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Improve CLI help (#1025)
* launch option changes * more CLI help improvements * change plot help * additional changes requested * change metavars for options and subcommand
This commit is contained in:
Bruce Martin
+70
-34
@@ -13,7 +13,7 @@ import click
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from server.app.app import Server
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from server.app.util.errors import ScanpyFileError
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from server.app.util.utils import custom_format_warning
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from server.utils.utils import find_available_port, is_port_available
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from server.utils.utils import find_available_port, is_port_available, sort_options
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from server.app.util.data_locator import DataLocator
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# anything bigger than this will generate a special message
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@@ -25,55 +25,70 @@ def common_args(func):
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Decorator to contain CLI args that will be common to both CLI and GUI: title and engine args.
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"""
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@click.option("--title", "-t", help="Title to display (if omitted will use file name).")
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@click.option("--about",
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help="A URL to more information about the dataset."
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"(This must be an absolute URL including HTTP(S) protocol)")
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@click.option(
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"--title",
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"-t",
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metavar="<text>",
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help="Title to display. If omitted will use file name.")
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@click.option(
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"--about",
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metavar="<URL>",
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help="URL providing more information about the dataset "
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"(hint: must be a fully specified absolute URL).")
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@click.option(
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"--embedding",
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"-e",
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default=[],
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multiple=True,
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show_default=False,
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metavar="<text>",
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help="Embedding name, eg, 'umap'. Repeat option for multiple embeddings. Defaults to all."
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)
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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(
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"--obs-names",
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"-obs",
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default=None,
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metavar="<text>",
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help="Name of annotation field to use for observations. If not specified cellxgene will use the the obs index.")
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@click.option(
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"--var-names",
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"-var",
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default=None,
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metavar="<text>",
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help="Name of annotation to use for variables. If not specified cellxgene will use the the var index.")
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@click.option(
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"--max-category-items",
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default=1000,
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metavar="",
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metavar="<integer>",
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show_default=True,
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help="Categories with more distinct values than this will not be displayed.",
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)
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help="Will not display categories with more distinct values than specified.",)
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@click.option(
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"--diffexp-lfc-cutoff",
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"-de",
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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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metavar="<float>",
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help="Minimum log fold change threshold for differential expression.",)
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@click.option(
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"--experimental-label-file",
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default=None,
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show_default=True,
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multiple=False,
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metavar="<user labels CSV file>",
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help="CSV file containing user annotations; will be overwritten. Created if does not exist.",
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)
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metavar="<path>",
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help="CSV file containing user annotations; will be overwritten. Created if does not exist.",)
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@click.option(
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"--backed",
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"-b",
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is_flag=True,
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default=False,
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show_default=False,
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help="Load data in file-backed mode, which may save memory, but result in slower overall performance."
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)
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help="Load data in file-backed mode. This may save memory, but may result in slower overall performance.")
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@click.option(
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"--disable-diffexp",
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is_flag=True,
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default=False,
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show_default=False,
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help="Disable on-demand differential expression."
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)
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help="Disable on-demand differential expression.")
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@functools.wraps(func)
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def wrapper(*args, **kwargs):
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return func(*args, **kwargs)
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@@ -96,17 +111,26 @@ def parse_engine_args(embedding, obs_names, var_names, max_category_items,
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}
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@click.command()
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@click.argument("data", nargs=1, metavar="<data file>", required=True)
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@sort_options
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@click.command(short_help="Launch the cellxgene data viewer. "
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"Run `cellxgene launch --help` for more information.",
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options_metavar="<options>",)
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@click.argument("data", nargs=1, metavar="<path to data file>", required=True)
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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", is_flag=True, default=False, show_default=True, help="Run in debug mode.")
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help="Provide verbose output, including warnings and all server requests.",)
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@click.option(
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"--debug",
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"-d",
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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="Run in debug mode. This is helpful for cellxgene developers, "
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"or when you want more information about an error condition.",)
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@click.option(
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"--open",
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"-o",
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@@ -114,18 +138,29 @@ def parse_engine_args(embedding, obs_names, var_names, max_category_items,
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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, if not specified cellxgene will find an available port.",
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metavar="", show_default=True)
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@click.option("--host", default="127.0.0.1", help="Host IP address")
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help="Open web browser after launch.",)
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@click.option(
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"--port",
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"-p",
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metavar="<port>",
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show_default=True,
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help="Port to run server on. If not specified cellxgene will find an available port.",)
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@click.option(
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"--host",
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metavar="<IP address>",
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default="127.0.0.1",
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show_default=False,
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help="Host IP address. By default cellxgene will use localhost (e.g. 127.0.0.1).")
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@click.option(
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"--scripts",
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"-s",
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default=[],
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multiple=True,
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help="Additional script files to include in html page",
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show_default=True,
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)
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metavar="<text>",
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help="Additional script files to include in HTML page. If not specified, "
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"no additional script files will be included.",
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show_default=False,)
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@click.help_option("--help", "-h", help="Show this message and exit.")
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@common_args
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def launch(
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data,
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@@ -148,8 +183,9 @@ def launch(
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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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"getting started" guide.
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Data must be in a format that cellxgene expects.
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Read the "getting started" guide to learn more:
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https://chanzuckerberg.github.io/cellxgene/getting-started.html
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Examples:
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