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Black -- formatter for python (#508)

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* Add black

* use black to format code

* Black version
This commit is contained in:
Charlotte Weaver
2018-12-12 09:44:47 -08:00
committed by GitHub
parent a847951658
commit 83154577e4
18 changed files with 636 additions and 791 deletions
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server/cli/prepare.py
+48 -17
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@@ -7,22 +7,48 @@ from scipy.sparse.csc import csc_matrix
@click.command()
@click.argument("data", nargs=1, metavar="<dataset: file or path to data>", required=True)
@click.option("--layout", "-l", default=["umap", "tsne"], multiple=True, type=click.Choice(["umap", "tsne"]),
help="Layout algorithm", show_default=True)
@click.option("--recipe", "-r", default="none", type=click.Choice(["none", "seurat", "zheng17"]),
help="Preprocessing to run.", show_default=True)
@click.option(
"--layout",
"-l",
default=["umap", "tsne"],
multiple=True,
type=click.Choice(["umap", "tsne"]),
help="Layout algorithm",
show_default=True,
)
@click.option(
"--recipe",
"-r",
default="none",
type=click.Choice(["none", "seurat", "zheng17"]),
help="Preprocessing to run.",
show_default=True,
)
@click.option("--output", "-o", default="", help="Save a new file to filename.", metavar="<filename>")
@click.option("--plotting", "-p", default=False, is_flag=True, help="Whether to generate plots.", show_default=True)
@click.option("--sparse", default=False, is_flag=True, help="Whether to force sparsity.", show_default=True)
@click.option("--overwrite", default=False, is_flag=True, help="Allow file overwriting.", show_default=True)
@click.option("--set-obs-names", default="", help="Named field to set as index for obs.", metavar="<name>")
@click.option("--set-var-names", default="", help="Named field to set as index for var.", metavar="<name>")
@click.option("--make-obs-names-unique", default=True, is_flag=True,
help="Ensure obs index is unique.", show_default=True)
@click.option("--make-var-names-unique", default=True, is_flag=True,
help="Ensure var index is unique.", show_default=True)
def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
set_obs_names, set_var_names, make_obs_names_unique, make_var_names_unique):
@click.option(
"--make-obs-names-unique", default=True, is_flag=True, help="Ensure obs index is unique.", show_default=True
)
@click.option(
"--make-var-names-unique", default=True, is_flag=True, help="Ensure var index is unique.", show_default=True
)
def prepare(
data,
layout,
recipe,
output,
plotting,
sparse,
overwrite,
set_obs_names,
set_var_names,
make_obs_names_unique,
make_var_names_unique,
):
"""Preprocesses data for use with cellxgene.
This tool runs a series of scanpy routines for preparing a dataset
@@ -35,6 +61,7 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
# collect slow imports here to make CLI startup more responsive
click.echo("[cellxgene] Starting CLI...")
import matplotlib
matplotlib.use("Agg")
import scanpy.api as sc
@@ -49,8 +76,10 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
output = expanduser(output)
if not output:
click.echo("Warning: No file will be saved, to save the results of cellxgene prepare include "
"--output <filename> to save output to a new file")
click.echo(
"Warning: No file will be saved, to save the results of cellxgene prepare include "
"--output <filename> to save output to a new file"
)
if isfile(output) and not overwrite:
raise click.UsageError(f"Cannot overwrite existing file {output}, try using the flag --overwrite")
@@ -119,9 +148,11 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
try:
sc.tl.louvain(adata)
except ModuleNotFoundError:
click.echo("\nWarning: louvain module is not installed, no clusters will be calculated. "
"To fix this please install cellxgene with the optional feature louvain enabled: "
"`pip install cellxgene[louvain]`")
click.echo(
"\nWarning: louvain module is not installed, no clusters will be calculated. "
"To fix this please install cellxgene with the optional feature louvain enabled: "
"`pip install cellxgene[louvain]`"
)
def run_layout(adata):
if len(unique(adata.obs["louvain"].values)) < 10:
@@ -142,11 +173,11 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
def show_step(item):
names = {
"make_sparse": "Ensuring sparsity",
"run_recipe": f"Running preprocessing recipe \"{recipe}\"",
"run_recipe": f'Running preprocessing recipe "{recipe}"',
"run_pca": "Running PCA",
"run_neighbors": "Calculating neighbors",
"run_louvain": "Calculating clusters",
"run_layout": "Computing layout"
"run_layout": "Computing layout",
}
if item is not None:
return names[item.__name__]