Improve CLI help (#1025)

* launch option changes

* more CLI help improvements

* change plot help

* additional changes requested

* change metavars for options and subcommand

server/cli/cli.py

@@ -4,8 +4,17 @@ from .launch import launch
 from .prepare import prepare
 
 
-@click.group(name="cellxgene", context_settings=dict(max_content_width=85))
+@click.group(name="cellxgene",
-@click.version_option(version="0.12.0", prog_name="cellxgene", message="[%(prog)s] Version %(version)s")
+             subcommand_metavar="COMMAND <args>",
+             options_metavar="<options>",
+             context_settings=dict(max_content_width=85,
+                                   help_option_names=['-h', '--help']))
+@click.help_option("--help", "-h", help="Show this message and exit.")
+@click.version_option(
+    version="0.12.0",
+    prog_name="cellxgene",
+    message="[%(prog)s] Version %(version)s",
+    help="Show the software version and exit.")
 def cli():
     pass
 

server/cli/launch.py

@@ -13,7 +13,7 @@ import click
 from server.app.app import Server
 from server.app.util.errors import ScanpyFileError
 from server.app.util.utils import custom_format_warning
-from server.utils.utils import find_available_port, is_port_available
+from server.utils.utils import find_available_port, is_port_available, sort_options
 from server.app.util.data_locator import DataLocator
 
 # anything bigger than this will generate a special message
@@ -25,55 +25,70 @@ def common_args(func):
     Decorator to contain CLI args that will be common to both CLI and GUI: title and engine args.
     """
 
-    @click.option("--title", "-t", help="Title to display (if omitted will use file name).")
+    @click.option(
-    @click.option("--about",
+        "--title",
-                  help="A URL to more information about the dataset."
+        "-t",
-                       "(This must be an absolute URL including HTTP(S) protocol)")
+        metavar="<text>",
+        help="Title to display. If omitted will use file name.")
+    @click.option(
+        "--about",
+        metavar="<URL>",
+        help="URL providing more information about the dataset "
+             "(hint: must be a fully specified absolute URL).")
     @click.option(
         "--embedding",
         "-e",
         default=[],
         multiple=True,
         show_default=False,
+        metavar="<text>",
         help="Embedding name, eg, 'umap'. Repeat option for multiple embeddings. Defaults to all."
     )
-    @click.option("--obs-names", default=None, metavar="", help="Name of annotation field to use for observations.")
+    @click.option(
-    @click.option("--var-names", default=None, metavar="", help="Name of annotation to use for variables.")
+        "--obs-names",
+        "-obs",
+        default=None,
+        metavar="<text>",
+        help="Name of annotation field to use for observations. If not specified cellxgene will use the the obs index.")
+    @click.option(
+        "--var-names",
+        "-var",
+        default=None,
+        metavar="<text>",
+        help="Name of annotation to use for variables. If not specified cellxgene will use the the var index.")
     @click.option(
         "--max-category-items",
         default=1000,
-        metavar="",
+        metavar="<integer>",
         show_default=True,
-        help="Categories with more distinct values than this will not be displayed.",
+        help="Will not display categories with more distinct values than specified.",)
-    )
     @click.option(
         "--diffexp-lfc-cutoff",
+        "-de",
         default=0.01,
         show_default=True,
-        help="Relative expression cutoff used when selecting top N differentially expressed genes",
+        metavar="<float>",
-    )
+        help="Minimum log fold change threshold for differential expression.",)
     @click.option(
         "--experimental-label-file",
         default=None,
         show_default=True,
         multiple=False,
-        metavar="<user labels CSV file>",
+        metavar="<path>",
-        help="CSV file containing user annotations; will be overwritten.  Created if does not exist.",
+        help="CSV file containing user annotations; will be overwritten.  Created if does not exist.",)
-    )
     @click.option(
         "--backed",
+        "-b",
         is_flag=True,
         default=False,
         show_default=False,
-        help="Load data in file-backed mode, which may save memory, but result in slower overall performance."
+        help="Load data in file-backed mode. This may save memory, but may result in slower overall performance.")
-    )
     @click.option(
         "--disable-diffexp",
         is_flag=True,
         default=False,
         show_default=False,
-        help="Disable on-demand differential expression."
+        help="Disable on-demand differential expression.")
-    )
     @functools.wraps(func)
     def wrapper(*args, **kwargs):
         return func(*args, **kwargs)
@@ -96,17 +111,26 @@ def parse_engine_args(embedding, obs_names, var_names, max_category_items,
     }
 
 
-@click.command()
+@sort_options
-@click.argument("data", nargs=1, metavar="<data file>", required=True)
+@click.command(short_help="Launch the cellxgene data viewer. "
+                          "Run `cellxgene launch --help` for more information.",
+               options_metavar="<options>",)
+@click.argument("data", nargs=1, metavar="<path to data file>", required=True)
 @click.option(
     "--verbose",
     "-v",
     is_flag=True,
     default=False,
     show_default=True,
-    help="Provide verbose output, including warnings and all server requests.",
+    help="Provide verbose output, including warnings and all server requests.",)
-)
+@click.option(
-@click.option("--debug", is_flag=True, default=False, show_default=True, help="Run in debug mode.")
+    "--debug",
+    "-d",
+    is_flag=True,
+    default=False,
+    show_default=True,
+    help="Run in debug mode. This is helpful for cellxgene developers, "
+         "or when you want more information about an error condition.",)
 @click.option(
     "--open",
     "-o",
@@ -114,18 +138,29 @@ def parse_engine_args(embedding, obs_names, var_names, max_category_items,
     is_flag=True,
     default=False,
     show_default=True,
-    help="Open the web browser after launch.",
+    help="Open web browser after launch.",)
-)
+@click.option(
-@click.option("--port", "-p", help="Port to run server on, if not specified cellxgene will find an available port.",
+    "--port",
-              metavar="", show_default=True)
+    "-p",
-@click.option("--host", default="127.0.0.1", help="Host IP address")
+    metavar="<port>",
+    show_default=True,
+    help="Port to run server on. If not specified cellxgene will find an available port.",)
+@click.option(
+    "--host",
+    metavar="<IP address>",
+    default="127.0.0.1",
+    show_default=False,
+    help="Host IP address. By default cellxgene will use localhost (e.g. 127.0.0.1).")
 @click.option(
     "--scripts",
+    "-s",
     default=[],
     multiple=True,
-    help="Additional script files to include in html page",
+    metavar="<text>",
-    show_default=True,
+    help="Additional script files to include in HTML page. If not specified, "
-)
+         "no additional script files will be included.",
+    show_default=False,)
+@click.help_option("--help", "-h", help="Show this message and exit.")
 @common_args
 def launch(
         data,
@@ -148,8 +183,9 @@ def launch(
 ):
     """Launch the cellxgene data viewer.
     This web app lets you explore single-cell expression data.
-    Data must be in a format that cellxgene expects, read the
+    Data must be in a format that cellxgene expects.
-    "getting started" guide.
+    Read the "getting started" guide to learn more:
+    https://chanzuckerberg.github.io/cellxgene/getting-started.html
 
     Examples:
 

server/cli/prepare.py

@@ -4,16 +4,21 @@ import click
 from numpy import ndarray, unique
 from scipy.sparse.csc import csc_matrix
 
+from server.utils.utils import sort_options
 
-@click.command()
+
-@click.argument("data", nargs=1, metavar="<dataset: file or path to data>", required=True)
+@sort_options
+@click.command(short_help="Preprocess data for use with cellxgene. "
+                          "Run `cellxgene prepare --help` for more information.",
+               options_metavar="<options>",)
+@click.argument("data", nargs=1, metavar="<path to data file>", required=True)
 @click.option(
     "--embedding",
     "-e",
     default=["umap", "tsne"],
     multiple=True,
     type=click.Choice(["umap", "tsne"]),
-    help="Embedding algorithm",
+    help="Embedding algorithm(s). Repeat option for multiple embeddings.",
     show_default=True,
 )
 @click.option(
@@ -25,21 +30,29 @@ from scipy.sparse.csc import csc_matrix
     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("--plotting", "-p", default=False, is_flag=True, help="Generate plots.", show_default=True)
-@click.option("--sparse", default=False, is_flag=True, help="Whether to force sparsity.", show_default=True)
+@click.option("--sparse", default=False, is_flag=True, help="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("--skip-qc", default=False, is_flag=True,
+              help="Do not run quality control metrics. By default cellxgene runs them "
+                   "(saved to adata.obs and adata.var; see scanpy.pp.calculate_qc_metrics for details).")
 @click.option(
-    "--run-qc/--skip-qc", default=True, is_flag=True,
+    "--make-obs-names-unique",
-    help="Whether to calculate QC metrics (saved to adata.obs and adata.var). \
+    default=True,
-    See scanpy.pp.calculate_qc_metrics for details.", show_default=True)
+    is_flag=True,
-@click.option(
+    help="Ensure obs index is unique.",
-    "--make-obs-names-unique", default=True, is_flag=True, help="Ensure obs index is unique.", show_default=True
+    show_default=True
 )
 @click.option(
-    "--make-var-names-unique", default=True, is_flag=True, help="Ensure var index is unique.", show_default=True
+    "--make-var-names-unique",
+    default=True,
+    is_flag=True,
+    help="Ensure var index is unique.",
+    show_default=True
 )
+@click.help_option("--help", "-h", help="Show this message and exit.")
 def prepare(
         data,
         embedding,
@@ -50,18 +63,18 @@ def prepare(
         overwrite,
         set_obs_names,
         set_var_names,
-        run_qc,
+        skip_qc,
         make_obs_names_unique,
         make_var_names_unique,
 ):
-    """Preprocesses data for use with cellxgene.
+    """
-
+    Preprocess data for use with cellxgene.
-    This tool runs a series of scanpy routines for preparing a dataset
+    This tool runs a series of scanpy routines for preparing a dataset for use
-    for use with cellxgene. It loads data from different formats
+    with cellxgene. It loads data from different formats
     (h5ad, loom, or a 10x directory), runs dimensionality reduction,
     computes nearest neighbors, computes an embedding, performs clustering,
-    and saves the results. Includes additional options for naming
+    and saves the results. Includes additional options for naming annotations,
-    annotations, ensuring sparsity, and plotting results."""
+    ensuring sparsity, and plotting results."""
 
     # collect slow imports here to make CLI startup more responsive
     click.echo("[cellxgene] Starting CLI...")
@@ -129,7 +142,7 @@ def prepare(
         return adata
 
     def calculate_qc_metrics(adata):
-        if run_qc:
+        if not skip_qc:
             sc.pp.calculate_qc_metrics(adata, inplace=True)
         return adata
 
@@ -179,7 +192,7 @@ def prepare(
                 sc.pl.tsne(adata, color="louvain", palette=palette, save="_louvain")
 
     def show_step(item):
-        if run_qc:
+        if not skip_qc:
             qc_name = "Calculating QC metrics"
         else:
             qc_name = "Skipping QC"

server/utils/utils.py

@@ -24,3 +24,12 @@ def is_port_available(host, port):
         except socket.error:
             pass
     return is_available
+
+
+def sort_options(command):
+    """
+    Helper for the click options - will sort options in a command, and can
+    be used as a decorator.
+    """
+    command.params.sort(key=lambda p: p.name)
+    return command