Update setup.py

Author: mehdijoodaki

setup.py

@@ -8,29 +8,71 @@
     url='https://github.com/CostaLab/PILOT',
     python_requires='>=3.11.5,<3.12',
     install_requires=[
-            "cycler>=0.11.0,<0.12.0",
-            "joypy>=0.2.6,<0.3.0",
-            "leidenalg>=0.10.1,<0.11.0",
-            "numpy>=1.24.4,<1.25.0",
-            "matplotlib==3.8.0",
-            "pandas>=2.0.3,<2.1.0",
-            "plotly>=5.22.0,<5.23.0",
-            "plotnine>=0.12.3,<0.13.0",
-            "pot>=0.9.1,<0.10.0",
-            "pydiffmap>=0.2.0.1,<0.3.0",
-            "scanpy>=1.9.5,<1.10.0",
-            "scikit-learn>=1.3.0,<1.4.0",
-            "scikit-network>=0.31.0,<0.32.0",
-            "scipy>=1.11.2,<1.12.0",
-            "seaborn>=0.12.2,<0.13.0",
-            "shap>=0.42.1,<0.43.0",
-            "statsmodels>=0.14.0,<0.15.0",
-            "elpigraph-python>=0.3.1,<0.4.0",
-            "adjusttext>=0.8,<0.9",
-            "gprofiler-official>=1.0.0,<1.1.0",
-            "rpy2>=3.5.11",
-            "gseapy>=1.1.7"
-        ],
-        packages=find_packages()
+        "adjustText>=0.8,<0.9",
+        "anndata>=0.11.4,<0.12.0",
+        "array-api-compat>=1.12.0,<1.13.0",
+        "certifi>=2025.7.9",
+        "cffi>=1.17.1,<1.18.0",
+        "charset-normalizer>=3.4.2,<3.5.0",
+        "cloudpickle>=3.1.1,<3.2.0",
+        "contourpy>=1.3.2,<1.4.0",
+        "cycler>=0.11.0,<0.12.0",
+        "elpigraph-python>=0.3.2,<0.4.0",
+        "fonttools>=4.58.5,<4.59.0",
+        "gprofiler-official>=1.0.0,<1.1.0",
+        "h5py>=3.14.0,<3.15.0",
+        "idna>=3.10,<3.11",
+        "igraph>=0.11.9,<0.12.0",
+        "Jinja2>=3.1.6,<3.2.0",
+        "joblib>=1.5.1,<1.6.0",
+        "joypy>=0.2.6,<0.3.0",
+        "kiwisolver>=1.4.8,<1.5.0",
+        "leidenalg>=0.10.2,<0.11.0",
+        "llvmlite>=0.44.0,<0.45.0",
+        "MarkupSafe>=3.0.2,<3.1.0",
+        "matplotlib>=3.10.3,<3.11.0",
+        "mizani>=0.9.3,<0.10.0",
+        "natsort>=8.4.0,<8.5.0",
+        "networkx>=3.5,<3.6",
+        "numba>=0.61.2,<0.62.0",
+        "numexpr>=2.11.0,<2.12.0",
+        "numpy>=1.26.4,<1.27.0",
+        "packaging>=25.0,<26.0",
+        "pandas>=2.3.1,<2.4.0",
+        "patsy>=1.0.1,<1.1.0",
+        "pillow>=11.3.0,<11.4.0",
+        "plotly>=5.24.1,<5.25.0",
+        "plotnine>=0.12.4,<0.13.0",
+        "POT>=0.9.5,<0.10.0",
+        "pycparser>=2.22,<2.23",
+        "pydiffmap>=0.2.0.1,<0.3.0",
+        "pynndescent>=0.5.13,<0.6.0",
+        "pyparsing>=3.2.3,<3.3.0",
+        "python-dateutil>=2.9.0",
+        "pytz>=2025.2",
+        "requests>=2.32.4,<2.33.0",
+        "rpy2>=3.5.11,<3.6.0",
+        "scanpy>=1.9.6,<1.10.0",
+        "scikit-learn>=1.7.0,<1.8.0",
+        "scikit-network>=0.31.0,<0.32.0",
+        "scipy>=1.16.0,<1.17.0",
+        "seaborn>=0.12.2,<0.13.0",
+        "session_info>=1.0.1,<1.1.0",
+        "shap>=0.42.1,<0.43.0",
+        "shapely>=2.1.1,<2.2.0",
+        "six>=1.17.0,<1.18.0",
+        "slicer>=0.0.7,<0.0.8",
+        "statsmodels>=0.14.5,<0.15.0",
+        "stdlib-list>=0.11.1,<0.12.0",
+        "tenacity>=9.1.2,<9.2.0",
+        "texttable>=1.7.0,<1.8.0",
+        "threadpoolctl>=3.6.0,<3.7.0",
+        "tqdm>=4.67.1,<4.68.0",
+        "tzdata>=2025.2",
+        "tzlocal>=5.3.1,<5.4.0",
+        "umap-learn>=0.5.9,<0.6.0",
+        "urllib3>=2.5.0,<2.6.0",
+        "gseapy>=1.1.7,<1.2.0"
+    ],
+    packages=find_packages()
 )
-