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Changelog

0.2.0 (2024-04-10)

New

  • Add pre-commit. [Matthew Upson]
  • Add CITATION.cff file. [Matthew Upson]
  • Upload artefacts to codecov. [Matthew Upson]
  • Run tests on windows instance. [Matthew Upson]

Changes

  • Add codecov config. [Matthew Upson]
  • Remove .travis.yml. [Matthew Upson]
  • Update tox.ini. [Matthew Upson]
  • Update versions to test. [Matthew Upson]
  • Add tox tests as github action. [Matthew Upson]

Fix

  • Grant write permission to CICD workflow. [Matthew Upson]
  • Run on windows and linux matrix. [Matthew Upson]

Other

  • Updates README to reflect new functionality. [Jack Boylan]

  • Removes extra 'indices' printed. [Jack Boylan]

  • Bump black from 23.3.0 to 24.3.0. [dependabot[bot]]

    Bumps [black](https://github.com/psf/black) from 23.3.0 to 24.3.0. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](https://github.com/psf/black/compare/23.3.0...24.3.0)

    --- updated-dependencies: - dependency-name: black

    dependency-type: direct:development

    ...

  • Fixed Typo in README. [Giovanni Casari]

  • Reformats quotes in test_nervaluate.py [Jack Boylan]

  • Initial import. [David S. Batista]

  • Handles case when predictions is empty. [Jack Boylan]

  • Adds unit tests for evaluation indices output. [Jack Boylan]

  • Adds summary print functions for overall indices and per-entity indices results. [Jack Boylan]

  • Adds within_instance_index to evaluation indices outputs. [Jack Boylan]

  • Ensures compatibility with existing unit tests. [Jack Boylan]

  • Adheres to code quality checks. [Jack Boylan]

  • Adds more descriptive variable names. [Jack Boylan]

  • Adds correct indices to result indices output. [Jack Boylan]

  • Moves evaluation indices to separate data structures. [Jack Boylan]

  • Adds index lists to output for examples with incorrect, partial, spurious, and missed entities. [Jack Boylan]

  • Docs: fix typo "spurius" > "spurious" [DanShatford]

  • Added test for issue #40. [g.casari]

  • Solved issue #40. [g.casari]

  • Update README.md. [David S. Batista]

  • Cleaning README.MD. [David S. Batista]

  • Attending PR comments. [David S. Batista]

  • Fixing links on README.MD. [David S. Batista]

  • Updating pyproject.toml. [David S. Batista]

  • Updating pyproject.toml. [David S. Batista]

  • Updating README.MD and bumping version to 0.2.0. [David S. Batista]

  • Updating README.MD. [David S. Batista]

  • Reverting to Python 3.8. [David S. Batista]

  • Adding some badges to the README. [David S. Batista]

  • Initial commit. [David S. Batista]

  • Wip: adding poetry. [David S. Batista]

  • Full working example. [David S. Batista]

  • Nit. [David S. Batista]

  • Wip: adding summary report and examples. [David S. Batista]

  • Wip: adding summary report and examples. [David S. Batista]

  • Wip: adding summary report and examples. [David S. Batista]

  • Wip: adding summary report and examples. [David S. Batista]

  • Wip: adding summary report and examples. [David S. Batista]

  • Wip: adding summary report. [David S. Batista]

  • Wip: adding summary report. [David S. Batista]

  • Removed codecov from requirements.txt. [David S. Batista]

  • Removing duplicated code and fixing type hit. [David S. Batista]

  • Updated Makefile: install package in editable mode. [David S. Batista]

  • Updated name. [David S. Batista]

  • Minimum version Python 3.8. [David S. Batista]

  • Fixing Makefile and pre-commit. [David S. Batista]

  • Adding DS_Store and .idea to gitignore. [David S. Batista]

  • Updating Makefile. [David S. Batista]

  • WIP: pre-commit. [David S. Batista]

  • WIP: pre-commit. [David S. Batista]

  • WIP: pre-commit. [David S. Batista]

  • WIP: pre-commit. [David S. Batista]

  • WIP: pre-commit. [David S. Batista]

  • WIP: pre-commit. [David S. Batista]

  • WIP: pre-commit. [David S. Batista]

  • WIP: pre-commit. [David S. Batista]

  • Fixing types. [David S. Batista]

  • Finished adding type hints, some were skipped, code needs refactoring. [David S. Batista]

  • WIP: adding type hints. [David S. Batista]

  • WIP: adding type hints. [David S. Batista]

  • WIP: adding type hints. [David S. Batista]

  • WIP: adding type hints. [David S. Batista]

  • Adding some execptions, code needs refactoring. [David S. Batista]

  • Fixing pyling and flake8 issues. [David S. Batista]

  • Replaced setup.py with pyproject.toml. [David S. Batista]

  • Reverting utils import. [David S. Batista]

  • Fixing types and wrappint at 120 characters. [David S. Batista]

  • Update CITATION.cff. [David S. Batista]

    updating orcid

  • Fix recall formula readme. [fgh95]

  • Update LICENSE. [ivyleavedtoadflax]

  • Update LICENSE. [ivyleavedtoadflax]

  • Delete .python-version. [ivyleavedtoadflax]

0.1.8 (2020-10-16)

New

  • Add test for whole span length entities (see #32) [Matthew Upson]
  • Summarise blog post in README. [Matthew Upson]

Changes

  • Bump version in setup.py. [Matthew Upson]
  • Update CHANGELOG (#36) [ivyleavedtoadflax]
  • Fix tests to match #32. [Matthew Upson]

Fix

  • Correct catch sequence of just one entity. [Matthew Upson]

    Incorporate edits in #28 but includes tests.

Other

  • Add code coverage. [ivyleavedtoadflax]

  • Crucial fixes for evaluation. [Alex Flückiger]

  • Update utils.py. [ivyleavedtoadflax]

    Tiny change to kick off CI

  • Fix to catch last entites Small change to catch entities that go up until last character when there is no tag. [pim]

0.1.7 (2019-12-07)

New

  • Add tests. [Matthew Upson]
    • Linting
    • Rename existing tests to disambiguate
  • Add loaders to nervaluate. [Matthew Upson]
    • Add list and conll formats

Changes

  • Update README. [Matthew Upson]

Fix

  • Issue with setup.py. [Matthew Upson]
    • Add docstring to __version__.py

0.1.6 (2019-12-07)

New

  • Add gitchangelog and Makefile recipe. [Matthew Upson]

Changes

  • Bump version to 0.1.6. [Matthew Upson]

  • Remove examples. [Matthew Upson]

    These are not accessible from the package in any case.

  • Add dev requirements. [Matthew Upson]

0.1.5 (2019-12-06)

Changes

  • Bump version to 0.1.5. [Matthew Upson]
  • Update setup.py. [Matthew Upson]
  • Update package url to point at pypi. [Matthew Upson]

0.1.4 (2019-12-06)

New

  • Add dist to .gitignore. [Matthew Upson]
  • Create pypi friendly README/long description. [Matthew Upson]
  • Clean entity dicts of extraneous keys. [Matthew Upson]
    • Failing to do this can cause problems in evaluations
    • Add tests

Changes

  • Bump version to 0.1.4. [Matthew Upson]
  • Make setup.py pypi compliant. [Matthew Upson]

0.1.2 (2019-12-04)

New

  • Add missing prodigy format tests. [Matthew Upson]

  • Pass argument when using list. [Matthew Upson]

  • Setup module structure. [Matthew Upson]

  • Add get_tags() and tests. [Matthew Upson]

    Adds function to extract all the NER tags from a list of sentences.

  • Add Evaluator class. [Matthew Upson]

    • Add some logging statements
    • Add input checks on number of documents and tokens per document
    • Allow target labels to be passed as argument to compute_metrics. Note
      that if a label is predicted and it is not in this list, then it will be classed as spurious for the aggregated scores, and on each entity level result (because it is unclear where the spurious value should be applied, it is applied to all)
    • linting
    • Add many new tests

  • Don't evaluate precision and recall for each sentence. [Matthew Upson]

    Rather than automatically calculate precision and recall at the sentence level, this change adds a new function compute_precision_recall_wrapper which can be run after all the metrics whether for 1 document, or 1000, have been calculated. This has the benefit that we can reuse the same code for calculating precision/recall, and allows us to calculate entity level precision/recall if required.

  • Calculate entity level score. [Matthew Upson]

  • Add compute_actual_possible function. [Matthew Upson]

  • Record results for each entity type. [Matthew Upson]

  • Add scenario comments matching blog table. [Matthew Upson]

  • Test results at individual entity level. [Matthew Upson]

  • Add .gitinore file. [Matthew Upson]

  • Add requirements.txt. [Matthew Upson]

Changes

  • Bump version to 0.1.2. [Matthew Upson]

  • Bump version number to 0.1.1. [Matthew Upson]

  • Reduce logging verbosity. [ivyleavedtoadflax]

  • Add example to README.md. [Matthew Upson]

  • Create virtualenv recipe. [Matthew Upson]

    • Move example dependencies to requirements_example.txt
    • Add virtualenv recipe to Makefile
    • Update .gitignore

  • Remove unused dependencies. [Matthew Upson]

    • Dependencies for the examples should not be included in setup.py, instead

    move them to requirements_examples.txt

  • Update example notebook. [Matthew Upson]

  • Remove unwanted tags from pred_named_entities. [Matthew Upson]

  • Remove superfluous get_tags() function. [Matthew Upson]

  • Update notebook. [Matthew Upson]

  • Update notebook. [Matthew Upson]

  • Update tests. [Matthew Upson]

  • Update .gitignore. [Matthew Upson]

  • Replace spurius with spurious. [Matthew Upson]

  • Update README with requirements and test info. [Matthew Upson]

  • Update setup.cfg with source and omit paths. [Matthew Upson]

  • Use pytest instead of unittest. [Matthew Upson]

Other

  • Revert "Remove tox and use pytest" [Matthew Upson]

    • Better to keep tox for local testing in the Makefile and resolve issues running tox on the developers machine.

    This reverts commit 8578795e62ca384adf054c1b85a1c1d7f0d089d5.

  • Remove tox and use pytest. [Elizabeth Gallagher]

  • Add f1 output to nervaluate and update all tests. [Elizabeth Gallagher]

  • Update .travis.yml. [ivyleavedtoadflax]

  • Update README.md. [Matt Upson]

  • Build(deps): bump nltk from 3.4.4 to 3.4.5. [dependabot[bot]]

    Bumps [nltk](https://github.com/nltk/nltk) from 3.4.4 to 3.4.5. - [Release notes](https://github.com/nltk/nltk/releases) - [Changelog](https://github.com/nltk/nltk/blob/develop/ChangeLog) - [Commits](https://github.com/nltk/nltk/compare/3.4.4...3.4.5)

  • Update __version__.py. [Matt Upson]

  • PEPed8 things a bit. [David Soares Batista]

  • Update README.md. [David S. Batista]

  • Update README.md. [David S. Batista]

  • Notebook. [David Soares Batista]

  • Updated notebook. [David Soares Batista]

  • Update README.md. [David S. Batista]

  • Update README.md. [David S. Batista]

  • Renamed notebook. [David Soares Batista]

  • Bug fixing. [David Soares Batista]

  • Test. [David Soares Batista]

  • Typo in comment. [David Soares Batista]

  • Use find_overlap to find all overlap cases. [Matthew Upson]

    Adds the find_overlap function which captures the three possible overlap scenarios (Total, Start, and End). This is examplained in graph below.

    Character Offset: | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | True: | | | |LOC|LOC|LOC|LOC|LOC| | | Total Overlap: | | |LOC|LOC|LOC|LOC|LOC|LOC|LOC| | Start Overlap: | | |LOC|LOC|LOC| | | | | | End Overlap: | | | | | | |LOC|LOC|LOC| |

  • Removed debug stamt. [David Soares Batista]

  • Added partial and exact evaluation and tests. [David Soares Batista]

  • Update. [David Soares Batista]

  • Updated README. [David Soares Batista]

    • fixed bugs and added tests - added pytest. [David Soares Batista]

  • Update ner_evaluation.py. [David S. Batista]

  • Redefined evaluation according to discussion here: davidsbatista/NER-Evaluation#2. [David Soares Batista]

  • Fixed a BUG in collect_named_entites() issued by rjlotok.dblma@gmail.com. [David Soares Batista]

  • Update README.md. [David S. Batista]

  • Update README.md. [David S. Batista]

  • Major refactoring. [David Soares Batista]

  • Create README.md. [David S. Batista]

  • Initial import. [David Soares Batista]

  • Initial commit. [David S. Batista]