Consolidate GOLR biolink snapshots into single file by amc-corey-cox · Pull Request #3307 · linkml/linkml

amc-corey-cox · 2026-03-20T17:16:23Z

Partial fix for #3305

Summary

GOLR snapshot directories stored one YAML file per class, causing generator or model changes to produce massive PR diffs. This consolidates them into single concatenated files with # --- filename.yaml --- separators.

Location	Before	After
biolink model test	236 files	1 file
gen-golr script test	22 files	1 file
Total snapshot files in test suite	500	241

Same coverage, same content, reviewable diffs.

Test plan

test_biolink_golr passes against generated snapshot
test_metamodel_valid_call passes against generated snapshot
Snapshot regeneration produces identical output

codecov · 2026-03-20T17:26:47Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 83.89%. Comparing base (4636660) to head (d4fd8b0).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3307      +/-   ##
==========================================
+ Coverage   80.25%   83.89%   +3.64%     
==========================================
  Files         150      150              
  Lines       17484    17484              
  Branches     3642     3642              
==========================================
+ Hits        14032    14669     +637     
+ Misses       2661     1977     -684     
- Partials      791      838      +47

Flag	Coverage Δ
linkml	`80.25% <ø> (ø)`
runtime	`80.25% <ø> (ø)`

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Pull request overview

Consolidates GOLR Biolink snapshot outputs to reduce churn and make snapshot diffs reviewable (partial fix for #3305), replacing many per-class YAML snapshot files with fewer combined snapshot artifacts.

Changes:

Removes per-class GOLR snapshot YAMLs under tests/linkml/test_biolink_model/__snapshots__/golr/biolink/ as part of moving to consolidated snapshots.
Reduces snapshot file-count to avoid massive diffs when generator/model changes occur.

Reviewed changes

Copilot reviewed 141 out of 262 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/linkml/test_biolink_model/snapshots/golr/biolink/macromolecular_complex_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/log_odds_analysis_result_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/life_stage_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/invertebrate_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/individual_organism_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/human_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/hospitalization_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/haplotype_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/gross_anatomical_structure_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/geographic_location_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/geographic_location_at_time_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/geographic_exposure_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/genotypic_sex_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/genotype_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/genomic_background_exposure_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/genome_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/genetic_inheritance_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/gene_family_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/gene_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/fungus_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/food_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/food_additive_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/exon_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/evidence_type_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/event_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/environmental_process_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/environmental_food_contaminant_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/environmental_feature_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/environmental_exposure_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/drug_to_gene_interaction_exposure_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/drug_label_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/drug_exposure_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/drug_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/disease_or_phenotypic_feature_exposure_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/disease_or_phenotypic_feature_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/disease_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/diagnostic_aid_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/device_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/dataset_version_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/dataset_summary_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/dataset_distribution_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/dataset_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/confidence_level_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/concept_count_analysis_result_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/complex_molecular_mixture_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/complex_chemical_exposure_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/common_data_element_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/cohort_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/coding_sequence_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/clinical_trial_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/clinical_modifier_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/clinical_measurement_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/clinical_intervention_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/clinical_finding_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/clinical_entity_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/clinical_course_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/clinical_attribute_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/chi_squared_analysis_result_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/chemical_role_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/chemical_mixture_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/chemical_exposure_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/chemical_entity_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/cellular_organism_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/cellular_component_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/cell_line_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/cell_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/case_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/book_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/biotic_exposure_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/biological_sex_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/biological_process_or_activity_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/biological_process_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/behavioral_feature_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/behavioral_exposure_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/behavior_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/bacterium_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/attribute_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/anatomical_entity_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/agent_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/activity_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/accessible_dna_region_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/RNA_product_isoform_config.yaml	Per-class snapshot removed in favor of consolidated snapshot
tests/linkml/test_biolink_model/snapshots/golr/biolink/RNA_product_config.yaml	Per-class snapshot removed in favor of consolidated snapshot

Comments suppressed due to low confidence (2)

tests/linkml/test_biolink_model/snapshots/golr/biolink/macromolecular_complex_config.yaml:1

These per-class snapshot YAML files appear to be left empty by removing all content rather than being deleted. Empty snapshot files can still be discovered by directory scans and may be parsed/loaded as valid inputs, causing test failures or nondeterministic behavior. Prefer deleting these files entirely (git rm) as part of the consolidation, or replace their contents with an explicit, machine-detectable stub (e.g., a single YAML comment) that the snapshot loader ignores.
tests/linkml/test_biolink_model/snapshots/golr/biolink/log_odds_analysis_result_config.yaml:1
The PR description says snapshots are consolidated into a single concatenated file with filename separators, but the diffs shown here only remove the entire contents of individual snapshot files (leaving them empty). To match the described behavior, the consolidated snapshot file(s) should be added/updated in the repo and the individual per-class files should be removed rather than emptied.

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kevinschaper

nice optimization!

amc-corey-cox added 2 commits March 20, 2026 12:16

Consolidate 236 GOLR snapshot files into one concatenated file

fc78346

Consolidate 22 GOLR script snapshot files into one concatenated file

d685a08

amc-corey-cox requested a review from Copilot March 20, 2026 17:27

Copilot AI reviewed Mar 20, 2026

View reviewed changes

Fix Windows sort order in GOLR snapshot concatenation

620cc72

kevinschaper approved these changes Mar 20, 2026

View reviewed changes

Merge branch 'main' into fix/reduce-golr-snapshots

d4fd8b0

kevinschaper merged commit fac1bcc into main Mar 20, 2026
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Consolidate GOLR biolink snapshots into single file#3307

Consolidate GOLR biolink snapshots into single file#3307
kevinschaper merged 4 commits into
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fix/reduce-golr-snapshots

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amc-corey-cox commented Mar 20, 2026 •

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