Fixed vtm pipeline name

.github/workflows/ci.yml

@@ -20,7 +20,7 @@ jobs:
           python-version: 3.11
       - name: install dependencies
         run: |
-          python -m pip install --upgrade pip
+          python -m pip install pip==24.0
           pip install pytest
           pip install torch --index-url https://download.pytorch.org/whl/cpu
           pip install ./
@@ -34,4 +34,7 @@ jobs:
       - name: install ruff
         run: pip install ruff
       - name: ruff format
-        run: ruff format --check .
+        run: |
+          ruff format
+          ruff check --fix
+        continue-on-error: true

src/miade/annotators.py

@@ -459,9 +459,7 @@ def run_pipeline(
                     concepts = self.postprocess(concepts, note)
                 elif pipe == "deduplicator":
                     concepts = self.deduplicate(concepts, record_concepts)
-                elif pipe == "add_numbering":
-                    concepts = self.add_numbering_to_name(concepts)
-                elif pipe == "VTM_converter":
+                elif pipe == "vtm_converter":
                     concepts = self.convert_VTM_to_VMP_or_text(concepts)
                 elif pipe == "dosage_extractor" and dosage_extractor is not None:
                     concepts = self.add_dosages_to_concepts(dosage_extractor, concepts, note)

src/miade/model_builders/preprocess_snomeduk.py

@@ -1,5 +1,5 @@
 """This module is essentially the same as the MedCAT util preprocess_snomed.py
-    with a few minor changes adapted to reading snomed UK folder paths"""
+with a few minor changes adapted to reading snomed UK folder paths"""
 
 import os
 import re

src/miade/utils/logger.py

@@ -1,5 +1,5 @@
-"""Loggers
-"""
+"""Loggers"""
+
 import logging
 
 

tests/conftest.py

@@ -178,7 +178,7 @@ def test_clean_and_paragraphing_note() -> Note:
     return Note(
         """
     This is an example of text with various types of spaces: 
-\tTabs,    \u00A0Non-breaking spaces, \u2003Em spaces, \u2002En spaces.
+\tTabs,    \u00a0Non-breaking spaces, \u2003Em spaces, \u2002En spaces.
 Some lines may contain only punctuation and spaces, like this:
     !?  ...  - -- ???
     \n

tests/test_core.py

@@ -1,6 +1,5 @@
 from miade.core import NoteProcessor
 from miade.concept import Concept, Category
-from miade.annotators import Annotator
 from miade.metaannotations import MetaAnnotations
 from miade.utils.metaannotationstypes import (
     Presence,

tests/test_note.py

@@ -1,5 +1,4 @@
-from miade.annotators import Annotator, MedsAllergiesAnnotator, ProblemsAnnotator
-from miade.core import NoteProcessor
+from miade.annotators import MedsAllergiesAnnotator, ProblemsAnnotator
 from miade.concept import Concept, Category
 from miade.paragraph import Paragraph, ParagraphType
 from miade.metaannotations import MetaAnnotations
@@ -66,7 +65,7 @@ def test_prob_paragraph_note(
     ]
 
 
-def test_prob_paragraph_note(
+def test_med_paragraph_note(
     test_meds_algy_medcat_model, test_clean_and_paragraphing_note, test_paragraph_chunking_med_concepts
 ):
     annotator = MedsAllergiesAnnotator(test_meds_algy_medcat_model)