mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-02 12:28:11 +08:00
Black -- formatter for python (#508)
* Add black * use black to format code * Black version
This commit is contained in:
Charlotte Weaver
+70
-26
@@ -13,30 +13,76 @@ from server.app.util.utils import custom_format_warning
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@click.command()
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@click.argument("data", metavar="<data file>", type=click.Path(exists=True, file_okay=True, dir_okay=False))
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@click.option("--layout", "-l", type=click.Choice(["umap", "tsne"]), default="umap", show_default=True,
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help="Method for layout.")
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@click.option("--diffexp", "-d", type=click.Choice(["ttest"]), default="ttest", show_default=True,
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help="Method for differential expression.")
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@click.option(
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"--layout", "-l", type=click.Choice(["umap", "tsne"]), default="umap", show_default=True, help="Method for layout."
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)
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@click.option(
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"--diffexp",
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"-d",
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type=click.Choice(["ttest"]),
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default="ttest",
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show_default=True,
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help="Method for differential expression.",
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)
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@click.option("--title", "-t", help="Title to display (if omitted will use file name).", metavar="")
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@click.option("--verbose", "-v", is_flag=True, default=False, show_default=True,
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help="Provide verbose output, including warnings and all server requests.")
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@click.option("--debug", "-d", is_flag=True, default=False, show_default=True,
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help="Run in debug mode.")
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@click.option("--open", "-o", "open_browser", is_flag=True, default=False, show_default=True,
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help="Open the web browser after launch.")
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@click.option(
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"--verbose",
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"-v",
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is_flag=True,
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default=False,
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show_default=True,
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help="Provide verbose output, including warnings and all server requests.",
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)
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@click.option("--debug", "-d", is_flag=True, default=False, show_default=True, help="Run in debug mode.")
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@click.option(
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"--open",
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"-o",
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"open_browser",
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is_flag=True,
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default=False,
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show_default=True,
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help="Open the web browser after launch.",
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)
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@click.option("--port", "-p", help="Port to run server on.", metavar="", default=5005, show_default=True)
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@click.option("--obs-names", default=None, metavar="", help="Name of annotation field to use for observations.")
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@click.option("--var-names", default=None, metavar="", help="Name of annotation to use for variables.")
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@click.option("--host", default="127.0.0.1", help="Host IP address")
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@click.option("--max-category-items", default=100, metavar="", show_default=True,
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help="Limits the number of categorical annotation items displayed.")
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@click.option("--diffexp-lfc-cutoff", default=0.01, show_default=True,
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help="Relative expression cutoff used when selecting top N differentially expressed genes")
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@click.option("--nan-to-num", is_flag=True, default=False, show_default=True,
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help="Replace all floating point NaN with zero, and infinities with finite numbers")
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def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
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open_browser, port, host, max_category_items, diffexp_lfc_cutoff,
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nan_to_num):
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@click.option(
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"--max-category-items",
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default=100,
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metavar="",
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show_default=True,
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help="Limits the number of categorical annotation items displayed.",
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)
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@click.option(
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"--diffexp-lfc-cutoff",
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default=0.01,
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show_default=True,
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help="Relative expression cutoff used when selecting top N differentially expressed genes",
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)
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@click.option(
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"--nan-to-num",
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is_flag=True,
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default=False,
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show_default=True,
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help="Replace all floating point NaN with zero, and infinities with finite numbers",
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)
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def launch(
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data,
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layout,
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diffexp,
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title,
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verbose,
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debug,
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obs_names,
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var_names,
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open_browser,
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port,
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host,
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max_category_items,
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diffexp_lfc_cutoff,
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nan_to_num,
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):
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"""Launch the cellxgene data viewer.
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This web app lets you explore single-cell expression data.
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Data must be in a format that cellxgene expects, read the
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@@ -76,10 +122,7 @@ def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
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# Import Flask app
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from server.app.app import app
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app.config.update(
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DATASET_TITLE=title,
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CXG_API_BASE=api_base
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)
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app.config.update(DATASET_TITLE=title, CXG_API_BASE=api_base)
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if not verbose:
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log = logging.getLogger("werkzeug")
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@@ -90,7 +133,8 @@ def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
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# Fix for anaconda python. matplotlib typically expects python to be installed as a framework TKAgg is usually
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# available and fixes this issue. See https://matplotlib.org/faq/virtualenv_faq.html
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import matplotlib as mpl
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mpl.use('TkAgg')
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mpl.use("TkAgg")
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from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
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args = {
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@@ -100,7 +144,7 @@ def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
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"diffexp_lfc_cutoff": diffexp_lfc_cutoff,
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"obs_names": obs_names,
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"var_names": var_names,
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"nan_to_num": nan_to_num
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"nan_to_num": nan_to_num,
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}
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try:
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@@ -117,7 +161,7 @@ def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
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click.echo("[cellxgene] Type CTRL-C at any time to exit.")
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if not verbose:
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f = open(devnull, 'w')
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f = open(devnull, "w")
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sys.stdout = f
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app.run(host=host, debug=debug, port=port, threaded=True)
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+48
-17
@@ -7,22 +7,48 @@ from scipy.sparse.csc import csc_matrix
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@click.command()
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@click.argument("data", nargs=1, metavar="<dataset: file or path to data>", required=True)
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@click.option("--layout", "-l", default=["umap", "tsne"], multiple=True, type=click.Choice(["umap", "tsne"]),
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help="Layout algorithm", show_default=True)
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@click.option("--recipe", "-r", default="none", type=click.Choice(["none", "seurat", "zheng17"]),
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help="Preprocessing to run.", show_default=True)
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@click.option(
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"--layout",
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"-l",
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default=["umap", "tsne"],
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multiple=True,
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type=click.Choice(["umap", "tsne"]),
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help="Layout algorithm",
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show_default=True,
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)
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@click.option(
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"--recipe",
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"-r",
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default="none",
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type=click.Choice(["none", "seurat", "zheng17"]),
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help="Preprocessing to run.",
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show_default=True,
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)
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@click.option("--output", "-o", default="", help="Save a new file to filename.", metavar="<filename>")
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@click.option("--plotting", "-p", default=False, is_flag=True, help="Whether to generate plots.", show_default=True)
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@click.option("--sparse", default=False, is_flag=True, help="Whether to force sparsity.", show_default=True)
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@click.option("--overwrite", default=False, is_flag=True, help="Allow file overwriting.", show_default=True)
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@click.option("--set-obs-names", default="", help="Named field to set as index for obs.", metavar="<name>")
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@click.option("--set-var-names", default="", help="Named field to set as index for var.", metavar="<name>")
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@click.option("--make-obs-names-unique", default=True, is_flag=True,
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help="Ensure obs index is unique.", show_default=True)
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@click.option("--make-var-names-unique", default=True, is_flag=True,
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help="Ensure var index is unique.", show_default=True)
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def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
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set_obs_names, set_var_names, make_obs_names_unique, make_var_names_unique):
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@click.option(
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"--make-obs-names-unique", default=True, is_flag=True, help="Ensure obs index is unique.", show_default=True
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)
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@click.option(
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"--make-var-names-unique", default=True, is_flag=True, help="Ensure var index is unique.", show_default=True
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)
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def prepare(
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data,
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layout,
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recipe,
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output,
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plotting,
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sparse,
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overwrite,
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set_obs_names,
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set_var_names,
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make_obs_names_unique,
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make_var_names_unique,
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):
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"""Preprocesses data for use with cellxgene.
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This tool runs a series of scanpy routines for preparing a dataset
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@@ -35,6 +61,7 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
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# collect slow imports here to make CLI startup more responsive
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click.echo("[cellxgene] Starting CLI...")
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import matplotlib
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matplotlib.use("Agg")
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import scanpy.api as sc
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@@ -49,8 +76,10 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
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output = expanduser(output)
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if not output:
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click.echo("Warning: No file will be saved, to save the results of cellxgene prepare include "
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"--output <filename> to save output to a new file")
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click.echo(
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"Warning: No file will be saved, to save the results of cellxgene prepare include "
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"--output <filename> to save output to a new file"
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)
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if isfile(output) and not overwrite:
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raise click.UsageError(f"Cannot overwrite existing file {output}, try using the flag --overwrite")
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@@ -119,9 +148,11 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
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try:
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sc.tl.louvain(adata)
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except ModuleNotFoundError:
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click.echo("\nWarning: louvain module is not installed, no clusters will be calculated. "
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"To fix this please install cellxgene with the optional feature louvain enabled: "
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"`pip install cellxgene[louvain]`")
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click.echo(
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"\nWarning: louvain module is not installed, no clusters will be calculated. "
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"To fix this please install cellxgene with the optional feature louvain enabled: "
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"`pip install cellxgene[louvain]`"
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)
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def run_layout(adata):
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if len(unique(adata.obs["louvain"].values)) < 10:
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@@ -142,11 +173,11 @@ def prepare(data, layout, recipe, output, plotting, sparse, overwrite,
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def show_step(item):
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names = {
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"make_sparse": "Ensuring sparsity",
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"run_recipe": f"Running preprocessing recipe \"{recipe}\"",
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"run_recipe": f'Running preprocessing recipe "{recipe}"',
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"run_pca": "Running PCA",
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"run_neighbors": "Calculating neighbors",
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"run_louvain": "Calculating clusters",
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"run_layout": "Computing layout"
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"run_layout": "Computing layout",
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}
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if item is not None:
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return names[item.__name__]
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