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Make progress bar optional #1234

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merged 2 commits into from
Apr 12, 2024
Merged

Make progress bar optional #1234

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4c154bb
Update `recover_dynamics`
WeilerP Apr 12, 2024
61e437a
Update `velocity_graph.py`
WeilerP Apr 12, 2024
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5 changes: 4 additions & 1 deletion scvelo/tools/_em_model_core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down Expand Up @@ -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
-------
Expand Down Expand Up @@ -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,
Expand Down
12 changes: 10 additions & 2 deletions scvelo/tools/velocity_graph.py
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Expand Up @@ -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)

Expand All @@ -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))

Expand Down Expand Up @@ -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.

Expand Down Expand Up @@ -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
-------
Expand Down Expand Up @@ -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
Expand Down
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