ENH/DOC: no_args_is_help; note in a comment (#236)

marbl · Mar 9, 2023 · 3a939eb · 3a939eb
1 parent 30b23bc
commit 3a939eb
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diff --git a/metagenomescope/_cli.py b/metagenomescope/_cli.py
@@ -31,8 +31,11 @@
 )
 
 
-# Make mgsc -h show the help text
-@click.command(context_settings={"help_option_names": ["-h", "--help"]})
+# Make mgsc -h (or just mgsc by itself) show the help text
+@click.command(
+    context_settings={"help_option_names": ["-h", "--help"]},
+    no_args_is_help=True,
+)
 @click.option("-i", "--input-file", required=True, help=INPUT)
 @click.option("-o", "--output-dir", required=True, help=OUTPUT_DIR)
 # @click.option(

diff --git a/metagenomescope/graph_objects/assembly_graph.py b/metagenomescope/graph_objects/assembly_graph.py
@@ -206,7 +206,8 @@ def reindex_digraph(self):
         layout and internal storage of nodes. This way, we can have multiple
         nodes with the same name without causing a problem.
 
-        Also calls self.save_orig_src_and_tgt() on every edge in the digraph.
+        Also calls self.save_orig_src_and_tgt() on every edge in the digraph
+        (critically, that's done *after* assigning nodes unique integer IDs).
         """
         self.digraph = nx.convert_node_labels_to_integers(
             self.digraph, label_attribute="name"