Fix linting errors, mostly import sorting

penman/__init__.py

@@ -35,35 +35,35 @@
     __version__,
     __version_info__,
 )
-from penman.exceptions import (
-    PenmanError,
-    DecodeError,
-)
-from penman.tree import Tree
-from penman.graph import (
-    Triple,
-    Graph,
-)
-from penman.layout import (
-    interpret,
-    configure,
+from penman._format import (
+    format,
+    format_triples,
 )
 from penman._parse import (
-    parse,
     iterparse,
+    parse,
     parse_triples,
 )
-from penman._format import (
-    format,
-    format_triples,
-)
 from penman.codec import (
     PENMANCodec,
     _decode as decode,
-    _iterdecode as iterdecode,
+    _dump as dump,
+    _dumps as dumps,
     _encode as encode,
+    _iterdecode as iterdecode,
     _load as load,
     _loads as loads,
-    _dump as dump,
-    _dumps as dumps,
 )
+from penman.exceptions import (
+    DecodeError,
+    PenmanError,
+)
+from penman.graph import (
+    Graph,
+    Triple,
+)
+from penman.layout import (
+    configure,
+    interpret,
+)
+from penman.tree import Tree

penman/__main__.py

@@ -1,16 +1,14 @@
 # -*- coding: utf-8 -*-
-import sys
-import os
 import argparse
 import json
 import logging
+import os
+import sys
 
+from penman import layout, transform
 from penman.__about__ import __version__
-from penman.model import Model
-from penman import layout
 from penman.codec import PENMANCodec
-from penman import transform
-
+from penman.model import Model
 
 # Names of functions allowed for ordering triples/branches; we cannot
 # resolve them to the actual functions until the model is loaded.  If
@@ -108,13 +106,13 @@ def _check(g, model):
     i = 1
     errors = model.errors(g)
     if errors:
-        for triple, errors in errors.items():
+        for triple, error_messages in errors.items():
             if triple:
                 context = '({}) '.format(' '.join(map(str, triple)))
             else:
                 context = ''
-            for error in errors:
-                g.metadata[f'error-{i}'] = context + error
+            for error_message in error_messages:
+                g.metadata[f'error-{i}'] = context + error_message
             i += 1
         return 1
     else:

penman/_format.py

@@ -1,8 +1,8 @@
 
-from typing import Optional, Union, List, Iterable
+from typing import Iterable, List, Optional, Union
 
+from penman.tree import Tree, is_atomic
 from penman.types import BasicTriple
-from penman.tree import (Tree, is_atomic)
 
 
 def format(tree: Tree,

penman/_lexer.py

@@ -4,13 +4,12 @@
 Classes and functions for lexing PENMAN strings.
 """
 
-from typing import Union, Iterable, Iterator, NamedTuple, Pattern, Optional
-import re
 import logging
+import re
+from typing import Iterable, Iterator, NamedTuple, Optional, Pattern, Union
 
 from penman.exceptions import DecodeError
 
-
 logger = logging.getLogger(__name__)
 
 
@@ -126,7 +125,7 @@ def expect(self, *choices):
         try:
             token = self.next()
         except StopIteration:
-            raise self.error('Unexpected end of input')
+            raise self.error('Unexpected end of input') from None
         if token.type not in choices:
             raise self.error('Expected: {}'.format(', '.join(choices)),
                              token=token)

penman/_parse.py

@@ -1,19 +1,18 @@
 
-from typing import Union, Iterable, Iterator, List
 import logging
+from typing import Iterable, Iterator, List, Union
 
-from penman.types import (
-    Target,
-    BasicTriple,
-)
-from penman.tree import Tree
 from penman._lexer import (
     PENMAN_RE,
     TRIPLE_RE,
-    lex,
     TokenIterator,
+    lex,
+)
+from penman.tree import Tree
+from penman.types import (
+    BasicTriple,
+    Target,
 )
-
 
 logger = logging.getLogger('penman')
 

penman/codec.py

@@ -3,27 +3,26 @@
 """
 Serialization of PENMAN graphs.
 """
-from typing import Optional, Union, Iterable, Iterator, List, IO
 from pathlib import Path
+from typing import IO, Iterable, Iterator, List, Optional, Union
 
-from penman.types import (
-    Variable,
-    BasicTriple,
+from penman import layout
+from penman._format import (
+    format,
+    format_triples,
 )
-from penman.tree import Tree
-from penman.graph import Graph
-from penman.model import Model
 from penman._parse import (
-    parse,
     iterparse,
+    parse,
     parse_triples,
 )
-from penman._format import (
-    format,
-    format_triples,
+from penman.graph import Graph
+from penman.model import Model
+from penman.tree import Tree
+from penman.types import (
+    BasicTriple,
+    Variable,
 )
-from penman import layout
-
 
 # "Utility" types; not Penman-specific
 

penman/constant.py

@@ -3,13 +3,12 @@
 Functions for working with constant values.
 """
 
-from typing import Union
-from enum import Enum
 import json
+from enum import Enum
+from typing import Union
 
-from penman.types import Constant
 from penman.exceptions import ConstantError
-
+from penman.types import Constant
 
 pytype = type  # store because type() is redefined below
 

penman/graph.py

@@ -4,21 +4,20 @@
 Data structures for Penman graphs and triples.
 """
 
-from typing import (Union, Optional, Mapping, List, Dict, Set, NamedTuple)
-from collections import defaultdict
 import copy
+from collections import defaultdict
+from typing import Dict, List, Mapping, NamedTuple, Optional, Set, Union
 
+from penman.epigraph import Epidata
 from penman.exceptions import GraphError
 from penman.types import (
-    Variable,
+    BasicTriple,
     Constant,
     Role,
     Target,
-    BasicTriple,
     Triples,
+    Variable,
 )
-from penman.epigraph import Epidata
-
 
 CONCEPT_ROLE = ':instance'
 

penman/interface.py

@@ -10,15 +10,17 @@
 
 from penman.codec import (  # noqa: F401
     _decode as decode,
-    _iterdecode as iterdecode,
+    _dump as dump,
+    _dumps as dumps,
     _encode as encode,
+    _iterdecode as iterdecode,
     _load as load,
     _loads as loads,
-    _dump as dump,
-    _dumps as dumps,
 )
 
 warnings.warn(
     'The penman.interface module is deprecated. Use the functions from '
     'the penman module directly, e.g., penman.decode().',
-    DeprecationWarning)
+    DeprecationWarning,
+    stacklevel=2,
+)

penman/layout.py

@@ -50,18 +50,17 @@
                           ('b', ':ARG0', 'd')]            : POP
 """
 
-from typing import Union, Mapping, Callable, Any, List, Set, cast, Optional
 import copy
 import logging
+from typing import Any, Callable, List, Mapping, Optional, Set, Union, cast
 
-from penman.exceptions import LayoutError
-from penman.types import (Variable, Role, BasicTriple, Branch, Node)
 from penman.epigraph import Epidatum
-from penman.surface import (Alignment, RoleAlignment)
-from penman.tree import (Tree, is_atomic)
-from penman.graph import (Graph, CONCEPT_ROLE)
+from penman.exceptions import LayoutError
+from penman.graph import CONCEPT_ROLE, Graph
 from penman.model import Model
-
+from penman.surface import Alignment, RoleAlignment
+from penman.tree import Tree, is_atomic
+from penman.types import BasicTriple, Branch, Node, Role, Variable
 
 logger = logging.getLogger(__name__)
 

penman/model.py

@@ -4,22 +4,14 @@
 Semantic models for interpreting graphs.
 """
 
-from typing import (
-    cast, Optional, Tuple, List, Dict, Set, Iterable, Mapping, Any)
+import random
 import re
 from collections import defaultdict
-import random
+from typing import Any, Dict, Iterable, List, Mapping, Optional, Set, Tuple, cast
 
 from penman.exceptions import ModelError
-from penman.types import (
-    Variable,
-    Role,
-    Constant,
-    Target,
-    BasicTriple
-)
 from penman.graph import CONCEPT_ROLE, Graph
-
+from penman.types import BasicTriple, Constant, Role, Target, Variable
 
 _ReificationSpec = Tuple[Role, Constant, Role, Role]
 _Reified = Tuple[Constant, Role, Role]

penman/models/amr.py

@@ -5,7 +5,6 @@
 
 from penman.model import Model
 
-
 #: The roles are the edge labels of reifications. The purpose of roles
 #: in a :class:`~penman.model.Model` is mainly to define the set of
 #: valid roles, but they map to arbitrary data which is not used by

penman/models/noop.py

@@ -2,8 +2,8 @@
 No-op semantic model definition.
 """
 
-from penman.types import BasicTriple
 from penman.model import Model
+from penman.types import BasicTriple
 
 
 class NoOpModel(Model):

penman/surface.py

@@ -4,13 +4,12 @@
 Surface strings, tokens, and alignments.
 """
 
-from typing import TypeVar, Type, Mapping, Tuple, Optional
+from typing import Mapping, Optional, Tuple, Type, TypeVar
 
-from penman.types import BasicTriple
-from penman.graph import Graph
 from penman.epigraph import Epidatum
 from penman.exceptions import SurfaceError
-
+from penman.graph import Graph
+from penman.types import BasicTriple
 
 T = TypeVar('T', bound='AlignmentMarker')  # for classmethods
 

penman/transform.py

@@ -3,24 +3,23 @@
 Tree and graph transformations.
 """
 
-from typing import Optional, Dict, Set, List, Tuple
 import logging
+from typing import Dict, List, Optional, Set, Tuple
 
-from penman.types import (Variable, Target, BasicTriple, Node)
+from penman.epigraph import Epidata, Epidatum
 from penman.exceptions import ModelError
-from penman.epigraph import (Epidatum, Epidata)
-from penman.surface import (Alignment, RoleAlignment, alignments)
-from penman.tree import (Tree, is_atomic)
-from penman.graph import (Graph, CONCEPT_ROLE)
-from penman.model import Model
+from penman.graph import CONCEPT_ROLE, Graph
 from penman.layout import (
-    Push,
-    Pop,
     POP,
+    Pop,
+    Push,
     appears_inverted,
     get_pushed_variable,
 )
-
+from penman.model import Model
+from penman.surface import Alignment, RoleAlignment, alignments
+from penman.tree import Tree, is_atomic
+from penman.types import BasicTriple, Node, Target, Variable
 
 logger = logging.getLogger(__name__)
 
@@ -60,7 +59,7 @@ def canonicalize_roles(t: Tree, model: Model) -> Tree:
 def _canonicalize_node(node: Node, model: Model) -> Node:
     var, edges = node
     canonical_edges = []
-    for i, edge in enumerate(edges):
+    for edge in edges:
         role, tgt = edge
         # alignments aren't parsed off yet, so handle them superficially
         role, tilde, alignment = role.partition('~')