Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add LinkGraph to replace ObjectLink and LinkCollection #252

Merged
merged 14 commits into from
Jun 10, 2024
Merged

Add LinkGraph to replace ObjectLink and LinkCollection #252

merged 14 commits into from
Jun 10, 2024

Conversation

CunliangGeng
Copy link
Member

@CunliangGeng CunliangGeng commented Jun 6, 2024 •
edited
Loading

The LinkGraph class is a wrapper of networkx.Graph, which treats links as edges between objects or nodes (e.g. GCF, spectrum) while the scoring data of the links is treated as the attributes of the edges in the graph. This graph data structure can perfectly replace the legacy ObjectLink and LinkCollection classes.

This was referenced Jun 6, 2024
Merged
Merged
Merged
Merged
Merged
Merged
@CunliangGeng Graphite App
Copy link
Member Author

CunliangGeng commented Jun 6, 2024 •
edited
Loading

This stack of pull requests is managed by Graphite. Learn more about stacking.

Join @CunliangGeng and the rest of your teammates on Graphite Graphite

@CunliangGeng CunliangGeng requested a review from gcroci2 June 6, 2024 07:03
@CunliangGeng CunliangGeng self-assigned this Jun 6, 2024
@CunliangGeng CunliangGeng marked this pull request as ready for review June 6, 2024 07:09
@CunliangGeng CunliangGeng force-pushed the merge_DataLinks_to_ObjectLink branch from 7f9f439 to 9711915 Compare June 6, 2024 07:16
@CunliangGeng CunliangGeng force-pushed the replace_ObjectLink_and_LinkCollection_with_LinkGraph branch from 640d787 to e8a3a3f Compare June 6, 2024 07:16
@CunliangGeng CunliangGeng force-pushed the merge_DataLinks_to_ObjectLink branch from 9711915 to 8dade37 Compare June 6, 2024 07:21
@CunliangGeng CunliangGeng force-pushed the replace_ObjectLink_and_LinkCollection_with_LinkGraph branch from e8a3a3f to 9d5d264 Compare June 6, 2024 07:21
@CunliangGeng CunliangGeng force-pushed the merge_DataLinks_to_ObjectLink branch from 8dade37 to 6674ba0 Compare June 6, 2024 07:24
@CunliangGeng CunliangGeng force-pushed the replace_ObjectLink_and_LinkCollection_with_LinkGraph branch from 9d5d264 to 48fafc8 Compare June 6, 2024 07:24
@CunliangGeng CunliangGeng force-pushed the merge_DataLinks_to_ObjectLink branch from 6674ba0 to 063ecdc Compare June 6, 2024 13:49
@CunliangGeng CunliangGeng force-pushed the replace_ObjectLink_and_LinkCollection_with_LinkGraph branch from 48fafc8 to 62ad2f8 Compare June 6, 2024 13:49
@CunliangGeng CunliangGeng mentioned this pull request Jun 7, 2024
Merged
@gcroci2 gcroci2 mentioned this pull request Jun 7, 2024
Closed
gcroci2
gcroci2 approved these changes Jun 7, 2024
View reviewed changes
Copy link
Contributor

@gcroci2 gcroci2 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Very nice additions :D

This was referenced Jun 7, 2024
Merged
Closed
@CunliangGeng Graphite App
Copy link
Member Author

CunliangGeng commented Jun 10, 2024 •
edited
Loading

Merge activity

  • Jun 10, 3:24 AM EDT: @CunliangGeng started a stack merge that includes this pull request via Graphite.
  • Jun 10, 3:28 AM EDT: Graphite rebased this pull request as part of a merge.
  • Jun 10, 3:29 AM EDT: @CunliangGeng merged this pull request with Graphite.

@CunliangGeng CunliangGeng force-pushed the merge_DataLinks_to_ObjectLink branch from 063ecdc to 230162e Compare June 10, 2024 07:25
Base automatically changed from merge_DataLinks_to_ObjectLink to dev June 10, 2024 07:27
@CunliangGeng
Create score.py
d456254
@CunliangGeng
Create link_graph.py
9b15418
@CunliangGeng
Update __init__.py
5d0e8d9
@CunliangGeng
Create test_score.py
240c301
@CunliangGeng
Create test_scoring_method.py
2c19db0
@CunliangGeng
Create test_link_graph.py
9720fef
@CunliangGeng
update abc.py to use LinkGraph
55458a9
@CunliangGeng
Update MetcalfScoring to use LinkGraph
d3b8713 
- Use LinkGraph to replace ObjectLink and LinkCollection
- remove attribute `cutoff` and `standardised`. Now users have to pass them as parameters
@CunliangGeng
update NPLinker and other scoring methods to use LinkGraph
9894232 
These updates are just to make sure code can import. Further refactoring is needed to ensure the correct output.
@CunliangGeng
Update test_nplinker_scoring.py
91b2510
@CunliangGeng CunliangGeng force-pushed the replace_ObjectLink_and_LinkCollection_with_LinkGraph branch from 62ad2f8 to 91b2510 Compare June 10, 2024 07:28
@CunliangGeng CunliangGeng merged commit c7d2be8 into dev Jun 10, 2024
1 of 2 checks passed
@CunliangGeng CunliangGeng deleted the replace_ObjectLink_and_LinkCollection_with_LinkGraph branch June 10, 2024 07:29
This was referenced Jun 10, 2024
Merged
Merged
Merged
Merged
Merged
@CunliangGeng CunliangGeng mentioned this pull request Jun 18, 2024
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@gcroci2 gcroci2 gcroci2 approved these changes

Assignees

@CunliangGeng CunliangGeng

Labels
None yet
Projects
dev
Status: Done
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@CunliangGeng @gcroci2