Fix download actions

src/sos/actions.py

@@ -2,29 +2,38 @@
 #
 # Copyright (c) Bo Peng and the University of Texas MD Anderson Cancer Center
 # Distributed under the terms of the 3-clause BSD License.
-
 import copy
+import gzip
 import os
 import shlex
 import shutil
 import subprocess
 import sys
+import tarfile
 import tempfile
 import textwrap
 import time
+import urllib
+import urllib.error
+import urllib.parse
+import urllib.request
 import uuid
+import zipfile
 from collections.abc import Sequence
+from concurrent.futures import ProcessPoolExecutor
 from functools import wraps
 from typing import Any, Callable, Dict, List, Tuple, Union
 
+from tqdm import tqdm as ProgressBar
+
 from .controller import send_message_to_controller
 from .eval import interpolate
 from .messages import decode_msg, encode_msg
 from .parser import SoS_Script
 from .syntax import SOS_ACTION_OPTIONS
 from .targets import executable, file_target, path, paths, sos_targets
-from .utils import (TimeoutInterProcessLock, env, load_config_files,
-                    short_repr, textMD5, transcribe)
+from .utils import (TimeoutInterProcessLock, env, fileMD5, get_traceback,
+                    load_config_files, short_repr, textMD5, transcribe)
 
 __all__ = [
     "SoS_Action",
@@ -758,6 +767,7 @@ def script(script, interpreter="", suffix="", args="", entrypoint="", **kwargs):
 # download file with progress bar
 #
 
+
 def downloadURL(URL, dest, decompress=False, index=None):
     dest = os.path.abspath(os.path.expanduser(dest))
     dest_dir, filename = os.path.split(dest)
@@ -953,6 +963,7 @@ def downloadURL(URL, dest, decompress=False, index=None):
             os.remove(dest_tmp)
     return os.path.isfile(dest)
 
+
 @SoS_Action(acceptable_args=["URLs", "workdir", "dest_dir", "dest_file", "decompress", "max_jobs"])
 def download(URLs, dest_dir=".", dest_file=None, decompress=False, max_jobs=5):
     """Download files from specified URL, which should be space, tab or

src/sos/functions.py

@@ -1,21 +1,7 @@
-import gzip
-import tarfile
-import urllib
-import urllib.error
-import urllib.parse
-import urllib.request
-import zipfile
-from concurrent.futures import ProcessPoolExecutor
-
-import pkg_resources
-from tqdm import tqdm as ProgressBar
-
-from .utils import (StopInputGroup, TerminateExecution, env, fileMD5,
-                    get_traceback)
+from .utils import (StopInputGroup, TerminateExecution, env)
 
 # g_action_map = {}
 
-
 # def _load_actions():
 #     global g_action_map  # pylint: disable=global-variable-not-assigned
 #     for _entrypoint in pkg_resources.iter_entry_points(group="sos_actions"):
@@ -31,7 +17,6 @@
 #             # look for sos version requirement
 #             get_logger().warning(f"Failed to load script running action {_entrypoint.name}: {e}")
 
-
 # def sos_run_script(action, script, *args, **kwargs):
 #     '''Call script-execution actions.'''
 #     if not g_action_map:

test/test_task.py

@@ -2,7 +2,6 @@
 #
 # Copyright (c) Bo Peng and the University of Texas MD Anderson Cancer Center
 # Distributed under the terms of the 3-clause BSD License.
-
 import os
 import shutil
 import subprocess
@@ -841,7 +840,6 @@ def test_remote_output(clear_now_and_after):
         assert res.read() == "100"
 
 
-
 def test_runtime_max_walltime():
     """Test server max_walltime option"""
     # only warning messages will be yielded