Fix/formatting

.flake8

@@ -4,6 +4,8 @@ extend-ignore =
     E203,
     E402,
     E741,
+    E742,
+    E743,
     F403,
     F405,
     W503

allensdk/__init__.py

@@ -54,8 +54,7 @@ def one(x):
     except TypeError:
         return x
     if xlen != 1:
-        raise OneResultExpectedError("Expected length one result, received: "
-                                     f"{x} results from query")
+        raise OneResultExpectedError(f"Expected length one result, received: {x} results from query")
     if isinstance(x, set):
         return list(x)[0]
     else:
@@ -65,11 +64,9 @@ def one(x):
 logging.getLogger(__name__).addHandler(logging.NullHandler())
 
 if True:
-    file_download_log = logging.getLogger(
-        'allensdk.api.api.retrieve_file_over_http')
+    file_download_log = logging.getLogger("allensdk.api.api.retrieve_file_over_http")
     file_download_log.setLevel(logging.INFO)
     console = logging.StreamHandler()
-    formatter = logging.Formatter("%(asctime)s %(name)-12s "
-                                  "%(levelname)-8s %(message)s")
+    formatter = logging.Formatter("%(asctime)s %(name)-12s %(levelname)-8s %(message)s")
     console.setFormatter(formatter)
     file_download_log.addHandler(console)

allensdk/api/__init__.py

@@ -33,6 +33,6 @@
 # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 #
-''' Subclasses of allensdk.api.api.Api to implement specific queries to the
+"""Subclasses of allensdk.api.api.Api to implement specific queries to the
 `Allen Brain Atlas Data Portal <http://www.brain-map.org/api/index.html>`_.
-'''
+"""

allensdk/api/cloud_cache/file_attributes.py

@@ -22,22 +22,15 @@ class CacheFileAttributes(object):
         (probably computed by the Manifest class)
     """
 
-    def __init__(self,
-                 url: str,
-                 version_id: str,
-                 file_hash: str,
-                 local_path: pathlib.Path):
-
+    def __init__(self, url: str, version_id: str, file_hash: str, local_path: pathlib.Path):
         if not isinstance(url, str):
             raise ValueError(f"url must be str; got {type(url)}")
         if not isinstance(version_id, str):
             raise ValueError(f"version_id must be str; got {type(version_id)}")
         if not isinstance(file_hash, str):
-            raise ValueError(f"file_hash must be str; "
-                             f"got {type(file_hash)}")
+            raise ValueError(f"file_hash must be str; got {type(file_hash)}")
         if not isinstance(local_path, pathlib.Path):
-            raise ValueError(f"local_path must be pathlib.Path; "
-                             f"got {type(local_path)}")
+            raise ValueError(f"local_path must be pathlib.Path; got {type(local_path)}")
 
         self._url = url
         self._version_id = version_id
@@ -61,9 +54,11 @@ def local_path(self) -> pathlib.Path:
         return self._local_path
 
     def __str__(self):
-        output = {'url': self.url,
-                  'version_id': self.version_id,
-                  'file_hash': self.file_hash,
-                  'local_path': str(self.local_path)}
+        output = {
+            "url": self.url,
+            "version_id": self.version_id,
+            "file_hash": self.file_hash,
+            "local_path": str(self.local_path),
+        }
         output = json.dumps(output, indent=2, sort_keys=True)
-        return f'CacheFileParameters{output}'
+        return f"CacheFileParameters{output}"

allensdk/api/cloud_cache/manifest.py

@@ -35,39 +35,28 @@ class Manifest(object):
         local paths for remote resources. Defaults to False.
     """
 
-    def __init__(
-        self,
-        cache_dir: Union[str, pathlib.Path],
-        json_input,
-        use_static_project_dir: bool = False
-    ):
+    def __init__(self, cache_dir: Union[str, pathlib.Path], json_input, use_static_project_dir: bool = False):
         if isinstance(cache_dir, str):
             self._cache_dir = pathlib.Path(cache_dir).resolve()
         elif isinstance(cache_dir, pathlib.Path):
             self._cache_dir = cache_dir.resolve()
         else:
-            raise ValueError("cache_dir must be either a str "
-                             "or a pathlib.Path; "
-                             f"got {type(cache_dir)}")
+            raise ValueError(f"cache_dir must be either a str or a pathlib.Path; got {type(cache_dir)}")
 
         self._use_static_project_dir = use_static_project_dir
 
         self._data: Dict[str, Any] = json.load(json_input)
         if not isinstance(self._data, dict):
-            raise ValueError("Expected to deserialize manifest into a dict; "
-                             f"instead got {type(self._data)}")
+            raise ValueError(f"Expected to deserialize manifest into a dict; instead got {type(self._data)}")
         self._project_name: str = self._data["project_name"]
-        self._version: str = self._data['manifest_version']
-        self._file_id_column: str = self._data['metadata_file_id_column_name']
+        self._version: str = self._data["manifest_version"]
+        self._file_id_column: str = self._data["metadata_file_id_column_name"]
         self._data_pipeline: str = self._data["data_pipeline"]
 
-        self._metadata_file_names: List[str] = [
-            file_name for file_name in self._data['metadata_files']
-        ]
+        self._metadata_file_names: List[str] = [file_name for file_name in self._data["metadata_files"]]
         self._metadata_file_names.sort()
 
-        self._file_id_values: List[Any] = [ii for ii in
-                                           self._data['data_files'].keys()]
+        self._file_id_values: List[Any] = [ii for ii in self._data["data_files"].keys()]
         self._file_id_values.sort()
 
     @property
@@ -107,10 +96,7 @@ def file_id_values(self):
         """
         return self._file_id_values
 
-    def _create_file_attributes(self,
-                                remote_path: str,
-                                version_id: str,
-                                file_hash: str) -> CacheFileAttributes:
+    def _create_file_attributes(self, remote_path: str, version_id: str, file_hash: str) -> CacheFileAttributes:
         """
         Create the cache_file_attributes describing a file.
         This method does the work of assigning a local_path for a remote file.
@@ -151,19 +137,11 @@ def _create_file_attributes(self,
 
         local_path = project_dir / shaved_rel_path
 
-        obj = CacheFileAttributes(
-            remote_path,
-            version_id,
-            file_hash,
-            local_path
-        )
+        obj = CacheFileAttributes(remote_path, version_id, file_hash, local_path)
 
         return obj
 
-    def metadata_file_attributes(
-        self,
-        metadata_file_name: str
-    ) -> CacheFileAttributes:
+    def metadata_file_attributes(self, metadata_file_name: str) -> CacheFileAttributes:
         """
         Return the CacheFileAttributes associated with a metadata file
 
@@ -186,19 +164,15 @@ def metadata_file_attributes(
             If the metadata_file_name is not a valid option
         """
         if self._data is None:
-            raise RuntimeError("You cannot retrieve "
-                               "metadata_file_attributes;\n"
-                               "you have not yet loaded a manifest.json file")
+            raise RuntimeError(
+                "You cannot retrieve metadata_file_attributes;\nyou have not yet loaded a manifest.json file"
+            )
 
         if metadata_file_name not in self._metadata_file_names:
-            raise ValueError(f"{metadata_file_name}\n"
-                             "is not in self.metadata_file_names:\n"
-                             f"{self._metadata_file_names}")
+            raise ValueError(f"{metadata_file_name}\nis not in self.metadata_file_names:\n{self._metadata_file_names}")
 
-        file_data = self._data['metadata_files'][metadata_file_name]
-        return self._create_file_attributes(file_data['url'],
-                                            file_data['version_id'],
-                                            file_data['file_hash'])
+        file_data = self._data["metadata_files"][metadata_file_name]
+        return self._create_file_attributes(file_data["url"], file_data["version_id"], file_data["file_hash"])
 
     def data_file_attributes(self, file_id) -> CacheFileAttributes:
         """
@@ -224,17 +198,14 @@ def data_file_attributes(self, file_id) -> CacheFileAttributes:
             If the file_id is not a valid option
         """
         if self._data is None:
-            raise RuntimeError("You cannot retrieve data_file_attributes;\n"
-                               "you have not yet loaded a manifest.json file")
+            raise RuntimeError(
+                "You cannot retrieve data_file_attributes;\nyou have not yet loaded a manifest.json file"
+            )
 
-        if file_id not in self._data['data_files']:
-            valid_keys = list(self._data['data_files'].keys())
+        if file_id not in self._data["data_files"]:
+            valid_keys = list(self._data["data_files"].keys())
             valid_keys.sort()
-            raise ValueError(f"file_id: {file_id}\n"
-                             "Is not a data file listed in manifest:\n"
-                             f"{valid_keys}")
-
-        file_data = self._data['data_files'][file_id]
-        return self._create_file_attributes(file_data['url'],
-                                            file_data['version_id'],
-                                            file_data['file_hash'])
+            raise ValueError(f"file_id: {file_id}\nIs not a data file listed in manifest:\n{valid_keys}")
+
+        file_data = self._data["data_files"][file_id]
+        return self._create_file_attributes(file_data["url"], file_data["version_id"], file_data["file_hash"])

allensdk/api/cloud_cache/utils.py

@@ -28,7 +28,7 @@ def bucket_name_from_url(url: str) -> Optional[str]:
     here
     https://aws.amazon.com/blogs/aws/amazon-s3-path-deprecation-plan-the-rest-of-the-story/
     """
-    s3_pattern = re.compile('\.s3[\.,a-z,0-9,\-]*\.amazonaws.com')  # noqa: W605, E501
+    s3_pattern = re.compile("\.s3[\.,a-z,0-9,\-]*\.amazonaws.com")  # noqa: W605, E501
     url_params = url_parse.urlparse(url)
     raw_location = url_params.netloc
     s3_match = s3_pattern.search(raw_location)
@@ -37,8 +37,8 @@ def bucket_name_from_url(url: str) -> Optional[str]:
         warnings.warn(f"{s3_pattern} does not occur in url {url}")
         return None
 
-    s3_match = raw_location[s3_match.start():s3_match.end()]
-    return url_params.netloc.replace(s3_match, '')
+    s3_match = raw_location[s3_match.start() : s3_match.end()]
+    return url_params.netloc.replace(s3_match, "")
 
 
 def relative_path_from_url(url: str) -> str:
@@ -81,7 +81,7 @@ def file_hash_from_path(file_path: Union[str, Path]) -> str:
         The file hash (Blake2b; hexadecimal) of the file
     """
     hasher = hashlib.blake2b()
-    with open(file_path, 'rb') as in_file:
+    with open(file_path, "rb") as in_file:
         chunk = in_file.read(1000000)
         while len(chunk) > 0:
             hasher.update(chunk)

allensdk/api/queries/__init__.py

@@ -32,4 +32,4 @@
 # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
-#
+#