Running tutorial and dependencies

[leonardogolinelli]

Hello,
I tried to run the tutorial locally and encountered some problems, here is the list of problems and solutions:

1) Jax method ShapedArray is deprecated.
ImportError: cannot import name 'ShapedArray' from 'jax'
solution: downgrade Jax to 0.4.7

2) error on velocity graph computation using scvelo
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (1, 4) + inhomogeneous part.
solution:
install scvelo from the master branch (as already explained in scvelo repo issues)

3) multi dimensional indexing on pandas is deprecated.
"Multi-dimensional indexing (e.g. obj[:, None]) is no longer supported. Convert to a numpy array before indexing instead."
solution:
add line:
scaling = scaling.to_numpy()
before:
adata.layers["fit_t"] = latent_time.values * scaling[np.newaxis, :]
in function:
add_velovi_outputs_to_adata

4) df output is tuple instead of dataframe in the function:
compute_extrinisic_uncertainty
solution:
substitute:
df = _compute_directional_statistics_tensor(extrapolated_cells, n_jobs=-1, n_cells=adata.n_obs)
with:
df, cosine_sims = _compute_directional_statistics_tensor(extrapolated_cells, n_jobs=-1, n_cells=adata.n_obs)
(this was already reported in #15 )

Here's how I installed the environment on linux (the order sometimes is important):
remark 1 - recommend using mamba instead of conda whenever possible
remark 2 -Probably better to follow these steps when using an active gpu

1. install pytorch following https://pytorch.org/ - mamba install.. (follow link)
2. install conda notebook - mamba install -c anaconda notebook
3. install scvelo from master branch - cd to scvelo cloned repo then pip install .
4. install velovi from master branch - cd to velovi cloned repo then pip install .
5. downgrade jax to 0.4.7 - mamba install -c conda-forge jax=0.4.7

Hope it helps.