Merge pull request #266 from multinet-app/add-flake8-plugins

Add flake8 plugins

.flake8

@@ -5,7 +5,8 @@ max-line-length = 88
 exclude =
     __pycache__,
     build,
-    scripts
+    scripts,
+    docs
 extend-ignore =
     # See https://github.com/PyCQA/pycodestyle/issues/373
     E203,

Pipfile

@@ -20,14 +20,18 @@ flake8-black = "==0.1.0"
 flake8-bugbear = "==19.8.0"
 flake8-docstrings = "==1.3.1"
 flake8-quotes = "==2.1.0"
+flake8-builtins = "==1.4.2"
+flake8-comprehensions = "==3.2.2"
+flake8-eradicate = "==0.2.4"
+flake8-mutable = "==1.2.0"
+flake8-mypy = "==17.8.0"
+pep8-naming = "==0.9.1"
 sphinx = "==2.3.1"
 pytest = "==5.1.0"
 pytest-cov = "==2.7.1"
 pytest-xdist = "==1.29.0"
 recommonmark = "==0.5.0"
 pre-commit = "==1.18.2"
-flake8-mypy = "*"
-pep8-naming = "*"
 flasgger = "*"
 uwsgi = "*"
 

data/openflights/script/process.py

@@ -9,7 +9,7 @@ def main():
 
     with open(sys.argv[1]) as nodes:
         reader = csv.DictReader(nodes)
-        ids = set(n["_key"] for n in reader)
+        ids = {n["_key"] for n in reader}
 
     reader = csv.DictReader(sys.stdin)
     writer = csv.DictWriter(sys.stdout, reader.fieldnames)

multinet/api.py

@@ -38,7 +38,7 @@ def get_workspace(workspace: str) -> Any:
 @bp.route("/workspaces/<workspace>/tables", methods=["GET"])
 @use_kwargs({"type": fields.Str()})
 @swag_from("swagger/workspace_tables.yaml")
-def get_workspace_tables(workspace: str, type: TableType = "all") -> Any:
+def get_workspace_tables(workspace: str, type: TableType = "all") -> Any:  # noqa: A002
     """Retrieve the tables of a single workspace."""
     tables = db.workspace_tables(workspace, type)
     return util.stream(tables)

multinet/db.py

@@ -137,7 +137,7 @@ def get_workspaces(arango: ArangoClient) -> Generator[str, None, None]:
 
 @with_client
 def workspace_tables(
-    workspace: str, type: TableType, arango: ArangoClient
+    workspace: str, table_type: TableType, arango: ArangoClient
 ) -> Generator[str, None, None]:
     """Return a list of all table names in the workspace named `workspace`."""
 
@@ -163,14 +163,14 @@ def is_edge(x: Tuple[Any, bool]) -> bool:
     def is_node(x: Tuple[Any, bool]) -> bool:
         return not is_edge(x)
 
-    if type == "all":
+    if table_type == "all":
         desired_type = pass_all
-    elif type == "node":
+    elif table_type == "node":
         desired_type = is_node
-    elif type == "edge":
+    elif table_type == "edge":
         desired_type = is_edge
     else:
-        raise BadQueryArgument("type", type, ["all", "node", "edge"])
+        raise BadQueryArgument("type", table_type, ["all", "node", "edge"])
 
     return (table[0] for table in tables if desired_type(table))
 

multinet/downloaders/d3_json.py

@@ -66,10 +66,10 @@ def download(workspace: str, graph: str) -> Any:
             links.append(edge)
 
     response = make_response(
-        dict(
-            nodes=list(generate_filtered_docs(nodes)),
-            links=list(generate_filtered_docs(links)),
-        )
+        {
+            "nodes": list(generate_filtered_docs(nodes)),
+            "links": list(generate_filtered_docs(links)),
+        }
     )
     response.headers["Content-Disposition"] = f"attachment; filename={graph}.json"
     response.headers["Content-type"] = "application/json"

multinet/errors.py

@@ -28,14 +28,14 @@ def flask_response(self) -> FlaskTuple:
 class NotFound(ServerError):
     """Base exception for 404 errors of various types."""
 
-    def __init__(self, type: str, item: str):
+    def __init__(self, item_type: str, item: str):
         """
         Initialize the instance with the type and identity of the missing item.
 
-        `type` - the kind of item that is not found
+        `item_type` - the kind of item that is not found
         `item` - the name of the not found item
         """
-        self.type = type
+        self.type = item_type
         self.item = item
 
     def flask_response(self) -> FlaskTuple:
@@ -98,9 +98,9 @@ def flask_response(self) -> FlaskTuple:
 class AlreadyExists(ServerError):
     """Exception for attempting to create a resource that already exists."""
 
-    def __init__(self, type: str, item: str):
+    def __init__(self, item_type: str, item: str):
         """Initialize the exception."""
-        self.type = type
+        self.type = item_type
         self.item = item
 
     def flask_response(self) -> FlaskTuple:

multinet/uploaders/csv.py

@@ -100,4 +100,4 @@ def upload(workspace: str, table: str) -> Any:
 
     # Insert the data into the collection.
     results = coll.insert_many(rows)
-    return dict(count=len(results))
+    return {"count": len(results)}

multinet/uploaders/d3_json.py

@@ -58,7 +58,7 @@ def validate_d3_json(data: dict) -> Sequence[ValidationFailure]:
         data_errors.append(InconsistentLinkKeys())
 
     # Check for duplicated nodes
-    ids = set(row["id"] for row in data["nodes"])
+    ids = {row["id"] for row in data["nodes"]}
     if len(data["nodes"]) != len(ids):
         data_errors.append(NodeDuplicates())
 
@@ -113,4 +113,4 @@ def upload(workspace: str, table: str) -> Any:
     nodes_coll.insert_many(nodes)
     links_coll.insert_many(links)
 
-    return dict(nodecount=len(nodes), edgecount=len(links))
+    return {"nodecount": len(nodes), "edgecount": len(links)}

multinet/uploaders/nested_json.py

@@ -22,15 +22,14 @@ def analyze_nested_json(
     `data` - the text of a nested_json file
     `(nodes, edges)` - a node and edge table describing the tree.
     """
-    id = itertools.count(100)
+    ident = itertools.count(100)
     data = json.loads(raw_data)
 
     def keyed(rec: dict) -> dict:
         if "_key" in rec:
             return rec
 
-        # keyed = dict(rec)
-        rec["_key"] = str(next(id))
+        rec["_key"] = str(next(ident))
 
         return rec
 
@@ -115,6 +114,8 @@ def upload(workspace: str, table: str) -> Any:
     int_nodetable.insert_many(nodes[0])
     leaf_nodetable.insert_many(nodes[1])
 
-    return dict(
-        edgecount=len(edges), int_nodecount=len(nodes[0]), leaf_nodecount=len(nodes[1])
-    )
+    return {
+        "edgecount": len(edges),
+        "int_nodecount": len(nodes[0]),
+        "leaf_nodecount": len(nodes[1]),
+    }

multinet/uploaders/newick.py

@@ -119,4 +119,4 @@ def read_tree(parent: Optional[str], node: newick.Node) -> None:
 
     read_tree(None, tree[0])
 
-    return dict(edgecount=edgecount, nodecount=nodecount)
+    return {"edgecount": edgecount, "nodecount": nodecount}

multinet/util.py

@@ -54,7 +54,11 @@ def get_edge_table_properties(workspace: str, edge_table: str) -> EdgeTablePrope
             else:
                 tables_to_keys[table] = {key}
 
-    return dict(table_keys=tables_to_keys, from_tables=from_tables, to_tables=to_tables)
+    return {
+        "table_keys": tables_to_keys,
+        "from_tables": from_tables,
+        "to_tables": to_tables,
+    }
 
 
 def generate(iterator: Sequence[Any]) -> Generator[str, None, None]:
@@ -80,10 +84,10 @@ def require_db() -> None:
         raise DatabaseNotLive()
 
 
-def decode_data(input: bytes) -> str:
+def decode_data(data: bytes) -> str:
     """Decode the request data assuming utf8 encoding."""
     try:
-        body = input.decode("utf8")
+        body = data.decode("utf8")
     except UnicodeDecodeError as e:
         raise DecodeFailed(str(e))
 

test/test_csv_uploader.py

@@ -32,7 +32,7 @@ def test_validate_csv():
 
     validation_resp = v_error.value.errors
     correct = [err.asdict() for err in [DuplicateKey(key="2"), DuplicateKey(key="5")]]
-    assert all([err in validation_resp for err in correct])
+    assert all(err in validation_resp for err in correct)
 
     # Test invalid syntax
     with open(invalid_headers_file_path) as test_file:
@@ -51,7 +51,7 @@ def test_validate_csv():
             InvalidRow(row=5, fields=["_from", "_to"]),
         ]
     ]
-    assert all([err in validation_resp for err in correct])
+    assert all(err in validation_resp for err in correct)
 
     # Test unicode decode errors
     test_data = b"\xff\xfe_\x00k\x00e\x00y\x00,\x00n\x00a\x00m\x00e\x00\n"