Add LinkGraph to replace ObjectLink and LinkCollection (#252)

* Update pyproject.toml

* Delete link_collection.py

* Delete object_link.py

* Create scoring_method.py

* Create score.py

* Create link_graph.py

* Update __init__.py

* Create test_score.py

* Create test_scoring_method.py

* Create test_link_graph.py

* update abc.py to use LinkGraph

* Update MetcalfScoring to use LinkGraph

- Use LinkGraph to replace ObjectLink and LinkCollection
- remove attribute `cutoff` and `standardised`. Now users have to pass them as parameters

* update NPLinker and other scoring methods to use LinkGraph

These updates are just to make sure code can import. Further refactoring is needed to ensure the correct output.

* Update test_nplinker_scoring.py

pyproject.toml

@@ -34,6 +34,7 @@ dependencies = [
     "httpx",
     "jsonschema",
     "numpy",
+    "networkx",
     "pandas",
     "pyteomics",
     "rich",

src/nplinker/nplinker.py

@@ -15,7 +15,6 @@
 from .metabolomics import Spectrum
 from .pickler import save_pickled_data
 from .scoring.abc import ScoringBase
-from .scoring.link_collection import LinkCollection
 from .scoring.metcalf_scoring import MetcalfScoring
 from .scoring.np_class_scoring import NPClassScoring
 from .scoring.rosetta_scoring import RosettaScoring

src/nplinker/scoring/__init__.py

@@ -1,7 +1,14 @@
 from .abc import ScoringBase
-from .link_collection import LinkCollection
+from .link_graph import LinkGraph
 from .metcalf_scoring import MetcalfScoring
-from .object_link import ObjectLink
+from .score import Score
+from .scoring_method import ScoringMethod
 
 
-__all__ = ["LinkCollection", "MetcalfScoring", "ScoringBase", "ObjectLink"]
+__all__ = [
+    "LinkGraph",
+    "MetcalfScoring",
+    "Score",
+    "ScoringBase",
+    "ScoringMethod",
+]

src/nplinker/scoring/abc.py

@@ -6,8 +6,8 @@
 
 
 if TYPE_CHECKING:
-    from nplinker import NPLinker
-    from . import LinkCollection
+    from nplinker.nplinker import NPLinker
+    from .link_graph import LinkGraph
 
 logger = logging.getLogger(__name__)
 
@@ -36,15 +36,19 @@ def setup(cls, npl: NPLinker):
         """Setup class level attributes."""
 
     @abstractmethod
-    def get_links(self, *objects, link_collection: LinkCollection) -> LinkCollection:
+    def get_links(
+        self,
+        *objects,
+        **parameters,
+    ) -> LinkGraph:
         """Get links information for the given objects.
 
         Args:
-            objects: A set of objects.
-            link_collection: The LinkCollection object.
+            objects: A list of objects to get links for.
+            parameters: The parameters used for scoring.
 
         Returns:
-            The LinkCollection object.
+            The LinkGraph object.
         """
 
     @abstractmethod