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chore(medcat-trainer): lint fixes and package upgrades - #640
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…exposing training params. (#647) * fixing tokenization of gold label entities and adding detected name to stats * mypy! * mypy fix * fixed testing * fixed test set up * changed from AutoModelForTokenClassification to AutoModel for consistency * changed loss weighting, exposed training params * chore(medcat-trainer): lint fixes and package upgrades (#640) * feat(medcat-trainer): metrics report filter, on row, on low performing metrics (#642) * feat(medcat-trainer): Solr backed full text search of clinical notes (#634) * feat(medcat-trainer): Add text and name contains filters to documents API Co-authored-by: tomolopolis <tomolopolis@users.noreply.github.com> * feat(medcat-trainer): Search clinical notes by text span in annotate view Co-authored-by: tomolopolis <tomolopolis@users.noreply.github.com> * feat(medcat-trainer): Index dataset documents into Solr on upload and add Solr backed document search endpoint Co-authored-by: tomolopolis <tomolopolis@users.noreply.github.com> * feat(medcat-trainer): Use Solr document search for clinical notes text search Co-authored-by: tomolopolis <tomolopolis@users.noreply.github.com> * docs(medcat-trainer): Document Solr document search settings Co-authored-by: tomolopolis <tomolopolis@users.noreply.github.com> * feat(medcat-trainer): Put clinical notes summary in a resizable split pane Co-authored-by: tomolopolis <tomolopolis@users.noreply.github.com> * feat(medcat-trainer): improved styles and UX of doc search function --------- Co-authored-by: Cursor Agent <cursoragent@cursor.com> Co-authored-by: tomolopolis <tomolopolis@users.noreply.github.com> * fix(medcat-trainer): open FP, FN, and TP example dialogs (#635) * fix(medcat-trainer): open FP/FN/TP example dialogs reliably Clicking a concept count failed when the metrics table did not hand back the original row, so the example dialog never opened. Current MedCAT stats examples also use snake_case fields, which left the dialog unable to show or link those occurrences, and unescaped clinical text could break rendering. Resolve examples without object identity, accept both key styles, escape note text, and mount the dialog on document.body. Co-authored-by: tomolopolis <tomolopolis@users.noreply.github.com> * fix(medcat-trainer): restore TP, FN, and FP count colors type=button matched Vuetify's color:inherit rule and overrode the outline button colors. Keep true positives green, false negatives grey, and false positives red. Co-authored-by: tomolopolis <tomolopolis@users.noreply.github.com> * fix(medcat-trainer): paint non-zero TP, FN, and FP counts Bootstrap outline colors were still lost once later button rules reset --bs-btn-color. Set the NHS green, grey, and red on the count buttons themselves so a non-zero number keeps its colour. Co-authored-by: tomolopolis <tomolopolis@users.noreply.github.com> * fix(medcat-trainer): use theme variables for count colours Non-zero TP, FN, and FP counts take --success, --warning, and --danger from the NHS theme map instead of hardcoded hex values. Co-authored-by: tomolopolis <tomolopolis@users.noreply.github.com> * fix(medcat-trainer): fix styling of metrics * fix(medcat-trainer): fix test, fix clickable mention in span in modal appearing alongside the context to the right of the mention --------- Co-authored-by: Cursor Agent <cursoragent@cursor.com> Co-authored-by: tomolopolis <tomolopolis@users.noreply.github.com> * feat(medcat-trainer): mct client project groups creation (#643) * feat(medcat-trainer): add project group changes in mct-client * chore(medcat-trainer): update to latest release * build: bump pypa/gh-action-pypi-publish (#646) Bumps the actions-deps group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish). Updates `pypa/gh-action-pypi-publish` from 1.14.2 to 1.14.3 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](pypa/gh-action-pypi-publish@v1.14.2...v1.14.3) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions-deps ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * mypy! --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: tomolopolis <tom@cogstack.org> Co-authored-by: Cursor Agent <cursoragent@cursor.com> Co-authored-by: tomolopolis <tomolopolis@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mart Ratas <mart.ratas@gmail.com>
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npm lintfixes, i.e.lettoconstnpm audit fix --forcefor front end lib upgrade