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* 'Paper.ipynb' contains notebook to open manual annotations and replicate paper experiments
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Dataset schema for automated tools is in "code/Documentation/Dataset_structure.md"
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Annotations protocol is in "code/Documentation/miniatura_protocol.md"
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Annotations schema is as follows:
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* 'annotated_data' contains json files extracted from label studio
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* prefix letter of name of file denotes annotator, for instance "A_1_24.json" was annotated by annotator "A"
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* in file there is a list of annotations, each entry on the list has fields containing
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** bug description and metadata in "data" field
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** results of annotators actions in "result" field
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* Following entries are stored in "result" field as directory
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** entries with type 'choices' like "annotations-were-problematic", "reviewer-is-sure", "bug-type" contain selected answers
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** entry with type 'cve' contains line and file annotations
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*** subentry "diffsFiles" contains "fileName", assigned category "category" and annotated lines in "lines", divided into "afterChange" and "beforeChange" of specific commit
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Example first "data/cve" entry
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```
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{'id': 'CVE-2019-11340',
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'publicationDate': '19-04-2019',
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'severityScore': '4.3',
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'summary': 'util/emailutils.py in Matrix Sydent before 1.0.2 mishandles registration restrictions that are based on e-mail domain, if the allowed_local_3pids option is enabled. This occurs because of potentially unwanted behavior in Python, in which an email.utils.parseaddr call on [email protected]@good.example.com returns the [email protected] substring.'}
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```
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Corresponding example first "result" entry taken from "A_1_24.json" file, for manual annotatios of 'sydent/util/emailutils.py':
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```
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[{'value': {'choices': ['application/library']},
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'id': 'g4UOah3mt_',
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'from_name': 'bug-type',
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'to_name': 'text-bug-type',
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'type': 'choices',
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'origin': 'manual'},
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{'value': {'choices': ['yes']},
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'id': 'OhaMoaD2UT',
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'from_name': 'reviewer-is-sure',
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'to_name': 'text-reviewer-is-sure',
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'type': 'choices',
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'origin': 'manual'},
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{'value': {'choices': ['no']},
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'id': '3VdKlaBUh9',
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'from_name': 'annotations-were-problematic',
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'to_name': 'text-annotations-were-problematic',
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'type': 'choices',
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'origin': 'manual'},
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{'type': 'cve',
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'value': {'hyperlinks': [{'url': 'https://matrix.org/blog/2019/04/18/security-update-sydent-1-0-2/',
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'dates': {'min': '2019-04-18', 'max': '2019-04-18'},
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'labels': ['Release Notes', 'Vendor Advisory']},
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{'url': 'https://twitter.com/matrixdotorg/status/1118934335963500545',
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'dates': {'min': None, 'max': None},
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'labels': ['Third Party Advisory']},
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{'url': 'https://github.com/matrix-org/sydent/commit/4e1cfff53429c49c87d5c457a18ed435520044fc',
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'dates': {'min': '2019-04-18', 'max': '2019-04-26'},
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'labels': ['Patch', 'Third Party Advisory']},
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{'url': 'https://github.com/matrix-org/sydent/compare/7c002cd...09278fb',
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'dates': {'min': '2019-04-18', 'max': '2019-04-18'},
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'labels': ['Patch', 'Third Party Advisory']}],
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'diffsFiles': [[{'fileName': 'sydent/util/emailutils.py',
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'category': 'programming',
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'lines': {'afterChange': [{'lineNumber': 58, 'category': 'other'},
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{'lineNumber': 59, 'category': 'bug(fix)'},
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{'lineNumber': 60, 'category': 'bug(fix)'},
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{'lineNumber': 61, 'category': 'bug(fix)'},
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{'lineNumber': 64, 'category': 'refactoring'},
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{'lineNumber': 81, 'category': 'refactoring'},
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{'lineNumber': 82, 'category': 'documentation'},
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{'lineNumber': 83, 'category': 'documentation'},
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{'lineNumber': 84, 'category': 'documentation'},
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{'lineNumber': 85, 'category': 'documentation'},
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{'lineNumber': 86, 'category': 'bug(fix)'}],
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'beforeChange': [{'lineNumber': 58, 'category': 'other'},
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{'lineNumber': 59, 'category': 'bug(fix)'},
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{'lineNumber': 60, 'category': 'bug(fix)'},
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{'lineNumber': 61, 'category': 'bug(fix)'},
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{'lineNumber': 80, 'category': 'bug(fix)'}]}}]]}}]
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```
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‎code/.gitignore

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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pip-wheel-metadata/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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.python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# PyCharm
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.idea/
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# Script output files
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data/
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# node.js
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node_modules
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package-lock.json

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