258 remove strand groups #259
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…lib-histogram-of-nearest-neighbor-energies closes #255 matplotlib histogram of nearest neighbor energies
dave-doty
requested changes
May 1, 2024
nuad/constraints.py
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| @@ -72,7 +72,7 @@ | |||
| domain_pools_num_sampled_key = 'domain_pools_num_sampled' | |||
| domain_names_key = 'domain_names' | |||
| starred_domain_indices_key = 'starred_domain_indices' | |||
| group_key = 'group' | |||
| group_key = 'label' | |||
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we should just remove the field group (and the constant group_key)
nuad/constraints.py
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| @@ -2169,7 +2169,8 @@ def evaluate(seqs: Tuple[str, ...], | |||
| @dataclass | |||
| class VendorFields(JSONSerializable): | |||
| """Data required when ordering DNA strands from a synthesis company such as | |||
| `IDT (Integrated DNA Technologies) <https://www.idtdna.com/>`_. | |||
| `IDT (Integrated DNA Technologies) <https://www. | |||
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Looks like this URL got messed up.
| @@ -2247,7 +2248,7 @@ def _check_vendor_string_not_none_or_empty(value: str, field_name: str) -> None: | |||
| raise ValueError(f'field {field_name} in VendorFields cannot be empty') | |||
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| default_strand_group = 'default_strand_group' | |||
| default_strand_label = 'default_strand_label' | |||
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we don't have a default label since it is an optional field
| name: str | None = None, | ||
| label: str | None = None, | ||
| label: str = default_strand_label, |
| @@ -2526,7 +2520,7 @@ def to_json_serializable(self, suppress_indent: bool = True) -> NoIndent | Dict[ | |||
| Dictionary ``d`` representing this :any:`Strand` that is "naturally" JSON serializable, | |||
| by calling ``json.dumps(d)``. | |||
| """ | |||
| dct: Dict[str, Any] = {name_key: self.name, group_key: self.group} | |||
| dct: Dict[str, Any] = {name_key: self.name, label_key: self.label} | |||
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only include label_key if the label is not None
| @@ -3078,7 +3069,7 @@ class Design(JSONSerializable): | |||
| Computed from :data:`Design.strands`, so not specified in constructor. | |||
| """ | |||
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| strands_by_group_name: Dict[str, List[Strand]] = field(init=False) | |||
| strands_by_label_name: Dict[str, List[Strand]] = field(init=False) | |||
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