v1.1.1

What's Changed

• Documentation refactor by @Thomas-Rowlands in #106
• Updated authors. by @Thomas-Rowlands in #107
• Hackathon_BugFixes by @Thomas-Rowlands in #108
• Update the IAO dicts to include additional terms by @jmp111 in #109
• Add auto-merge workflow by @AdrianDAlessandro in #128
• Bump abatilo/actions-poetry from 3.0.1 to 4.0.0 by @dependabot in #101
• Bump regex from 2024.9.11 to 2024.11.6 by @dependabot in #83
• Bump ruff from 0.7.1 to 0.9.3 by @dependabot in #105
• Bump mkdocs-material from 9.5.42 to 9.5.50 by @dependabot in #103
• Bump mkdocstrings from 0.26.2 to 0.27.0 by @dependabot in #85
• Bump pytest-cov from 5.0.0 to 6.0.0 by @dependabot in #81
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #91
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #147
• Added the HTML mermaid chart to the index.md page by @Thomas-Rowlands in #125
• Add XML parsing script by @AdrianDAlessandro in #129
• Remove all commented-out code by @alexdewar in #148
• Enforce Pydocstyle by @AdrianDAlessandro in #152
• Add macos-latest to the CI runners by @AdrianDAlessandro in #158
• Add some more files to .gitignore and some default VS Code settings by @alexdewar in #156
• Bump lxml from 5.3.0 to 5.3.1 by @dependabot in #159
• Bump ruff from 0.10.0 to 0.11.2 by @dependabot in #161
• Bump python-levenshtein from 0.26.1 to 0.27.1 by @dependabot in #163
• Bump mkdocstrings-python from 1.12.2 to 1.16.8 by @dependabot in #162
• Bump opencv-contrib-python from 4.10.0.84 to 4.11.0.86 by @dependabot in #160
• Bump beautifulsoup4 from 4.12.3 to 4.13.3 by @dependabot in #164
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #165
• Add pre-commit to dependencies by @alexdewar in #166
• Refactored config file loading logic for easier default config usage. by @Thomas-Rowlands in #149
• pytest: Ignore site/ folder by @alexdewar in #167
• Fix GH Pages docs build by @AdrianDAlessandro in #170
• Remove dead code throughout code base by @alexdewar in #151
• Fix broken table headers in table output files by @alexdewar in #154
• Fix JSON schema and add tests by @alexdewar in #175
• Use Python's logging module for writing to console and file by @alexdewar in #176
• Mypy by @AdrianDAlessandro in #187
• Tidy autocorpus.py by @alexdewar in #192
• Remove unused ruff ignore by @AdrianDAlessandro in #195
• IAO default allocation by @Antoinelfr in #189
• Added a test for the current version of PMC articles, using the pmc c… by @Thomas-Rowlands in #188
• Bump mkdocstrings from 0.29.0 to 0.29.1 by @dependabot in #198
• Bump mkdocs-material from 9.6.9 to 9.6.10 by @dependabot in #197
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #199
• move IAO term functions out of Section class by @AdrianDAlessandro in #200
• Bump types-regex from 2024.11.6.20250318 to 2024.11.6.20250403 by @dependabot in #207
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #213
• Bump lxml from 5.3.1 to 5.3.2 by @dependabot in #208
• Bump types-tqdm from 4.67.0.20250319 to 4.67.0.20250404 by @dependabot in #210
• Bump pytest-cov from 6.0.0 to 6.1.1 by @dependabot in #212
• Bump mkdocs-material from 9.6.10 to 9.6.11 by @dependabot in #211
• Bump ruff from 0.11.2 to 0.11.4 by @dependabot in #209
• Converted BioCDocument class to a function by @Thomas-Rowlands in #205
• Converted Table class to functions by @Thomas-Rowlands in #206
• Convert BioCPassage to a dataclass by @alexdewar in #201
• Converted BioCFormatter class to a function by @Thomas-Rowlands in #204
• Bump mkdocs-section-index from 0.3.9 to 0.3.10 by @dependabot in #215
• Bump mkdocstrings-python from 1.16.8 to 1.16.10 by @dependabot in #214
• Bump ruff from 0.11.4 to 0.11.5 by @dependabot in #216
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #217
• Bump types-tqdm from 4.67.0.20250404 to 4.67.0.20250417 by @dependabot in #223
• Bump ruff from 0.11.5 to 0.11.6 by @dependabot in #226
• Bump beautifulsoup4 from 4.13.3 to 4.13.4 by @dependabot in #225
• Bump mkdocs-material from 9.6.11 to 9.6.12 by @dependabot in #224
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #227
• Convert Section class to functions by @alexdewar in #228
• Various fixes for documentation by @alexdewar in #230
• Bump ruff from 0.11.6 to 0.11.7 by @dependabot in #232
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #234
• Bump lxml from 5.3.2 to 5.4.0 by @dependabot in #233
• Converted the "References" class to a function by @Thomas-Rowlands in #203
• A few reference-related renamings by @alexdewar in #237
• Convert Abbreviations class to functions by @alexdewar in #236
• Bump ruff from 0.11.7 to 0.11.8 by @dependabot in #238
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #239
• Reduce the code in the main module by @AdrianDAlessandro in #240
• Bump mkdocs-material from 9.6.12 to 9.6.13 by @dependabot in #242
• Bump ruff from 0.11.8 to 0.11.9 by @dependabot in #241
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #243
• Bump types-tqdm from 4.67.0.20250417 to 4.67.0.20250516 by @dependabot in #250
• Bump types-jsonschema from 4.23.0.20241208 to 4.23.0.20250516 by @dependabot in #252
• Bump types-beautifulsoup4 from 4.12.0.20250204 to 4.12.0.20250516 by @dependabot in #253
• Bump mkdocs-material from 9.6.13 to 9.6.14 by @dependabot in #254
• Bump ruff from 0.11.9 to 0.11.10 by @dependabot in #251
• Skip the PDF regression test in MacOS if running in CI by @AdrianDAlessandro in #249
• PDF Processing Functionality by @Thomas-Rowlands in #235
• Post-review changes and refactoring of supplementary bioc builder classes by @AdrianDAlessandro in #259
• Enable codecov for this repo by @alexdewar in #247
• Make PDF-related dependencies optional by @alexdewar in #261
• Fix running Auto-CORPus from command line by @alexdewar in #262
• Fix: Accidental reference to marker outside pdf module by @alexdewar in #266
• Bump mkdocstrings-python from 1.16.10 to 1.16.11 by @dependabot in #267
• Bump ruff from 0.11.10 to 0.11.11 by @dependabot in #269
• Bump pytest-mock from 3.14.0 to 3.14.1 by @dependabot in #270
• Bump marker-pdf from 1.6.2 to 1.7.3 by @dependabot in #268
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #255
• File type checking by @Thomas-Rowlands in #172
• Fix is_abbreviation by @alexdewar in #245
• Make tables output file ordering deterministic by @alexdewar in #276
• Add Inputs and Outputs to documentation by @AdrianDAlessandro in #273
• Add regression tests for private test data by @alexdewar in #265
• README.md: Use built-in config argument for example usage by @alexdewar in #277
• Refactor autocorpus class by @AdrianDAlessandro in #264
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #284
• Word test additions and old .doc document conversion by @Thomas-Rowlands in #260

New Contributors

• @jmp111 made their first contribution in #109
• @pre-commit-ci made their first contribution in #91
• @Antoinelfr made their first contribution in #189

Full Changelog: v1.1.0...v1.1.1