Release 0.9.2

Changes since 0.9.1

• fix doc generation

Release 0.9.1

Release 0.9.1 is available !

Changelog from 0.8.1

[Added/Changed]

• [text] attrs_to_copy for segmentation operations
• [text] store section names in Attribute rather than metadata
• Trainer logging changes
• [text] change default params for RegexpMatcherRule
• [text] add default rules for rule-based operations
• [text][preprocessing] Change Normalizer name
• Add e3c corpus support

[Fixed]

• [text] fix syntagma tokenizer rules
• [text] Harmonize kb_id field between EntityNormAttribute and other places
• [text] fix duplicate finder
• [umls-coder-normalizer] Don't crash on empty list of entities

[Config]

• Drop python 3.7 for bumping to torch 2.0
• [audio] remove pyannote-audio dependency from medkit package

[Docs]

• Add doc for load_text_documents
• [readme] add contact and link to CONTRIBUTING.md
• update medkit logo

You will find the documentation at: https://medkit.readthedocs.io/en/0.9.1

Finally, to install medkit, the package is available on PyPI under the name of medkit-lib

We strongly recommend to create virtual environments (using venv or conda) before installing medkit.

# Install medkit with only required dependencies
pip install medkit-lib

To install with extra dependencies (e.g., hf-translator, hf-entity-matcher, hf-transcriber, quick-umls, resampler, rush-sentence-tokenizer, umls-coder-normalizer, webrtc-voice-detector, ...):

# Install medkit with all extra optional dependencies
pip install 'medkit-lib[optional]'

Release 0.8.1

Changes since 0.8.0

• fix doc generation

Release 0.8.0

Release 0.8.0 is available !

Changelog from 0.7.1

[Added]

• add simstring matcher operation
• add mtsamples loader
• add doccano converter
• add edsnlp date matcher operation
• add post-processing operation to filter overlapping entities

[Fixed]

• change rule-based operation strategy for special characters
• [regexpmatcher] Change label to category (like semgroup)
• [medkit-json] don't force ascii chars only when exporting
• fix "Too much padding in HFEntityMatcherTrainable"

[Docs]

• add documentation for custom operation
• fix links in documentation
• fix inheritance in generated docs

You will find the documentation at: https://medkit.readthedocs.io/en/0.8.1

Finally, to install medkit, the package is available on PyPI under the name of medkit-lib

We strongly recommend to create virtual environments (using venv or conda) before installing medkit.

# Install medkit with only required dependencies
pip install medkit-lib

To install with extra dependencies (e.g., hf-translator, hf-entity-matcher, hf-transcriber, quick-umls, resampler, rush-sentence-tokenizer, umls-coder-normalizer, webrtc-voice-detector, ...):

# Install medkit with all extra optional dependencies
pip install 'medkit-lib[optional]'

Release 0.7.1

Release 0.7.1 is available !

Changelog from 0.7.1

[Fixed]

• Fix umls coder normalizer gpu support
• Fix message for provenance error
• Fix missing save rules in rule-based text operations

You will find the documentation at: https://medkit.readthedocs.io/en/0.7.1

Finally, to install medkit, the package is available on PyPI under the name of medkit-lib

We strongly recommend to create virtual environments (using venv or conda) before installing medkit.

# Install medkit with only required dependencies
pip install medkit-lib

To install with extra dependencies (e.g., hf-translator, hf-entity-matcher, hf-transcriber, quick-umls, resampler, rush-sentence-tokenizer, umls-coder-normalizer, webrtc-voice-detector, ...):

# Install medkit with all extra optional dependencies
pip install 'medkit-lib[optional]'

Release 0.7.0

Release 0.7.0 is available !

Changelog from 0.6.0

[Added]

• Add duplicate finder
• Add char replacer
• Add alignment utils

[Fixed]

• Fix encoding for medkit-json-io

[Docs]

• Add doc for training
• Update docs

You will find the documentation at: https://medkit.readthedocs.io/en/0.7.0

Finally, to install medkit, the package is available on PyPI under the name of medkit-lib

We strongly recommend to create virtual environments (using venv or conda) before installing medkit.

# Install medkit with only required dependencies
pip install medkit-lib

To install with extra dependencies (e.g., hf-translator, hf-entity-matcher, hf-transcriber, quick-umls, resampler, rush-sentence-tokenizer, umls-coder-normalizer, webrtc-voice-detector, ...):

# Install medkit with all extra optional dependencies
pip install 'medkit-lib[optional]'

Release 0.6.0

Release 0.6.0 is available !

Changelog from 0.5.0

[Added]

• Add NER metrics : seqeval

[Fixed]

• Fix label mapping quickumls
• Fix extra characters in segmentation operation : add strip functions
• Fix iamsystem : attrs_to_copy #12

[Docs]

• Add examples for segmentation operations, in particular rules files
• Add example for finetuning of HF model
• Move docs to readthedocs

[Other stuff]

• Remove develop branch

You will find the documentation at: https://medkit.readthedocs.io/en/0.6.0

Finally, to install medkit, the package is available on PyPI under the name of medkit-lib

We strongly recommend to create virtual environments (using venv or conda) before installing medkit.

# Install medkit with only required dependencies
pip install medkit-lib

To install with extra dependencies (e.g., hf-translator, hf-entity-matcher, hf-transcriber, quick-umls, resampler, rush-sentence-tokenizer, umls-coder-normalizer, webrtc-voice-detector, ...):

# Install medkit with all extra optional dependencies
pip install 'medkit-lib[optional]'

Release 0.5.0

Release 0.5.0 is available !

Changelog from 0.4.1

[Added]

• text: add iam system #111
• training: add finetuning of HF model #110
• text: add edsnlp

[Fixed]

• Skip empty sentences in SentenceTokenizer #119
• Fix duckling matcher #11
• Fix minor issues #75 !129
• Fix encoding #117
• Fix docs : tuto !138
• Fix spans example #127

You will find the documentation at: https://heka.gitlabpages.inria.fr/medkit.

Finally, to install medkit 0.5.0, the package is available on PyPI under the name of medkit-lib

We strongly recommend to create virtual environments (using venv or conda) before installing medkit.

# Install medkit with only required dependencies
python -m pip install medkit-lib

To install with extra dependencies (e.g., hf-translator, hf-entity-matcher, hf-transcriber, quick-umls, resampler, rush-sentence-tokenizer, umls-coder-normalizer, webrtc-voice-detector):

# Install medkit with all extra optional dependencies
python -m pip install 'medkit-lib[optional]'

Release 0.4.1

Release 0.4.1 is available !

Changelog from 0.3.1

[Added]

• audio: add io converter for audio annotation formats .rttm and .str #85
• audio: add speechbrain transcriber !102
• text: add attribute propagation using interval tree !90
• audio: add audio diarization/speaker detection with pyannote !105
• docs: add io and text examples !77
• text: add entity normalization attributes !107
• text: add custom text operation #108
• training: introduce training architecture in medkit #109 !22
• io: add new medkit json format !123

[Fixed]

• Fix SyntacticRelationExtractor !92
• Fix HF translator issues !66
• Fix BratOutputConverter !89
• Fix miscs !28
• Fix HFEntity matcher #114
• Fix RegexpMatcher !128 (Github issue #10)

[Changed]

• Refactor anotation and operation ids !108
• Make medkit_doc_to_displacy support Segment #106
• Add names to Operations and their descriptions #71
• Change label for QuickUMLSMatcher #65
• Make text and audio mandatory !117
• Refactor Collection class !116
• Rework medkit data model !119

[Development]

• Commit poetry.lock #91
• Add github mirroring
• Simplify deps testing !112
• Add API generation for docs !123

You will find the documentation at: https://heka.gitlabpages.inria.fr/medkit.

Finally, to install medkit 0.4.1, the package is available on PyPI under the name of medkit-lib

We strongly recommend to create virtual environments (using venv or conda) before installing medkit.

# Install medkit with only required dependencies
python -m pip install medkit-lib

To install with extra dependencies (e.g., hf-translator, hf-entity-matcher, hf-transcriber, quick-umls, resampler, rush-sentence-tokenizer, umls-coder-normalizer, webrtc-voice-detector):

# Install medkit with all extra optional dependencies
python -m pip install medkit-lib[optional]

Release 0.3.1

This release 0.3.1 fixes a pip install issue found for release 0.3.0.

You will find the documentation at: https://heka.gitlabpages.inria.fr/medkit.
Finally, to install medkit 0.3.1, download the package in release assets and install the package.
For example:

# Install medkit with only required dependencies
python -m pip install 'medkit-0.3.1.tar.gz'

To install with extra dependencies (e.g., hf-translator, hf-entity-matcher, hf-transcriber, quick-umls, resampler, rush-sentence-tokenizer, umls-coder-normalizer, webrtc-voice-detector):

# Install medkit with all extra optional dependencies
python -m pip install 'medkit-0.3.1.tar.gz[optional]'

If you have some issues during installation, it is possible that you may need some additional packages:

sudo apt-get install -y gcc g++ libsndfile1 graphviz python3 python3-dev