fix transformers config

.github/workflows/publish.yml

@@ -11,6 +11,9 @@ jobs:
   publish:
     name: Build and Publish to PyPI
     runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
     steps:
       - name: Git checkout
         uses: actions/checkout@v4
@@ -27,8 +30,8 @@ jobs:
       - name: Install dependencies
         run: poetry install --no-interaction
 
-      - name: Login to PyPI
-        run: poetry config pypi-token.pypi "${{ secrets.PYPI_API_KEY }}"
+      - name: Build package
+        run: poetry build
 
-      - name: Publish package
-        run: poetry publish --build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

cprex/__init__.py

@@ -0,0 +1,5 @@
+"""Chemical Properties Relation EXtractor"""
+
+__version__ = "0.3.0"
+
+from .pipeline import get_pipeline as get_pipeline

cprex/rel/configs/rel_trf.cfg

@@ -30,7 +30,7 @@ set_extra_annotations = {"@annotation_setters":"spacy-transformers.null_annotati
 # name = "microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext"
 name = "michiyasunaga/BioLinkBERT-large"
 tokenizer_config = {"use_fast": true}
-transformers_config = {"output_attentions": True}
+transformer_config = {"output_attentions": true}
 
 [components.transformer.model.get_spans]
 @span_getters = "spacy-transformers.strided_spans.v1"

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cprex"
-version = "0.2.0"
+version = "0.3.0"
 description = "Chemical Properties Relation Extraction"
 authors = ["Jonas Renault <[email protected]>", "Lucie Chasseur <[email protected]>"]
 readme = "README.md"
@@ -71,15 +71,18 @@ exclude = [
     "dist",
     "venv",
 ]
-lint.ignore = []
+src = ["cprex", "tests"]
 line-length = 90
-lint.select = [
+
+[tool.ruff.lint]
+ignore-init-module-imports = true
+ignore = []
+select = [
     "E",
     "F",
     "W",
     "I001",
 ]
-src = ["cprex", "tests"]
 
 [tool.mypy]
 files = ["cprex"]