diff --git a/.github/workflows/github_test.yml b/.github/workflows/github_test.yml
index bab1088..e1fc875 100644
--- a/.github/workflows/github_test.yml
+++ b/.github/workflows/github_test.yml
@@ -1,8 +1,8 @@
# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-name: Tests
-run-name: Unit Testing on ${{ github.event_name }}
+name: CI Tests
+run-name: CI Testing on ${{ github.event_name }}
on:
push:
diff --git a/README.md b/README.md
index 90808cc..5b5e1b6 100644
--- a/README.md
+++ b/README.md
@@ -14,6 +14,8 @@
+ 
+ 
## Installation
diff --git a/requirements.txt b/requirements.txt
index cf8334d..f932ccf 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,16 +1,16 @@
-Owlready2~=0.44
+owlready2~=0.46
argparse~=1.4.0
-pandas~=2.0.3
-numpy~=1.24.2
-gensim~=4.3.0
-scipy~=1.10.1
-scikit-learn~=1.2.1
-setuptools~=68.2.2
-requests~=2.31.0
+pandas~=2.2.2
+numpy~=1.26.4
+gensim~=4.3.2
+scipy~=1.12.0
+scikit-learn~=1.5.1
+setuptools~=70.2.0
+requests~=2.32.3
tqdm~=4.66.1
-sparse_dot_topn~=0.3.4
-bioregistry~=0.10.6
+sparse-dot-topn~=1.1.3
+bioregistry~=0.11.10
nltk~=3.8.1
-rapidfuzz~=2.13.7
+rapidfuzz~=3.9.4
shortuuid~=1.0.11
-myst_parser~=2.0.0
\ No newline at end of file
+myst-parser~=2.0.0
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 7292f02..d6d71c5 100644
--- a/setup.py
+++ b/setup.py
@@ -1,7 +1,7 @@
from setuptools import setup, find_packages
from text2term.config import VERSION
-description = 'A tool for mapping free-text descriptions of (biomedical) entities to controlled terms in ontologies'
+description = 'a tool for mapping free-text descriptions of entities to ontology terms'
long_description = open('README.md').read()
with open('requirements.txt') as f:
@@ -24,9 +24,13 @@
'Development Status :: 4 - Beta',
'License :: OSI Approved :: MIT License',
'Operating System :: OS Independent',
+ 'Environment :: Console',
'Programming Language :: Python',
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.9',
+ 'Programming Language :: Python :: 3.10',
+ 'Programming Language :: Python :: 3.11',
+ 'Programming Language :: Python :: 3.12',
'Topic :: Scientific/Engineering'
],
python_requires=">=3.9",
diff --git a/text2term/__main__.py b/text2term/__main__.py
index 9560fac..ed94223 100644
--- a/text2term/__main__.py
+++ b/text2term/__main__.py
@@ -4,7 +4,6 @@
from t2t import map_terms, cache_ontology
from onto_cache import cache_exists
from mapper import Mapper
-from term import OntologyTermType
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='A tool for mapping free-text descriptions of (biomedical) '
@@ -25,7 +24,7 @@
"that contains the terms to map, optionally followed by the name of the column that "
"contains identifiers for the terms (eg 'my_terms,my_term_ids')")
parser.add_argument("-sep", "--separator", required=False, type=str, default=',',
- help="Specifies the cell separator to be used when reading a non-comma-separated tabular file")
+ help="Specifies the cell separator to be used when reading a table")
parser.add_argument("-top", "--top_mappings", required=False, type=int, default=3,
help="Maximum number of top-ranked mappings returned per source term (default=3)")
parser.add_argument("-min", "--min_score", required=False, type=float, default=0.5,
@@ -38,9 +37,9 @@
parser.add_argument("-g", "--save_term_graphs", required=False, default=False, action="store_true",
help="Save vis.js graphs representing the neighborhood of each ontology term (default=False)")
parser.add_argument("-c", "--store_in_cache", required=False, type=str, default="",
- help="Store the target ontology into local cache under acronym")
+ help="Cache the target ontology using the name given here")
parser.add_argument("-type", "--term_type", required=False, type=str, default="class",
- help="Define whether to return ontology classes, properties, or both")
+ help="Define whether to map to ontology classes, properties, or both")
parser.add_argument('-u', "--incl_unmapped", required=False, default=False, action="store_true",
help="Include all unmapped terms in the output")
diff --git a/text2term/config.py b/text2term/config.py
index 60e3b39..773464b 100644
--- a/text2term/config.py
+++ b/text2term/config.py
@@ -1 +1 @@
-VERSION = "4.1.4"
+VERSION = "4.2.0"
diff --git a/text2term/syntactic_mapper.py b/text2term/syntactic_mapper.py
index 5316303..ea84dbe 100644
--- a/text2term/syntactic_mapper.py
+++ b/text2term/syntactic_mapper.py
@@ -79,7 +79,7 @@ def compare_levenshtein(self, s1, s2):
Calculates the normalized Levenshtein distance between s1 and s2.
:return similarity between s1 and s2 as a float between 0 and 1
"""
- similarity = rapidfuzz.string_metric.normalized_levenshtein(s1, s2)/100
+ similarity = rapidfuzz.distance.Levenshtein.normalized_similarity(s1, s2)
return similarity
def compare_jaro(self, s1, s2):
@@ -87,7 +87,7 @@ def compare_jaro(self, s1, s2):
Calculates the Jaro similarity between s1 and s2.
:return similarity between s1 and s2 as a float between 0 and 1
"""
- similarity = rapidfuzz.string_metric.jaro_similarity(s1, s2)/100
+ similarity = rapidfuzz.distance.Jaro.normalized_similarity(s1, s2)
return similarity
def compare_jarowinkler(self, s1, s2):
@@ -95,16 +95,15 @@ def compare_jarowinkler(self, s1, s2):
Calculates the Jaro-Winkler similarity between s1 and s2.
:return similarity between s1 and s2 as a float between 0 and 1
"""
- similarity = rapidfuzz.string_metric.jaro_winkler_similarity(s1, s2)/100
+ similarity = rapidfuzz.distance.Jaro.normalized_similarity(s1, s2)
return similarity
def compare_indel(self, s1, s2):
"""
Calculates the normalized Indel distance between s1 and s2.
- See: https://maxbachmann.github.io/RapidFuzz/Usage/fuzz.html#ratio
:return similarity between s1 and s2 as a float between 0 and 1
"""
- similarity = rapidfuzz.fuzz.ratio(s1, s2)/100
+ similarity = rapidfuzz.distance.Indel.normalized_similarity(s1, s2)
return similarity
def compare_fuzzy_ratio(self, s1, s2):