flake8-aided fixes

README.md

@@ -15,7 +15,7 @@ to output to multiple formats.
 Requirements:
 * python >= 3.8
 * numpy
-* klamath (used for `gdsii` i/o and library management)
+* klamath (optional, used for `gdsii` i/o)
 * matplotlib (optional, used for `visualization` functions and `text`)
 * ezdxf (optional, used for `dxf` i/o)
 * fatamorgana (optional, used for `oasis` i/o)
@@ -49,9 +49,3 @@ pip3 install git+https://mpxd.net/code/jan/masque.git@release
     - boolean ops
 * Construct polygons from bitmap using `skimage.find_contours`
 * Deal with shape repetitions for dxf, svg
-
-* this approach has an issue: how add devices together?
-   - need to add the other device by name
-   - need to know the other device's ports
-   - 
-   - also: device doesn't know its own name, can't wrap itself into a ref

examples/pic2mask.py

@@ -0,0 +1,41 @@
+# pip install pillow scikit-image
+# or
+# sudo apt install python3-pil python3-skimage
+
+from PIL import Image
+from skimage.measure import find_contours
+from matplotlib import pyplot
+import numpy
+
+from masque import Pattern, Library, Polygon
+from masque.file.gdsii import writefile
+
+#
+# Read the image into a numpy array
+#
+im = Image.open('./Desktop/Camera/IMG_20220626_091101.jpg')
+
+aa = numpy.array(im.convert(mode='L').getdata()).reshape(im.height, im.width)
+
+threshold = (aa.max() - aa.min()) / 2
+
+#
+# Find edge contours and plot them
+#
+contours = find_contours(aa, threshold)
+
+pyplot.imshow(aa)
+for contour in contours:
+    pyplot.plot(contour[:, 1], contour[:, 0], linewidth=2)
+pyplot.show(block=False)
+
+#
+# Create the layout from the contours
+#
+pat = Pattern()
+pat.shapes = [Polygon(vertices=vv) for vv in contours if len(vv) < 1_000]
+
+lib = {}
+lib['my_mask_name'] = pat
+
+writefile(lib, 'test_contours.gds', meters_per_unit=1e-9)

masque/__init__.py

@@ -28,7 +28,7 @@
 """
 
 from .error import MasqueError, PatternError, LibraryError, BuildError
-from .shapes import Shape
+from .shapes import Shape, Polygon, Path, Circle, Arc, Ellipse
 from .label import Label
 from .ref import Ref
 from .pattern import Pattern

masque/builder/builder.py

@@ -1,17 +1,12 @@
-from typing import Dict, Iterable, List, Tuple, Union, TypeVar, Any, Iterator, Optional, Sequence
+from typing import Dict, Tuple, Union, TypeVar, Optional, Sequence
-from typing import overload, KeysView, ValuesView, MutableMapping, Mapping
+from typing import MutableMapping, Mapping
 import copy
-import warnings
-import traceback
 import logging
-from collections import Counter
-from abc import ABCMeta
 
 import numpy
 from numpy import pi
-from numpy.typing import ArrayLike, NDArray
+from numpy.typing import ArrayLike
 
-from ..traits import PositionableImpl, Rotatable, PivotableImpl, Copyable, Mirrorable
 from ..pattern import Pattern
 from ..ref import Ref
 from ..library import MutableLibrary
@@ -241,8 +236,6 @@ class Builder(PortList):
             `PortError` if applying the prefixes results in duplicate port
                 names.
         """
-        from ..pattern import Pattern
-
         if library is None:
             if hasattr(source, 'library') and isinstance(source, MutableLibrary):
                 library = source.library

masque/builder/port_utils.py

@@ -82,6 +82,7 @@ def pat2dev(
 
     ports = {}
     annotated_cells = set()
+
     def find_ports_each(pat, hierarchy, transform, memo) -> Pattern:
         if len(hierarchy) > max_depth:
             if max_depth >= 999_999:

masque/builder/utils.py

@@ -1,5 +1,5 @@
-from typing import Dict, Tuple, List, Mapping, Sequence, SupportsFloat
+from typing import Dict, Mapping, Sequence, SupportsFloat
-from typing import Optional, Union, Any, cast, TYPE_CHECKING
+from typing import Optional, Union, cast, TYPE_CHECKING
 from pprint import pformat
 
 import numpy

masque/file/dxf.py

@@ -1,7 +1,7 @@
 """
 DXF file format readers and writers
 """
-from typing import List, Any, Dict, Tuple, Callable, Union, Sequence, Iterable, Mapping
+from typing import List, Any, Dict, Tuple, Callable, Union, Iterable, Mapping
 import re
 import io
 import base64
@@ -17,7 +17,6 @@ from .. import Pattern, Ref, PatternError, Label, Shape
 from ..shapes import Polygon, Path
 from ..repetition import Grid
 from ..utils import rotation_matrix_2d, layer_t
-from .gdsii import check_valid_names
 
 
 logger = logging.getLogger(__name__)
@@ -52,8 +51,11 @@ def write(
     DXF does not support shape repetition (only block repeptition). Please call
     library.wrap_repeated_shapes() before writing to file.
 
-    If you want pattern polygonized with non-default arguments, just call `pattern.polygonize()`
+    Other functions you may want to call:
-     prior to calling this function.
+        - `masque.file.oasis.check_valid_names(library.keys())` to check for invalid names
+        - `library.dangling_references()` to check for references to missing patterns
+        - `pattern.polygonize()` for any patterns with shapes other
+            than `masque.shapes.Polygon` or `masque.shapes.Path`
 
     Only `Grid` repetition objects with manhattan basis vectors are preserved as arrays. Since DXF
      rotations apply to basis vectors while `masque`'s rotations do not, the basis vectors of an
@@ -70,8 +72,6 @@ def write(
     """
     #TODO consider supporting DXF arcs?
 
-    check_valid_names(library.keys())
-
     pattern = library[top_name]
 
     # Create library
@@ -83,7 +83,7 @@ def write(
 
     # Now create a block for each referenced pattern, and add in any shapes
     for name, pat in library.items():
-        assert(pat is not None)
+        assert pat is not None
         block = lib.blocks.new(name=name)
 
         _shapes_to_elements(block, pat.shapes)
@@ -173,8 +173,9 @@ def read(
     msp = lib.modelspace()
 
     npat = _read_block(msp, clean_vertices)
-    patterns_dict = dict([npat]
+    patterns_dict = dict(
-        + [_read_block(bb, clean_vertices) for bb in lib.blocks if bb.name != '*Model_Space'])
+        [npat] + [_read_block(bb, clean_vertices) for bb in lib.blocks if bb.name != '*Model_Space']
+        )
 
     library_info = {
         'layers': [ll.dxfattribs() for ll in lib.layers]
@@ -323,8 +324,10 @@ def _shapes_to_elements(
     #   Could set do paths with width setting, but need to consider endcaps.
     for shape in shapes:
         if shape.repetition is not None:
-            raise PatternError('Shape repetitions are not supported by DXF.'
+            raise PatternError(
-                ' Please call library.wrap_repeated_shapes() before writing to file.')
+                'Shape repetitions are not supported by DXF.'
+                ' Please call library.wrap_repeated_shapes() before writing to file.'
+                )
 
         attribs = {'layer': _mlayer2dxf(shape.layer)}
         for polygon in shape.to_polygons():

masque/file/gdsii.py

@@ -18,14 +18,10 @@ Notes:
  * GDS does not support library- or structure-level annotations
  * Creation/modification/access times are set to 1900-01-01 for reproducibility.
 """
-from typing import List, Any, Dict, Tuple, Callable, Union, Iterable, Optional
+from typing import List, Any, Dict, Tuple, Callable, Union, Iterable
-from typing import Sequence, BinaryIO, Mapping, cast
+from typing import BinaryIO, Mapping
-import re
 import io
 import mmap
-import copy
-import base64
-import struct
 import logging
 import pathlib
 import gzip
@@ -83,10 +79,13 @@ def write(
             otherwise `0`
 
     GDS does not support shape repetition (only cell repeptition). Please call
-    library.wrap_repeated_shapes() before writing to file.
+    `library.wrap_repeated_shapes()` before writing to file.
 
-    If you want pattern polygonized with non-default arguments, just call `pattern.polygonize()`
+    Other functions you may want to call:
-     prior to calling this function.
+        - `masque.file.gdsii.check_valid_names(library.keys())` to check for invalid names
+        - `library.dangling_references()` to check for references to missing patterns
+        - `pattern.polygonize()` for any patterns with shapes other
+            than `masque.shapes.Polygon` or `masque.shapes.Path`
 
     Args:
         library: A {name: Pattern} mapping of patterns to write.
@@ -98,10 +97,6 @@ def write(
         library_name: Library name written into the GDSII file.
             Default 'masque-klamath'.
     """
-    check_valid_names(library.keys())
-
-    # TODO check all hierarchy present
-
     if not isinstance(library, MutableLibrary):
         if isinstance(library, dict):
             library = WrapLibrary(library)
@@ -504,56 +499,6 @@ def _labels_to_texts(labels: List[Label]) -> List[klamath.elements.Text]:
     return texts
 
 
-def disambiguate_pattern_names(
-        names: Iterable[str],
-        max_name_length: int = 32,
-        suffix_length: int = 6,
-        ) -> List[str]:
-    """
-    Args:
-        names: List of pattern names to disambiguate
-        max_name_length: Names longer than this will be truncated
-        suffix_length: Names which get truncated are truncated by this many extra characters. This is to
-            leave room for a suffix if one is necessary.
-    """
-    new_names = []
-    for name in names:
-        # Shorten names which already exceed max-length
-        if len(name) > max_name_length:
-            shortened_name = name[:max_name_length - suffix_length]
-            logger.warning(f'Pattern name "{name}" is too long ({len(name)}/{max_name_length} chars),\n'
-                           + f' shortening to "{shortened_name}" before generating suffix')
-        else:
-            shortened_name = name
-
-        # Remove invalid characters
-        sanitized_name = re.compile(r'[^A-Za-z0-9_\?\$]').sub('_', shortened_name)
-
-        # Add a suffix that makes the name unique
-        i = 0
-        suffixed_name = sanitized_name
-        while suffixed_name in new_names or suffixed_name == '':
-            suffix = base64.b64encode(struct.pack('>Q', i), b'$?').decode('ASCII')
-
-            suffixed_name = sanitized_name + '$' + suffix[:-1].lstrip('A')
-            i += 1
-
-        if sanitized_name == '':
-            logger.warning(f'Empty pattern name saved as "{suffixed_name}"')
-
-        # Encode into a byte-string and perform some final checks
-        encoded_name = suffixed_name.encode('ASCII')
-        if len(encoded_name) == 0:
-            # Should never happen since zero-length names are replaced
-            raise PatternError(f'Zero-length name after sanitize+encode,\n originally "{name}"')
-        if len(encoded_name) > max_name_length:
-            raise PatternError(f'Pattern name "{encoded_name!r}" length > {max_name_length} after encode,\n'
-                               + f' originally "{name}"')
-
-        new_names.append(suffixed_name)
-    return new_names
-
-
 def load_library(
         stream: BinaryIO,
         *,

masque/file/oasis.py

@@ -12,11 +12,7 @@ Note that OASIS references follow the same convention as `masque`,
    vectors or offsets.
 """
 from typing import List, Any, Dict, Tuple, Callable, Union, Sequence, Iterable, Mapping, Optional, cast
-import re
 import io
-import copy
-import base64
-import struct
 import logging
 import pathlib
 import gzip
@@ -77,8 +73,11 @@ def build(
         If a layer map is provided, layer strings will be converted
             automatically, and layer names will be written to the file.
 
-    If you want pattern polygonized with non-default arguments, just call `pattern.polygonize()`
+    Other functions you may want to call:
-     prior to calling this function.
+        - `masque.file.oasis.check_valid_names(library.keys())` to check for invalid names
+        - `library.dangling_references()` to check for references to missing patterns
+        - `pattern.polygonize()` for any patterns with shapes other
+            than `masque.shapes.Polygon`, `masque.shapes.Path`, or `masque.shapes.Circle`
 
     Args:
         library: A {name: Pattern} mapping of patterns to write.
@@ -97,10 +96,6 @@ def build(
     Returns:
         `fatamorgana.OasisLayout`
     """
-    check_valid_names(library.keys())
-
-    # TODO check all hierarchy present
-
     if not isinstance(library, MutableLibrary):
         if isinstance(library, dict):
             library = WrapLibrary(library)
@@ -130,7 +125,7 @@ def build(
                 for tt in (True, False)]
 
         def layer2oas(mlayer: layer_t) -> Tuple[int, int]:
-            assert(layer_map is not None)
+            assert layer_map is not None
             layer_num = layer_map[mlayer] if isinstance(mlayer, str) else mlayer
             return _mlayer2oas(layer_num)
     else:
@@ -270,7 +265,7 @@ def read(
                 # note XELEMENT has no repetition
                 continue
 
-            assert(not isinstance(element.repetition, fatamorgana.ReuseRepetition))
+            assert not isinstance(element.repetition, fatamorgana.ReuseRepetition)
             repetition = repetition_fata2masq(element.repetition)
 
             # Switch based on element type:
@@ -481,7 +476,7 @@ def _placement_to_ref(placement: fatrec.Placement, lib: fatamorgana.OasisLayout)
     """
     Helper function to create a Ref from a placment. Sets ref.target to the placement name.
     """
-    assert(not isinstance(placement.repetition, fatamorgana.ReuseRepetition))
+    assert not isinstance(placement.repetition, fatamorgana.ReuseRepetition)
     xy = numpy.array((placement.x, placement.y))
     mag = placement.magnification if placement.magnification is not None else 1
 
@@ -659,7 +654,7 @@ def repetition_masq2fata(
         frep = fatamorgana.ArbitraryRepetition(diff_ints[:, 0], diff_ints[:, 1])        # type: ignore
         offset = rep.displacements[0, :]
     else:
-        assert(rep is None)
+        assert rep is None
         frep = None
         offset = (0, 0)
     return frep, offset
@@ -682,14 +677,14 @@ def properties_to_annotations(
         ) -> annotations_t:
     annotations = {}
     for proprec in properties:
-        assert(proprec.name is not None)
+        assert proprec.name is not None
         if isinstance(proprec.name, int):
             key = propnames[proprec.name].string
         else:
             key = proprec.name.string
         values: List[Union[str, float, int]] = []
 
-        assert(proprec.values is not None)
+        assert proprec.values is not None
         for value in proprec.values:
             if isinstance(value, (float, int)):
                 values.append(value)

masque/file/svg.py

@@ -1,7 +1,7 @@
 """
 SVG file format readers and writers
 """
-from typing import Dict, Optional, Mapping
+from typing import Mapping
 import warnings
 
 import numpy

masque/file/utils.py

@@ -1,14 +1,11 @@
 """
 Helper functions for file reading and writing
 """
-from typing import Set, Tuple, List, Iterable, Mapping
 import re
-import copy
 import pathlib
 import logging
 
 from .. import Pattern, PatternError
-from ..library import Library, WrapROLibrary
 from ..shapes import Polygon, Path
 
 

masque/label.py

@@ -1,4 +1,4 @@
-from typing import Tuple, Dict, Optional, TypeVar
+from typing import Dict, Optional, TypeVar
 import copy
 
 import numpy

masque/library.py

@@ -3,9 +3,8 @@ Library class for managing unique name->pattern mappings and
  deferred loading or creation.
 """
 from typing import List, Dict, Callable, TypeVar, Generic, Type, TYPE_CHECKING
-from typing import Any, Tuple, Union, Iterator, Mapping, MutableMapping, Set, Optional, Sequence
+from typing import Tuple, Union, Iterator, Mapping, MutableMapping, Set, Optional, Sequence
 import logging
-import copy
 import base64
 import struct
 import re
@@ -14,7 +13,7 @@ from collections import defaultdict
 from abc import ABCMeta, abstractmethod
 
 import numpy
-from numpy.typing import ArrayLike, NDArray, NDArray
+from numpy.typing import ArrayLike
 
 from .error import LibraryError, PatternError
 from .utils import rotation_matrix_2d, normalize_mirror
@@ -45,21 +44,51 @@ class Library(Mapping[str, Pattern], metaclass=ABCMeta):
     def __repr__(self) -> str:
         return '<Library with keys ' + repr(list(self.keys())) + '>'
 
-    def referenced_patterns(
+    def dangling_references(
             self,
-            tops: Union[str, Sequence[str]],
+            tops: Union[None, str, Sequence[str]] = None,
-            skip: Optional[Set[Optional[str]]] = None,
             ) -> Set[Optional[str]]:
         """
-        Get the set of all pattern names referenced by `top`. Recursively traverses into any refs.
+        Get the set of all pattern names not present in the library but referenced
+        by `tops`, recursively traversing any refs.
+
+        If `tops` are not given, all patterns in the library are checked.
 
         Args:
-            top: Name of the top pattern(s) to check.
+            tops: Name(s) of the pattern(s) to check.
+                Default is all patterns in the library.
             skip: Memo, set patterns which have already been traversed.
 
         Returns:
             Set of all referenced pattern names
         """
+        if tops is None:
+            tops = tuple(self.keys())
+
+        referenced = self.referenced_patterns(tops)
+        return referenced - set(self.keys())
+
+    def referenced_patterns(
+            self,
+            tops: Union[None, str, Sequence[str]] = None,
+            skip: Optional[Set[Optional[str]]] = None,
+            ) -> Set[Optional[str]]:
+        """
+        Get the set of all pattern names referenced by `tops`. Recursively traverses into any refs.
+
+        If `tops` are not given, all patterns in the library are checked.
+
+        Args:
+            tops: Name(s) of the pattern(s) to check.
+                Default is all patterns in the library.
+            skip: Memo, set patterns which have already been traversed.
+
+        Returns:
+            Set of all referenced pattern names
+        """
+        if tops is None:
+            tops = tuple(self.keys())
+
         if skip is None:
             skip = set([None])
 
@@ -73,17 +102,17 @@ class Library(Mapping[str, Pattern], metaclass=ABCMeta):
 
         # Perform recursive lookups, but only once for each name
         for target in targets - skip:
-            assert(target is not None)
+            assert target is not None
-            self.referenced_patterns(target, skip)
+            if target in self:
+                targets |= self.referenced_patterns(target, skip=skip)
             skip.add(target)
 
         return targets
 
-    # TODO maybe not for immutable?
     def subtree(
             self,
             tops: Union[str, Sequence[str]],
-            ) -> Library:
+            ) -> 'Library':
         """
          Return a new `Library`, containing only the specified patterns and the patterns they
         reference (recursively).
@@ -184,7 +213,7 @@ class Library(Mapping[str, Pattern], metaclass=ABCMeta):
         for top in tops:
             flatten_single(top)
 
-        assert(None not in flattened.values())
+        assert None not in flattened.values()
         return flattened    # type: ignore
 
     def get_name(
@@ -364,7 +393,7 @@ class MutableLibrary(Generic[VVV], Library, metaclass=ABCMeta):
     #def __len__(self) -> int:
 
     @abstractmethod
-    def __setitem__(self, key: str, value: VVV) -> None:  # TODO
+    def __setitem__(self, key: str, value: VVV) -> None:
         pass
 
     @abstractmethod
@@ -390,7 +419,7 @@ class MutableLibrary(Generic[VVV], Library, metaclass=ABCMeta):
 
         Args:
             other: The library to insert keys from
-            use_ours: Decision function for name conflicts, called with cell name.
+            use_ours: Decision function for name conflicts, called with pattern name.
                 Should return `True` if the value from `self` should be used.
             use_theirs: Decision function for name conflicts. Same format as `use_ours`.
                 Should return `True` if the value from `other` should be used.
@@ -451,13 +480,14 @@ class MutableLibrary(Generic[VVV], Library, metaclass=ABCMeta):
             exclude_types = ()
 
         if label2name is None:
-            label2name = lambda label: self.get_name('_shape')
+            def label2name(label):
-
+                return self.get_name('_shape_')
+            #label2name = lambda label: self.get_name('_shape')
 
         shape_counts: MutableMapping[Tuple, int] = defaultdict(int)
         shape_funcs = {}
 
-        ### First pass ###
+        # ## First pass ##
         #  Using the label tuple from `.normalized_form()` as a key, check how many of each shape
         # are present and store the shape function for each one
         for pat in tuple(self.values()):
@@ -476,7 +506,7 @@ class MutableLibrary(Generic[VVV], Library, metaclass=ABCMeta):
             shape_pat = Pattern(shapes=[shape_func()])
             shape_pats[label] = shape_pat
 
-        ### Second pass ###
+        # ## Second pass ##
         for pat in tuple(self.values()):
             #  Store `[(index_in_shapes, values_from_normalized_form), ...]` for all shapes which
             # are to be replaced.
@@ -534,7 +564,9 @@ class MutableLibrary(Generic[VVV], Library, metaclass=ABCMeta):
         from .pattern import Pattern
 
         if name_func is None:
-            name_func = lambda _pat, _shape: self.get_name('_rep')
+            def name_func(_pat, _shape):
+                return self.get_name('_rep_')
+            #name_func = lambda _pat, _shape: self.get_name('_rep')
 
         for pat in tuple(self.values()):
             new_shapes = []
@@ -710,7 +742,7 @@ class LazyLibrary(MutableLibrary):
     def clear_cache(self: LL) -> LL:
         """
         Clear the cache of this library.
-        This is usually used before modifying or deleting cells, e.g. when merging
+        This is usually used before modifying or deleting patterns, e.g. when merging
           with another library.
 
         Returns:

masque/pattern.py

@@ -2,11 +2,10 @@
  Base object representing a lithography mask.
 """
 
-from typing import List, Callable, Tuple, Dict, Union, Set, Sequence, Optional, Type, overload, cast
+from typing import List, Callable, Dict, Union, Set, Sequence, Optional, cast
-from typing import Mapping, MutableMapping, Iterable, TypeVar, Any
+from typing import Mapping, TypeVar, Any
 import copy
 from itertools import chain
-from collections import defaultdict
 
 import numpy
 from numpy import inf
@@ -14,9 +13,9 @@ from numpy.typing import NDArray, ArrayLike
 # .visualize imports matplotlib and matplotlib.collections
 
 from .ref import Ref
-from .shapes import Shape, Polygon
+from .shapes import Shape
 from .label import Label
-from .utils import rotation_matrix_2d, normalize_mirror, AutoSlots, annotations_t
+from .utils import rotation_matrix_2d, AutoSlots, annotations_t
 from .error import PatternError
 from .traits import AnnotatableImpl, Scalable, Mirrorable, Rotatable, Positionable, Repeatable
 from .ports import Port, PortList
@@ -30,7 +29,11 @@ class Pattern(PortList, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
     2D layout consisting of some set of shapes, labels, and references to other Pattern objects
      (via Ref). Shapes are assumed to inherit from masque.shapes.Shape or provide equivalent functions.
     """
-    __slots__ = ('shapes', 'labels', 'refs', 'ports')
+    __slots__ = (
+        'shapes', 'labels', 'refs', 'ports',
+        # inherited
+        '_offset', '_annotations'
+        )
 
     shapes: List[Shape]
     """ List of all shapes in this Pattern.
@@ -116,7 +119,7 @@ class Pattern(PortList, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
             )
         return new
 
-    def append(self: P, other_pattern: Pattern) -> P:
+    def append(self: P, other_pattern: 'Pattern') -> P:
         """
         Appends all shapes, labels and refs from other_pattern to self's shapes,
           labels, and supbatterns.
@@ -321,7 +324,7 @@ class Pattern(PortList, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
             `[[x_min, y_min], [x_max, y_max]]`
         """
         bounds = self.get_bounds(library)
-        assert(bounds is not None)
+        assert bounds is not None
         return bounds
 
     def translate_elements(self: P, offset: ArrayLike) -> P:

masque/ports.py

@@ -1,6 +1,5 @@
-from typing import Dict, Iterable, List, Tuple, Iterator, Optional, Sequence, MutableMapping
+from typing import Dict, Iterable, List, Tuple, KeysView, ValuesView, ItemsView
-from typing import overload, KeysView, ValuesView, ItemsView, TYPE_CHECKING, Union, TypeVar, Any
+from typing import overload, Union, Optional, TypeVar
-import copy
 import warnings
 import traceback
 import logging
@@ -14,17 +13,11 @@ from numpy.typing import ArrayLike, NDArray
 from .traits import PositionableImpl, Rotatable, PivotableImpl, Copyable, Mirrorable
 from .utils import AutoSlots, rotate_offsets_around
 from .error import PortError
-from .library import MutableLibrary
-from .builder import Tool
-
-if TYPE_CHECKING:
-    from .builder import Builder
 
 
 logger = logging.getLogger(__name__)
 
 
-
 P = TypeVar('P', bound='Port')
 PL  = TypeVar('PL',  bound='PortList')
 PL2 = TypeVar('PL2', bound='PortList')
@@ -200,8 +193,6 @@ class PortList(metaclass=ABCMeta):
         Returns:
             self
         """
-
-
         new_ports = {
             names[0]: Port(offset, rotation=rotation, ptype=ptype),
             names[1]: Port(offset, rotation=rotation + pi, ptype=ptype),
@@ -335,7 +326,6 @@ class PortList(metaclass=ABCMeta):
         type_conflicts = numpy.array([st != ot and st != 'unk' and ot != 'unk'
                                       for st, ot in zip(s_types, o_types)])
         if type_conflicts.any():
-            ports = numpy.where(type_conflicts)
             msg = 'Ports have conflicting types:\n'
             for nn, (k, v) in enumerate(map_in.items()):
                 if type_conflicts[nn]:
@@ -353,7 +343,7 @@ class PortList(metaclass=ABCMeta):
 
         if not numpy.allclose(rotations[:1], rotations):
             rot_deg = numpy.rad2deg(rotations)
-            msg = f'Port orientations do not match:\n'
+            msg = 'Port orientations do not match:\n'
             for nn, (k, v) in enumerate(map_in.items()):
                 msg += f'{k} | {rot_deg[nn]:g} | {v}\n'
             raise PortError(msg)
@@ -362,7 +352,7 @@ class PortList(metaclass=ABCMeta):
         rotate_offsets_around(o_offsets, pivot, rotations[0])
         translations = s_offsets - o_offsets
         if not numpy.allclose(translations[:1], translations):
-            msg = f'Port translations do not match:\n'
+            msg = 'Port translations do not match:\n'
             for nn, (k, v) in enumerate(map_in.items()):
                 msg += f'{k} | {translations[nn]} | {v}\n'
             raise PortError(msg)

masque/ref.py

@@ -4,7 +4,7 @@
 """
 #TODO more top-level documentation
 
-from typing import Dict, Tuple, Optional, Sequence, Mapping, TYPE_CHECKING, Any, TypeVar
+from typing import Dict, Optional, Sequence, Mapping, TYPE_CHECKING, Any, TypeVar
 import copy
 
 import numpy
@@ -12,7 +12,7 @@ from numpy import pi
 from numpy.typing import NDArray, ArrayLike
 
 from .error import PatternError
-from .utils import is_scalar, AutoSlots, annotations_t
+from .utils import is_scalar, annotations_t
 from .repetition import Repetition
 from .traits import (
     PositionableImpl, RotatableImpl, ScalableImpl,
@@ -121,8 +121,8 @@ class Ref(
     def as_pattern(
             self,
             *,
-            pattern: Optional[Pattern] = None,
+            pattern: Optional['Pattern'] = None,
-            library: Optional[Mapping[str, Pattern]] = None,
+            library: Optional[Mapping[str, 'Pattern']] = None,
             ) -> 'Pattern':
         """
         Args:
@@ -138,7 +138,7 @@ class Ref(
             if library is None:
                 raise PatternError('as_pattern() must be given a pattern or library.')
 
-            assert(self.target is not None)
+            assert self.target is not None
             pattern = library[self.target]
 
         pattern = pattern.deepcopy()
@@ -196,6 +196,8 @@ class Ref(
             raise PatternError('as_pattern() must be given a pattern or library.')
         if pattern is None and self.target is None:
             return None
+        if self.target not in library:
+            raise PatternError(f'get_bounds() called on dangling reference to "{self.target}"')
         return self.as_pattern(pattern=pattern, library=library).get_bounds()
 
     def __repr__(self) -> str:

masque/repetition.py

@@ -3,7 +3,7 @@
      instances of an object .
 """
 
-from typing import Union, Dict, Optional, Sequence, Any, Type
+from typing import Union, Dict, Optional, Any, Type
 import copy
 from abc import ABCMeta, abstractmethod
 

masque/shapes/arc.py

@@ -171,9 +171,9 @@ class Arc(Shape, metaclass=AutoSlots):
             raw: bool = False,
             ) -> None:
         if raw:
-            assert(isinstance(radii, numpy.ndarray))
+            assert isinstance(radii, numpy.ndarray)
-            assert(isinstance(angles, numpy.ndarray))
+            assert isinstance(angles, numpy.ndarray)
-            assert(isinstance(offset, numpy.ndarray))
+            assert isinstance(offset, numpy.ndarray)
             self._radii = radii
             self._angles = angles
             self._width = width

masque/shapes/circle.py

@@ -59,7 +59,7 @@ class Circle(Shape, metaclass=AutoSlots):
             raw: bool = False,
             ) -> None:
         if raw:
-            assert(isinstance(offset, numpy.ndarray))
+            assert isinstance(offset, numpy.ndarray)
             self._radius = radius
             self._offset = offset
             self._repetition = repetition

masque/shapes/ellipse.py

@@ -106,8 +106,8 @@ class Ellipse(Shape, metaclass=AutoSlots):
             raw: bool = False,
             ) -> None:
         if raw:
-            assert(isinstance(radii, numpy.ndarray))
+            assert isinstance(radii, numpy.ndarray)
-            assert(isinstance(offset, numpy.ndarray))
+            assert isinstance(offset, numpy.ndarray)
             self._radii = radii
             self._offset = offset
             self._rotation = rotation

masque/shapes/path.py

@@ -162,9 +162,9 @@ class Path(Shape, metaclass=AutoSlots):
         self._cap_extensions = None     # Since .cap setter might access it
 
         if raw:
-            assert(isinstance(vertices, numpy.ndarray))
+            assert isinstance(vertices, numpy.ndarray)
-            assert(isinstance(offset, numpy.ndarray))
+            assert isinstance(offset, numpy.ndarray)
-            assert(isinstance(cap_extensions, numpy.ndarray) or cap_extensions is None)
+            assert isinstance(cap_extensions, numpy.ndarray) or cap_extensions is None
             self._vertices = vertices
             self._offset = offset
             self._repetition = repetition
@@ -409,7 +409,7 @@ class Path(Shape, metaclass=AutoSlots):
         if self.cap == PathCap.Square:
             extensions = numpy.full(2, self.width / 2)
         elif self.cap == PathCap.SquareCustom:
-            assert(isinstance(self.cap_extensions, numpy.ndarray))
+            assert isinstance(self.cap_extensions, numpy.ndarray)
             extensions = self.cap_extensions
         else:
             # Flush or Circle

masque/shapes/polygon.py

@@ -88,8 +88,8 @@ class Polygon(Shape, metaclass=AutoSlots):
             raw: bool = False,
             ) -> None:
         if raw:
-            assert(isinstance(vertices, numpy.ndarray))
+            assert isinstance(vertices, numpy.ndarray)
-            assert(isinstance(offset, numpy.ndarray))
+            assert isinstance(offset, numpy.ndarray)
             self._vertices = vertices
             self._offset = offset
             self._repetition = repetition
@@ -212,17 +212,17 @@ class Polygon(Shape, metaclass=AutoSlots):
         """
         if lx is None:
             if xctr is None:
-                assert(xmin is not None)
+                assert xmin is not None
-                assert(xmax is not None)
+                assert xmax is not None
                 xctr = 0.5 * (xmax + xmin)
                 lx = xmax - xmin
             elif xmax is None:
-                assert(xmin is not None)
+                assert xmin is not None
-                assert(xctr is not None)
+                assert xctr is not None
                 lx = 2 * (xctr - xmin)
             elif xmin is None:
-                assert(xctr is not None)
+                assert xctr is not None
-                assert(xmax is not None)
+                assert xmax is not None
                 lx = 2 * (xmax - xctr)
             else:
                 raise PatternError('Two of xmin, xctr, xmax, lx must be None!')
@@ -230,29 +230,29 @@ class Polygon(Shape, metaclass=AutoSlots):
             if xctr is not None:
                 pass
             elif xmax is None:
-                assert(xmin is not None)
+                assert xmin is not None
-                assert(lx is not None)
+                assert lx is not None
                 xctr = xmin + 0.5 * lx
             elif xmin is None:
-                assert(xmax is not None)
+                assert xmax is not None
-                assert(lx is not None)
+                assert lx is not None
                 xctr = xmax - 0.5 * lx
             else:
                 raise PatternError('Two of xmin, xctr, xmax, lx must be None!')
 
         if ly is None:
             if yctr is None:
-                assert(ymin is not None)
+                assert ymin is not None
-                assert(ymax is not None)
+                assert ymax is not None
                 yctr = 0.5 * (ymax + ymin)
                 ly = ymax - ymin
             elif ymax is None:
-                assert(ymin is not None)
+                assert ymin is not None
-                assert(yctr is not None)
+                assert yctr is not None
                 ly = 2 * (yctr - ymin)
             elif ymin is None:
-                assert(yctr is not None)
+                assert yctr is not None
-                assert(ymax is not None)
+                assert ymax is not None
                 ly = 2 * (ymax - yctr)
             else:
                 raise PatternError('Two of ymin, yctr, ymax, ly must be None!')
@@ -260,12 +260,12 @@ class Polygon(Shape, metaclass=AutoSlots):
             if yctr is not None:
                 pass
             elif ymax is None:
-                assert(ymin is not None)
+                assert ymin is not None
-                assert(ly is not None)
+                assert ly is not None
                 yctr = ymin + 0.5 * ly
             elif ymin is None:
-                assert(ly is not None)
+                assert ly is not None
-                assert(ymax is not None)
+                assert ymax is not None
                 yctr = ymax - 0.5 * ly
             else:
                 raise PatternError('Two of ymin, yctr, ymax, ly must be None!')
@@ -331,7 +331,6 @@ class Polygon(Shape, metaclass=AutoSlots):
         poly.rotate(rotation)
         return poly
 
-
     def to_polygons(
             self,
             poly_num_points: Optional[int] = None,        # unused

masque/shapes/text.py

@@ -79,8 +79,8 @@ class Text(RotatableImpl, Shape, metaclass=AutoSlots):
             raw: bool = False,
             ) -> None:
         if raw:
-            assert(isinstance(offset, numpy.ndarray))
+            assert isinstance(offset, numpy.ndarray)
-            assert(isinstance(mirrored, numpy.ndarray))
+            assert isinstance(mirrored, numpy.ndarray)
             self._offset = offset
             self._layer = layer
             self._string = string

masque/traits/lockable.py

@@ -1,103 +0,0 @@
-from typing import TypeVar, Dict, Tuple, Any
-from abc import ABCMeta, abstractmethod
-
-#from ..error import PatternLockedError
-
-
-T = TypeVar('T', bound='Lockable')
-I = TypeVar('I', bound='LockableImpl')
-
-
-class Lockable(metaclass=ABCMeta):
-    """
-    Abstract class for all lockable entities
-    """
-    __slots__ = ()      # type: Tuple[str, ...]
-
-    '''
-    ---- Methods
-    '''
-    @abstractmethod
-    def lock(self: T) -> T:
-        """
-        Lock the object, disallowing further changes
-
-        Returns:
-            self
-        """
-        pass
-
-    @abstractmethod
-    def unlock(self: T) -> T:
-        """
-        Unlock the object, reallowing changes
-
-        Returns:
-            self
-        """
-        pass
-
-    @abstractmethod
-    def is_locked(self) -> bool:
-        """
-        Returns:
-            True if the object is locked
-        """
-        pass
-
-    def set_locked(self: T, locked: bool) -> T:
-        """
-        Locks or unlocks based on the argument.
-        No action if already in the requested state.
-
-        Args:
-            locked: State to set.
-
-        Returns:
-            self
-        """
-        if locked != self.is_locked():
-            if locked:
-                self.lock()
-            else:
-                self.unlock()
-        return self
-
-
-class LockableImpl(Lockable, metaclass=ABCMeta):
-    """
-    Simple implementation of Lockable
-    """
-    __slots__ = ()      # type: Tuple[str, ...]
-
-    locked: bool
-    """ If `True`, disallows changes to the object """
-
-    '''
-    ---- Non-abstract methods
-    '''
-    def __setattr__(self, name, value):
-        if self.locked and name != 'locked':
-            raise PatternLockedError()
-        object.__setattr__(self, name, value)
-
-    def __getstate__(self) -> Dict[str, Any]:
-        if hasattr(self, '__slots__'):
-            return {key: getattr(self, key) for key in self.__slots__}
-        else:
-            return self.__dict__
-
-    def __setstate__(self, state: Dict[str, Any]) -> None:
-        for k, v in state.items():
-            object.__setattr__(self, k, v)
-
-    def lock(self: I) -> I:
-        object.__setattr__(self, 'locked', True)
-        return self
-
-    def unlock(self: I) -> I:
-        object.__setattr__(self, 'locked', False)
-        return self
-
-    def is_locked(self) -> bool:
-        return self.locked

masque/traits/positionable.py

@@ -80,7 +80,7 @@ class Positionable(metaclass=ABCMeta):
         This is handy for destructuring like `xy_min, xy_max = entity.get_bounds_nonempty()`
         """
         bounds = self.get_bounds()
-        assert(bounds is not None)
+        assert bounds is not None
         return bounds
 
 

masque/traits/rotatable.py

@@ -3,11 +3,11 @@ from abc import ABCMeta, abstractmethod
 
 import numpy
 from numpy import pi
-from numpy.typing import ArrayLike, NDArray
+from numpy.typing import ArrayLike
 
 from .positionable import Positionable
 from ..error import MasqueError
-from ..utils import is_scalar, rotation_matrix_2d
+from ..utils import rotation_matrix_2d
 
 
 _empty_slots = ()     # Workaround to get mypy to ignore intentionally empty slots for superclass

masque/utils/pack2d.py

@@ -11,31 +11,6 @@ from ..pattern import Pattern
 from ..ref import Ref
 
 
-def pack_patterns(
-        library: Mapping[str, Pattern],
-        patterns: Sequence[str],
-        regions: numpy.ndarray,
-        spacing: Tuple[float, float],
-        presort: bool = True,
-        allow_rejects: bool = True,
-        packer: Callable = maxrects_bssf,
-        ) -> Tuple[Pattern, List[str]]:
-    half_spacing = numpy.array(spacing) / 2
-
-    bounds = [library[pp].get_bounds() for pp in patterns]
-    sizes = [bb[1] - bb[0] + spacing if bb is not None else spacing for bb in bounds]
-    offsets = [half_spacing - bb[0] if bb is not None else (0, 0) for bb in bounds]
-
-    locations, reject_inds = packer(sizes, regions, presort=presort, allow_rejects=allow_rejects)
-
-    pat = Pattern()
-    pat.refs = [Ref(pp, offset=oo + loc)
-                for pp, oo, loc in zip(patterns, offsets, locations)]
-
-    rejects = [patterns[ii] for ii in reject_inds]
-    return pat, rejects
-
-
 def maxrects_bssf(
         rects: ArrayLike,
         containers: ArrayLike,
@@ -165,3 +140,28 @@ def guillotine_bssf_sas(rect_sizes: numpy.ndarray,
                                 new_region0, new_region1))
 
     return rect_locs, rejected_inds
+
+
+def pack_patterns(
+        library: Mapping[str, Pattern],
+        patterns: Sequence[str],
+        regions: numpy.ndarray,
+        spacing: Tuple[float, float],
+        presort: bool = True,
+        allow_rejects: bool = True,
+        packer: Callable = maxrects_bssf,
+        ) -> Tuple[Pattern, List[str]]:
+    half_spacing = numpy.array(spacing) / 2
+
+    bounds = [library[pp].get_bounds() for pp in patterns]
+    sizes = [bb[1] - bb[0] + spacing if bb is not None else spacing for bb in bounds]
+    offsets = [half_spacing - bb[0] if bb is not None else (0, 0) for bb in bounds]
+
+    locations, reject_inds = packer(sizes, regions, presort=presort, allow_rejects=allow_rejects)
+
+    pat = Pattern()
+    pat.refs = [Ref(pp, offset=oo + loc)
+                for pp, oo, loc in zip(patterns, offsets, locations)]
+
+    rejects = [patterns[ii] for ii in reject_inds]
+    return pat, rejects

masque/utils/types.py

@@ -1,7 +1,7 @@
 """
 Type definitions
 """
-from typing import Union, Tuple, Sequence, Dict, List
+from typing import Union, Tuple, Dict, List
 
 
 layer_t = Union[int, Tuple[int, int], str]

masque/utils/vertices.py

@@ -83,7 +83,7 @@ def poly_contains_points(
     max_bounds = numpy.max(vertices, axis=0)[None, :]
 
     trivially_outside = ((points < min_bounds).any(axis=1)
-                       | (points > max_bounds).any(axis=1))
+                       | (points > max_bounds).any(axis=1))     # noqa: E128
 
     nontrivial = ~trivially_outside
     if trivially_outside.all():
@@ -101,10 +101,10 @@ def poly_contains_points(
 
     dv = numpy.roll(verts, -1, axis=0) - verts
     is_left = (dv[:, 0] * (ntpts[..., 1] - verts[:, 1])        # >0 if left of dv, <0 if right, 0 if on the line
-             - dv[:, 1] * (ntpts[..., 0] - verts[:, 0]))
+             - dv[:, 1] * (ntpts[..., 0] - verts[:, 0]))    # noqa: E128
 
     winding_number = ((upward & (is_left > 0)).sum(axis=0)
-                  - (downward & (is_left < 0)).sum(axis=0))
+                  - (downward & (is_left < 0)).sum(axis=0))    # noqa: E128
 
     nontrivial_inside = winding_number != 0        # filter nontrivial points based on winding number
     if include_boundary: