Refactor and optimize the tools module

[Sichao25]

Refactor and optimize the functions in dynamo.tl. Including:

• [x] Resolve the TODO list in graph_calculus.py
• [ ] Refactor dynamics.
• [x] Debug and optimize the reduceDimension function, and investigate the possibility of speeding up umap.
• [x] Updating the tools recipe with the updated preprocessing module.
• [ ] Fix the multiprocessing issues.
• [x] Merge some utils functions to the file calls them, for example, utils_reduceDimension.py to dimension_reduction.py.
• [x] Debug and optimize the clustering.py.
• [x] Add more tests.
• [x] Update docstrings and type hints if needed.
• [x] There are similar structures creating neighbors graphs again and again in tools, try to get rid of them by helper functions(e.g. k_nearest_neighbors in utils, neighbors in connectivity.py) or reusing existing results. Also, it can be helpful to have Hnswlib nearest neighbors supported.

[github-actions[bot]]

This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 14 days

[github-actions[bot]]

This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 14 days