Code

Dev#2

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rtbs-dev merged 130 commits intomasterusnistgov/nestor:masterfrom devusnistgov/nestor:devCopy head branch name to clipboardMar 7, 2024

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Commits

Commits on Oct 26, 2020

• Set up general workflow for new NER function in bio_output_creation.py

  

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Commits on Oct 28, 2020

• Tokens tagged with 'U' or 'X' in Nestor are 'O'

  

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• Fix string matching when searching vocab file for token

  

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• Move code into function

  

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• Move new (draft) function to keyword.py

  

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Commits on Nov 3, 2020

• add new keyword tests (token_to_alias example)

  

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• fixed iob_extractor, added test (failed)

  

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Commits on Nov 4, 2020

• Access 'tokens' column instead of index for string matching

  

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Commits on Nov 5, 2020

• Switch to nestor-native utility functions (load_excavators, generate_vocabulary_df)

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Commits on Nov 6, 2020

• Reformat iob_extractor output as DataFrame and move notebook to examples

  

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• Simplify tag logic

  

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• iob_extractor handles combined tokens (i.e. 'grease_line') and passes tests

  

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Commits on Nov 9, 2020

• use nestorParams for NE name groups

  

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• fix gitignore

  

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• Add unit tests for combined tag labeling, begin to label tokens that have molecular tag (not working yet)

  

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Commits on Nov 18, 2020

• Pass test_iob_extractor_2g_tokens unit test

  

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Commits on Nov 24, 2020

• Change loop behavior to pass test_iob_extractor_extended_tokens (all unit tests now pass)

  

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• Minor clean up/commenting in IOB function

  

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Commits on Nov 25, 2020

• Go through MWO with while loop for better control of indexing multi-word tokens, fixed doc_id bug

  

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• Delete bio_output_creation.ipynb

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Commits on Dec 14, 2020

• style edits to readme

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Commits on Dec 16, 2020

• fix dynamic-versioning issue (v0.10 poetry-core)

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• After 'poetry run task format'

  

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• Merge branch 'bio' of https://gitlab.nist.gov/gitlab/kea/nestor into bio

  

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Commits on Jan 28, 2021

• use nist header/footer

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• add docs branch to gitlab ci

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• ensure updated poetry-dynamic-versioning

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Commits on Jun 17, 2021

• rm tables dep

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Commits on Jun 21, 2021

• working mkdocstrings and pdf

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• optimize imports

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Commits on Aug 11, 2021

• subtitle pdf

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• nestor cache folder and remote excavators

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Commits on Aug 12, 2021

• get and test excavators from remote (uwa)

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• rm deprecated excavator csv's

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• rm csv from pyproject.toml

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• use mamba runner and modify ci/cd

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• don't test docs... unnecessary

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• cache pip and use base (poetry)

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• cache...nvm

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• switch to conda if headless-chrome is a prob?

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• no conda init?

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• headless-chrome was needed by render_js...

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Commits on Aug 13, 2021

• try to add roboto

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• set gitlab repo_url in ci yaml

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• mkdocs env var and apt-get fonts-roboto

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• spacessss

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• better stages

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• Merge branch 'dev' of gitlab.nist.gov:kea/nestor into dev

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• Update .gitlab-ci.yml

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• test report and apt-get -y

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• cache conda

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• fix mkdocs url and before_script

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• rules are array of str

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• texlive fonts?

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• apt -y

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• try new kea image

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• make poetry venv globally cached

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Commits on Aug 18, 2021

• merge conflict fix

  

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Commits on Aug 25, 2021

• Create script to demonstrate file format required for using spacy and spacy config file

  

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• Modify tag formatting to match IOB conventions, still not 100% functional

  

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Commits on Aug 31, 2021

• Update testing for correct IOB format (updated tests dont pass yet)

  

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• Cleanup unit tests

  

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Commits on Sep 2, 2021

• Update IOB function logic to handle inner tags, unit tests all pass

  

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• Update IOB to handle multi-token X/U tags

  

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Commits on Sep 8, 2021

• more cleanup of spacy example

  

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• Remove print statement from debugging

  

  amc8

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• Clean up keyword unit tests

  

  amc8

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• remove cache artefacts

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• modernize .gitignore

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• update to use isinstance rather than type() is

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• refactor iob test to group w/ fixtures

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Commits on Sep 9, 2021

• Add unit test for tokens not in vocab list

  

  amc8

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• working speed-up, needs non-vocab tokens to pass

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Commits on Sep 10, 2021

• working iob refactor

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• move notebooks to /notebooks

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• Updated the readme with new links, text about TLP

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• Merge remote-tracking branch 'nist-origin/bio' into bio-refactor

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• Merge branch 'bio-refactor' into 'bio'

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• Add headings/text to spacy example

  

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• new vocab interface (needs remote url's)

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• new way to get vocabs

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• Merge branch 'bio-vocab' into bio

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• move notebooks to docs/examples

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• Create notebook for NLTK example

  

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• Create notebook for NLTK example

  

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• Update spacy example

  

  amc8

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• fix spaces in vocab2g, add ner-example subfolder

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• fix nans in iob-extract vocab dict

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• Merge branch 'bio' of gitlab.nist.gov:kea/nestor into bio

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• rename to order mkdocs pages

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Commits on Sep 13, 2021

• move example files

  

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• Merge branch 'bio' of https://gitlab.nist.gov/gitlab/kea/nestor-suite/nestor into bio

  

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• Update nestor-docs conda env dependencies

  

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• Update NLTK example and include md with output

  

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• Update Spacy example and add associated .md file with output

  

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• new TagExtractor to group utils. also, properties

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Commits on Sep 14, 2021

• working tagextractor and goodies

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• convenience funcs

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• Merge branch 'tagextractor' into bio

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• add jupytext survival analysis

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• update survival analysis w/ TagExtractor

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• Merge branch 'bio' into 'dev'

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Commits on Sep 15, 2021

• add codemeta.yaml

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• add notebook export to mkdocs

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• Merge branch 'docs' of gitlab.nist.gov:kea/nestor into docs

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• jupytext auto-build for mkdocs

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• Merge branch 'docs-mknotebooks' into 'docs'

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• needs

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• nb build env stage

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• always test?

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• mamba env update

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• mamba env create

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• no quotations

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• try wrapping in quotes

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• rm extraneous stage

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• oh, micromamba

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• use conda again

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• correct container tag

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• job-specific vars

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• maybe auto github deploy from gitlab

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• oh right, it's bash not posix sh

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• nist-origin

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• Merge branch 'docs' of gitlab.nist.gov:kea/nestor into docs

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• try mv to nist-pages?

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Commits on Oct 4, 2021

• hopefully stage for gh-actions

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Commits on Oct 5, 2021

• add workflow for nist-pages

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• fix pattern type hint

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Commits on Oct 6, 2021

• cleaning up docs and api (mkdocstrings)

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Commits on Nov 24, 2021

• bugfix

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Commits on Nov 29, 2021

• fix excavators(raw) url

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