2023-05-14T06:26:43,485 Created temporary directory: /tmp/pip-build-tracker-q06pa4rj 2023-05-14T06:26:43,486 Initialized build tracking at /tmp/pip-build-tracker-q06pa4rj 2023-05-14T06:26:43,486 Created build tracker: /tmp/pip-build-tracker-q06pa4rj 2023-05-14T06:26:43,486 Entered build tracker: /tmp/pip-build-tracker-q06pa4rj 2023-05-14T06:26:43,487 Created temporary directory: /tmp/pip-wheel-winlutmo 2023-05-14T06:26:43,490 Created temporary directory: /tmp/pip-ephem-wheel-cache-3lupdx71 2023-05-14T06:26:43,515 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-05-14T06:26:43,518 2 location(s) to search for versions of medspacy: 2023-05-14T06:26:43,518 * https://pypi.org/simple/medspacy/ 2023-05-14T06:26:43,518 * https://www.piwheels.org/simple/medspacy/ 2023-05-14T06:26:43,518 Fetching project page and analyzing links: https://pypi.org/simple/medspacy/ 2023-05-14T06:26:43,519 Getting page https://pypi.org/simple/medspacy/ 2023-05-14T06:26:43,521 Found 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requirements to build wheel 2023-05-14T06:26:55,241 /tmp/pip-build-env-tyhrirxm/overlay/lib/python3.9/site-packages/setuptools/config/pyprojecttoml.py:66: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. 2023-05-14T06:26:55,241 config = read_configuration(filepath, True, ignore_option_errors, dist) 2023-05-14T06:26:55,280 /tmp/pip-build-env-tyhrirxm/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:62: _WouldIgnoreField: `readme` defined outside of `pyproject.toml` would be ignored. 2023-05-14T06:26:55,280 !! 2023-05-14T06:26:55,280 ******************************************************************************** 2023-05-14T06:26:55,280 ########################################################################## 2023-05-14T06:26:55,281 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-05-14T06:26:55,281 ########################################################################## 2023-05-14T06:26:55,281 The following seems to be defined outside of `pyproject.toml`: 2023-05-14T06:26:55,281 `readme = '[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n![Build Status](https://github.com/medspacy/medspacy/workflows/medspacy/badge.svg)\n\n# medspacy\nLibrary for clinical NLP with spaCy. \n\n![alt text](./images/medspacy_logo.png "medSpaCy logo")\n\n**MedSpaCy is currently in beta.**\n\n\n# Overview\nMedSpaCy is a library of tools for performing clinical NLP and text processing tasks with the popular [spaCy](https://spacy.io) \nframework. The `medspacy` package brings together a number of other packages, each of which implements specific \nfunctionality for common clinical text processing specific to the clinical domain, such as sentence segmentation, \ncontextual analysis and attribute assertion, and section detection.\n\n`medspacy` is modularized so that each component can be used independently. All of `medspacy` is designed to be used \nas part of a `spacy` processing pipeline. Each of the following modules is available as part of `medspacy`:\n- `medspacy.preprocess`: Destructive preprocessing for modifying clinical text before processing\n- `medspacy.sentence_splitter`: Clinical sentence segmentation\n- `medspacy.ner`: Utilities for extracting concepts from clinical text\n- `medspacy.context`: Implementation of the [ConText](https://www.sciencedirect.com/science/article/pii/S1532046409000744)\nfor detecting semantic modifiers and attributes of entities, including negation and uncertainty\n- `medspacy.section_detection`: Clinical section detection and segmentation\n- `medspacy.postprocess`: Flexible framework for modifying and removing extracted entities\n- `medspacy.io`: Utilities for converting processed texts to structured data and interacting with databases\n- `medspacy.visualization`: Utilities for visualizing concepts and relationships extracted from text\n- `SpacyQuickUMLS`: UMLS concept extraction compatible with spacy and medspacy implemented by [our fork](https://github.com/medspacy/QuickUMLS) of [QuickUMLS](https://github.com/Georgetown-IR-Lab/QuickUMLS). More detail on this component, how to use it, how to generate UMLS resources beyond the small UMLS sample can be found in [this notebook](notebooks/11-QuickUMLS_Extraction.ipynb).\n\nFuture work could include I/O, relations extraction, and pre-trained clinical models.\n\n**As of 10/2/2021 (version 0.2.0.0), medspaCy supports spaCy v3**\n\n# Usage\n## Installation\n\nYou can install `medspacy` using `setup.py`:\n```bash\npython setup.py install\n```\n\nOr with pip:\n```bash\npip install medspacy\n```\n\nTo install a previous version which uses spaCy 2:\n```bash\npip install medspacy==medspacy 0.1.0.2\n```\n\n### Requirements\nThe following packages are required and installed when `medspacy` is installed:\n- spaCy v3\n- [pyrush](https://github.com/medspacy/PyRuSH)\n\nIf you download other models, you can use them by providing the model itself or model name to `medspacy.load(model_name)`:\n```python\nimport spacy; import medspacy\n# Option 1: Load default\nnlp = medspacy.load()\n\n# Option 2: Load from existing model\nnlp = spacy.load("en_core_web_sm", disable={"ner"})\nnlp = medspacy.load(nlp)\n\n# Option 3: Load from model name\nnlp = medspacy.load("en_core_web_sm", disable={"ner"})\n```\n \n## Basic Usage\nHere is a simple example showing how to implement and visualize a simple rule-based pipeline using `medspacy`:\n```python\nimport medspacy\nfrom medspacy.ner import TargetRule\nfrom medspacy.visualization import visualize_ent\n\n# Load medspacy model\nnlp = medspacy.load()\nprint(nlp.pipe_names)\n\ntext = """\nPast Medical History:\n1. Atrial fibrillation\n2. Type II Diabetes Mellitus\n\nAssessment and Plan:\nThere is no evidence of pneumonia. Continue warfarin for Afib. Follow up for management of type 2 DM.\n"""\n\n# Add rules for target concept extraction\ntarget_matcher = nlp.get_pipe("medspacy_target_matcher")\ntarget_rules = [\n TargetRule("atrial fibrillation", "PROBLEM"),\n TargetRule("atrial fibrillation", "PROBLEM", pattern=[{"LOWER": "afib"}]),\n TargetRule("pneumonia", "PROBLEM"),\n TargetRule("Type II Diabetes Mellitus", "PROBLEM", \n pattern=[\n {"LOWER": "type"},\n {"LOWER": {"IN": ["2", "ii", "two"]}},\n {"LOWER": {"IN": ["dm", "diabetes"]}},\n {"LOWER": "mellitus", "OP": "?"}\n ]),\n TargetRule("warfarin", "MEDICATION")\n]\ntarget_matcher.add(target_rules)\n\ndoc = nlp(text)\nvisualize_ent(doc)\n```\n\n`Output:`\n![alt text](./images/simple_text_visualization.png "Example of clinical text processed by medSpaCy")\n\nFor more detailed examples and explanations of each component, see the [notebooks](./notebooks) folder.\n\n# Citing medspaCy\nIf you use medspaCy in your work, consider citing our paper! Presented at the AMIA Annual Symposium 2021, [preprint available on Arxiv](http://arxiv.org/abs/2106.07799).\n\n```\nH. Eyre, A.B. Chapman, K.S. Peterson, J. Shi, P.R. Alba, M.M. Jones, T.L. Box, S.L. DuVall, O. V Patterson,\nLaunching into clinical space with medspaCy: a new clinical text processing toolkit in Python,\nAMIA Annu. Symp. Proc. 2021 (in Press. (n.d.). \nhttp://arxiv.org/abs/2106.07799.\n```\n\n```\n@Article{medspacy,\n Author="Eyre, H. and Chapman, A. B. and Peterson, K. S. and Shi, J. and Alba, P. R. and Jones, M. M. and Box, T. L. and DuVall, S. L. and Patterson, O. V. ",\n Title="{{L}aunching into clinical space with medspa{C}y: a new clinical text processing toolkit in {P}ython}",\n Journal="AMIA Annu Symp Proc",\n Year="2021",\n Volume="2021",\n Pages="438--447"\n}\n\n}\n```\n\n# Made with medSpaCy\nHere are some links to projects or tutorials which use medSpacy. If you have a project which uses medSpaCy which you\'d like to use, let us know!\n- [VA_COVID-19_NLP_BSV](https://github.com/abchapman93/VA_COVID-19_NLP_BSV): An NLP pipeline for [identifying positive cases of COVID-19](https://aclanthology.org/2020.nlpcovid19-acl.10/) from clinical text. Deployed as part of the Department of Veterans Affairs response to COVID-19\n- [clinspacy](https://ml4lhs.github.io/clinspacy/index.html): An R wrapper for spaCy, sciSpaCy, and medSpaCy for performing clinical NLP and UMLS linking in R\n- [mimic34md2020_materials](https://github.com/Melbourne-BMDS/mimic34md2020_materials): A crash course in clinical data science from the University of Melbourne. For medSpaCy materials, see `notebooks/nlp-*.ipynb`\n- [ReHouSED NLP](https://github.com/abchapman93/ReHouSED): An NLP pipeline for [studying Veteran housing stability](https://www.sciencedirect.com/science/article/pii/S153204642100232X) and distinguishing between Veterans who are currently unstably housed and those who have exited homelessness\n'` 2023-05-14T06:26:55,282 According to the spec (see the link below), however, setuptools CANNOT 2023-05-14T06:26:55,282 consider this value unless `readme` is listed as `dynamic`. 2023-05-14T06:26:55,282 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-05-14T06:26:55,282 For the time being, `setuptools` will still consider the given value (as a 2023-05-14T06:26:55,282 **transitional** measure), but please note that future releases of setuptools will 2023-05-14T06:26:55,283 follow strictly the standard. 2023-05-14T06:26:55,283 To prevent this warning, you can list `readme` under `dynamic` or alternatively 2023-05-14T06:26:55,283 remove the `[project]` table from your file and rely entirely on other means of 2023-05-14T06:26:55,283 configuration. 2023-05-14T06:26:55,283 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-05-14T06:26:55,284 or your builds will no longer be supported. 2023-05-14T06:26:55,284 ******************************************************************************** 2023-05-14T06:26:55,284 !! 2023-05-14T06:26:55,284 _handle_missing_dynamic(dist, project_table) 2023-05-14T06:26:55,284 /tmp/pip-build-env-tyhrirxm/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:69: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-05-14T06:26:55,284 corresp(dist, value, root_dir) 2023-05-14T06:26:55,637 running egg_info 2023-05-14T06:26:55,644 writing medspacy.egg-info/PKG-INFO 2023-05-14T06:26:55,646 writing dependency_links to medspacy.egg-info/dependency_links.txt 2023-05-14T06:26:55,649 writing requirements to medspacy.egg-info/requires.txt 2023-05-14T06:26:55,650 writing top-level names to medspacy.egg-info/top_level.txt 2023-05-14T06:26:55,711 listing git files failed - pretending there aren't any 2023-05-14T06:26:55,719 reading manifest file 'medspacy.egg-info/SOURCES.txt' 2023-05-14T06:26:55,724 adding license file 'LICENSE' 2023-05-14T06:26:55,733 writing manifest file 'medspacy.egg-info/SOURCES.txt' 2023-05-14T06:26:55,847 Getting requirements to build wheel: finished with status 'done' 2023-05-14T06:26:55,858 Created temporary directory: /tmp/pip-modern-metadata-3c31c04b 2023-05-14T06:26:55,861 Preparing metadata (pyproject.toml): started 2023-05-14T06:26:55,862 Running command Preparing metadata (pyproject.toml) 2023-05-14T06:26:56,428 /tmp/pip-build-env-tyhrirxm/overlay/lib/python3.9/site-packages/setuptools/config/pyprojecttoml.py:66: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. 2023-05-14T06:26:56,429 config = read_configuration(filepath, True, ignore_option_errors, dist) 2023-05-14T06:26:56,469 /tmp/pip-build-env-tyhrirxm/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:62: _WouldIgnoreField: `readme` defined outside of `pyproject.toml` would be ignored. 2023-05-14T06:26:56,470 !! 2023-05-14T06:26:56,470 ******************************************************************************** 2023-05-14T06:26:56,470 ########################################################################## 2023-05-14T06:26:56,470 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-05-14T06:26:56,470 ########################################################################## 2023-05-14T06:26:56,471 The following seems to be defined outside of `pyproject.toml`: 2023-05-14T06:26:56,471 `readme = '[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n![Build Status](https://github.com/medspacy/medspacy/workflows/medspacy/badge.svg)\n\n# medspacy\nLibrary for clinical NLP with spaCy. \n\n![alt text](./images/medspacy_logo.png "medSpaCy logo")\n\n**MedSpaCy is currently in beta.**\n\n\n# Overview\nMedSpaCy is a library of tools for performing clinical NLP and text processing tasks with the popular [spaCy](https://spacy.io) \nframework. The `medspacy` package brings together a number of other packages, each of which implements specific \nfunctionality for common clinical text processing specific to the clinical domain, such as sentence segmentation, \ncontextual analysis and attribute assertion, and section detection.\n\n`medspacy` is modularized so that each component can be used independently. All of `medspacy` is designed to be used \nas part of a `spacy` processing pipeline. Each of the following modules is available as part of `medspacy`:\n- `medspacy.preprocess`: Destructive preprocessing for modifying clinical text before processing\n- `medspacy.sentence_splitter`: Clinical sentence segmentation\n- `medspacy.ner`: Utilities for extracting concepts from clinical text\n- `medspacy.context`: Implementation of the [ConText](https://www.sciencedirect.com/science/article/pii/S1532046409000744)\nfor detecting semantic modifiers and attributes of entities, including negation and uncertainty\n- `medspacy.section_detection`: Clinical section detection and segmentation\n- `medspacy.postprocess`: Flexible framework for modifying and removing extracted entities\n- `medspacy.io`: Utilities for converting processed texts to structured data and interacting with databases\n- `medspacy.visualization`: Utilities for visualizing concepts and relationships extracted from text\n- `SpacyQuickUMLS`: UMLS concept extraction compatible with spacy and medspacy implemented by [our fork](https://github.com/medspacy/QuickUMLS) of [QuickUMLS](https://github.com/Georgetown-IR-Lab/QuickUMLS). More detail on this component, how to use it, how to generate UMLS resources beyond the small UMLS sample can be found in [this notebook](notebooks/11-QuickUMLS_Extraction.ipynb).\n\nFuture work could include I/O, relations extraction, and pre-trained clinical models.\n\n**As of 10/2/2021 (version 0.2.0.0), medspaCy supports spaCy v3**\n\n# Usage\n## Installation\n\nYou can install `medspacy` using `setup.py`:\n```bash\npython setup.py install\n```\n\nOr with pip:\n```bash\npip install medspacy\n```\n\nTo install a previous version which uses spaCy 2:\n```bash\npip install medspacy==medspacy 0.1.0.2\n```\n\n### Requirements\nThe following packages are required and installed when `medspacy` is installed:\n- spaCy v3\n- [pyrush](https://github.com/medspacy/PyRuSH)\n\nIf you download other models, you can use them by providing the model itself or model name to `medspacy.load(model_name)`:\n```python\nimport spacy; import medspacy\n# Option 1: Load default\nnlp = medspacy.load()\n\n# Option 2: Load from existing model\nnlp = spacy.load("en_core_web_sm", disable={"ner"})\nnlp = medspacy.load(nlp)\n\n# Option 3: Load from model name\nnlp = medspacy.load("en_core_web_sm", disable={"ner"})\n```\n \n## Basic Usage\nHere is a simple example showing how to implement and visualize a simple rule-based pipeline using `medspacy`:\n```python\nimport medspacy\nfrom medspacy.ner import TargetRule\nfrom medspacy.visualization import visualize_ent\n\n# Load medspacy model\nnlp = medspacy.load()\nprint(nlp.pipe_names)\n\ntext = """\nPast Medical History:\n1. Atrial fibrillation\n2. Type II Diabetes Mellitus\n\nAssessment and Plan:\nThere is no evidence of pneumonia. Continue warfarin for Afib. Follow up for management of type 2 DM.\n"""\n\n# Add rules for target concept extraction\ntarget_matcher = nlp.get_pipe("medspacy_target_matcher")\ntarget_rules = [\n TargetRule("atrial fibrillation", "PROBLEM"),\n TargetRule("atrial fibrillation", "PROBLEM", pattern=[{"LOWER": "afib"}]),\n TargetRule("pneumonia", "PROBLEM"),\n TargetRule("Type II Diabetes Mellitus", "PROBLEM", \n pattern=[\n {"LOWER": "type"},\n {"LOWER": {"IN": ["2", "ii", "two"]}},\n {"LOWER": {"IN": ["dm", "diabetes"]}},\n {"LOWER": "mellitus", "OP": "?"}\n ]),\n TargetRule("warfarin", "MEDICATION")\n]\ntarget_matcher.add(target_rules)\n\ndoc = nlp(text)\nvisualize_ent(doc)\n```\n\n`Output:`\n![alt text](./images/simple_text_visualization.png "Example of clinical text processed by medSpaCy")\n\nFor more detailed examples and explanations of each component, see the [notebooks](./notebooks) folder.\n\n# Citing medspaCy\nIf you use medspaCy in your work, consider citing our paper! Presented at the AMIA Annual Symposium 2021, [preprint available on Arxiv](http://arxiv.org/abs/2106.07799).\n\n```\nH. Eyre, A.B. Chapman, K.S. Peterson, J. Shi, P.R. Alba, M.M. Jones, T.L. Box, S.L. DuVall, O. V Patterson,\nLaunching into clinical space with medspaCy: a new clinical text processing toolkit in Python,\nAMIA Annu. Symp. Proc. 2021 (in Press. (n.d.). \nhttp://arxiv.org/abs/2106.07799.\n```\n\n```\n@Article{medspacy,\n Author="Eyre, H. and Chapman, A. B. and Peterson, K. S. and Shi, J. and Alba, P. R. and Jones, M. M. and Box, T. L. and DuVall, S. L. and Patterson, O. V. ",\n Title="{{L}aunching into clinical space with medspa{C}y: a new clinical text processing toolkit in {P}ython}",\n Journal="AMIA Annu Symp Proc",\n Year="2021",\n Volume="2021",\n Pages="438--447"\n}\n\n}\n```\n\n# Made with medSpaCy\nHere are some links to projects or tutorials which use medSpacy. If you have a project which uses medSpaCy which you\'d like to use, let us know!\n- [VA_COVID-19_NLP_BSV](https://github.com/abchapman93/VA_COVID-19_NLP_BSV): An NLP pipeline for [identifying positive cases of COVID-19](https://aclanthology.org/2020.nlpcovid19-acl.10/) from clinical text. Deployed as part of the Department of Veterans Affairs response to COVID-19\n- [clinspacy](https://ml4lhs.github.io/clinspacy/index.html): An R wrapper for spaCy, sciSpaCy, and medSpaCy for performing clinical NLP and UMLS linking in R\n- [mimic34md2020_materials](https://github.com/Melbourne-BMDS/mimic34md2020_materials): A crash course in clinical data science from the University of Melbourne. For medSpaCy materials, see `notebooks/nlp-*.ipynb`\n- [ReHouSED NLP](https://github.com/abchapman93/ReHouSED): An NLP pipeline for [studying Veteran housing stability](https://www.sciencedirect.com/science/article/pii/S153204642100232X) and distinguishing between Veterans who are currently unstably housed and those who have exited homelessness\n'` 2023-05-14T06:26:56,471 According to the spec (see the link below), however, setuptools CANNOT 2023-05-14T06:26:56,471 consider this value unless `readme` is listed as `dynamic`. 2023-05-14T06:26:56,472 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-05-14T06:26:56,472 For the time being, `setuptools` will still consider the given value (as a 2023-05-14T06:26:56,472 **transitional** measure), but please note that future releases of setuptools will 2023-05-14T06:26:56,472 follow strictly the standard. 2023-05-14T06:26:56,473 To prevent this warning, you can list `readme` under `dynamic` or alternatively 2023-05-14T06:26:56,473 remove the `[project]` table from your file and rely entirely on other means of 2023-05-14T06:26:56,473 configuration. 2023-05-14T06:26:56,473 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-05-14T06:26:56,473 or your builds will no longer be supported. 2023-05-14T06:26:56,473 ******************************************************************************** 2023-05-14T06:26:56,474 !! 2023-05-14T06:26:56,474 _handle_missing_dynamic(dist, project_table) 2023-05-14T06:26:56,474 /tmp/pip-build-env-tyhrirxm/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:69: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-05-14T06:26:56,474 corresp(dist, value, root_dir) 2023-05-14T06:26:56,776 running dist_info 2023-05-14T06:26:56,783 creating /tmp/pip-modern-metadata-3c31c04b/medspacy.egg-info 2023-05-14T06:26:56,789 writing /tmp/pip-modern-metadata-3c31c04b/medspacy.egg-info/PKG-INFO 2023-05-14T06:26:56,792 writing dependency_links to /tmp/pip-modern-metadata-3c31c04b/medspacy.egg-info/dependency_links.txt 2023-05-14T06:26:56,795 writing requirements to /tmp/pip-modern-metadata-3c31c04b/medspacy.egg-info/requires.txt 2023-05-14T06:26:56,796 writing top-level names to /tmp/pip-modern-metadata-3c31c04b/medspacy.egg-info/top_level.txt 2023-05-14T06:26:56,797 writing manifest file '/tmp/pip-modern-metadata-3c31c04b/medspacy.egg-info/SOURCES.txt' 2023-05-14T06:26:56,854 listing git files failed - pretending there aren't any 2023-05-14T06:26:56,862 reading manifest file '/tmp/pip-modern-metadata-3c31c04b/medspacy.egg-info/SOURCES.txt' 2023-05-14T06:26:56,865 adding license file 'LICENSE' 2023-05-14T06:26:56,872 writing manifest file '/tmp/pip-modern-metadata-3c31c04b/medspacy.egg-info/SOURCES.txt' 2023-05-14T06:26:56,874 creating '/tmp/pip-modern-metadata-3c31c04b/medspacy-1.1.2.dist-info' 2023-05-14T06:26:57,027 Preparing metadata (pyproject.toml): finished with status 'done' 2023-05-14T06:26:57,034 Source in /tmp/pip-wheel-winlutmo/medspacy_120b16fdf6124f6dae12b2835a61b4ba has version 1.1.2, which satisfies requirement medspacy==1.1.2 from https://files.pythonhosted.org/packages/ab/0f/9f8e15d75266f3fb269e8ae4894e2db0aafb7375de505c0facbd7bc3cb30/medspacy-1.1.2.tar.gz 2023-05-14T06:26:57,035 Removed medspacy==1.1.2 from https://files.pythonhosted.org/packages/ab/0f/9f8e15d75266f3fb269e8ae4894e2db0aafb7375de505c0facbd7bc3cb30/medspacy-1.1.2.tar.gz from build tracker '/tmp/pip-build-tracker-q06pa4rj' 2023-05-14T06:26:57,043 Created temporary directory: /tmp/pip-unpack-c4qd0pqr 2023-05-14T06:26:57,044 Building wheels for collected packages: medspacy 2023-05-14T06:26:57,049 Created temporary directory: /tmp/pip-wheel-j54xdbu9 2023-05-14T06:26:57,049 Destination directory: /tmp/pip-wheel-j54xdbu9 2023-05-14T06:26:57,051 Building wheel for medspacy (pyproject.toml): started 2023-05-14T06:26:57,052 Running command Building wheel for medspacy (pyproject.toml) 2023-05-14T06:26:57,603 /tmp/pip-build-env-tyhrirxm/overlay/lib/python3.9/site-packages/setuptools/config/pyprojecttoml.py:66: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. 2023-05-14T06:26:57,604 config = read_configuration(filepath, True, ignore_option_errors, dist) 2023-05-14T06:26:57,638 /tmp/pip-build-env-tyhrirxm/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:62: _WouldIgnoreField: `readme` defined outside of `pyproject.toml` would be ignored. 2023-05-14T06:26:57,638 !! 2023-05-14T06:26:57,638 ******************************************************************************** 2023-05-14T06:26:57,638 ########################################################################## 2023-05-14T06:26:57,639 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-05-14T06:26:57,639 ########################################################################## 2023-05-14T06:26:57,639 The following seems to be defined outside of `pyproject.toml`: 2023-05-14T06:26:57,639 `readme = '[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n![Build Status](https://github.com/medspacy/medspacy/workflows/medspacy/badge.svg)\n\n# medspacy\nLibrary for clinical NLP with spaCy. \n\n![alt text](./images/medspacy_logo.png "medSpaCy logo")\n\n**MedSpaCy is currently in beta.**\n\n\n# Overview\nMedSpaCy is a library of tools for performing clinical NLP and text processing tasks with the popular [spaCy](https://spacy.io) \nframework. The `medspacy` package brings together a number of other packages, each of which implements specific \nfunctionality for common clinical text processing specific to the clinical domain, such as sentence segmentation, \ncontextual analysis and attribute assertion, and section detection.\n\n`medspacy` is modularized so that each component can be used independently. All of `medspacy` is designed to be used \nas part of a `spacy` processing pipeline. Each of the following modules is available as part of `medspacy`:\n- `medspacy.preprocess`: Destructive preprocessing for modifying clinical text before processing\n- `medspacy.sentence_splitter`: Clinical sentence segmentation\n- `medspacy.ner`: Utilities for extracting concepts from clinical text\n- `medspacy.context`: Implementation of the [ConText](https://www.sciencedirect.com/science/article/pii/S1532046409000744)\nfor detecting semantic modifiers and attributes of entities, including negation and uncertainty\n- `medspacy.section_detection`: Clinical section detection and segmentation\n- `medspacy.postprocess`: Flexible framework for modifying and removing extracted entities\n- `medspacy.io`: Utilities for converting processed texts to structured data and interacting with databases\n- `medspacy.visualization`: Utilities for visualizing concepts and relationships extracted from text\n- `SpacyQuickUMLS`: UMLS concept extraction compatible with spacy and medspacy implemented by [our fork](https://github.com/medspacy/QuickUMLS) of [QuickUMLS](https://github.com/Georgetown-IR-Lab/QuickUMLS). More detail on this component, how to use it, how to generate UMLS resources beyond the small UMLS sample can be found in [this notebook](notebooks/11-QuickUMLS_Extraction.ipynb).\n\nFuture work could include I/O, relations extraction, and pre-trained clinical models.\n\n**As of 10/2/2021 (version 0.2.0.0), medspaCy supports spaCy v3**\n\n# Usage\n## Installation\n\nYou can install `medspacy` using `setup.py`:\n```bash\npython setup.py install\n```\n\nOr with pip:\n```bash\npip install medspacy\n```\n\nTo install a previous version which uses spaCy 2:\n```bash\npip install medspacy==medspacy 0.1.0.2\n```\n\n### Requirements\nThe following packages are required and installed when `medspacy` is installed:\n- spaCy v3\n- [pyrush](https://github.com/medspacy/PyRuSH)\n\nIf you download other models, you can use them by providing the model itself or model name to `medspacy.load(model_name)`:\n```python\nimport spacy; import medspacy\n# Option 1: Load default\nnlp = medspacy.load()\n\n# Option 2: Load from existing model\nnlp = spacy.load("en_core_web_sm", disable={"ner"})\nnlp = medspacy.load(nlp)\n\n# Option 3: Load from model name\nnlp = medspacy.load("en_core_web_sm", disable={"ner"})\n```\n \n## Basic Usage\nHere is a simple example showing how to implement and visualize a simple rule-based pipeline using `medspacy`:\n```python\nimport medspacy\nfrom medspacy.ner import TargetRule\nfrom medspacy.visualization import visualize_ent\n\n# Load medspacy model\nnlp = medspacy.load()\nprint(nlp.pipe_names)\n\ntext = """\nPast Medical History:\n1. Atrial fibrillation\n2. Type II Diabetes Mellitus\n\nAssessment and Plan:\nThere is no evidence of pneumonia. Continue warfarin for Afib. Follow up for management of type 2 DM.\n"""\n\n# Add rules for target concept extraction\ntarget_matcher = nlp.get_pipe("medspacy_target_matcher")\ntarget_rules = [\n TargetRule("atrial fibrillation", "PROBLEM"),\n TargetRule("atrial fibrillation", "PROBLEM", pattern=[{"LOWER": "afib"}]),\n TargetRule("pneumonia", "PROBLEM"),\n TargetRule("Type II Diabetes Mellitus", "PROBLEM", \n pattern=[\n {"LOWER": "type"},\n {"LOWER": {"IN": ["2", "ii", "two"]}},\n {"LOWER": {"IN": ["dm", "diabetes"]}},\n {"LOWER": "mellitus", "OP": "?"}\n ]),\n TargetRule("warfarin", "MEDICATION")\n]\ntarget_matcher.add(target_rules)\n\ndoc = nlp(text)\nvisualize_ent(doc)\n```\n\n`Output:`\n![alt text](./images/simple_text_visualization.png "Example of clinical text processed by medSpaCy")\n\nFor more detailed examples and explanations of each component, see the [notebooks](./notebooks) folder.\n\n# Citing medspaCy\nIf you use medspaCy in your work, consider citing our paper! Presented at the AMIA Annual Symposium 2021, [preprint available on Arxiv](http://arxiv.org/abs/2106.07799).\n\n```\nH. Eyre, A.B. Chapman, K.S. Peterson, J. Shi, P.R. Alba, M.M. Jones, T.L. Box, S.L. DuVall, O. V Patterson,\nLaunching into clinical space with medspaCy: a new clinical text processing toolkit in Python,\nAMIA Annu. Symp. Proc. 2021 (in Press. (n.d.). \nhttp://arxiv.org/abs/2106.07799.\n```\n\n```\n@Article{medspacy,\n Author="Eyre, H. and Chapman, A. B. and Peterson, K. S. and Shi, J. and Alba, P. R. and Jones, M. M. and Box, T. L. and DuVall, S. L. and Patterson, O. V. ",\n Title="{{L}aunching into clinical space with medspa{C}y: a new clinical text processing toolkit in {P}ython}",\n Journal="AMIA Annu Symp Proc",\n Year="2021",\n Volume="2021",\n Pages="438--447"\n}\n\n}\n```\n\n# Made with medSpaCy\nHere are some links to projects or tutorials which use medSpacy. If you have a project which uses medSpaCy which you\'d like to use, let us know!\n- [VA_COVID-19_NLP_BSV](https://github.com/abchapman93/VA_COVID-19_NLP_BSV): An NLP pipeline for [identifying positive cases of COVID-19](https://aclanthology.org/2020.nlpcovid19-acl.10/) from clinical text. Deployed as part of the Department of Veterans Affairs response to COVID-19\n- [clinspacy](https://ml4lhs.github.io/clinspacy/index.html): An R wrapper for spaCy, sciSpaCy, and medSpaCy for performing clinical NLP and UMLS linking in R\n- [mimic34md2020_materials](https://github.com/Melbourne-BMDS/mimic34md2020_materials): A crash course in clinical data science from the University of Melbourne. For medSpaCy materials, see `notebooks/nlp-*.ipynb`\n- [ReHouSED NLP](https://github.com/abchapman93/ReHouSED): An NLP pipeline for [studying Veteran housing stability](https://www.sciencedirect.com/science/article/pii/S153204642100232X) and distinguishing between Veterans who are currently unstably housed and those who have exited homelessness\n'` 2023-05-14T06:26:57,640 According to the spec (see the link below), however, setuptools CANNOT 2023-05-14T06:26:57,640 consider this value unless `readme` is listed as `dynamic`. 2023-05-14T06:26:57,640 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-05-14T06:26:57,640 For the time being, `setuptools` will still consider the given value (as a 2023-05-14T06:26:57,641 **transitional** measure), but please note that future releases of setuptools will 2023-05-14T06:26:57,641 follow strictly the standard. 2023-05-14T06:26:57,641 To prevent this warning, you can list `readme` under `dynamic` or alternatively 2023-05-14T06:26:57,641 remove the `[project]` table from your file and rely entirely on other means of 2023-05-14T06:26:57,641 configuration. 2023-05-14T06:26:57,641 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-05-14T06:26:57,642 or your builds will no longer be supported. 2023-05-14T06:26:57,642 ******************************************************************************** 2023-05-14T06:26:57,642 !! 2023-05-14T06:26:57,642 _handle_missing_dynamic(dist, project_table) 2023-05-14T06:26:57,642 /tmp/pip-build-env-tyhrirxm/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:69: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-05-14T06:26:57,642 corresp(dist, value, root_dir) 2023-05-14T06:26:57,929 running bdist_wheel 2023-05-14T06:26:57,952 running build 2023-05-14T06:26:57,952 running build_py 2023-05-14T06:26:57,960 creating build 2023-05-14T06:26:57,960 creating build/lib 2023-05-14T06:26:57,961 creating build/lib/medspacy 2023-05-14T06:26:57,962 copying medspacy/ner.py -> build/lib/medspacy 2023-05-14T06:26:57,964 copying medspacy/_version.py -> build/lib/medspacy 2023-05-14T06:26:57,965 copying medspacy/visualization.py -> build/lib/medspacy 2023-05-14T06:26:57,968 copying medspacy/sentence_splitting.py -> build/lib/medspacy 2023-05-14T06:26:57,970 copying medspacy/__init__.py -> build/lib/medspacy 2023-05-14T06:26:57,971 copying medspacy/util.py -> build/lib/medspacy 2023-05-14T06:26:57,974 copying medspacy/components.py -> build/lib/medspacy 2023-05-14T06:26:57,975 copying medspacy/custom_tokenizer.py -> build/lib/medspacy 2023-05-14T06:26:57,977 copying medspacy/_extensions.py -> build/lib/medspacy 2023-05-14T06:26:57,980 creating build/lib/tests 2023-05-14T06:26:57,981 copying tests/test_medspacy.py -> build/lib/tests 2023-05-14T06:26:57,984 copying tests/__init__.py -> build/lib/tests 2023-05-14T06:26:57,985 copying tests/test_extensions.py -> build/lib/tests 2023-05-14T06:26:57,987 copying tests/test_notebooks.py -> build/lib/tests 2023-05-14T06:26:57,989 creating build/lib/medspacy/postprocess 2023-05-14T06:26:57,990 copying medspacy/postprocess/postprocessor.py -> build/lib/medspacy/postprocess 2023-05-14T06:26:57,992 copying medspacy/postprocess/postprocessing_functions.py -> build/lib/medspacy/postprocess 2023-05-14T06:26:57,995 copying medspacy/postprocess/__init__.py -> build/lib/medspacy/postprocess 2023-05-14T06:26:57,996 copying medspacy/postprocess/postprocessing_rule.py -> build/lib/medspacy/postprocess 2023-05-14T06:26:57,998 copying medspacy/postprocess/postprocessing_pattern.py -> build/lib/medspacy/postprocess 2023-05-14T06:26:58,001 creating build/lib/medspacy/context 2023-05-14T06:26:58,002 copying medspacy/context/context_rule.py -> build/lib/medspacy/context 2023-05-14T06:26:58,004 copying medspacy/context/__init__.py -> build/lib/medspacy/context 2023-05-14T06:26:58,006 copying medspacy/context/util.py -> build/lib/medspacy/context 2023-05-14T06:26:58,007 copying medspacy/context/context.py -> build/lib/medspacy/context 2023-05-14T06:26:58,010 copying medspacy/context/context_modifier.py -> build/lib/medspacy/context 2023-05-14T06:26:58,013 copying medspacy/context/context_graph.py -> build/lib/medspacy/context 2023-05-14T06:26:58,015 creating build/lib/medspacy/io 2023-05-14T06:26:58,016 copying medspacy/io/pipeline.py -> build/lib/medspacy/io 2023-05-14T06:26:58,018 copying medspacy/io/db.py -> build/lib/medspacy/io 2023-05-14T06:26:58,020 copying medspacy/io/config_example.py -> build/lib/medspacy/io 2023-05-14T06:26:58,022 copying medspacy/io/__init__.py -> build/lib/medspacy/io 2023-05-14T06:26:58,024 copying medspacy/io/db_connect.py -> build/lib/medspacy/io 2023-05-14T06:26:58,026 copying medspacy/io/db_writer.py -> build/lib/medspacy/io 2023-05-14T06:26:58,028 copying medspacy/io/doc_consumer.py -> build/lib/medspacy/io 2023-05-14T06:26:58,030 copying medspacy/io/db_reader.py -> build/lib/medspacy/io 2023-05-14T06:26:58,033 creating build/lib/medspacy/target_matcher 2023-05-14T06:26:58,034 copying medspacy/target_matcher/target_matcher.py -> build/lib/medspacy/target_matcher 2023-05-14T06:26:58,036 copying medspacy/target_matcher/target_rule.py -> build/lib/medspacy/target_matcher 2023-05-14T06:26:58,038 copying medspacy/target_matcher/__init__.py -> build/lib/medspacy/target_matcher 2023-05-14T06:26:58,040 copying medspacy/target_matcher/concept_tagger.py -> build/lib/medspacy/target_matcher 2023-05-14T06:26:58,042 creating build/lib/medspacy/section_detection 2023-05-14T06:26:58,043 copying medspacy/section_detection/section_rule.py -> build/lib/medspacy/section_detection 2023-05-14T06:26:58,046 copying medspacy/section_detection/sectionizer.py -> build/lib/medspacy/section_detection 2023-05-14T06:26:58,048 copying medspacy/section_detection/__init__.py -> build/lib/medspacy/section_detection 2023-05-14T06:26:58,050 copying medspacy/section_detection/section.py -> build/lib/medspacy/section_detection 2023-05-14T06:26:58,053 copying medspacy/section_detection/util.py -> build/lib/medspacy/section_detection 2023-05-14T06:26:58,055 creating build/lib/medspacy/common 2023-05-14T06:26:58,056 copying medspacy/common/base_rule.py -> build/lib/medspacy/common 2023-05-14T06:26:58,058 copying medspacy/common/medspacy_matcher.py -> build/lib/medspacy/common 2023-05-14T06:26:58,060 copying medspacy/common/__init__.py -> build/lib/medspacy/common 2023-05-14T06:26:58,062 copying medspacy/common/util.py -> build/lib/medspacy/common 2023-05-14T06:26:58,064 copying medspacy/common/regex_matcher.py -> build/lib/medspacy/common 2023-05-14T06:26:58,067 creating build/lib/medspacy/preprocess 2023-05-14T06:26:58,068 copying medspacy/preprocess/__init__.py -> build/lib/medspacy/preprocess 2023-05-14T06:26:58,070 copying medspacy/preprocess/preprocessor.py -> build/lib/medspacy/preprocess 2023-05-14T06:26:58,071 copying medspacy/preprocess/preprocessing_rule.py -> build/lib/medspacy/preprocess 2023-05-14T06:26:58,073 running egg_info 2023-05-14T06:26:58,085 writing medspacy.egg-info/PKG-INFO 2023-05-14T06:26:58,087 writing dependency_links to medspacy.egg-info/dependency_links.txt 2023-05-14T06:26:58,089 writing requirements to medspacy.egg-info/requires.txt 2023-05-14T06:26:58,090 writing top-level names to medspacy.egg-info/top_level.txt 2023-05-14T06:26:58,135 listing git files failed - pretending there aren't any 2023-05-14T06:26:58,142 reading manifest file 'medspacy.egg-info/SOURCES.txt' 2023-05-14T06:26:58,147 adding license file 'LICENSE' 2023-05-14T06:26:58,157 writing manifest file 'medspacy.egg-info/SOURCES.txt' 2023-05-14T06:26:58,183 creating build/lib/resources 2023-05-14T06:26:58,184 copying medspacy/../resources/context_rules.json -> build/lib/medspacy/../resources 2023-05-14T06:26:58,188 copying medspacy/../resources/rush_rules.tsv -> build/lib/medspacy/../resources 2023-05-14T06:26:58,191 copying medspacy/../resources/section_patterns.json -> build/lib/medspacy/../resources 2023-05-14T06:26:58,193 creating build/lib/resources/quickumls 2023-05-14T06:26:58,194 creating build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:26:58,195 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/README.md -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:26:58,197 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/database_backend.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:26:58,199 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/language.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:26:58,202 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/lowercase.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:26:58,203 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/normalize-unicode.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:26:58,205 creating build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db 2023-05-14T06:26:58,206 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db/cui.unqlite -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db 2023-05-14T06:26:58,209 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db/semtypes.unqlite -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db 2023-05-14T06:26:58,211 creating build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,212 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,215 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.120.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,218 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.14.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,220 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.15.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,222 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.17.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,224 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.20.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,226 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.21.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,229 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.22.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,231 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.24.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,233 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.26.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,235 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.27.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,237 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.28.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,240 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.29.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,242 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.30.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,244 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.31.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,247 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.32.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,250 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.33.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,253 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.35.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,255 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.37.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,258 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.38.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,261 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.39.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,263 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.40.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,266 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.43.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,268 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.79.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,271 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.8.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,273 creating build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:26:58,274 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/README.md -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:26:58,276 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/database_backend.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:26:58,278 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/language.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:26:58,280 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/lowercase.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:26:58,282 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/normalize-unicode.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:26:58,283 creating build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db 2023-05-14T06:26:58,284 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db/cui.unqlite -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db 2023-05-14T06:26:58,287 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db/semtypes.unqlite -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db 2023-05-14T06:26:58,290 creating build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,291 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,293 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.120.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,296 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.14.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,298 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.15.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,300 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.17.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,302 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.20.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,305 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.21.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,307 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.22.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,309 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.24.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,311 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.26.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,314 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.27.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,316 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.28.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,318 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.29.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,321 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.30.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,323 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.31.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,325 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.32.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,328 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.33.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,330 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.35.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,332 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.37.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,335 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.38.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,337 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.39.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,339 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.40.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,342 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.43.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,344 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.79.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,346 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.8.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,392 installing to build/bdist.linux-aarch64/wheel 2023-05-14T06:26:58,392 running install 2023-05-14T06:26:58,418 running install_lib 2023-05-14T06:26:58,424 creating build/bdist.linux-aarch64 2023-05-14T06:26:58,425 creating build/bdist.linux-aarch64/wheel 2023-05-14T06:26:58,427 creating build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:26:58,428 copying build/lib/medspacy/ner.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:26:58,430 creating build/bdist.linux-aarch64/wheel/medspacy/postprocess 2023-05-14T06:26:58,431 copying build/lib/medspacy/postprocess/postprocessor.py -> build/bdist.linux-aarch64/wheel/medspacy/postprocess 2023-05-14T06:26:58,433 copying build/lib/medspacy/postprocess/postprocessing_functions.py -> build/bdist.linux-aarch64/wheel/medspacy/postprocess 2023-05-14T06:26:58,436 copying build/lib/medspacy/postprocess/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy/postprocess 2023-05-14T06:26:58,437 copying build/lib/medspacy/postprocess/postprocessing_rule.py -> build/bdist.linux-aarch64/wheel/medspacy/postprocess 2023-05-14T06:26:58,439 copying build/lib/medspacy/postprocess/postprocessing_pattern.py -> build/bdist.linux-aarch64/wheel/medspacy/postprocess 2023-05-14T06:26:58,442 creating build/bdist.linux-aarch64/wheel/medspacy/context 2023-05-14T06:26:58,442 copying build/lib/medspacy/context/context_rule.py -> build/bdist.linux-aarch64/wheel/medspacy/context 2023-05-14T06:26:58,445 copying build/lib/medspacy/context/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy/context 2023-05-14T06:26:58,447 copying build/lib/medspacy/context/util.py -> build/bdist.linux-aarch64/wheel/medspacy/context 2023-05-14T06:26:58,448 copying build/lib/medspacy/context/context.py -> build/bdist.linux-aarch64/wheel/medspacy/context 2023-05-14T06:26:58,451 copying build/lib/medspacy/context/context_modifier.py -> build/bdist.linux-aarch64/wheel/medspacy/context 2023-05-14T06:26:58,454 copying build/lib/medspacy/context/context_graph.py -> build/bdist.linux-aarch64/wheel/medspacy/context 2023-05-14T06:26:58,456 copying build/lib/medspacy/_version.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:26:58,458 copying build/lib/medspacy/visualization.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:26:58,460 copying build/lib/medspacy/sentence_splitting.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:26:58,462 copying build/lib/medspacy/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:26:58,464 copying build/lib/medspacy/util.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:26:58,466 copying build/lib/medspacy/components.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:26:58,468 copying build/lib/medspacy/custom_tokenizer.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:26:58,470 creating build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:26:58,471 copying build/lib/medspacy/io/pipeline.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:26:58,473 copying build/lib/medspacy/io/db.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:26:58,475 copying build/lib/medspacy/io/config_example.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:26:58,477 copying build/lib/medspacy/io/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:26:58,479 copying build/lib/medspacy/io/db_connect.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:26:58,481 copying build/lib/medspacy/io/db_writer.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:26:58,483 copying build/lib/medspacy/io/doc_consumer.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:26:58,485 copying build/lib/medspacy/io/db_reader.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:26:58,487 creating build/bdist.linux-aarch64/wheel/medspacy/target_matcher 2023-05-14T06:26:58,488 copying build/lib/medspacy/target_matcher/target_matcher.py -> build/bdist.linux-aarch64/wheel/medspacy/target_matcher 2023-05-14T06:26:58,491 copying build/lib/medspacy/target_matcher/target_rule.py -> build/bdist.linux-aarch64/wheel/medspacy/target_matcher 2023-05-14T06:26:58,493 copying build/lib/medspacy/target_matcher/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy/target_matcher 2023-05-14T06:26:58,495 copying build/lib/medspacy/target_matcher/concept_tagger.py -> build/bdist.linux-aarch64/wheel/medspacy/target_matcher 2023-05-14T06:26:58,497 creating build/bdist.linux-aarch64/wheel/medspacy/section_detection 2023-05-14T06:26:58,498 copying build/lib/medspacy/section_detection/section_rule.py -> build/bdist.linux-aarch64/wheel/medspacy/section_detection 2023-05-14T06:26:58,500 copying build/lib/medspacy/section_detection/sectionizer.py -> build/bdist.linux-aarch64/wheel/medspacy/section_detection 2023-05-14T06:26:58,503 copying build/lib/medspacy/section_detection/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy/section_detection 2023-05-14T06:26:58,505 copying build/lib/medspacy/section_detection/section.py -> build/bdist.linux-aarch64/wheel/medspacy/section_detection 2023-05-14T06:26:58,507 copying build/lib/medspacy/section_detection/util.py -> build/bdist.linux-aarch64/wheel/medspacy/section_detection 2023-05-14T06:26:58,509 creating build/bdist.linux-aarch64/wheel/medspacy/common 2023-05-14T06:26:58,510 copying build/lib/medspacy/common/base_rule.py -> build/bdist.linux-aarch64/wheel/medspacy/common 2023-05-14T06:26:58,512 copying build/lib/medspacy/common/medspacy_matcher.py -> build/bdist.linux-aarch64/wheel/medspacy/common 2023-05-14T06:26:58,515 copying build/lib/medspacy/common/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy/common 2023-05-14T06:26:58,516 copying build/lib/medspacy/common/util.py -> build/bdist.linux-aarch64/wheel/medspacy/common 2023-05-14T06:26:58,519 copying build/lib/medspacy/common/regex_matcher.py -> build/bdist.linux-aarch64/wheel/medspacy/common 2023-05-14T06:26:58,521 copying build/lib/medspacy/_extensions.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:26:58,524 creating build/bdist.linux-aarch64/wheel/medspacy/preprocess 2023-05-14T06:26:58,524 copying build/lib/medspacy/preprocess/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy/preprocess 2023-05-14T06:26:58,526 copying build/lib/medspacy/preprocess/preprocessor.py -> build/bdist.linux-aarch64/wheel/medspacy/preprocess 2023-05-14T06:26:58,528 copying build/lib/medspacy/preprocess/preprocessing_rule.py -> build/bdist.linux-aarch64/wheel/medspacy/preprocess 2023-05-14T06:26:58,531 creating build/bdist.linux-aarch64/wheel/resources 2023-05-14T06:26:58,532 copying build/lib/resources/context_rules.json -> build/bdist.linux-aarch64/wheel/resources 2023-05-14T06:26:58,535 copying build/lib/resources/rush_rules.tsv -> build/bdist.linux-aarch64/wheel/resources 2023-05-14T06:26:58,538 creating build/bdist.linux-aarch64/wheel/resources/quickumls 2023-05-14T06:26:58,539 creating build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:26:58,541 creating build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db 2023-05-14T06:26:58,542 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db/semtypes.unqlite -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db 2023-05-14T06:26:58,545 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db/cui.unqlite -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db 2023-05-14T06:26:58,548 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/database_backend.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:26:58,549 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/normalize-unicode.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:26:58,551 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/lowercase.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:26:58,553 creating build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,554 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.35.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,556 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.37.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,558 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.38.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,560 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.39.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,562 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.27.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,564 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.14.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,566 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.79.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,568 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.8.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,570 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.24.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,572 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.43.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,574 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.20.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,576 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.120.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,578 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.15.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,580 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.28.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,582 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.21.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,584 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,586 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.22.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,588 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.30.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,591 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.29.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,593 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.31.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,595 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.26.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,597 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.17.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,599 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.32.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,601 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.33.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,603 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.40.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:26:58,605 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/language.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:26:58,607 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/README.md -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:26:58,610 creating build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:26:58,611 creating build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db 2023-05-14T06:26:58,612 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db/semtypes.unqlite -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db 2023-05-14T06:26:58,615 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db/cui.unqlite -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db 2023-05-14T06:26:58,617 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/database_backend.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:26:58,619 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/normalize-unicode.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:26:58,620 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/lowercase.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:26:58,623 creating build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,623 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.35.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,626 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.37.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,628 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.38.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,630 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.39.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,632 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.27.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,634 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.14.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,636 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.79.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,638 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.8.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,640 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.24.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,642 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.43.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,644 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.20.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,646 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.120.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,648 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.15.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,650 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.28.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,652 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.21.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,654 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,656 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.22.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,658 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.30.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,661 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.29.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,662 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.31.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,665 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.26.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,667 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.17.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,668 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.32.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,671 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.33.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,673 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.40.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:26:58,675 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/language.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:26:58,677 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/README.md -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:26:58,679 copying build/lib/resources/section_patterns.json -> build/bdist.linux-aarch64/wheel/resources 2023-05-14T06:26:58,682 creating build/bdist.linux-aarch64/wheel/tests 2023-05-14T06:26:58,683 copying build/lib/tests/test_medspacy.py -> build/bdist.linux-aarch64/wheel/tests 2023-05-14T06:26:58,685 copying build/lib/tests/__init__.py -> build/bdist.linux-aarch64/wheel/tests 2023-05-14T06:26:58,686 copying build/lib/tests/test_extensions.py -> build/bdist.linux-aarch64/wheel/tests 2023-05-14T06:26:58,688 copying build/lib/tests/test_notebooks.py -> build/bdist.linux-aarch64/wheel/tests 2023-05-14T06:26:58,690 running install_egg_info 2023-05-14T06:26:58,696 Copying medspacy.egg-info to build/bdist.linux-aarch64/wheel/medspacy-1.1.2-py3.9.egg-info 2023-05-14T06:26:58,707 running install_scripts 2023-05-14T06:26:58,724 creating build/bdist.linux-aarch64/wheel/medspacy-1.1.2.dist-info/WHEEL 2023-05-14T06:26:58,727 creating '/tmp/pip-wheel-j54xdbu9/.tmp-7ekwj9nc/medspacy-1.1.2-py3-none-any.whl' and adding 'build/bdist.linux-aarch64/wheel' to it 2023-05-14T06:26:58,729 adding 'medspacy/__init__.py' 2023-05-14T06:26:58,731 adding 'medspacy/_extensions.py' 2023-05-14T06:26:58,733 adding 'medspacy/_version.py' 2023-05-14T06:26:58,734 adding 'medspacy/components.py' 2023-05-14T06:26:58,735 adding 'medspacy/custom_tokenizer.py' 2023-05-14T06:26:58,736 adding 'medspacy/ner.py' 2023-05-14T06:26:58,738 adding 'medspacy/sentence_splitting.py' 2023-05-14T06:26:58,740 adding 'medspacy/util.py' 2023-05-14T06:26:58,742 adding 'medspacy/visualization.py' 2023-05-14T06:26:58,744 adding 'medspacy/common/__init__.py' 2023-05-14T06:26:58,745 adding 'medspacy/common/base_rule.py' 2023-05-14T06:26:58,747 adding 'medspacy/common/medspacy_matcher.py' 2023-05-14T06:26:58,748 adding 'medspacy/common/regex_matcher.py' 2023-05-14T06:26:58,750 adding 'medspacy/common/util.py' 2023-05-14T06:26:58,752 adding 'medspacy/context/__init__.py' 2023-05-14T06:26:58,755 adding 'medspacy/context/context.py' 2023-05-14T06:26:58,756 adding 'medspacy/context/context_graph.py' 2023-05-14T06:26:58,759 adding 'medspacy/context/context_modifier.py' 2023-05-14T06:26:58,761 adding 'medspacy/context/context_rule.py' 2023-05-14T06:26:58,762 adding 'medspacy/context/util.py' 2023-05-14T06:26:58,765 adding 'medspacy/io/__init__.py' 2023-05-14T06:26:58,766 adding 'medspacy/io/config_example.py' 2023-05-14T06:26:58,767 adding 'medspacy/io/db.py' 2023-05-14T06:26:58,769 adding 'medspacy/io/db_connect.py' 2023-05-14T06:26:58,770 adding 'medspacy/io/db_reader.py' 2023-05-14T06:26:58,772 adding 'medspacy/io/db_writer.py' 2023-05-14T06:26:58,774 adding 'medspacy/io/doc_consumer.py' 2023-05-14T06:26:58,775 adding 'medspacy/io/pipeline.py' 2023-05-14T06:26:58,777 adding 'medspacy/postprocess/__init__.py' 2023-05-14T06:26:58,779 adding 'medspacy/postprocess/postprocessing_functions.py' 2023-05-14T06:26:58,781 adding 'medspacy/postprocess/postprocessing_pattern.py' 2023-05-14T06:26:58,782 adding 'medspacy/postprocess/postprocessing_rule.py' 2023-05-14T06:26:58,784 adding 'medspacy/postprocess/postprocessor.py' 2023-05-14T06:26:58,786 adding 'medspacy/preprocess/__init__.py' 2023-05-14T06:26:58,788 adding 'medspacy/preprocess/preprocessing_rule.py' 2023-05-14T06:26:58,789 adding 'medspacy/preprocess/preprocessor.py' 2023-05-14T06:26:58,792 adding 'medspacy/section_detection/__init__.py' 2023-05-14T06:26:58,793 adding 'medspacy/section_detection/section.py' 2023-05-14T06:26:58,795 adding 'medspacy/section_detection/section_rule.py' 2023-05-14T06:26:58,798 adding 'medspacy/section_detection/sectionizer.py' 2023-05-14T06:26:58,800 adding 'medspacy/section_detection/util.py' 2023-05-14T06:26:58,801 adding 'medspacy/target_matcher/__init__.py' 2023-05-14T06:26:58,803 adding 'medspacy/target_matcher/concept_tagger.py' 2023-05-14T06:26:58,805 adding 'medspacy/target_matcher/target_matcher.py' 2023-05-14T06:26:58,806 adding 'medspacy/target_matcher/target_rule.py' 2023-05-14T06:26:58,810 adding 'resources/context_rules.json' 2023-05-14T06:26:58,813 adding 'resources/rush_rules.tsv' 2023-05-14T06:26:58,815 adding 'resources/section_patterns.json' 2023-05-14T06:26:58,818 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/README.md' 2023-05-14T06:26:58,819 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/database_backend.flag' 2023-05-14T06:26:58,820 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/language.flag' 2023-05-14T06:26:58,822 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/lowercase.flag' 2023-05-14T06:26:58,823 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/normalize-unicode.flag' 2023-05-14T06:26:58,825 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db/cui.unqlite' 2023-05-14T06:26:58,827 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db/semtypes.unqlite' 2023-05-14T06:26:58,829 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring' 2023-05-14T06:26:58,831 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.120.cdb' 2023-05-14T06:26:58,833 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.14.cdb' 2023-05-14T06:26:58,834 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.15.cdb' 2023-05-14T06:26:58,836 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.17.cdb' 2023-05-14T06:26:58,837 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.20.cdb' 2023-05-14T06:26:58,839 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.21.cdb' 2023-05-14T06:26:58,840 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.22.cdb' 2023-05-14T06:26:58,841 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.24.cdb' 2023-05-14T06:26:58,843 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.26.cdb' 2023-05-14T06:26:58,844 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.27.cdb' 2023-05-14T06:26:58,847 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.28.cdb' 2023-05-14T06:26:58,848 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.29.cdb' 2023-05-14T06:26:58,850 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.30.cdb' 2023-05-14T06:26:58,851 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.31.cdb' 2023-05-14T06:26:58,853 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.32.cdb' 2023-05-14T06:26:58,855 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.33.cdb' 2023-05-14T06:26:58,856 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.35.cdb' 2023-05-14T06:26:58,858 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.37.cdb' 2023-05-14T06:26:58,859 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.38.cdb' 2023-05-14T06:26:58,861 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.39.cdb' 2023-05-14T06:26:58,863 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.40.cdb' 2023-05-14T06:26:58,864 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.43.cdb' 2023-05-14T06:26:58,866 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.79.cdb' 2023-05-14T06:26:58,867 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.8.cdb' 2023-05-14T06:26:58,869 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/README.md' 2023-05-14T06:26:58,870 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/database_backend.flag' 2023-05-14T06:26:58,872 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/language.flag' 2023-05-14T06:26:58,873 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/lowercase.flag' 2023-05-14T06:26:58,874 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/normalize-unicode.flag' 2023-05-14T06:26:58,877 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db/cui.unqlite' 2023-05-14T06:26:58,879 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db/semtypes.unqlite' 2023-05-14T06:26:58,881 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring' 2023-05-14T06:26:58,883 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.120.cdb' 2023-05-14T06:26:58,884 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.14.cdb' 2023-05-14T06:26:58,886 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.15.cdb' 2023-05-14T06:26:58,887 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.17.cdb' 2023-05-14T06:26:58,888 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.20.cdb' 2023-05-14T06:26:58,890 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.21.cdb' 2023-05-14T06:26:58,891 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.22.cdb' 2023-05-14T06:26:58,893 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.24.cdb' 2023-05-14T06:26:58,894 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.26.cdb' 2023-05-14T06:26:58,895 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.27.cdb' 2023-05-14T06:26:58,897 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.28.cdb' 2023-05-14T06:26:58,899 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.29.cdb' 2023-05-14T06:26:58,900 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.30.cdb' 2023-05-14T06:26:58,902 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.31.cdb' 2023-05-14T06:26:58,903 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.32.cdb' 2023-05-14T06:26:58,905 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.33.cdb' 2023-05-14T06:26:58,906 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.35.cdb' 2023-05-14T06:26:58,908 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.37.cdb' 2023-05-14T06:26:58,910 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.38.cdb' 2023-05-14T06:26:58,911 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.39.cdb' 2023-05-14T06:26:58,913 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.40.cdb' 2023-05-14T06:26:58,914 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.43.cdb' 2023-05-14T06:26:58,916 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.79.cdb' 2023-05-14T06:26:58,917 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.8.cdb' 2023-05-14T06:26:58,919 adding 'tests/__init__.py' 2023-05-14T06:26:58,920 adding 'tests/test_extensions.py' 2023-05-14T06:26:58,922 adding 'tests/test_medspacy.py' 2023-05-14T06:26:58,924 adding 'tests/test_notebooks.py' 2023-05-14T06:26:58,925 adding 'medspacy-1.1.2.dist-info/LICENSE' 2023-05-14T06:26:58,927 adding 'medspacy-1.1.2.dist-info/METADATA' 2023-05-14T06:26:58,928 adding 'medspacy-1.1.2.dist-info/WHEEL' 2023-05-14T06:26:58,929 adding 'medspacy-1.1.2.dist-info/top_level.txt' 2023-05-14T06:26:58,931 adding 'medspacy-1.1.2.dist-info/RECORD' 2023-05-14T06:26:58,936 removing build/bdist.linux-aarch64/wheel 2023-05-14T06:26:59,083 Building wheel for medspacy (pyproject.toml): finished with status 'done' 2023-05-14T06:26:59,091 Created wheel for medspacy: filename=medspacy-1.1.2-py3-none-any.whl size=147920 sha256=2d1b734ace3ff4460cf578e7a60be5552c820063b36878102103b61d25712431 2023-05-14T06:26:59,093 Stored in directory: /tmp/pip-ephem-wheel-cache-3lupdx71/wheels/e2/71/05/df23d5a6731ea886c373b4c65f55179e540456f10ad7a4ecdd 2023-05-14T06:26:59,109 Successfully built medspacy 2023-05-14T06:26:59,116 Removed build tracker: '/tmp/pip-build-tracker-q06pa4rj'