export: Allow --node-data to be repeated to build up a file list

…instead of each repetition overriding the last values.  While there is
some theoretical utility in being able to override one list of node data
files with another in a subsequent option, I think it's more likely that
repetition is intended to built up a single list.  I was surprised, at
least.

See also <https://discussion.nextstrain.org/t/1194/4>.

augur/argparse_.py

@@ -57,3 +57,22 @@ class HideAsFalseAction(Action):
     """
     def __call__(self, parser, namespace, values, option_string=None):
         setattr(namespace, self.dest, option_string[2:6] != 'hide')
+
+
+# XXX TODO: Drop this when we drop support for 3.7 and use builtin "extend"
+# action.
+class ExtendAction(Action):
+    """
+    Loosely backported version of builtin "extend" action
+    (argparse._ExtendAction) in CPython v3.10.5-172-gf118661a18.  Some of the
+    ceremony we don't need has been ditched.
+
+    >>> import argparse
+    >>> p = argparse.ArgumentParser()
+    >>> a = p.add_argument("-x", action=ExtendAction, nargs="+")
+    >>> p.parse_args(["-x", "a", "b", "-x", "c", "-x", "d"]).x
+    ['a', 'b', 'c', 'd']
+    """
+    def __call__(self, parser, namespace, values, option_string=None):
+        current = getattr(namespace, self.dest, None) or []
+        setattr(namespace, self.dest, [*current, *values])

augur/export_v1.py

@@ -9,6 +9,7 @@
 from Bio import Phylo
 from argparse import SUPPRESS
 from collections import defaultdict
+from .argparse_ import ExtendAction
 from .io import read_metadata
 from .utils import read_node_data, write_json, read_config, read_lat_longs, read_colors
 
@@ -311,7 +312,7 @@ def add_core_args(parser):
     core = parser.add_argument_group("REQUIRED")
     core.add_argument('--tree','-t', required=True, help="tree to perform trait reconstruction on")
     core.add_argument('--metadata', required=True, metavar="FILE", help="sequence metadata, as CSV or TSV")
-    core.add_argument('--node-data', required=True, nargs='+', help="JSON files with meta data for each node")
+    core.add_argument('--node-data', required=True, nargs='+', action=ExtendAction, help="JSON files with meta data for each node")
     core.add_argument('--output-tree', help="JSON file name that is passed on to auspice (e.g., zika_tree.json).")
     core.add_argument('--output-meta', help="JSON file name that is passed on to auspice (e.g., zika_meta.json).")
     core.add_argument('--auspice-config', help="file with auspice configuration")

augur/export_v2.py

@@ -10,6 +10,7 @@
 import re
 from Bio import Phylo
 
+from .argparse_ import ExtendAction
 from .io import read_metadata
 from .utils import read_node_data, write_json, read_config, read_lat_longs, read_colors
 from .validate import export_v2 as validate_v2, auspice_config_v2 as validate_auspice_config_v2, ValidateError
@@ -826,7 +827,7 @@ def register_parser(parent_subparsers):
         title="REQUIRED"
     )
     required.add_argument('--tree','-t', metavar="newick", required=True, help="Phylogenetic tree, usually output from `augur refine`")
-    required.add_argument('--node-data', metavar="JSON", required=True, nargs='+', help="JSON files containing metadata for nodes in the tree")
+    required.add_argument('--node-data', metavar="JSON", required=True, nargs='+', action=ExtendAction, help="JSON files containing metadata for nodes in the tree")
     required.add_argument('--output', metavar="JSON", required=True, help="Ouput file (typically for visualisation in auspice)")
 
     config = parser.add_argument_group(