Merge pull request #36 from goodmami/v0.7.2

V0.7.2

CHANGELOG.md

@@ -2,11 +2,32 @@
 
 ## [Unreleased][unreleased]
 
-(no unreleased changes yet)
+(No unreleased changes)
+
+## [v0.7.2][v0.7.2]
+
+### Added
+
+* `-q` / `--quiet` command line option
+* `-v` / `--verbose` command line option
+* Loggers that print some diagnostic information at the DEBUG and INFO
+  levels
+
+### Fixed
+
+* Remove superfluous `POP` layout markers when graphs have duplicated
+  triples ([#34][])
+* Avoid `KeyError` on edge and attribute reification when graphs have
+  duplicated triples ([#35][])
+
+### Changed
+
+* `Model.reify()` no longer inverts the incoming triple
+
 
 ## [v0.7.1][v0.7.1]
 
-The [v0.7.0][v070] release was missing a declaration for the new
+The [v0.7.0](#v070) release was missing a declaration for the new
 `penman.models` sub-package, so it was not available for new
 installs. This release fixes that.
 
@@ -17,6 +38,7 @@ installs. This release fixes that.
   "in case", as I think the missing package problem was the real
   culprit for faulty documentation builds.)
 
+
 ## [v0.7.0][v0.7.0]
 
 This release comprises a major restructuring from previous
@@ -101,24 +123,24 @@ modules.
 * `penman.models.amr.normalizations`
 * `penman.models.amr.reifications`
 * `penman.models.amr.model`
-* `penman.surface` (#19)
+* `penman.surface` ([#19][])
 * `penman.surface.AlignmentMarker`
 * `penman.surface.Alignment`
 * `penman.surface.RoleAlignment`
 * `penman.surface.alignments()`
 * `penman.surface.role_alignments()`
 * `penman.transform`
 * `penman.transform.canonicalize_roles()`
-* `penman.transform.reify_edges()` (#27)
+* `penman.transform.reify_edges()` ([#27][])
 * `penman.transform.reify_attributes()`
 * `penman.transform.indicate_branches()`
-* `penman.tree` (#16)
+* `penman.tree` ([#16][])
 * `penman.tree.Tree`
 * `penman.tree.is_atomic()`
 
 ### Removed
 
-* [docopt](https://github.com/docopt/docopt) dependency (#20)
+* [docopt](https://github.com/docopt/docopt) dependency ([#20][])
 * `penman.EncodeError`
 * `penman.AMRCodec`
 * `penman.Triple.inverted`
@@ -132,11 +154,11 @@ modules.
 
 ### Fixed
 
-* Graphs can no longer be encoded with attributes as the top (#15)
+* Graphs can no longer be encoded with attributes as the top ([#15][])
 * For AMR, both `:mod` and `:domain` are for non-inverted relations,
-  although their inverses can be canonicalized to the other (#26)
+  although their inverses can be canonicalized to the other ([#26][])
 * Epigraphical layout markers allow the tree structure to be preserved
-  without modifying the pure graph's triples (#25)
+  without modifying the pure graph's triples ([#25][])
 
 ### Changed
 
@@ -151,10 +173,10 @@ modules.
   parameters
 * `penman.PENMANCodec.encode()` now takes `indent` and `compact`
   parameters
-* `penman.PENMANCodec.iterdecode()` works on streams (#21)
-* `penman.PENMANCodec` now reads comments with metadata (#23)
-* `penman.PENMANCodec` no longer accepts non-symbol variables (#13)
-* `penman.dump()` now writes iteratively to a stream (#22)
+* `penman.PENMANCodec.iterdecode()` works on streams ([#21][])
+* `penman.PENMANCodec` now reads comments with metadata ([#23][])
+* `penman.PENMANCodec` no longer accepts non-symbol variables ([#13][])
+* `penman.dump()` now writes iteratively to a stream ([#22][])
 * The following no longer take the `cls` parameter for a codec class,
   nor `**kwargs` to configure that class, but instead a `model`
   parameter for the semantic model:
@@ -170,21 +192,22 @@ modules.
   - `penman.dumps()`
   - `penman.dump()`
 * `penman.Graph.triples` is now a member variable instead of a method
-* `penman.Graph` class is mutable (#32)
+* `penman.Graph` class is mutable ([#32][])
 * Concepts (node labels) in `penman.Graph` now have a special role
   known to the `penman.graph` module, which can help avoid some
-  reentrancy issues (#29)
+  reentrancy issues ([#29][])
 
 
 ## [v0.6.2][v0.6.2]
 
 ### Fixed
 
-* Value-cast patterns terminated with `$` to invalid casts (#9)
-* Raise EncodeError when attempting to encode empty graphs (#14)
-* Redefine NODETYPE_RE for AMRCodec (#17)
+* Value-cast patterns terminated with `$` to invalid casts ([#9][])
+* Raise EncodeError when attempting to encode empty graphs ([#14][])
+* Redefine NODETYPE_RE for AMRCodec ([#17][])
 * Remove specific float and int parsing in variables/nodetypes for the
-  default parser (the numeric values are still parses as atoms) (#17)
+  default parser (the numeric values are still parses as atoms) ([#17][])
+
 
 ## [v0.6.1][v0.6.1]
 
@@ -203,6 +226,7 @@ modules.
 * Grammar in README now more accurately reflect parsing behavior (and
   vice versa)
 
+
 ## [v0.6.0][]
 
 ### Fixed
@@ -323,6 +347,7 @@ subclassed to customize behavior.
   parameter for a serialization codec, and any additional `**kwargs`
   are passed to its constructor.
 
+
 ## [v0.3.0][]
 
 ### Added
@@ -347,6 +372,7 @@ subclassed to customize behavior.
 * `load()`, `loads()`, `dump()`, and `dumps()` can now take a `triples=...`
   parameter (default: False); if True, read/write as triples
 
+
 ## [v0.2.0][]
 
 ### Changed
@@ -359,6 +385,7 @@ subclassed to customize behavior.
   of triples (e.g. `instance-of(b, bark-01) ^ ARG0(b, d) ^
   instance-of(d, dog)`).
 
+
 ## [v0.1.0][]
 
 First release with very basic functionality.
@@ -370,6 +397,7 @@ First release with very basic functionality.
 * `load()`/`loads()` reads Penman files/strings
 * `dump()`/`dumps()` writes Penman files/strings
 
+
 [unreleased]: ../../tree/develop
 [v0.1.0]: ../../releases/tag/v0.1.0
 [v0.2.0]: ../../releases/tag/v0.2.0
@@ -382,4 +410,26 @@ First release with very basic functionality.
 [v0.6.2]: ../../releases/tag/v0.6.2
 [v0.7.0]: ../../releases/tag/v0.7.0
 [v0.7.1]: ../../releases/tag/v0.7.1
+[v0.7.2]: ../../releases/tag/v0.7.2
 [README]: README.md
+
+[#4]: https://github.com/goodmami/penman/issues/4
+[#6]: https://github.com/goodmami/penman/issues/6
+[#9]: https://github.com/goodmami/penman/issues/9
+[#13]: https://github.com/goodmami/penman/issues/13
+[#14]: https://github.com/goodmami/penman/issues/14
+[#15]: https://github.com/goodmami/penman/issues/15
+[#16]: https://github.com/goodmami/penman/issues/16
+[#17]: https://github.com/goodmami/penman/issues/17
+[#19]: https://github.com/goodmami/penman/issues/19
+[#20]: https://github.com/goodmami/penman/issues/20
+[#21]: https://github.com/goodmami/penman/issues/21
+[#22]: https://github.com/goodmami/penman/issues/22
+[#23]: https://github.com/goodmami/penman/issues/23
+[#25]: https://github.com/goodmami/penman/issues/25
+[#26]: https://github.com/goodmami/penman/issues/26
+[#27]: https://github.com/goodmami/penman/issues/27
+[#29]: https://github.com/goodmami/penman/issues/29
+[#32]: https://github.com/goodmami/penman/issues/32
+[#34]: https://github.com/goodmami/penman/issues/34
+[#35]: https://github.com/goodmami/penman/issues/35

docs/conf.py

@@ -26,7 +26,7 @@
 # The short X.Y version
 version = 'v0.7'
 # The full version, including alpha/beta/rc tags
-release = 'v0.7.1'
+release = 'v0.7.2'
 
 
 # -- General configuration ---------------------------------------------------

penman/__about__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '0.7.1'
+__version__ = '0.7.2'
 __version_info__ = [
     int(x) if x.isdigit() else x
     for x in __version__.replace('.', ' ').replace('-', ' ').split()

penman/codec.py

@@ -6,6 +6,7 @@
 
 from typing import Optional, Union, Type, Iterable, Iterator, List
 import re
+import logging
 
 from penman.types import (
     Variable,
@@ -29,6 +30,9 @@
 from penman import layout
 
 
+logger = logging.getLogger(__name__)
+
+
 class PENMANCodec(object):
     """
     An encoder/decoder for PENMAN-serialized graphs.
@@ -102,9 +106,7 @@ def iterparse(self, lines: Union[Iterable[str], str]) -> Iterator[Tree]:
         """
         tokens = lex(lines, pattern=PENMAN_RE)
         while tokens and tokens.peek().type in ('COMMENT', 'LPAREN'):
-            metadata = self._parse_comments(tokens)
-            node = self._parse_node(tokens)
-            yield Tree(node, metadata=metadata)
+            yield self._parse(tokens)
 
     def parse(self, s: str) -> Tree:
         """
@@ -120,9 +122,14 @@ def parse(self, s: str) -> Tree:
             Tree(('b', [('/', 'bark', []), ('ARG1', ('d', [('/', 'dog', [])]), [])]))
         """
         tokens = lex(s, pattern=PENMAN_RE)
+        return self._parse(tokens)
+
+    def _parse(self, tokens: TokenIterator) -> Tree:
         metadata = self._parse_comments(tokens)
         node = self._parse_node(tokens)
-        return Tree(node, metadata=metadata)
+        tree = Tree(node, metadata=metadata)
+        logger.debug('Parsed: %s', tree)
+        return tree
 
     def _parse_comments(self, tokens: TokenIterator):
         """

penman/graph.py

@@ -109,6 +109,12 @@ def __repr__(self):
             id(self)
         )
 
+    def __str__(self):
+        triples = '[{}]'.format(',\n   '.join(map(repr, self.triples)))
+        epidata = '{{{}}}'.format(',\n    '.join(
+            map('{0[0]!r}: {0[1]!r}'.format, self.epidata.items())))
+        return 'Graph(\n  {},\n  epidata={})'.format(triples, epidata)
+
     def __eq__(self, other):
         if not isinstance(other, Graph):
             return NotImplemented

penman/layout.py

@@ -52,6 +52,7 @@
 
 from typing import Union, Mapping
 import copy
+import logging
 
 from penman.exceptions import LayoutError
 from penman.types import Variable
@@ -61,6 +62,9 @@
 from penman.model import Model
 
 
+logger = logging.getLogger(__name__)
+
+
 _Nodemap = Mapping[Variable, Union[Node, None]]
 
 
@@ -104,7 +108,9 @@ def interpret(t: Tree, model: Model = None) -> Graph:
     if model is None:
         model = Model()
     top, triples, epidata = _interpret_node(t.node, model)
-    return Graph(triples, top=top, epidata=epidata, metadata=t.metadata)
+    g = Graph(triples, top=top, epidata=epidata, metadata=t.metadata)
+    logger.info('Interpreted: %s', g)
+    return g
 
 
 def _interpret_node(t: Node, model: Model):
@@ -158,7 +164,12 @@ def configure(g: Graph,
         if len(data) >= data_count:
             raise LayoutError('possible cycle in configuration')
         data = skipped + data
-    return Tree(node, metadata=g.metadata)
+        # remove any superfluous POPs
+        while data and data[-1] is POP:
+            data.pop()
+    tree = Tree(node, metadata=g.metadata)
+    logger.debug('Configured: %s', tree)
+    return tree
 
 
 def _configure(g, top, model, strict):

penman/lexer.py

@@ -11,6 +11,9 @@
 from penman.exceptions import DecodeError
 
 
+logger = logging.getLogger(__name__)
+
+
 # These are the regex patterns for parsing. They must not have any
 # capturing groups. They are used during lexing and will be
 # checked by name during parsing.
@@ -200,17 +203,24 @@ def lex(lines: Union[Iterable[str], str],
     else:
         regex = PENMAN_RE
 
-    logging.debug('Lexing with pattern:\n{}'.format(regex.pattern))
-
     tokens = _lex(lines, regex)
     return TokenIterator(tokens)
 
 
 def _lex(lines: Iterable[str], regex: Pattern[str]) -> Iterator[Token]:
     for i, line in enumerate(lines, 1):
-        for m in regex.finditer(line):
+        logger.debug('Line %d: %r', i, line)
+        matches = list(regex.finditer(line))
+        tokens = []
+        for m in matches:
             if m.lastgroup is None:
                 raise ValueError(
                     'Lexer pattern generated a match without a named '
                     'capturing group:\n{}'.format(regex.pattern))
-            yield Token(m.lastgroup, m.group(), i, m.start(), line)
+            tokens.append(Token(m.lastgroup, m.group(), i, m.start(), line))
+
+        if logger.isEnabledFor(logging.DEBUG):
+            for token in tokens:
+                logger.debug(token)
+
+        yield from tokens