update min versions pip

pyproject.toml

@@ -35,25 +35,25 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
 ]
 dependencies = [
-    "notebook >= 7.0.6, < 8.0",
+    "notebook >= 7.2.1, < 8.0",
     "markov-clustering >= 0.0.6.dev0, < 1.0",
-    "tensorboard >= 1.0.0, < 2.0",
-    "protobuf >= 3.20.1, < 4.0",
+    "tensorboard >= 2.17.0, < 3.0",
+    "protobuf >= 5.27.1, < 6.0",
     "dill >= 0.3.8, < 1.0",
-    "pyarrow >= 15.0.0, < 16.0",
-    "tables >= 3.8.0, < 4.0",
-    "numpy >= 1.20, < 1.24",
+    "pyarrow >= 16.1.0, < 17.0",
+    "tables >= 3.9.2, < 4.0",
+    "numpy >= 1.25, < 2.0",
     "scipy >= 1.13.1, < 2.0",
-    "h5py >= 3.6.0, < 4.0",
-    "networkx >= 2.6.3, < 3.0",
-    "matplotlib >= 3.5.1, < 4.0",
-    "scikit-learn >= 1.0.2, < 2.0",
+    "h5py >= 3.11.0, < 4.0",
+    "networkx >= 3.3.3, < 4.0",
+    "matplotlib >= 3.9.0, < 4.0",
+    "scikit-learn >= 1.5.0, < 2.0",
     "chart-studio >= 1.1.0, < 2.0",
-    "pdb2sql >= 0.5.1, < 1.0",
+    "pdb2sql >= 0.5.3, < 1.0",
     "python-louvain >= 0.16, < 1.0",
-    "tqdm >= 4.63.0, < 5.0",
-    "freesasa >= 2.1.0, < 3.0",
-    "biopython >= 1.81, < 2.0"
+    "tqdm >= 4.66.4, < 5.0",
+    "freesasa >= 2.1.1, < 3.0",
+    "biopython >= 1.83, < 2.0"
     ]
 
 [project.optional-dependencies]