Update for v3 data #142
Merged
Update for v3 data #142
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
There was a problem hiding this comment.
Pull Request Overview
This PR updates the codebase to use the new v3 data column naming conventions (e.g. "parent_heavy"/"parent_light" instead of "parent_h"/"parent_l") throughout tests and core modules. Key changes include renaming columns in tests files, updating dataset preparation functions, and aligning the neutral model outputs to use the new naming conventions.
Reviewed Changes
Copilot reviewed 16 out of 16 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| tests/test_tokens.py | Updated tuple assignment to use "parent_heavy" and "parent_light" |
| tests/test_simulation.py | Renamed column accesses from "parent_h"/"child_h" to "parent_heavy"/"child_heavy" |
| tests/test_netam.py | Adapted DataFrame column keys to new naming convention |
| tests/test_multihit.py | Renamed DataFrame columns and tensor keys to reflect heavy chain naming |
| tests/test_molevol.py | Updated tensor column access for neutral model outputs |
| netam/sequences.py | Renamed parameter usage in sequence preparation |
| netam/multihit.py | Updated references to DataFrame column keys and neutral model outputs |
| netam/framework.py | Adjusted CSV loading and heavy/light chain column processing |
| netam/dxsm.py, dnsm.py, ddsm.py | Updated error messages and log probability calculations using new column keys |
| netam/data_format.py | Added new column definitions for heavy/light data |
| netam/dasm.py | Updated log probability stacking to use heavy/light nomenclature |
willdumm
force-pushed
the
dnsmex139-v3-data
branch
from
ecea364 to
853cb6f
Compare
matsen
approved these changes
Jun 13, 2025
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Addresses https://github.com/matsengrp/dnsm-experiments-1/issues/139
Also changes all anarci and plotter dict keys from "h" and "l" to "heavy" and "light", and introduces
netam.data_format.pywhich specifies pcp_df column types. The most notable change is that nowfamilyis always a string, instead of an int sometimes as was the case before.