velocity_graph fails outside of Jupyter notebook

[josiahbjorgaard]

velocity_graph uses tqdm.notebook via [the parallelize function].(

scvelo/scvelo/core/_parallelize.py

Line 29 in d89ca6a

def parallelize(

).
This causes an issue when running outside of a jupyter notebook, as shown below. I noted that there is a show_progress_bar option in parallelize, but no way of passing kwargs via an execution point of the velocity_graph function.

A fix for this would be to add an option to set show_progress_bar=False in parallelize when calling velocity_graph.

import os
import scvelo as scv
loomfile = 'combined_test1.loom'
ldata = scv.read_loom(loomfile, sparse=True)#cache=True)
scv.settings.verbosity = 0
scv.settings.set_figure_params('scvelo', facecolor='white', dpi=100, frameon=False)
cr.settings.verbosity = 0
barcodes = [bc.split(':')[1] for bc in ldata.obs.index.tolist()]
barcodes = [bc[0:len(bc)-1] + '_10' for bc in barcodes]
ldata.obs.index = barcodes
ldata.var_names_make_unique()
scv.pp.filter_and_normalize(ldata)
scv.pp.moments(ldata)
scv.tl.velocity(ldata, mode='stochastic', use_highly_variable=False)
scv.tl.velocity_graph(ldata, n_jobs=64)
scv.tl.umap(ldata)
scv.tl.louvain(ldata)
scv.pl.velocity_embedding(ldata, basis='umap', frameon=False, save='embedding.pdf')
scv.pl.velocity_embedding_grid(ldata, basis='umap', save='embedding_grid.pdf', title='', scale=0.25)
ldata.write_h5ad('combined_test1_loom_gzip.h5ad', compression="gzip")

Error output

Traceback (most recent call last):
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/traitlets/traitlets.py", line 653, in get
    value = obj._trait_values[self.name]
KeyError: 'layout'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "process_velocity_looms.py", line 29, in <module>
    scv.tl.velocity_graph(ldata, n_jobs=64)
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/scvelo/tools/velocity_graph.py", line 373, in v
elocity_graph
    vgraph.compute_cosines(n_jobs=n_jobs, backend=backend)
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/scvelo/tools/velocity_graph.py", line 185, in c
ompute_cosines
    res = parallelize(
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/scvelo/core/_parallelize.py", line 120, in wrap
per
    pbar = None if tqdm is None else tqdm(total=col_len, unit=unit)
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/tqdm/notebook.py", line 233, in __init__
    self.container = self.status_printer(self.fp, total, self.desc, self.ncols)
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/tqdm/notebook.py", line 110, in status_printer
    pbar = IProgress(min=0, max=total)
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/ipywidgets/widgets/widget_float.py", line 26, i
n __init__
    super().__init__(**kwargs)
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/ipywidgets/widgets/widget_description.py", line
 35, in __init__
    super().__init__(*args, **kwargs)
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/ipywidgets/widgets/widget.py", line 504, in __i
nit__
    self.open()
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/ipywidgets/widgets/widget.py", line 517, in ope
n
    state, buffer_paths, buffers = _remove_buffers(self.get_state())
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/ipywidgets/widgets/widget.py", line 615, in get
_state
    value = to_json(getattr(self, k), self)
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/traitlets/traitlets.py", line 700, in __get__
    return self.get(obj, cls)
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/traitlets/traitlets.py", line 656, in get
    default = obj.trait_defaults(self.name)
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/traitlets/traitlets.py", line 1868, in trait_defaults
    return self._get_trait_default_generator(names[0])(self)
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/traitlets/traitlets.py", line 624, in default
    return self.make_dynamic_default()
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/ipywidgets/widgets/trait_types.py", line 365, in make_dynamic_default
    return self.klass(*(self.default_args or ()),
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/ipywidgets/widgets/widget_layout.py", line 86, in __init__
    super().__init__(**kwargs)
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/ipywidgets/widgets/widget.py", line 504, in __init__
    self.open()
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/ipywidgets/widgets/widget.py", line 535, in open
    self.comm = create_comm(**args)
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/comm/__init__.py", line 27, in _create_comm
    raise NotImplementedError("Cannot ")
NotImplementedError: Cannot 
Exception ignored in: <function tqdm.__del__ at 0x7f2598201d30>
Traceback (most recent call last):
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/tqdm/std.py", line 1149, in __del__
    self.close()
  File "/shared/miniconda3/envs/geneformer/lib/python3.8/site-packages/tqdm/notebook.py", line 278, in close
    self.disp(bar_style='danger', check_delay=False)

Versions

scvelo==0.3.0  scanpy==1.9.3  anndata==0.9.2  loompy==3.0.7  numpy==1.24.3  scipy==1.8.1  matplotlib==3.7.1  sklearn==1.1.3  pandas==1.5.3  

[WeilerP]

Not a scvelo issue as far as I can tell but an issue in traitlets. I've added arguments to optionally display the progress bar, nonetheless. See #1234.