Releases · omicsNLP/Auto-CORPus

03 Jun 19:56

AdrianDAlessandro

v1.1.1

d607996

v1.1.1 Latest

Latest

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 http...