Clean up the requirement package

[YifanLu2000]

Clean up the requirement package @chansigit @Sichao25 @YifanLu2000

[YifanLu2000]

• [ ] adjustText
• [ ] anndata>=0.8.0
• [ ] colorcet>=2.0.1
• [ ] cvxopt>=1.2.3
• [ ] csbdeep>=0.6.3
• [ ] descartes
• [ ] dynamo-release>=1.3.0
• [ ] folium>=0.12.1
• [ ] geopandas>=0.10.2
• [ ] gpytorch
• [ ] ipywidgets>=7.7.1
• [ ] kneed>=0.7.0
• [ ] kornia>=0.6.4
• [ ] leidenalg>=0.10.0
• [ ] loompy>=3.0.5
• [ ] mapclassify>=2.4.2
• [ ] matplotlib<=3.5.3
• [ ] mpi4py
• [ ] nbconvert
• [ ] networkx>=2.6.3
• [ ] # ngs_tools>=1.6.0
• [ ] numba>=0.46.0
• [ ] numpy>=1.18.1
• [ ] opencv-python>=4.5.4.60
• [ ] pandana
• [ ] pandas>=0.25.1
• [ ] paste-bio>=1.4.0
• [ ] plotly>=5.1.0
• [ ] POT>=0.8.1
• [ ] psutil>=5.6.3
• [ ] pynndescent>=0.4.8
• [ ] pysal>=1.14.4
• [ ] pyro-ppl
• [ ] python-igraph>=0.7.1
• [ ] pyvista>=0.39.1
• [ ] scipy>=1.0
• [ ] scikit-image>=0.18.0
• [ ] scikit-learn>=0.19.1
• [ ] seaborn>=0.9.0
• [ ] setuptools>=58.0.4
• [ ] Shapely>=1.8.0
• [ ] statsmodels>=0.9.0
• [ ] tensorflow
• [ ] tqdm>=4.62.3
• [ ] torch
• [ ] trame>=2.2.5
• [ ] trame-server>=2.7.0
• [ ] typing_extensions>=4.0.1
• [ ] umap-learn>=0.5.1
• [ ] vtk>=9.2.2

[Sichao25]

Here are a few related issues to follow up on. Please correct me if anything is wrong.

• [x] Matplotlib requirement is out of date.
• [ ] python-igraph has been renamed to igraph on PyPi.
• [x] .A .H attributes were removed from the SciPy 0.14.0.
• [ ] Trame and Trame Server seem to be used mainly in the Spateo Viewer. Should we remove them here?
• [ ] Existing tools like Scvelo and scVI-tools restrict the usage of the latest version of NumPy (2.0). We may consider doing the same.
• [x] I feel like packages such as paste-bio, cvxopt, folium, pandana are likely dependencies of TensorFlow. We might be able to remove them from the requirements unless specific versions are needed to avoid conflicts. Need more tests on this.
• [ ] We could discuss making rarely used packages optional dependencies. For example, descartes