Update module docstring usage

augur/align.py

@@ -36,8 +36,8 @@ def register_arguments(parser):
     parser.add_argument('--debug', action="store_true", default=False, help="Produce extra files (e.g. pre- and post-aligner files) which can help with debugging poor alignments.")
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("align", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("align", **kwargs)
     register_arguments(parser)
     return parser
 

augur/ancestral.py

@@ -117,8 +117,8 @@ def collect_mutations_and_sequences(tt, infer_tips=False, full_sequences=False,
     return {"nodes": data, "mask": mask}
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("ancestral", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("ancestral", **kwargs)
     parser.add_argument('--tree', '-t', required=True, help="prebuilt Newick")
     parser.add_argument('--alignment', '-a', help="alignment in fasta or VCF format")
     parser.add_argument('--output-node-data', type=str, help='name of JSON file to save mutations and ancestral sequences to')

augur/argparse_.py

@@ -3,6 +3,8 @@
 """
 from argparse import Action, ArgumentDefaultsHelpFormatter
 
+from augur.utils import first_line
+
 
 def add_default_command(parser):
     """
@@ -37,7 +39,7 @@ def add_command_subparsers(subparsers, commands, command_attribute='__command__'
     """
     for command in commands:
         # Allow each command to register its own subparser
-        subparser = command.register_parser(subparsers)
+        subparser = command.register_parser(subparsers, help=first_line(command.__doc__))
 
         # Add default attribute for command module
         if command_attribute:
@@ -48,7 +50,7 @@ def add_command_subparsers(subparsers, commands, command_attribute='__command__'
         subparser.formatter_class = ArgumentDefaultsHelpFormatter
 
         if not subparser.description and command.__doc__:
-            subparser.description = command.__doc__
+            subparser.description = first_line(command.__doc__)
 
         # If a command doesn't have its own run() function, then print its help when called.
         if not getattr(command, "run", None):

augur/clades.py

@@ -248,8 +248,8 @@ def get_reference_sequence_from_root_node(all_muts, root_name):
     return ref
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("clades", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("clades", **kwargs)
     parser.add_argument('--tree', help="prebuilt Newick -- no tree will be built if provided")
     parser.add_argument('--mutations', nargs='+', help='JSON(s) containing ancestral and tip nucleotide and/or amino-acid mutations ')
     parser.add_argument('--reference', nargs='+', help='fasta files containing reference and tip nucleotide and/or amino-acid sequences ')

augur/curate/__init__.py

@@ -89,9 +89,9 @@ def create_shared_parser():
     return shared_parser
 
 
-def register_parser(parent_subparsers):
+def register_parser(parent_subparsers, **kwargs):
     shared_parser = create_shared_parser()
-    parser = parent_subparsers.add_parser("curate", help=__doc__)
+    parser = parent_subparsers.add_parser("curate", **kwargs)
 
     # Add print_help so we can run it when no subcommands are called
     parser.set_defaults(print_help = parser.print_help)

augur/curate/normalize_strings.py

@@ -6,13 +6,11 @@
 """
 import unicodedata
 
-from augur.utils import first_line
 
-
-def register_parser(parent_subparsers):
+def register_parser(parent_subparsers, **kwargs):
     parser = parent_subparsers.add_parser("normalize-strings",
         parents=[parent_subparsers.shared_parser],
-        help=first_line(__doc__))
+        **kwargs)
 
     optional = parser.add_argument_group(title="OPTIONAL")
     optional.add_argument("--form", default="NFC", choices=["NFC", "NFKC", "NFD", "NFKD"],

augur/curate/passthru.py

@@ -4,10 +4,10 @@
 """
 
 
-def register_parser(parent_subparsers):
+def register_parser(parent_subparsers, **kwargs):
     return parent_subparsers.add_parser("passthru",
         parents=[parent_subparsers.shared_parser],
-        help=__doc__)
+        **kwargs)
 
 
 def run(args, records):

augur/distance.py

@@ -159,7 +159,7 @@
 
 from .frequency_estimators import timestamp_to_float
 from .reconstruct_sequences import load_alignments
-from .utils import annotate_parents_for_tree, first_line, read_node_data, write_json
+from .utils import annotate_parents_for_tree, read_node_data, write_json
 
 
 def read_distance_map(map_file):
@@ -626,8 +626,8 @@ def get_distances_to_all_pairs(tree, sequences_by_node_and_gene, distance_map, e
     return distances_by_node
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("distance", help=first_line(__doc__))
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("distance", **kwargs)
     parser.add_argument("--tree", help="Newick tree", required=True)
     parser.add_argument("--alignment", nargs="+", help="sequence(s) to be used, supplied as FASTA files", required=True)
     parser.add_argument('--gene-names', nargs="+", type=str, help="names of the sequences in the alignment, same order assumed", required=True)

augur/export.py

@@ -10,8 +10,8 @@
 ]
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("export", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("export", **kwargs)
     # Add subparsers for subcommands
     metavar_msg ="Augur export now needs you to define the JSON version " + \
                  "you want, e.g. `augur export v2`."

augur/export_v1.py

@@ -331,8 +331,8 @@ def add_option_args(parser):
     return options
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("v1", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("v1", **kwargs)
     add_core_args(parser)
     add_option_args(parser)
     parser.add_argument("--v1", help=SUPPRESS, default=True)

augur/export_v2.py

@@ -820,8 +820,8 @@ def node_data_prop_is_normal_trait(name):
     return True
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("v2", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("v2", **kwargs)
 
     required = parser.add_argument_group(
         title="REQUIRED"

augur/filter/__init__.py

@@ -72,8 +72,8 @@ def register_arguments(parser):
     parser.set_defaults(probabilistic_sampling=True)
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("filter", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("filter", **kwargs)
     register_arguments(parser)
     return parser
 

augur/frequencies.py

@@ -14,8 +14,8 @@
 from .utils import read_node_data, write_json
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("frequencies", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("frequencies", **kwargs)
     # Shared arguments
     parser.add_argument('--method', choices=["diffusion", "kde"], required=True,
                         help="method by which frequencies should be estimated")

augur/import_/__init__.py

@@ -2,15 +2,14 @@
 Import analyses into augur pipeline from other systems
 """
 from augur.argparse_ import add_command_subparsers
-from augur.utils import first_line
 from . import beast
 
 SUBCOMMANDS = [
     beast,
 ]
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("import", help=first_line(__doc__))
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("import", **kwargs)
     metavar_msg = "Import analyses into augur pipeline from other systems"
     subparsers = parser.add_subparsers(title="TYPE",
                                        metavar=metavar_msg)

augur/import_/beast.py

@@ -1,4 +1,5 @@
-"""
+"""Import BEAST analysis.
+
 Parse a BEAST MCC tree for further analysis in augur or
 export for auspice v2+ (using `augur export v2` or greater).
 """
@@ -13,11 +14,11 @@
 from treetime import TreeAnc
 from augur.utils import write_json
 
-def register_parser(parent_subparsers):
+def register_parser(parent_subparsers, **kwargs):
     """
     Arguments available to `augur import beast`
     """
-    beast_parser = parent_subparsers.add_parser('beast', help="Import beast analysis")
+    beast_parser = parent_subparsers.add_parser('beast', **kwargs)
     beast_parser.add_argument("--beast", help=SUPPRESS, default=True) # used to disambiguate subcommands
     beast_parser.add_argument('--mcc', required=True, help="BEAST MCC tree")
     beast_parser.add_argument('--most-recent-tip-date', default=0, type=float, help='Numeric date of most recent tip in tree (--tip-date-regex, --tip-date-format and --tip-date-delimeter are ignored if this is set)')

augur/index.py

@@ -12,8 +12,8 @@
 from .io.sequences import read_sequences
 from .io.vcf import is_vcf, read_vcf
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("index", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("index", **kwargs)
     parser.add_argument('--sequences', '-s', required=True, help="sequences in FASTA or VCF formats. Augur will summarize the content of FASTA sequences and only report the names of strains found in a given VCF.")
     parser.add_argument('--output', '-o', help="tab-delimited file containing the number of bases per sequence in the given file. Output columns include strain, length, and counts for A, C, G, T, N, other valid IUPAC characters, ambiguous characters ('?' and '-'), and other invalid characters.", required=True)
     parser.add_argument('--verbose', '-v', action="store_true", help="print index statistics to stdout")

augur/lbi.py

@@ -79,8 +79,8 @@ def calculate_LBI(tree, attr="lbi", tau=0.4, transform=lambda x:x, normalize=Tru
         setattr(node, attr, node.attr[attr])
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("lbi", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("lbi", **kwargs)
     parser.add_argument("--tree", help="Newick tree", required=True)
     parser.add_argument("--branch-lengths", help="JSON with branch lengths and internal node dates estimated by TreeTime", required=True)
     parser.add_argument("--output", help="JSON file with calculated distances stored by node name and attribute name", required=True)

augur/mask.py

@@ -184,8 +184,8 @@ def register_arguments(parser):
     parser.add_argument('--no-cleanup', dest="cleanup", action="store_false",
                         help="Leave intermediate files around. May be useful for debugging")
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("mask", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("mask", **kwargs)
     register_arguments(parser)
     return parser
 

augur/measurements/__init__.py

@@ -2,7 +2,6 @@
 Create JSON files suitable for visualization within the measurements panel of Auspice.
 """
 from augur.argparse_ import add_command_subparsers
-from augur.utils import first_line
 from . import export, concat
 
 SUBCOMMANDS = [
@@ -11,8 +10,8 @@
 ]
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("measurements", help=first_line(__doc__))
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("measurements", **kwargs)
     # Add subparsers for subcommands
     subparsers = parser.add_subparsers(dest='subcommand')
     add_command_subparsers(subparsers, SUBCOMMANDS)

augur/measurements/concat.py

@@ -3,15 +3,15 @@
 """
 import sys
 
-from augur.utils import first_line, write_json
+from augur.utils import write_json
 from augur.validate import (
     measurements as read_measurements_json,
     ValidateError
 )
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("concat", help=first_line(__doc__))
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("concat", **kwargs)
 
     required = parser.add_argument_group(
         title="REQUIRED"

augur/measurements/export.py

@@ -6,7 +6,7 @@
 import sys
 
 from augur.argparse_ import HideAsFalseAction
-from augur.utils import first_line, write_json
+from augur.utils import write_json
 from augur.validate import (
     measurements as read_measurements_json,
     measurements_collection_config as read_collection_config_json,
@@ -22,8 +22,8 @@
 }
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("export", help=first_line(__doc__))
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("export", **kwargs)
 
     required = parser.add_argument_group(
         title="REQUIRED"

augur/parse.py

@@ -138,8 +138,8 @@ def parse_sequence(sequence, fields, strain_key="strain", separator="|", prettif
     return sequence, metadata
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("parse", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("parse", **kwargs)
     parser.add_argument('--sequences', '-s', required=True, help="sequences in fasta or VCF format")
     parser.add_argument('--output-sequences', help="output sequences file")
     parser.add_argument('--output-metadata', help="output metadata file")

augur/reconstruct_sequences.py

@@ -11,8 +11,8 @@
 
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("reconstruct-sequences", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("reconstruct-sequences", **kwargs)
     parser.add_argument('--tree', required=True, help="tree as Newick file")
     parser.add_argument('--gene', type=str, help="gene to translate (list or file containing list)")
     parser.add_argument('--mutations', required=True, type=str, help="json file containing mutations "

augur/refine.py

@@ -93,8 +93,8 @@ def collect_node_data(T, attributes):
     return data
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("refine", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("refine", **kwargs)
     parser.add_argument('--alignment', '-a', help="alignment in fasta or VCF format")
     parser.add_argument('--tree', '-t', required=True, help="prebuilt Newick")
     parser.add_argument('--metadata', type=str, metavar="FILE", help="sequence metadata, as CSV or TSV")

augur/sequence_traits.py

@@ -290,8 +290,8 @@ def attach_features(annotations, label, count):
     return seq_feature_dict
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("sequence-traits", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("sequence-traits", **kwargs)
     parser.add_argument('--ancestral-sequences', type=str, help="nucleotide alignment (VCF) to search for sequence traits in (can be generated from 'ancestral' using '--output-vcf')")
     parser.add_argument('--translations', type=str, help="AA alignment to search for sequence traits in (can include ancestral sequences)")
     parser.add_argument('--vcf-reference', type=str, help='fasta file of the sequence the nucleotide VCF was mapped to')

augur/titers.py

@@ -13,8 +13,8 @@
 from .argparse_ import add_default_command
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("titers", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("titers", **kwargs)
     subparsers = parser.add_subparsers()
     add_default_command(parser)
 

augur/traits.py

@@ -97,15 +97,15 @@ def mugration_inference(tree=None, seq_meta=None, field='country', confidence=Tr
     return tt.tree, tt.gtr, letter_to_state
 
 
-def register_parser(parent_subparsers):
+def register_parser(parent_subparsers, **kwargs):
     """Add subcommand specific arguments
 
     Parameters
     ----------
     parser : argparse
         subcommand argument parser
     """
-    parser = parent_subparsers.add_parser("traits", help=__doc__)
+    parser = parent_subparsers.add_parser("traits", **kwargs)
     parser.add_argument('--tree', '-t', required=True, help="tree to perform trait reconstruction on")
     parser.add_argument('--metadata', required=True, metavar="FILE", help="table with metadata, as CSV or TSV")
     parser.add_argument('--weights', required=False, help="tsv/csv table with equilibrium probabilities of discrete states")

augur/translate.py

@@ -302,8 +302,8 @@ def get_genes_from_file(fname):
     return unique_genes
 
 
-def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("translate", help=__doc__)
+def register_parser(parent_subparsers, **kwargs):
+    parser = parent_subparsers.add_parser("translate", **kwargs)
     parser.add_argument('--tree', help="prebuilt Newick -- no tree will be built if provided")
     parser.add_argument('--ancestral-sequences', type=str, help='JSON (fasta input) or VCF (VCF input) containing ancestral and tip sequences')
     parser.add_argument('--reference-sequence', required=True,