nerdd-module 0.3.15__tar.gz → 0.3.17__tar.gz

{nerdd_module-0.3.15 → nerdd_module-0.3.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nerdd-module
-Version: 0.3.15
+Version: 0.3.17
 Summary: Base package to create NERDD modules
 Author-email: Steffen Hirte <steffen.hirte@univie.ac.at>
 Maintainer-email: Steffen Hirte <steffen.hirte@univie.ac.at>

{nerdd_module-0.3.15 → nerdd_module-0.3.17}/nerdd_module/config/models.py

@@ -1,6 +1,7 @@
 from typing import Any, List, Optional, Union
 
-from pydantic import BaseModel, model_validator
+from pydantic import BaseModel, computed_field, model_validator
+from stringcase import spinalcase
 
 from ..polyfills import Literal
 
@@ -98,9 +99,22 @@ class ResultProperty(BaseModel):
 
 
 class Module(BaseModel):
+    @computed_field  # type: ignore[prop-decorator]
+    @property
+    def id(self) -> str:
+        # TODO: incorporate versioning
+        # compute the primary key from name and version
+        # if "version" in module.keys():
+        #     version = module["version"]
+        # else:
+        #     version = "1.0.0"
+        # name = module["name"]
+
+        return spinalcase(self.name)
+
     task: Optional[Task] = None
     rank: Optional[int] = None
-    name: Optional[str] = None
+    name: str
     batch_size: int = 100
     version: Optional[str] = None
     visible_name: Optional[str] = None

{nerdd_module-0.3.15 → nerdd_module-0.3.17}/nerdd_module/converters/__init__.py

@@ -2,7 +2,6 @@ from .basic_type_converter import *
 from .converter import *
 from .converter_config import *
 from .mol_converter import *
-from .mol_to_image_converter import *
 from .problem_list_converter import *
 from .representation_converter import *
 from .void_converter import *

{nerdd_module-0.3.15 → nerdd_module-0.3.17}/nerdd_module/model/model.py

@@ -85,7 +85,7 @@ class Model(ABC):
     def _get_batch_size(self) -> int:
         return 1
 
-    batch_size = property(_get_batch_size)
+    batch_size = property(fget=lambda self: self._get_batch_size())
 
     def _get_name(self) -> str:
         return snakecase(self.__class__.__name__)

{nerdd_module-0.3.15 → nerdd_module-0.3.17}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nerdd-module
-Version: 0.3.15
+Version: 0.3.17
 Summary: Base package to create NERDD modules
 Author-email: Steffen Hirte <steffen.hirte@univie.ac.at>
 Maintainer-email: Steffen Hirte <steffen.hirte@univie.ac.at>

{nerdd_module-0.3.15 → nerdd_module-0.3.17}/nerdd_module.egg-info/SOURCES.txt

@@ -25,7 +25,6 @@ nerdd_module/converters/basic_type_converter.py
 nerdd_module/converters/converter.py
 nerdd_module/converters/converter_config.py
 nerdd_module/converters/mol_converter.py
-nerdd_module/converters/mol_to_image_converter.py
 nerdd_module/converters/problem_list_converter.py
 nerdd_module/converters/representation_converter.py
 nerdd_module/converters/void_converter.py

{nerdd_module-0.3.15 → nerdd_module-0.3.17}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nerdd-module"
-version = "0.3.15"
+version = "0.3.17"
 description = "Base package to create NERDD modules"
 readme = "README.md"
 license = { file = "LICENSE" }

nerdd_module-0.3.15/nerdd_module/converters/mol_to_image_converter.py

@@ -1,62 +0,0 @@
-from typing import Any
-from xml.dom import minidom
-
-from rdkit.Chem import Mol
-from rdkit.Chem.Draw import MolDraw2DSVG
-
-from .converter import Converter
-from .converter_config import ConverterConfig
-
-__all__ = ["MolToImageConverter"]
-
-default_width = 300
-default_height = 180
-
-
-class MolToImageConverter(Converter):
-    def _convert(self, input: Any, context: dict) -> Any:
-        width = self.result_property.image_width
-        height = self.result_property.image_height
-
-        if width is None:
-            width = default_width
-        if height is None:
-            height = default_height
-
-        mol = input
-        if mol is None:
-            return None
-
-        assert isinstance(mol, Mol), f"Expected RDKit Mol object, but got {type(mol)}"
-
-        svg = MolDraw2DSVG(width, height)
-
-        # remove background
-        opts = svg.drawOptions()
-        opts.clearBackground = False
-
-        # add highlight circles around atoms during drawing
-        # (we will remove them later in post processing)
-        atoms = range(mol.GetNumAtoms())
-        colors = [[(0.8, 1, 1)]] * mol.GetNumAtoms()
-        radii = [0.5] * mol.GetNumAtoms()
-        atom_highlight = dict(zip(atoms, colors))
-        atom_radii = dict(zip(atoms, radii))
-        svg.DrawMoleculeWithHighlights(mol, "", atom_highlight, {}, atom_radii, [])
-        svg.FinishDrawing()
-
-        # post process SVG
-        xml = svg.GetDrawingText()
-        tree = minidom.parseString(xml)
-        root = tree.getElementsByTagName("svg")[0]
-
-        # make highlight circles invisible
-        for ellipse in root.getElementsByTagName("ellipse"):
-            ellipse.setAttribute("style", "opacity:0")
-
-        xml = tree.toxml()
-
-        return xml
-
-    # TODO: move to nerdd-link
-    config = ConverterConfig(data_types="mol", output_formats="json")