Merge pull request datalad#7643 from courtois-neuromod/fix/pre-commit…

…-all

pre-commit fixes on all files to avoid other PR to contain unrelated changes

.github/ISSUE_TEMPLATE/issue_template.yml

@@ -5,4 +5,4 @@ description: Report a generic issue which is not necessarily a bug
 body:
   - type: textarea
     attributes:
-      label: Description
+      label: Description

.github/ISSUE_TEMPLATE/issue_template_bug.yml

@@ -18,7 +18,7 @@ body:
     attributes:
       label: DataLad information
       description: |
-        What version of DataLad and git-annex do you use (run `datalad --version`)? 
+        What version of DataLad and git-annex do you use (run `datalad --version`)?
 
         On what operating system (consider running `datalad wtf`)?
 

.zenodo.json

@@ -157,4 +157,4 @@
     "access_right": "open",
     "license": "MIT",
     "upload_type": "software"
-}
+}

README.md

@@ -36,7 +36,7 @@
 
 # 10000-ft. overview
 
-DataLad's purpose is to make data management and data distribution more accessible. 
+DataLad's purpose is to make data management and data distribution more accessible.
 To do so, it stands on the shoulders of [Git] and [Git-annex] to deliver a
 decentralized system for data exchange. This includes automated ingestion of
 data from online portals and exposing it in readily usable form as Git(-annex)

datalad/__init__.py

@@ -109,6 +109,7 @@ def enable_librarymode():
     ConfigManager,
     warn_on_undefined_git_identity,
 )
+
 cfg = ConfigManager()
 warn_on_undefined_git_identity(cfg)
 

datalad/__main__.py

@@ -9,6 +9,7 @@
 """Helper to use datalad as a "runnable" module with  -m datalad"""
 
 import sys
+
 from . import __version__
 from .log import lgr
 
@@ -44,8 +45,8 @@ def runctx(cmd, globals=None, locals=None):
 
 
 def main(argv=None):
-    import os
     import getopt
+    import os
 
     if argv is None:
         argv = sys.argv

datalad/_version.py

@@ -11,12 +11,15 @@
 """Git implementation of _version.py."""
 
 import errno
+import functools
 import os
 import re
 import subprocess
 import sys
-from typing import Callable, Dict
-import functools
+from typing import (
+    Callable,
+    Dict,
+)
 
 
 def get_keywords():

datalad/api.py

@@ -15,12 +15,15 @@
 def _command_summary():
     # Import here to avoid polluting the datalad.api namespace.
     from collections import defaultdict
-    from datalad.interface.base import alter_interface_docs_for_api
-    from datalad.interface.base import get_api_name
-    from datalad.interface.base import get_cmd_doc
-    from datalad.interface.base import get_cmd_summaries
-    from datalad.interface.base import get_interface_groups
-    from datalad.interface.base import load_interface
+
+    from datalad.interface.base import (
+        alter_interface_docs_for_api,
+        get_api_name,
+        get_cmd_doc,
+        get_cmd_summaries,
+        get_interface_groups,
+        load_interface,
+    )
 
     groups = get_interface_groups()
     grp_short_descriptions = defaultdict(list)
@@ -43,13 +46,13 @@ def _command_summary():
 def _generate_extension_api():
     """Auto detect all available extensions and generate an API from them
     """
-    from datalad.support.entrypoints import iter_entrypoints
+    import logging
+
     from datalad.interface.base import (
         get_api_name,
         load_interface,
     )
-
-    import logging
+    from datalad.support.entrypoints import iter_entrypoints
     lgr = logging.getLogger('datalad.api')
 
     for ename, _, (grp_descr, interfaces) in iter_entrypoints(

datalad/cli/__init__.py

@@ -8,4 +8,5 @@
 __docformat__ = 'restructuredtext'
 
 import logging
+
 lgr = logging.getLogger('datalad.cli')

datalad/cli/common_args.py

@@ -13,13 +13,13 @@
 
 __all__ = ['common_args']
 
+from datalad.interface.base import eval_params
+from datalad.utils import ensure_unicode
+
 from .helpers import (
     HelpAction,
     LogLevelAction,
 )
-from datalad.interface.base import eval_params
-from datalad.utils import ensure_unicode
-
 
 _log_level_names = ['critical', 'error', 'warning', 'info', 'debug']
 

datalad/cli/exec.py

@@ -13,13 +13,8 @@
 # caused unconditionally by .main, and .parser.
 
 from datalad import cfg
-
-from datalad.interface.base import (
-    is_api_arg,
-)
-from datalad.utils import (
-    getargspec,
-)
+from datalad.interface.base import is_api_arg
+from datalad.utils import getargspec
 
 # only imported during command execution
 # .interface._has_eval_results_call
@@ -50,6 +45,7 @@ def call_from_parser(cls, args):
     """
     # XXX needs safety check for name collisions
     import inspect
+
     from datalad.interface.base import _has_eval_results_call
 
     argspec = getargspec(cls.__call__, include_kwonlyargs=True)
@@ -82,6 +78,7 @@ def call_from_parser(cls, args):
         kwargs['result_xfm'] = None
         if '{' in args.common_result_renderer:
             from .renderer import DefaultOutputRenderer
+
             # stupid hack, could and should become more powerful
             kwargs['result_renderer'] = DefaultOutputRenderer(
                 args.common_result_renderer)

datalad/cli/helpers.py

@@ -12,25 +12,26 @@
 __docformat__ = 'restructuredtext'
 
 import argparse
+import gzip
 import os
 import re
 import sys
-import gzip
 import textwrap
 from textwrap import wrap
 
+from platformdirs import AppDirs
+
 from datalad import __version__
 # delay?
 from datalad.support.exceptions import CapturedException
 from datalad.ui.utils import get_console_width
 from datalad.utils import is_interactive
 
-from platformdirs import AppDirs
-
 dirs = AppDirs("datalad", "datalad.org")
 
 
 from logging import getLogger
+
 lgr = getLogger('datalad.cli.helpers')
 
 
@@ -88,9 +89,10 @@ def _get_long_help(self, parser):
             get_cmd_doc,
             load_interface,
         )
+
         from .interface import (
-            get_cmdline_command_name,
             alter_interface_docs_for_cmdline,
+            get_cmdline_command_name,
         )
         preamble = get_description_with_cmd_summary(
             # produce a mapping of command groups to
@@ -153,6 +155,7 @@ def _get_all_interfaces(self):
     def _try_manpage(self, parser):
         try:
             import subprocess
+
             # get the datalad manpage to use
             manfile = os.environ.get('MANPATH', '/usr/share/man') \
                 + '/man1/{0}.1.gz'.format(parser.prog.replace(' ', '-'))
@@ -221,10 +224,9 @@ def _fix_datalad_ri(s):
 
 def get_description_with_cmd_summary(grp_short_descriptions, interface_groups,
                                      parser_description):
-    from .interface import (
-        dedent_docstring,
-    )
     from datalad.interface.base import get_cmd_summaries
+
+    from .interface import dedent_docstring
     lgr.debug("Generating detailed description for the parser")
 
     console_width = get_console_width()

datalad/cli/renderer.py

@@ -1,9 +1,8 @@
 """Render results in a terminal"""
 
-from collections import (
-    defaultdict,
-)
 import string
+from collections import defaultdict
+
 from datalad.ui import ui
 
 NA_STRING = 'N/A'  # we might want to make it configurable via config

datalad/cli/tests/test_exec.py

@@ -174,4 +174,3 @@ def __call__(pos_arg, **kwargs):
     args = parser.parse_args(["val"])
     eq_(call_from_parser(Cmd, args),
         "val")
-

datalad/cli/tests/test_renderer.py

@@ -21,6 +21,3 @@ def test_nadict():
     d = nadict({1: 2})
     eq_(d[1], 2)
     eq_(str(d[2]), NA_STRING)
-
-
-

datalad/cli/tests/test_utils.py

@@ -40,6 +40,3 @@ def our_post_mortem(tb):
             our_exceptionhook(type_, value_, tb_)
 
     eq_(old_exceptionhook, sys.excepthook)
-
-
-

datalad/cli/utils.py

@@ -4,7 +4,6 @@
 
 from datalad.log import is_interactive
 
-
 _sys_excepthook = sys.excepthook  # Just in case we ever need original one
 
 

datalad/cmdline/__init__.py

@@ -10,6 +10,7 @@
 """
 
 import warnings
+
 warnings.warn(
     "All of datalad.cmdline is deprecated/discontinued as of datalad 0.16. "
     "A new CLI implementation is available at datalad.cli. "

datalad/cmdline/helpers.py

@@ -13,8 +13,8 @@
 
 import os
 import warnings
-
 from logging import getLogger
+
 lgr = getLogger('datalad.cmdline')
 
 
@@ -44,10 +44,10 @@ def get_repo_instance(path=os.curdir, class_=None):
                   "It will be removed in a future release.",
                   DeprecationWarning)
 
-    from datalad.utils import get_dataset_root
     from datalad.distribution.dataset import Dataset
     from datalad.support.annexrepo import AnnexRepo
     from datalad.support.gitrepo import GitRepo
+    from datalad.utils import get_dataset_root
 
     if class_ is not None:
         if class_ == AnnexRepo:

datalad/cmdline/main.py

@@ -12,6 +12,7 @@
 """
 
 import warnings
+
 warnings.warn("datalad.cmdline.main was replaced by datalad.cli.main in "
               "datalad 0.16. Please update and reinstall extensions.",
               DeprecationWarning)

datalad/config.py

@@ -16,13 +16,13 @@
 import threading
 import warnings
 from collections import namedtuple
-from fasteners import InterProcessLock
 from functools import (
     lru_cache,
     wraps,
 )
 from pathlib import Path
 
+from fasteners import InterProcessLock
 
 import datalad
 from datalad.consts import DATASET_CONFIG_FILE

datalad/consts.py

@@ -10,8 +10,8 @@
 """
 
 import os
-from os.path import join
 import re
+from os.path import join
 
 # directory containing prepared metadata of a dataset repository:
 DATALAD_DOTDIR = ".datalad"

datalad/core/distributed/clone.py

@@ -25,7 +25,7 @@
 from datalad.interface.base import (
     Interface,
     build_doc,
-    eval_results
+    eval_results,
 )
 from datalad.interface.common_opts import (
     location_description,
@@ -45,8 +45,8 @@
 )
 from datalad.support.param import Parameter
 from datalad.utils import (
-    knows_annex,
     PurePath,
+    knows_annex,
     rmtree,
 )
 
@@ -60,7 +60,10 @@
     _test_existing_clone_target,
     _try_clone_candidates,
     decode_source_spec,
-    # RIA imports needed b/c datalad-next imports it from here ATM;
+)
+
+from .clone_utils import ( # isort: skip
+    # RIA imports needed b/c datalad-next imports it from here ATM
     # Remove after core was released and next dropped the ria patch.
     postclone_preannex_cfg_ria,
     postclonecfg_ria,

datalad/core/distributed/clone_ria.py

@@ -6,14 +6,14 @@
 from typing import Dict
 
 from datalad.distribution.dataset import Dataset
+
+from . import clone as mod_clone
 # For now kept in clone_utils, to avoid circular import (see datalad-next)
 from .clone_utils import (
     postclone_preannex_cfg_ria,
     postclonecfg_ria,
 )
 
-from . import clone as mod_clone
-
 # we need to preserve the original functions to be able to call them
 # in the patch
 orig_post_git_init_processing_ = mod_clone._post_git_init_processing_

datalad/core/distributed/clone_utils.py

@@ -32,7 +32,7 @@
 from datalad.support.annexrepo import AnnexRepo
 from datalad.support.exceptions import (
     CapturedException,
-    DownloadError
+    DownloadError,
 )
 from datalad.support.gitrepo import GitRepo
 from datalad.support.network import (
@@ -54,7 +54,6 @@
     rmtree,
 )
 
-
 __docformat__ = 'restructuredtext'
 
 lgr = logging.getLogger('datalad.core.distributed.clone')