Make progress bar optional (#1234)

* Update `recover_dynamics`

Add option to show progressbar or not.

* Update `velocity_graph.py`

Add argument `show_progress_bar` to `VelocityGraph::compute_cosines` and
`velocity_graph`.

scvelo/tools/_em_model_core.py

@@ -419,6 +419,7 @@ def recover_dynamics(
  copy=False,
  n_jobs=None,
  backend="loky",
+ show_progress_bar: bool = True,
  **kwargs,
 ):
  """Recovers the full splicing kinetics of specified genes.
@@ -476,6 +477,8 @@ def recover_dynamics(
  backend: `str` (default: "loky")
  Backend used for multiprocessing. See :class:`joblib.Parallel` for valid
  options.
+ show_progress_bar
+ Whether to show a progress bar.
 
  Returns
  -------
@@ -557,7 +560,7 @@ def recover_dynamics(
  unit="gene",
  as_array=False,
  backend=backend,
- show_progress_bar=len(var_names) > 9,
+ show_progress_bar=show_progress_bar,
  )(
  adata=adata,
  use_raw=use_raw,

scvelo/tools/velocity_graph.py

@@ -175,7 +175,9 @@ def __init__(
  self.adata = adata
 
  # TODO: Add docstrings
- def compute_cosines(self, n_jobs=None, backend="loky"):
+ def compute_cosines(
+ self, n_jobs=None, backend="loky", show_progress_bar: bool = True
+ ):
  """TODO."""
  n_jobs = get_n_jobs(n_jobs=n_jobs)
 
@@ -189,6 +191,7 @@ def compute_cosines(self, n_jobs=None, backend="loky"):
  unit="cells",
  backend=backend,
  as_array=False,
+ show_progress_bar=show_progress_bar,
  )()
  uncertainties, vals, rows, cols = map(_flatten, zip(*res))
 
@@ -277,6 +280,7 @@ def velocity_graph(
  copy=False,
  n_jobs=None,
  backend="loky",
+ show_progress_bar: bool = True,
 ):
  r"""Computes velocity graph based on cosine similarities.
 
@@ -329,6 +333,8 @@ def velocity_graph(
  backend: `str` (default: "loky")
  Backend used for multiprocessing. See :class:`joblib.Parallel` for valid
  options.
+ show_progress_bar
+ Whether to show a progress bar.
 
  Returns
  -------
@@ -370,7 +376,9 @@ def velocity_graph(
  logg.info(
  f"computing velocity graph (using {n_jobs}/{os.cpu_count()} cores)", r=True
  )
- vgraph.compute_cosines(n_jobs=n_jobs, backend=backend)
+ vgraph.compute_cosines(
+ n_jobs=n_jobs, backend=backend, show_progress_bar=show_progress_bar
+ )
 
  adata.uns[f"{vkey}_graph"] = vgraph.graph
  adata.uns[f"{vkey}_graph_neg"] = vgraph.graph_neg