dependency upgrade #63

Author: HamedBabaei

CHANGELOG.md

@@ -1,5 +1,11 @@
 ## Changelog
 
+### V1.5.1 Changelog (September 7, 2025)
+- Update dependencies.
+- Make versioning standardized.
+- Minor fix to the readme.
+- Add bash script for requirement update based on pyproject.toml
+
 ### V1.5.0 Changelog (July 29, 2025)
 - Added 17 Knowledge Graph Embedding (KGE) aligner models.
 - Major documentation update: improved structure, clarity, sectioning, etc.

CITATION.cff

@@ -17,5 +17,5 @@ keywords:
   - "Alignment"
   - "Python Library"
 license: "Apache-2.0"
-version: "1.5.0"
+version: "1.5.1"
 date-released: "2025-07-29"

README.md

@@ -33,6 +33,14 @@ git clone [email protected]:sciknoworg/OntoAligner.git
 pip install ./ontoaligner
 ```
 
+Next, verify the installation:
+
+```python
+import ontoaligner
+
+print(ontoaligner.__version__)
+```
+
 ## 📚 Documentation
 
 Comprehensive documentation for OntoAligner, including detailed guides and examples, is available at **[ontoaligner.readthedocs.io](https://ontoaligner.readthedocs.io/)**. Below are some key tutorials with links to both the documentation and the corresponding example codes.

ontoaligner/VERSION

@@ -0,0 +1 @@
+1.5.1

ontoaligner/__init__.py

@@ -11,7 +11,10 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-__version__ = "1.5.0"
+from pathlib import Path
+
+# Load version from VERSION file
+__version__ = (Path(__file__).parent / "VERSION").read_text().strip()
 
 from .pipeline import OntoAlignerPipeline
 from ontoaligner import ontology, base, encoder, aligner, utils, postprocess

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "OntoAligner"
-version = "1.5.0"
+version = "0.0.0"
 description = "OntoAligner: A Comprehensive Modular and Robust Python Toolkit for Ontology Alignment."
 authors = ["Hamed Babaei Giglou <[email protected]>"]
 license="Apache-2.0"
@@ -10,7 +10,7 @@ repository = "https://github.com/sciknoworg/OntoAligner/"
 include = ["images/logo-with-background.png"]
 
 [tool.poetry.dependencies]
-python = ">=3.10,<4.0.0"
+python = ">=3.10,<3.14"
 pathlib = "*"
 argparse = "*"
 numpy = "*"
@@ -20,14 +20,14 @@ scikit-learn = "*"
 tqdm = "*"
 owlready2 = "0.44"
 rdflib = "7.1.1"
-torch = "2.6.0"
+torch = "^2.8.0"
 transformers = "4.50.0"
 rapidfuzz = "3.5.2"
 openai = "1.56.0"
 rank_bm25 = "0.2.2"
-huggingface_hub="0.28.1"
-sentence-transformers = "4.1.0"
-bitsandbytes="0.45.1"
+huggingface-hub = "^0.34.4"
+sentence-transformers = "^5.1.0"
+bitsandbytes="^0.45.1"
 pykeen="1.11.1"
 
 [tool.poetry.dev-dependencies]
@@ -38,6 +38,12 @@ wheel = "*"
 twine = "*"
 pytest = "*"
 
+[tool.poetry-dynamic-versioning]
+enable = true
+style = "semver"
+source = "attr"
+attr = "ontoaligner.__version__"
+
 [build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
+requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.4.0"]
+build-backend = "poetry_dynamic_versioning.backend"

requirements.sh

@@ -0,0 +1,45 @@
+#!/usr/bin/env bash
+
+set -e
+
+if [ ! -f pyproject.toml ]; then
+    echo "pyproject.toml not found!"
+    exit 1
+fi
+
+echo "Generating clean requirements.txt with direct dependencies..."
+
+> requirements.txt
+
+awk '
+/^\[tool\.poetry\.dependencies\]/ {section="deps"; next}
+/^\[tool\.poetry\.dev-dependencies\]/ {section="dev"; next}
+/^\[/ {section=""; next}
+
+section!="" && NF>0 {
+    if ($1 ~ /^python/) next
+
+    gsub(/"/, "", $0)
+    gsub(/ /, "", $0)
+
+    split($0, a, "=")
+    pkg=a[1]
+    ver=a[2]
+
+    # Leave hyphens as-is (do not convert to underscores)
+
+    if(ver=="" || ver=="*") {
+        print pkg
+    } else {
+        # Remove ^ or ~ for pip-friendly pin
+        gsub(/\^|~/, "", ver)
+        # Add == only if not already present
+        if(index(ver, "==")==0) {
+            print pkg "==" ver
+        } else {
+            print pkg ver
+        }
+    }
+}' pyproject.toml > requirements.txt
+
+echo "Done! requirements.txt created."

requirements.txt

@@ -3,21 +3,22 @@ argparse
 numpy
 pandas
 datasets
-scikit_learn
-openai==1.56.0
+scikit-learn
+tqdm
 owlready2==0.44
-rank_bm25==0.2.2
-rapidfuzz==3.5.2
 rdflib==7.1.1
-sentence_transformers==4.1.0
-torch==2.6.0
-tqdm
+torch==2.8.0
 transformers==4.50.0
-huggingface_hub==0.28.1
+rapidfuzz==3.5.2
+openai==1.56.0
+rank_bm25==0.2.2
+huggingface-hub==0.34.4
+sentence-transformers==5.1.0
 bitsandbytes==0.45.1
+pykeen==1.11.1
+ruff
 pre-commit
 setuptools
 wheel
 twine
-ruff
-pykeen==1.11.1
+pytest

setup.py

@@ -1,11 +1,12 @@
 from setuptools import setup, find_packages
+import os
 
 with open("README.md", encoding="utf-8") as f:
     long_description = f.read()
 
 setup(
     name="OntoAligner",
-    version="1.5.0",
+    version=open(os.path.join(os.path.dirname(__file__), 'ontoaligner/VERSION')).read().strip(),
     author="Hamed Babaei Giglou",
     author_email="[email protected]",
     description="OntoAligner: A Comprehensive Modular and Robust Python Toolkit for Ontology Alignment",
@@ -26,11 +27,11 @@
         "rank_bm25==0.2.2",
         "rapidfuzz==3.5.2",
         "rdflib==7.1.1",
-        "sentence-transformers==4.1.0",
-        "torch==2.6.0",
-        "transformers==4.50.0",
-        "huggingface_hub==0.28.1",
-        "bitsandbytes==0.45.1",
+        "sentence-transformers>=5.1.0,<6.0.0",
+        "torch>=2.8.0,<3.0.0",
+        "transformers>=4.56.0,<5.0.0",
+        "huggingface-hub>=0.34.4,<1.0.0",
+        "bitsandbytes>=0.45.1,<1.0.0",
         "pykeen==1.11.1"
     ],
     classifiers=[