use pie-modules instead of pytorch-ie

see https://github.com/ArneBinder/pie-datasets/pull/204 for further information

README.md

@@ -15,13 +15,13 @@ and the following annotation layers:
 
 - `entities` (annotation type: `LabeledSpan`, target: `text`)
 
-See [here](https://github.com/ChristophAlt/pytorch-ie/blob/main/src/pytorch_ie/annotations.py) for the annotation type definitions.
+See [here](https://github.com/ArneBinder/pie-modules/blob/main/src/pie_modules/annotations.py) for the annotation type definitions.
 
 ## Document Converters
 
 The dataset provides document converters for the following target document types:
 
-- `pytorch_ie.documents.TextDocumentWithLabeledSpans`
+- `pie_modules.documents.TextDocumentWithLabeledSpans`
 
-See [here](https://github.com/ChristophAlt/pytorch-ie/blob/main/src/pytorch_ie/documents.py) for the document type
+See [here](https://github.com/ArneBinder/pie-modules/blob/main/src/pie_modules/documents.py) for the document type
 definitions.

conll2003.py

@@ -1,17 +1,40 @@
 from dataclasses import dataclass
+from typing import List, Sequence, Tuple
 
 import datasets
-from pytorch_ie.annotations import LabeledSpan
-from pytorch_ie.core import AnnotationList, annotation_field
-from pytorch_ie.documents import TextDocument, TextDocumentWithLabeledSpans
-from pytorch_ie.utils.span import tokens_and_tags_to_text_and_labeled_spans
+from pie_core import AnnotationLayer, annotation_field
+from pie_modules.annotations import LabeledSpan
+from pie_modules.documents import TextBasedDocument, TextDocumentWithLabeledSpans
+from pie_modules.utils.sequence_tagging import tag_sequence_to_token_spans
 
 from pie_datasets import GeneratorBasedBuilder
 
 
+def tokens_and_tags_to_text_and_labeled_spans(
+    tokens: Sequence[str], tags: Sequence[str]
+) -> Tuple[str, Sequence[LabeledSpan]]:
+    start = 0
+    token_offsets: List[Tuple[int, int]] = []
+    for token in tokens:
+        end = start + len(token)
+        token_offsets.append((start, end))
+        # we add a space after each token
+        start = end + 1
+
+    text = " ".join(tokens)
+
+    spans: List[LabeledSpan] = []
+    for label, (start, end) in tag_sequence_to_token_spans(tag_sequence=tags):
+        spans.append(
+            LabeledSpan(start=token_offsets[start][0], end=token_offsets[end][1], label=label)
+        )
+
+    return text, spans
+
+
 @dataclass
-class CoNLL2003Document(TextDocument):
-    entities: AnnotationList[LabeledSpan] = annotation_field(target="text")
+class CoNLL2003Document(TextBasedDocument):
+    entities: AnnotationLayer[LabeledSpan] = annotation_field(target="text")
 
 
 class Conll2003(GeneratorBasedBuilder):

requirements.txt

@@ -1 +1,2 @@
-pie-datasets>=0.8.1,<0.9.0
+pie-datasets>=0.10.11,<0.11.0
+pie-modules>=0.15.9,<0.16.0