update requirements.txt using pipreqs

requirements.txt

-pip==21.3.1
-pytest==6.2.4
-snakemake==7.1.1
 matplotlib==3.3.4
 numpy==1.22.3
-scipy==1.8.0
+pip==21.3.1
+pytest==6.2.4
 pyvista==0.33.0
-PyYaml==6.0
-pandas==1.3.3
-tqdm==4.59.0
-importlib_resources==5.4.0
-pythreejs==2.3.0
+PyYAML==6.0
+scipy==1.8.0
+setuptools==61.2.0
+vtk==9.1.0