Fix(JAQPOT-86): update requirements (#15)

* fix: Update the versions of dependencies.

This commit sets all dependecies of jaqpotpy to updated and fixed versions, both in setup.py and requirements.txt files.

* fix: Just deleted some empty lines

requirements.txt

@@ -1,28 +1,20 @@
-pandas
-pyjwt
-simplejson
-pydotplus
-requests
-pydantic
-rdkit-pypi
-mordred
-scikit-learn
-tqdm
-torch
-torch-scatter
-torch-sparse
-torch-cluster
-torch-spline-conv
-torch-geometric
-kennard-stone
-mendeleev
-pymatgen
+pandas==2.2.2
+pyjwt==2.8.0
+simplejson==3.19.2
+pydotplus==2.0.2
+requests==2.32.2
+pydantic==2.7.1
+rdkit-pypi==2022.9.5
+mordred==1.2.0
+scikit-learn==1.5.0
+tqdm==4.66.4
+kennard-stone==2.2.1
+mendeleev==0.16.2
+pymatgen==2024.5.1
+skl2onnx==1.16.0
+onnxruntime==1.18.0
 
-# TORCH - GEOMETRIC (KEEP IT LAST)
--f https://data.pyg.org/whl/torch-1.13.0+cpu.html
-torch-scatter
-torch-sparse
-torch-cluster
-torch-spline-conv
-torch-geometric
-# pyg-lib
+# Torch requirements
+torch==2.3.0
+torch-geometric==2.3.1
+torchvision==0.18.0

setup.py

@@ -20,7 +20,25 @@
       packages=find_packages(exclude=["*.tests"]),
       package_data={'jaqpotpy': ['data/*.gz']},
       install_requires=[
-          'pandas', 'requests', 'pydantic', 'rdkit-pypi', 'mordred', 'pyjwt', 'scikit-learn', 'tqdm',
-          'skl2onnx', 'onnxruntime'
+            'pandas==2.2.2',
+            'pyjwt==2.8.0',
+            'simplejson==3.19.2',
+            'pydotplus==2.0.2',
+            'requests==2.32.2',
+            'pydantic==2.7.1',
+            'rdkit-pypi==2022.9.5',
+            'mordred==1.2.0',
+            'scikit-learn==1.5.0',
+            'tqdm==4.66.4',
+            'kennard-stone==2.2.1',
+            'mendeleev==0.16.2',
+            'pymatgen==2024.5.1',
+            'skl2onnx==1.16.0',
+            'onnxruntime==1.18.0',
+
+            # Torch requirements
+            'torch==2.3.0',
+            'torch-geometric==2.3.1',
+            'torchvision==0.18.0',
       ],
-      zip_safe=False)
+      zip_safe=False)