Release 0.9.0

README.md

@@ -75,6 +75,7 @@ Other papers related to SeqScore include:
 * [If You Build Your Own NER Scorer, Non-replicable Results Will Come](https://aclanthology.org/2020.insights-1.15.pdf)
 * [Toward More Meaningful Resources for Lower-resourced Languages](https://aclanthology.org/2022.findings-acl.44/)
 * [CoNLL#: Fine-grained Error Analysis and a Corrected Test Set for CoNLL-03 English](https://aclanthology.org/2024.lrec-main.330/)
+* [OpenNER 1.0: Standardized Open-Access Named Entity Recognition Datasets in 50+ Languages](https://aclanthology.org/2025.emnlp-main.1708/)
 
 # Usage
 
@@ -86,7 +87,7 @@ For a list of commands, run `seqscore --help`:
 $ seqscore --help
 Usage: seqscore [OPTIONS] COMMAND [ARGS]...
 
-  Provides scoring and analysis tools for NER/chunking files (version 0.6.0)
+  Provides scoring and analysis tools for NER/chunking files (version 0.9.0)
 
 Options:
   --version  Show the version and exit.
@@ -209,7 +210,7 @@ scoring will fail:
 
 ```
 seqscore.encoding.EncodingError: Stopping due to validation errors in invalid.bio:
-Invalid transition 'O' -> 'I-ORG' for token 'University' on line 7
+Invalid transition 'O' -> 'I-ORG' for token 'University' on line 7 of invalid.bio
 ```
 
 To score output with invalid transitions, we need to specify a repair method which can
@@ -218,8 +219,8 @@ we refer to as "begin" repair in our paper):
 `seqscore score --labels BIO --repair-method conlleval --reference samples/reference.bio samples/invalid.bio`:
 
 ```
-Validation errors in sequence at line 7 of invalid.bio:
-Invalid transition 'O' -> 'I-ORG' for token 'University' on line 7
+Validation errors in sequence beginning at line 7 of invalid.bio:
+Invalid transition 'O' -> 'I-ORG' for token 'University' on line 7 of invalid.bio
 Used method conlleval to repair:
 Old: ('I-ORG', 'I-ORG', 'I-ORG', 'O', 'O', 'B-LOC', 'I-LOC', 'O', 'B-LOC', 'O')
 New: ('B-ORG', 'I-ORG', 'I-ORG', 'O', 'O', 'B-LOC', 'I-LOC', 'O', 'B-LOC', 'O')
@@ -271,14 +272,14 @@ To check if a file has any invalid transitions, we can run
 `seqscore validate --labels BIO samples/reference.bio`:
 
 ```
-No errors found in 0 tokens, 2 sequences, and 1 documents in reference.bio
+No errors found in 15 tokens, 2 sequences, and 1 document(s) in reference.bio
 ```
 
 For the example of the [samples/invalid.bio](samples/invalid.bio), we can run
 `seqscore validate --labels BIO samples/invalid.bio`:
 
 ```
-Encountered 1 errors in 1 tokens, 2 sequences, and 1 documents in invalid.bio
+Encountered 1 errors in 15 tokens, 2 sequences, and 1 document(s) in invalid.bio
 Invalid transition 'O' -> 'I-ORG' for token 'University' on line 7
 ```
 
@@ -313,11 +314,21 @@ We can get a list of available chunk encodings by running `seqscore convert --he
 ```
 Usage: seqscore convert [OPTIONS] FILE OUTPUT_FILE
 
+  convert between mention encodings
+
 Options:
   --file-encoding TEXT            [default: UTF-8]
-  --ignore-comment-lines
-  --ignore-document-boundaries / --use-document-boundaries
-  --output-delim TEXT             [default: space]
+  --allow-comment-lines           allow comment lines starting with # before
+                                  sequences
+  --ignore-document-boundaries    ignore any document boundaries in the input
+  --token-index INTEGER           index of the input field to use for the
+                                  token  [default: 0]
+  --label-index INTEGER           index of the input field to use for the
+                                  label  [default: -1]
+  --output-delim TEXT             the delimiter to be used for output (has no
+                                  effect on input) [default: tab]
+  --discard-extra-fields          discard any fields other than the token and
+                                  label when writing output files
   --input-labels [BIO|BIOES|BILOU|BMES|BMEOW|IO|IOB]
                                   [required]
   --output-labels [BIO|BIOES|BILOU|BMES|BMEOW|IO|IOB]
@@ -387,11 +398,13 @@ For example, if we run `seqscore summarize --labels BIO samples/reference.bio` w
 the following output:
 
 ```
-File 'samples/reference.bio' contains 1 document(s) with the following mentions:
+File 'samples/reference.bio' contains 1 document(s) and 2 sentences
 | Entity Type   |   Count |
 |---------------|---------|
 | LOC           |       2 |
 | ORG           |       1 |
+|---------------|---------|
+| TOTAL         |       3 |
 ```
 
 If the quiet (`-q`) flag is provided, the first line giving the filename and document
@@ -574,10 +587,13 @@ For development, check out the `dev` branch (latest, but less tested than `main`
 
 ## Setting up an environment for development
 
+Python 3.10 (the minimum version SeqScore supports) is used for development to avoid
+accidentally using newer Python features.
+
 ### Using uv
 
-1. Create an environment: `uv venv --python 3.10 .venv`
-2. Install seqscore and development dependencies: `uv pip install -e ".[dev]"`
+Create an environment and install seqscore with development dependencies:
+`uv sync --python 3.10 --extra dev`
 
 ### Using conda
 

pyproject.toml

@@ -13,8 +13,8 @@ authors = [
 ]
 requires-python = ">=3.10"
 dependencies = [
-    "attrs>=19.2.0",
     "click",
+    "pydantic>=2.0",
     "tabulate",
 ]
 classifiers = [

seqscore/__init__.py

@@ -1 +1 @@
-__version__ = "0.8.0"
+__version__ = "0.9.0"