Merge pull request #119 from templateflow/sty/run-ruff

MAINT: Run ruff and address some issues

Author: oesteban

templateflow/__init__.py

@@ -1,38 +1,38 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """TemplateFlow is the Zone of Templates."""
-__packagename__ = "templateflow"
-__copyright__ = "2020, The TemplateFlow developers"
+__packagename__ = 'templateflow'
+__copyright__ = '2020, The TemplateFlow developers'
 try:
     from ._version import __version__
 except ModuleNotFoundError:
-    from importlib.metadata import version, PackageNotFoundError
+    from importlib.metadata import PackageNotFoundError, version
     try:
         __version__ = version(__packagename__)
     except PackageNotFoundError:
-        __version__ = "0+unknown"
+        __version__ = '0+unknown'
     del version
     del PackageNotFoundError
 
 import os
-from . import api
-from .conf import update, TF_USE_DATALAD
 
+from . import api
+from .conf import TF_USE_DATALAD, update
 
-if not TF_USE_DATALAD and os.getenv("TEMPLATEFLOW_AUTOUPDATE", "1") not in (
-    "false",
-    "off",
-    "0",
-    "no",
-    "n",
+if not TF_USE_DATALAD and os.getenv('TEMPLATEFLOW_AUTOUPDATE', '1') not in (
+    'false',
+    'off',
+    '0',
+    'no',
+    'n',
 ):
     # trigger skeleton autoupdate
     update(local=True, overwrite=False, silent=True)
 
 __all__ = [
-    "__copyright__",
-    "__packagename__",
-    "__version__",
-    "api",
-    "update",
+    '__copyright__',
+    '__packagename__',
+    '__version__',
+    'api',
+    'update',
 ]

templateflow/_loader.py

@@ -27,7 +27,7 @@
 except ImportError:  # pragma: no cover
     from importlib_resources.abc import Traversable
 
-__all__ = ["Loader"]
+__all__ = ['Loader']
 
 
 class Loader:
@@ -119,19 +119,19 @@ def _doc(self):
         directory.
         """
         top_level = sorted(
-            os.path.relpath(p, self.files) + "/"[: p.is_dir()]
+            os.path.relpath(p, self.files) + '/'[: p.is_dir()]
             for p in self.files.iterdir()
-            if p.name[0] not in (".", "_") and p.name != "tests"
+            if p.name[0] not in ('.', '_') and p.name != 'tests'
         )
         doclines = [
-            f"Load package files relative to ``{self._anchor}``.",
-            "",
-            "This package contains the following (top-level) files/directories:",
-            "",
-            *(f"* ``{path}``" for path in top_level),
+            f'Load package files relative to ``{self._anchor}``.',
+            '',
+            'This package contains the following (top-level) files/directories:',
+            '',
+            *(f'* ``{path}``' for path in top_level),
         ]
 
-        return "\n".join(doclines)
+        return '\n'.join(doclines)
 
     def readable(self, *segments) -> Traversable:
         """Provide read access to a resource through a Path-like interface.

templateflow/api.py

@@ -2,12 +2,19 @@
 import sys
 from json import loads
 from pathlib import Path
+
 from bids.layout import Query
 
-from .conf import TF_LAYOUT, TF_S3_ROOT, TF_USE_DATALAD, requires_layout
+from templateflow.conf import (
+    TF_GET_TIMEOUT,
+    TF_LAYOUT,
+    TF_S3_ROOT,
+    TF_USE_DATALAD,
+    requires_layout,
+)
 
 _layout_dir = tuple(
-    item for item in dir(TF_LAYOUT) if item.startswith("get_")
+    item for item in dir(TF_LAYOUT) if item.startswith('get_')
 )
 
 
@@ -59,13 +66,13 @@ def ls(template, **kwargs):
 
     """
     # Normalize extensions to always have leading dot
-    if "extension" in kwargs:
-        kwargs["extension"] = _normalize_ext(kwargs["extension"])
+    if 'extension' in kwargs:
+        kwargs['extension'] = _normalize_ext(kwargs['extension'])
 
     return [
         Path(p) for p in TF_LAYOUT.get(
             template=Query.ANY if template is None else template,
-            return_type="file",
+            return_type='file',
             **kwargs
         )
     ]
@@ -130,7 +137,7 @@ def get(template, raise_empty=False, **kwargs):
     out_file = ls(template, **kwargs)
 
     if raise_empty and not out_file:
-        raise Exception("No results found")
+        raise Exception('No results found')
 
     # Try DataLad first
     dl_missing = [p for p in out_file if not p.is_file()]
@@ -147,7 +154,7 @@ def get(template, raise_empty=False, **kwargs):
     not_fetched = [str(p) for p in out_file if not p.is_file() or p.stat().st_size == 0]
 
     if not_fetched:
-        msg = "Could not fetch template files: %s." % ", ".join(not_fetched)
+        msg = 'Could not fetch template files: %s.' % ', '.join(not_fetched)
         if dl_missing and not TF_USE_DATALAD:
             msg += (
                 """\
@@ -222,7 +229,7 @@ def get_metadata(template):
 
     """
     tf_home = Path(TF_LAYOUT.root)
-    filepath = tf_home / ("tpl-%s" % template) / "template_description.json"
+    filepath = tf_home / ('tpl-%s' % template) / 'template_description.json'
 
     # Ensure that template is installed and file is available
     if not filepath.is_file():
@@ -243,9 +250,9 @@ def get_citations(template, bibtex=False):
 
     """
     data = get_metadata(template)
-    refs = data.get("ReferencesAndLinks", [])
+    refs = data.get('ReferencesAndLinks', [])
     if isinstance(refs, dict):
-        refs = [x for x in refs.values()]
+        refs = list(refs.values())
 
     if not bibtex:
         return refs
@@ -255,10 +262,10 @@ def get_citations(template, bibtex=False):
 
 @requires_layout
 def __getattr__(key: str):
-    key = key.replace("ls_", "get_")
+    key = key.replace('ls_', 'get_')
     if (
-        key.startswith("get_")
-        and key not in ("get_metadata", "get_citations")
+        key.startswith('get_')
+        and key not in ('get_metadata', 'get_citations')
         and key not in _layout_dir
     ):
         return TF_LAYOUT.__getattr__(key)
@@ -277,7 +284,7 @@ def _datalad_get(filepath):
     try:
         api.get(filepath, dataset=str(TF_LAYOUT.root))
     except IncompleteResultsError as exc:
-        if exc.failed[0]["message"] == "path not associated with any dataset":
+        if exc.failed[0]['message'] == 'path not associated with any dataset':
             from .conf import TF_GITHUB_SOURCE
 
             api.install(path=TF_LAYOUT.root, source=TF_GITHUB_SOURCE, recursive=True)
@@ -288,47 +295,50 @@ def _datalad_get(filepath):
 
 def _s3_get(filepath):
     from sys import stderr
-    from tqdm import tqdm
+
     import requests
+    from tqdm import tqdm
 
     path = filepath.relative_to(TF_LAYOUT.root).as_posix()
-    url = f"{TF_S3_ROOT}/{path}"
+    url = f'{TF_S3_ROOT}/{path}'
 
-    print("Downloading %s" % url, file=stderr)
+    print('Downloading %s' % url, file=stderr)
     # Streaming, so we can iterate over the response.
-    r = requests.get(url, stream=True)
+    r = requests.get(url, stream=True, timeout=TF_GET_TIMEOUT)
 
     # Total size in bytes.
-    total_size = int(r.headers.get("content-length", 0))
+    total_size = int(r.headers.get('content-length', 0))
     block_size = 1024
     wrote = 0
     if not filepath.is_file():
         filepath.unlink()
 
-    with filepath.open("wb") as f:
-        with tqdm(total=total_size, unit="B", unit_scale=True) as t:
+    with filepath.open('wb') as f:
+        with tqdm(total=total_size, unit='B', unit_scale=True) as t:
             for data in r.iter_content(block_size):
                 wrote = wrote + len(data)
                 f.write(data)
                 t.update(len(data))
 
     if total_size != 0 and wrote != total_size:
-        raise RuntimeError("ERROR, something went wrong")
+        raise RuntimeError('ERROR, something went wrong')
 
 
 def _to_bibtex(doi, template, idx):
-    if "doi.org" not in doi:
+    if 'doi.org' not in doi:
         return doi
 
     # Is a DOI URL
     import requests
 
     response = requests.post(
-        doi, headers={"Accept": "application/x-bibtex; charset=utf-8"}
+        doi,
+        headers={'Accept': 'application/x-bibtex; charset=utf-8'},
+        timeout=TF_GET_TIMEOUT,
     )
     if not response.ok:
         print(
-            f"Failed to convert DOI <{doi}> to bibtex, returning URL.",
+            f'Failed to convert DOI <{doi}> to bibtex, returning URL.',
             file=sys.stderr,
         )
         return doi

templateflow/conf/__init__.py

@@ -1,26 +1,28 @@
 """Configuration and settings."""
-from os import getenv
 import re
-from warnings import warn
-from pathlib import Path
 from contextlib import suppress
 from functools import wraps
+from os import getenv
+from pathlib import Path
+from warnings import warn
+
 from .._loader import Loader
 
 load_data = Loader(__package__)
 
-TF_DEFAULT_HOME = Path.home() / ".cache" / "templateflow"
-TF_HOME = Path(getenv("TEMPLATEFLOW_HOME", str(TF_DEFAULT_HOME)))
-TF_GITHUB_SOURCE = "https://github.com/templateflow/templateflow.git"
-TF_S3_ROOT = "https://templateflow.s3.amazonaws.com"
-TF_USE_DATALAD = getenv("TEMPLATEFLOW_USE_DATALAD", "false").lower() in (
-    "true",
-    "on",
-    "1",
-    "yes",
-    "y",
+TF_DEFAULT_HOME = Path.home() / '.cache' / 'templateflow'
+TF_HOME = Path(getenv('TEMPLATEFLOW_HOME', str(TF_DEFAULT_HOME)))
+TF_GITHUB_SOURCE = 'https://github.com/templateflow/templateflow.git'
+TF_S3_ROOT = 'https://templateflow.s3.amazonaws.com'
+TF_USE_DATALAD = getenv('TEMPLATEFLOW_USE_DATALAD', 'false').lower() in (
+    'true',
+    'on',
+    '1',
+    'yes',
+    'y',
 )
 TF_CACHED = True
+TF_GET_TIMEOUT = 10
 
 
 def _init_cache():
@@ -34,6 +36,7 @@ def _init_cache():
 If the path reported above is not the desired location for TemplateFlow, \
 please set the TEMPLATEFLOW_HOME environment variable.""",
             ResourceWarning,
+            stacklevel=2,
         )
         if TF_USE_DATALAD:
             try:
@@ -64,7 +67,7 @@ def wrapper(*args, **kwargs):
             from bids import __version__
 
             raise RuntimeError(
-                f"A layout with PyBIDS <{__version__}> could not be initiated"
+                f'A layout with PyBIDS <{__version__}> could not be initiated'
             )
         return func(*args, **kwargs)
 
@@ -85,6 +88,7 @@ def update(local=False, overwrite=True, silent=False):
         init_layout()
         # ensure the api uses the updated layout
         import importlib
+
         from .. import api
 
         importlib.reload(api)
@@ -96,19 +100,20 @@ def wipe():
     global TF_USE_DATALAD, TF_HOME
 
     if TF_USE_DATALAD:
-        print("TemplateFlow is configured in DataLad mode, wipe() has no effect")
+        print('TemplateFlow is configured in DataLad mode, wipe() has no effect')
         return
 
     import importlib
     from shutil import rmtree
+
     from templateflow import api
 
     def _onerror(func, path, excinfo):
         from pathlib import Path
 
         if Path(path).exists():
             print(
-                f"Warning: could not delete <{path}>, please clear the cache manually."
+                f'Warning: could not delete <{path}>, please clear the cache manually.'
             )
 
     rmtree(TF_HOME, onerror=_onerror)
@@ -132,32 +137,37 @@ def setup_home(force=False):
 def _update_datalad():
     from datalad.api import update
 
-    print("Updating TEMPLATEFLOW_HOME using DataLad ...")
+    print('Updating TEMPLATEFLOW_HOME using DataLad ...')
     try:
         update(dataset=str(TF_HOME), recursive=True, merge=True)
-    except Exception as e:
-        warn(f"Error updating TemplateFlow's home directory (using DataLad): {e}")
+    except Exception as e:  # noqa: BLE001
+        warn(
+            f"Error updating TemplateFlow's home directory (using DataLad): {e}",
+            stacklevel=2,
+        )
+        return False
     return True
 
 
 TF_LAYOUT = None
 
 
 def init_layout():
-    from templateflow.conf.bids import Layout
     from bids.layout.index import BIDSLayoutIndexer
 
+    from templateflow.conf.bids import Layout
+
     global TF_LAYOUT
     TF_LAYOUT = Layout(
         TF_HOME,
         validate=False,
-        config="templateflow",
+        config='templateflow',
         indexer=BIDSLayoutIndexer(
             validate=False,
             ignore=(
-                re.compile(r"scripts/"),
-                re.compile(r"/\."),
-                re.compile(r"^\."),
+                re.compile(r'scripts/'),
+                re.compile(r'/\.'),
+                re.compile(r'^\.'),
             ),
         ),
     )