Skip to content

Main #3

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

Merged
breakthewall merged 6 commits into from
Jun 2, 2026
Merged

Main #3

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
6db5a9e
build(environment.yaml): update rplibs min ver
breakthewall Jun 1, 2026
3975216
build(MANIFEST.in): add models in conda package
breakthewall Jun 1, 2026
162a38c
chore(rpscore/__main__.py): rm comments
breakthewall Jun 1, 2026
615f716
test(tests/data/pathway.xml): add target_id tag to test file
breakthewall Jun 1, 2026
2f01c7e
build(environment.yaml): update rplibs min ver
breakthewall Jun 2, 2026
52dc25f
trigger
breakthewall Jun 2, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions MANIFEST.in
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
graft rptools/rpscore/models
2 changes: 1 addition & 1 deletion environment.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,4 +10,4 @@ dependencies:
- scikit-learn
- xgboost=3.0.2
- brs_utils>=1.26.0
- rplibs>=6.9.3
- rplibs>=6.9.5
16 changes: 0 additions & 16 deletions rpscore/__main__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,22 +37,6 @@ def entry_point():
logger.error(e)
exit(2)

# if len(pathways) > 1:
# if not os_path.exists(args.outdir):
# makedirs(args.outdir)
# for i in range(len(pathways)):
# # Write results into the pathway
# pathways[i].set_global_score(
# scores[i]
# )
# # Write pathway into file
# pathways[i].to_rpSBML().write_to_file(
# os_path.join(
# args.outdir,
# os_path.basename(args.pathways[i])
# )
# )
# else:
# Write results into the pathway
pathway.set_global_score(score)
# Write pathway into file
Expand Down
2 changes: 2 additions & 0 deletions rpscore/rpscore.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -263,6 +263,8 @@ def transform_to_matrix(dset, model_file):


###############################################################


def score_prediction(
features_dset_train, features_dset_pred, models_path, out_filename
):
Expand Down
1 change: 1 addition & 0 deletions tests/data/pathway.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -357,6 +357,7 @@
<brsynth:error value="5.336452836371218"/>
<brsynth:units value="kilojoule / mole"/>
</brsynth:thermo_dG>
<brsynth:target_id value="TARGET_0000000001"/>
</brsynth:brsynth>
</rdf:BRSynth>
</rdf:RDF>
Expand Down
Loading