From 21b8708196a66d71fcd8cb2f9b35c13b46e4f69d Mon Sep 17 00:00:00 2001
From: Haibao Tang <tanghaibao@gmail.com>
Date: Wed, 8 May 2024 05:54:38 -0700
Subject: [PATCH] remove set_usage()

---
 jcvi/apps/base.py  | 10 +++++-----
 jcvi/apps/fetch.py |  8 ++++----
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/jcvi/apps/base.py b/jcvi/apps/base.py
index f7079dc3..b69946d7 100644
--- a/jcvi/apps/base.py
+++ b/jcvi/apps/base.py
@@ -12,6 +12,7 @@
 import sys
 import time
 
+from argparse import ArgumentParser, SUPPRESS
 from collections.abc import Iterable
 from configparser import (
     ConfigParser,
@@ -20,14 +21,13 @@
     NoSectionError,
     ParsingError,
 )
-
-from argparse import ArgumentParser, SUPPRESS
 from http.client import HTTPSConnection
 from socket import gethostname
 from subprocess import CalledProcessError, PIPE, call, check_output
 from time import ctime
 from typing import Any, Collection, List, Optional, Tuple, Union
 from urllib.parse import urlencode
+
 from natsort import natsorted
 from rich.console import Console
 from rich.logging import RichHandler
@@ -277,7 +277,7 @@ def set_outfile(self, outfile: Optional[str] = "stdout"):
         """
         self.add_argument("-o", "--outfile", default=outfile, help="Outfile name")
 
-    def set_outdir(self, outdir="."):
+    def set_outdir(self, outdir: Optional[str] = "."):
         self.add_argument("--outdir", default=outdir, help="Specify output directory")
 
     def set_email(self):
@@ -735,7 +735,7 @@ def set_pairs(self):
         part, e.g. /1, /2, or .f, .r, default behavior is to truncate until last
         char.
         """
-        self.set_usage(self.set_pairs.__doc__)
+        self.usage = self.set_pairs.__doc__
 
         self.add_argument(
             "--pairsfile", default=None, help="Write valid pairs to pairsfile"
@@ -2225,7 +2225,7 @@ def inspect(object):
         print("{}: {}".format(k, details), file=sys.stderr)
 
 
-def sample_N(a: Collection[Any], N: int, seed: Optional[int] = None) -> List[Any]:
+def sample_N(a: Collection, N: int, seed: Optional[int] = None) -> List:
     """
     When size of N is > size of a, random.sample() will emit an error:
     ValueError: sample larger than population
diff --git a/jcvi/apps/fetch.py b/jcvi/apps/fetch.py
index 41b18037..3ce134ca 100644
--- a/jcvi/apps/fetch.py
+++ b/jcvi/apps/fetch.py
@@ -158,7 +158,7 @@ def ensembl(args):
 
     valid_species = [x for x in ls_ftp(fasta_url) if "." not in x]
     doc = "\n".join((ensembl.__doc__, tile(valid_species)))
-    p.set_usage(doc)
+    p.usage = doc
 
     if len(args) != 1:
         sys.exit(not p.print_help())
@@ -273,7 +273,7 @@ def phytozome(args):
             downloader=downloader,
         )
         g = GlobusXMLParser(directory_listing)
-    except:
+    except Exception as _:
         logger.error("Error downloading directory listing ... cleaning up")
         cleanup(directory_listing, cookies)
         sys.exit(1)
@@ -281,7 +281,7 @@ def phytozome(args):
     genomes = g.get_genomes()
     valid_species = genomes.keys()
     species_tile = tile(valid_species)
-    p.set_usage("\n".join((phytozome.__doc__, species_tile)))
+    p.usage = "\n".join((phytozome.__doc__, species_tile))
 
     if len(args) != 1:
         sys.exit(not p.print_help())
@@ -383,7 +383,7 @@ def phytozome9(args):
     valid_species = [x for x in ls_ftp(url) if "." not in x]
 
     doc = "\n".join((phytozome9.__doc__, tile(valid_species)))
-    p.set_usage(doc)
+    p.usage = doc
 
     if len(args) != 1:
         sys.exit(not p.print_help())