upgrade dependencies

Author: Roland Sauter

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gemcat"
-version = "1.2.1"
+version = "1.3.0"
 
 description = "A toolbox for gene expression-based prediction of metabolic alterations"
 keywords = ["python", "bioinformatics", "modeling", "metabolites", "omics"]
@@ -15,22 +15,22 @@ readme = "README.md"
 
 requires-python=">=3.10"
 dependencies = [
-    "numpy==1.26.*",
-    "pandas==2.1.*",
+    "numpy==2.1.*",
+    "pandas==2.2.*",
     "cobra==0.29.*",
-    "networkx==3.2.*",
-    "scipy==1.11.*",
-    "sympy==1.12.*",
+    "networkx==3.3.*",
+    "scipy==1.14.*",
+    "sympy==1.13.*",
 ]
 
 [project.optional-dependencies]
 dev = [
-  "pytest==7.4.*",
-  "black==23.7.*",
-  "isort==5.12.*",
-  "pylint==3.1.*",
-  "ruff==0.0.*",
-  "requests==2.31.*",
+  "pytest==8.3.*",
+  "black==24.8.*",
+  "isort==5.13.*",
+  "pylint==3.2.*",
+  "ruff==0.6.*",
+  "requests==2.32.*",
 
 ]