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removed all string type hints and replaced with forward references (n…
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…ot supported in Python 3.6)
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@dave-doty
dave-doty committed Jul 18, 2023
1 parent 602575d commit a292757
Showing 1 changed file with 23 additions and 47 deletions.
70 changes: 23 additions & 47 deletions scadnano/scadnano.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1023,7 +1023,7 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D

@staticmethod
def from_json(
json_map: Dict[str, Any]) -> 'Modification': # remove quotes when Py3.6 support dropped
json_map: Dict[str, Any]) -> Modification:
location = json_map[mod_location_key]
if location == "5'":
return Modification5Prime.from_json(json_map)
Expand Down Expand Up @@ -1061,9 +1061,8 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D
ret[mod_location_key] = "5'"
return ret

# remove quotes when Py3.6 support dropped
@staticmethod
def from_json(json_map: Dict[str, Any]) -> 'Modification5Prime':
def from_json(json_map: Dict[str, Any]) -> Modification5Prime:
display_text = json_map[mod_display_text_key]
location = json_map[mod_location_key]
assert location == "5'"
Expand Down Expand Up @@ -1098,9 +1097,8 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D
ret[mod_location_key] = "3'"
return ret

# remove quotes when Py3.6 support dropped
@staticmethod
def from_json(json_map: Dict[str, Any]) -> 'Modification3Prime':
def from_json(json_map: Dict[str, Any]) -> Modification3Prime:
display_text = json_map[mod_display_text_key]
location = json_map[mod_location_key]
assert location == "3'"
Expand Down Expand Up @@ -1138,9 +1136,8 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D
list(self.allowed_bases)) if suppress_indent else list(self.allowed_bases)
return ret

# remove quotes when Py3.6 support dropped
@staticmethod
def from_json(json_map: Dict[str, Any]) -> 'ModificationInternal':
def from_json(json_map: Dict[str, Any]) -> ModificationInternal:
display_text = json_map[mod_display_text_key]
location = json_map[mod_location_key]
assert location == "internal"
Expand Down Expand Up @@ -1186,7 +1183,7 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D
return dct

@staticmethod
def from_json(json_map: Dict[str, Any]) -> 'Position3D': # remove quotes when Py3.6 support dropped
def from_json(json_map: Dict[str, Any]) -> Position3D:
if position_origin_key in json_map:
origin_ = json_map[position_origin_key]
x = origin_[position_x_key]
Expand Down Expand Up @@ -1317,7 +1314,7 @@ def _assign_default_helices_view_order(self, helices_in_group: Dict[int, 'Helix'
self.helices_view_order = _check_helices_view_order_and_return(self.helices_view_order, helix_idxs)

@staticmethod
def from_json(json_map: dict, **kwargs: Any) -> 'HelixGroup': # remove quotes when Py3.6 support dropped
def from_json(json_map: dict, **kwargs: Any) -> HelixGroup:
grid: Grid = optional_field(Grid.none, json_map, grid_key, transformer=Grid)
# grid: Grid = Grid.none
# if grid_key in json_map:
Expand Down Expand Up @@ -1398,7 +1395,7 @@ def is_default(self) -> bool:
return self == _default_geometry

@staticmethod
def from_json(json_map: dict) -> 'Geometry': # remove quotes when Py3.6 support dropped
def from_json(json_map: dict) -> Geometry:
geometry = Geometry()
geometry.rise_per_base_pair = optional_field(_default_geometry.rise_per_base_pair, json_map,
rise_per_base_pair_key,
Expand Down Expand Up @@ -1621,7 +1618,7 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D
return NoIndent(dct) if suppress_indent and use_no_indent_helix else dct

@staticmethod
def from_json(json_map: dict) -> 'Helix': # remove quotes when Py3.6 support dropped
def from_json(json_map: dict) -> Helix:
grid_position: Optional[Tuple[int, int]] = None
if grid_position_key in json_map:
gp_list = json_map[grid_position_key]
Expand Down Expand Up @@ -1815,7 +1812,7 @@ class Domain(_JSONSerializable):
"""

# not serialized; for efficiency
# remove quotes when Py3.6 support dropped

_parent_strand: Optional[Strand] = field(init=False, repr=False, compare=False, default=None)

def __post_init__(self) -> None:
Expand All @@ -1841,7 +1838,7 @@ def to_json_serializable(self, suppress_indent: bool = True,
return NoIndent(dct) if suppress_indent else dct

@staticmethod
def from_json(json_map: Dict[str, Any]) -> Domain: # remove quotes when Py3.6 support dropped
def from_json(json_map: Dict[str, Any]) -> Domain:
helix = mandatory_field(Domain, json_map, helix_idx_key)
forward = mandatory_field(Domain, json_map, forward_key, legacy_keys=legacy_forward_keys)
start = mandatory_field(Domain, json_map, start_key)
Expand Down Expand Up @@ -1881,7 +1878,7 @@ def __repr__(self) -> str:
def __str__(self) -> str:
return repr(self) if self.name is None else self.name

def strand(self) -> Strand: # remove quotes when Py3.6 support dropped
def strand(self) -> Strand:
"""
:return: The :any:`Strand` that contains this :any:`Domain`.
"""
Expand Down Expand Up @@ -2090,7 +2087,6 @@ def overlaps(self, other: Domain) -> bool:
return (self.forward == (not other.forward) and
self.compute_overlap(other)[0] >= 0)

# remove quotes when Py3.6 support dropped
# def overlaps_illegally(self, other: Domain):
def overlaps_illegally(self, other: Domain) -> bool:
r"""Indicates if this :any:`Domain`'s set of offsets (the set
Expand All @@ -2105,8 +2101,6 @@ def overlaps_illegally(self, other: Domain) -> bool:
return (self.forward == other.forward and
self.compute_overlap(other)[0] >= 0)

# remove quotes when Py3.6 support dropped
# def compute_overlap(self, other: Domain) -> Tuple[int, int]:
def compute_overlap(self, other: Domain) -> Tuple[int, int]:
"""Return [left,right) offset indicating overlap between this Domain and `other`.
Expand Down Expand Up @@ -2216,7 +2210,7 @@ class Loopout(_JSONSerializable):
"""

# not serialized; for efficiency
# remove quotes when Py3.6 support dropped

_parent_strand: Optional[Strand] = field(init=False, repr=False, compare=False, default=None)

def to_json_serializable(self, suppress_indent: bool = True,
Expand All @@ -2231,7 +2225,7 @@ def to_json_serializable(self, suppress_indent: bool = True,
return NoIndent(dct) if suppress_indent else dct

@staticmethod
def from_json(json_map: Dict[str, Any]) -> 'Loopout': # remove quotes when Py3.6 support dropped
def from_json(json_map: Dict[str, Any]) -> Loopout:
# XXX: this should never fail since we detect whether to call this from_json by the presence
# of a length key in json_map
length_str = mandatory_field(Loopout, json_map, loopout_key)
Expand All @@ -2242,7 +2236,7 @@ def from_json(json_map: Dict[str, Any]) -> 'Loopout': # remove quotes when Py3.
color = Color.from_json(color_json)
return Loopout(length=length, name=name, label=label, color=color)

def strand(self) -> Strand: # remove quotes when Py3.6 support dropped
def strand(self) -> Strand:
"""
:return: The :any:`Strand` that contains this :any:`Loopout`.
"""
Expand Down Expand Up @@ -2378,7 +2372,7 @@ class Extension(_JSONSerializable):
"""

# not serialized; for efficiency
# remove quotes when Py3.6 support dropped

_parent_strand: Optional[Strand] = field(init=False, repr=False, compare=False, default=None)

def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) \
Expand Down Expand Up @@ -2577,7 +2571,6 @@ def strand(self) -> Strand:
raise ValueError('no Strand created yet; make at least one domain first')
return self._strand

# remove quotes when Py3.6 support dropped
def cross(self, helix: int, offset: Optional[int] = None, move: Optional[int] = None) \
-> StrandBuilder:
"""
Expand Down Expand Up @@ -2616,7 +2609,6 @@ def _most_recently_added_substrand_is_instance_of_class(self, cls: Type) -> bool
def _most_recently_added_substrand_is_extension(self):
return self._most_recently_added_substrand_is_instance_of_class(Extension)

# remove quotes when Py3.6 support dropped
def loopout(self, helix: int, length: int, offset: Optional[int] = None, move: Optional[int] = None) \
-> StrandBuilder:
"""
Expand Down Expand Up @@ -2706,7 +2698,6 @@ def _verify_extension_5p_is_valid(self):
'Cannot add a 5\' extension when there are already domains. '
'Did you mean to create a 3\' extension?')

# remove quotes when Py3.6 support dropped
def move(self, delta: int) -> StrandBuilder:
"""
Extends this :any:`StrandBuilder` on the current helix to offset given by the current offset
Expand All @@ -2729,7 +2720,6 @@ def move(self, delta: int) -> StrandBuilder:
"""
return self.to(self.current_offset + delta)

# remove quotes when Py3.6 support dropped
def to(self, offset: int) -> StrandBuilder:
"""
Extends this :any:`StrandBuilder` on the current helix to offset `offset`,
Expand Down Expand Up @@ -2791,7 +2781,6 @@ def _most_recently_added_substrand_is_extension_3p(self) -> bool:
return False
return len(self._strand.domains) > 1 and self._most_recently_added_substrand_is_extension()

# remove quotes when Py3.6 support dropped
def update_to(self, offset: int) -> StrandBuilder:
"""
Like :py:meth:`StrandBuilder.to`, but changes the current offset without creating
Expand Down Expand Up @@ -2839,7 +2828,6 @@ def as_circular(self) -> StrandBuilder:
self._strand.set_circular()
return self

# remove quotes when Py3.6 support dropped
def as_scaffold(self) -> StrandBuilder:
"""
Makes :any:`Strand` being built a scaffold.
Expand Down Expand Up @@ -2875,7 +2863,6 @@ def with_idt(self, scale: str = default_idt_scale,
plate=plate, well=well)
return self

# remove quotes when Py3.6 support dropped
def with_modification_5p(self, mod: Modification5Prime) -> StrandBuilder:
"""
Sets Strand being built to have given 5' modification.
Expand All @@ -2888,7 +2875,6 @@ def with_modification_5p(self, mod: Modification5Prime) -> StrandBuilder:
self._strand.set_modification_5p(mod)
return self

# remove quotes when Py3.6 support dropped
def with_modification_3p(self, mod: Modification3Prime) -> StrandBuilder:
"""
Sets Strand being built to have given 3' modification.
Expand All @@ -2901,7 +2887,6 @@ def with_modification_3p(self, mod: Modification3Prime) -> StrandBuilder:
self._strand.set_modification_3p(mod)
return self

# remove quotes when Py3.6 support dropped
def with_modification_internal(self, idx: int, mod: ModificationInternal, warn_on_no_dna: bool) \
-> StrandBuilder:
"""
Expand All @@ -2917,7 +2902,6 @@ def with_modification_internal(self, idx: int, mod: ModificationInternal, warn_o
self._strand.set_modification_internal(idx, mod, warn_on_no_dna)
return self

# remove quotes when Py3.6 support dropped
def with_color(self, color: Color) -> StrandBuilder:
"""
Sets Strand being built to have given color.
Expand All @@ -2930,7 +2914,6 @@ def with_color(self, color: Color) -> StrandBuilder:
self._strand.set_color(color)
return self

# remove quotes when Py3.6 support dropped
def with_sequence(self, sequence: str, assign_complement: bool = False) \
-> StrandBuilder:
"""
Expand All @@ -2952,7 +2935,6 @@ def with_sequence(self, sequence: str, assign_complement: bool = False) \
self.design.assign_dna(strand=self._strand, sequence=sequence, assign_complement=assign_complement)
return self

# remove quotes when Py3.6 support dropped
def with_domain_sequence(self, sequence: str, assign_complement: bool = False) \
-> StrandBuilder:
"""
Expand Down Expand Up @@ -2990,7 +2972,6 @@ def with_domain_sequence(self, sequence: str, assign_complement: bool = False) \
assign_complement=assign_complement)
return self

# remove quotes when Py3.6 support dropped
def with_domain_color(self, color: Color) -> StrandBuilder:
"""
Sets most recent :any:`Domain`/:any:`Loopout`/:any:`Extension`
Expand All @@ -3007,7 +2988,6 @@ def with_domain_color(self, color: Color) -> StrandBuilder:
last_domain.color = color
return self

# remove quotes when Py3.6 support dropped
def with_name(self, name: str) -> StrandBuilder:
"""
Assigns `name` as name of the :any:`Strand` being built.
Expand All @@ -3024,7 +3004,6 @@ def with_name(self, name: str) -> StrandBuilder:
self._strand.set_name(name)
return self

# remove quotes when Py3.6 support dropped
def with_label(self, label: str) -> StrandBuilder:
"""
Assigns `label` as label of the :any:`Strand` being built.
Expand All @@ -3041,7 +3020,6 @@ def with_label(self, label: str) -> StrandBuilder:
self._strand.set_label(label)
return self

# remove quotes when Py3.6 support dropped
def with_domain_name(self, name: str) -> StrandBuilder:
"""
Assigns `name` as of the most recently created :any:`Domain` or :any:`Loopout` in
Expand All @@ -3066,7 +3044,6 @@ def with_domain_name(self, name: str) -> StrandBuilder:
last_domain.set_name(name)
return self

# remove quotes when Py3.6 support dropped
def with_domain_label(self, label: str) -> StrandBuilder:
"""
Assigns `label` as label of the most recently created :any:`Domain` or :any:`Loopout` in
Expand Down Expand Up @@ -3402,12 +3379,12 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D
dct[modifications_int_key] = NoIndent(mods_dict) if suppress_indent else mods_dict

if self.label is not None:
dct[strand_label_key] = NoIndent(self.label) if suppress_indent else self.label
dct[strand_label_key] = self.label

return dct

@staticmethod
def from_json(json_map: dict) -> Strand: # remove quotes when Py3.6 support dropped
def from_json(json_map: dict) -> Strand:
substrand_jsons = mandatory_field(Strand, json_map, domains_key, legacy_keys=legacy_domains_keys)
if len(substrand_jsons) == 0:
raise IllegalDesignError(f'{domains_key} list cannot be empty')
Expand Down Expand Up @@ -3465,7 +3442,7 @@ def from_json(json_map: dict) -> Strand: # remove quotes when Py3.6 support dro
label=label,
)

def __eq__(self, other: Any) -> bool: # remove quotes when Py3.6 support dropped
def __eq__(self, other: Any) -> bool:
if not isinstance(other, Strand):
return False
return self.domains == other.domains
Expand Down Expand Up @@ -3751,7 +3728,7 @@ def offset_3p(self) -> int:
"""3' offset of this entire :any:`Strand`, INCLUSIVE."""
return self.last_domain().offset_3p()

def overlaps(self, other: Strand) -> bool: # remove quotes when Py3.6 support dropped
def overlaps(self, other: Strand) -> bool:
"""Indicates whether `self` overlaps `other_strand`, meaning that the set of offsets occupied
by `self` has nonempty intersection with those occupied by `other_strand`."""
for domain_self in self.bound_domains():
Expand All @@ -3760,7 +3737,7 @@ def overlaps(self, other: Strand) -> bool: # remove quotes when Py3.6 support d
return True
return False

def assign_dna_complement_from(self, other: Strand) -> None: # remove quotes when Py3.6 support dropped
def assign_dna_complement_from(self, other: Strand) -> None:
"""Assuming a DNA sequence has been assigned to `other`, assign its Watson-Crick
complement to the portions of this Strand that are bound to `other`.
Expand Down Expand Up @@ -5186,7 +5163,7 @@ def roll_of_helix(self, helix: Helix) -> float:
return self.groups[helix.group].roll + helix.roll

@staticmethod
def from_scadnano_file(filename: str) -> 'Design': # remove quotes when Py3.6 support dropped
def from_scadnano_file(filename: str) -> Design:
"""
Loads a :any:`Design` from the file with the given name.
Expand All @@ -5198,7 +5175,7 @@ def from_scadnano_file(filename: str) -> 'Design': # remove quotes when Py3.6 s
return Design.from_scadnano_json_str(json_str)

@staticmethod
def from_scadnano_json_str(json_str: str) -> 'Design': # remove quotes when Py3.6 support dropped
def from_scadnano_json_str(json_str: str) -> Design:
"""
Loads a :any:`Design` from the given JSON string.
Expand Down Expand Up @@ -5406,7 +5383,7 @@ def _helices_and_groups_and_grid_from_json(json_map: Dict) \

@staticmethod
def from_scadnano_json_map(
json_map: dict) -> 'Design': # remove quotes when Py3.6 support dropped
json_map: dict) -> Design:
"""
Loads a :any:`Design` from the given JSON object (i.e., Python object obtained by calling
json.loads(json_str) from a string representing contents of a JSON file.
Expand Down Expand Up @@ -5796,7 +5773,6 @@ def _cadnano_v2_import_explore_strand(vstrands: VStrands,

return strand

# remove quotes when Py3.6 support dropped
@staticmethod
def from_cadnano_v2(directory: str = '', filename: Optional[str] = None,
json_dict: Optional[dict] = None) -> 'Design':
Expand Down

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