From edc48ad7b003b0d14eb99bde7e926686917c845b Mon Sep 17 00:00:00 2001
From: Vassilis Minadakis <vassilisminadakis@gmail.com>
Date: Tue, 28 May 2024 13:08:02 +0300
Subject: [PATCH 1/2] 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.
---
 requirements.txt | 46 +++++++++++++++++++---------------------------
 setup.py         | 33 +++++++++++++++++++++++++++++----
 2 files changed, 48 insertions(+), 31 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 5045c40a..1b8b6c80 100644
--- a/requirements.txt
+++ b/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
\ No newline at end of file
+# Torch requirements
+torch==2.3.0
+torch-geometric==2.3.1
+torchvision==0.18.0
\ No newline at end of file
diff --git a/setup.py b/setup.py
index ca663f5a..d5099931 100644
--- a/setup.py
+++ b/setup.py
@@ -33,9 +33,34 @@
       #           , 'jaqpotpy.datasets', 'jaqpotpy.descriptors', 'jaqpotpy.descriptors.molecular'
       #           , 'jaqpotpy.descriptors.graph'],
       install_requires=[
-            'pandas', 'requests', 'pydantic', 'rdkit-pypi', 'mordred', 'pyjwt', 'scikit-learn', "tqdm"
-            , 'skl2onnx', 'onnxruntime'
-            # ,'tornado', 'scikit-learn', 'torch', 'torch-scatter', 'torch-sparse', 'torch-cluster'
-            # , 'torch-spline-conv', 'torch-geometric', 'dgl', 'torch_sparse', 'kennard-stone'
+      #     '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',
+            # 'torch-scatter==2.1.2',
+            # 'torch-sparse==0.6.18',
+            # 'torch-cluster==1.6.3',
+            # 'torch-spline-conv==1.2.2'
+            # # ,'tornado', 'scikit-learn', 'torch', 'torch-scatter', 'torch-sparse', 'torch-cluster'
+            # # , 'torch-spline-conv', 'torch-geometric', 'dgl', 'torch_sparse', 'kennard-stone'
       ],
       zip_safe=False)

From 78584eaad6f957affaaa9a0f6de1df46677be997 Mon Sep 17 00:00:00 2001
From: Vassilis Minadakis <vassilisminadakis@gmail.com>
Date: Tue, 28 May 2024 13:50:15 +0300
Subject: [PATCH 2/2] fix: Just deleted some empty lines

---
 setup.py | 19 ++-----------------
 1 file changed, 2 insertions(+), 17 deletions(-)

diff --git a/setup.py b/setup.py
index d5099931..9bca8f4f 100644
--- a/setup.py
+++ b/setup.py
@@ -26,16 +26,7 @@
       license='MIT License',
       packages=find_packages(exclude=["*.tests"]),
       package_data={'jaqpotpy': ['data/*.gz']},
-      # package_data={find_packages(exclude=["*.tests"]): ['data/*.gz']},
-      # packages=['jaqpotpy', 'jaqpotpy.api', 'jaqpotpy.mappers', 'jaqpotpy.utils'
-      #           , 'jaqpotpy.entities', 'jaqpotpy.dto', 'jaqpotpy.doa'
-      #           , 'jaqpotpy.helpers', 'jaqpotpy.colorlog', 'jaqpotpy.models', 'jaqpotpy.cfg'
-      #           , 'jaqpotpy.datasets', 'jaqpotpy.descriptors', 'jaqpotpy.descriptors.molecular'
-      #           , 'jaqpotpy.descriptors.graph'],
       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',
@@ -52,15 +43,9 @@
             'skl2onnx==1.16.0',
             'onnxruntime==1.18.0',
 
-            # # Torch requirements
+            # Torch requirements
             'torch==2.3.0',
             'torch-geometric==2.3.1',
             'torchvision==0.18.0',
-            # 'torch-scatter==2.1.2',
-            # 'torch-sparse==0.6.18',
-            # 'torch-cluster==1.6.3',
-            # 'torch-spline-conv==1.2.2'
-            # # ,'tornado', 'scikit-learn', 'torch', 'torch-scatter', 'torch-sparse', 'torch-cluster'
-            # # , 'torch-spline-conv', 'torch-geometric', 'dgl', 'torch_sparse', 'kennard-stone'
       ],
-      zip_safe=False)
+      zip_safe=False)
\ No newline at end of file