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0.6.0: multivalued output_ids, no test_env on test cases, Python 3.10+ #43

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Merged
maximusunc merged 4 commits into from
Oct 29, 2026
Merged

0.6.0: multivalued output_ids, no test_env on test cases, Python 3.10+ #43

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fad362a
Replace TestAsset.output_id with multivalued output_ids
claude Oct 29, 2026
39609c1
Remove test_env from test cases
claude Oct 29, 2026
2282964
Pin Poetry 1.8.5 in CI
claude Oct 29, 2026
48308bf
Drop Python 3.9
claude Oct 29, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/deploy-docs.yaml
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Expand Up @@ -16,7 +16,7 @@ jobs:
- name: Set up Python 3.
uses: actions/setup-python@v5
with:
python-version: 3.9
python-version: "3.10"

- name: Install Poetry.
uses: snok/install-poetry@v1.3
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2 changes: 1 addition & 1 deletion .github/workflows/main.yaml
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Expand Up @@ -12,7 +12,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.9", "3.10"]
python-version: ["3.10", "3.11", "3.12"]

steps:

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2 changes: 1 addition & 1 deletion .github/workflows/pypi-publish.yaml
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Expand Up @@ -16,7 +16,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: 3.9
python-version: "3.10"

- name: Install Poetry
run: |
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3 changes: 2 additions & 1 deletion examples/Bad-TestAsset-001.yaml
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Expand Up @@ -8,7 +8,8 @@ name: TestAsset001
description: Fingolimod treats multiple sclerosis
input_id: PUBCHEM.COMPOUND:107970
predicate_name: treats
output_id: MONDO:0005301
output_ids:
- MONDO:0005301
expected_output: Acceptable
test_runner_settings:
- "inferred"
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3 changes: 2 additions & 1 deletion examples/Good-AcceptanceTestAsset-001.yaml
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Expand Up @@ -26,7 +26,8 @@ name: AcceptanceTestAsset001
description: Iron treats Aceruloplasminemia
input_id: MONDO:0011426
predicate_name: treats
output_id: DRUGBANK:DB01592
output_ids:
- DRUGBANK:DB01592
expected_output: NeverShow
test_metadata:
id: "test:1"
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3 changes: 2 additions & 1 deletion examples/Good-AcceptanceTestCase-001.yaml
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Expand Up @@ -22,7 +22,8 @@ test_assets:
description: Iron treats Aceruloplasminemia
input_id: MONDO:0011426
predicate_name: treats
output_id: DRUGBANK:DB01592
output_ids:
- DRUGBANK:DB01592
expected_output: NeverShow
test_runner_settings:
- "inferred"
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2 changes: 1 addition & 1 deletion examples/Good-TestAsset-001.json
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Expand Up @@ -4,7 +4,7 @@
"description": "Fingolimod treats multiple sclerosis",
"input_id": "PUBCHEM.COMPOUND:107970",
"predicate_name": "treats",
"output_id": "MONDO:0005301",
"output_ids": ["MONDO:0005301"],
"expected_output": "Acceptable",
"test_runner_settings": ["inferred", "test"],
"test_metadata": {
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5 changes: 3 additions & 2 deletions examples/Good-TestAsset-001.yaml
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Expand Up @@ -16,7 +16,7 @@
# - input_category
# - predicate_id
# - predicate_name
# - output_id
# - output_ids
# - output_name
# - output_category
# - association
Expand Down Expand Up @@ -45,7 +45,8 @@ description: Iron treats Aceruloplasminemia
input_id: MONDO:0011426
input_name: Aceruloplasminemia
predicate_name: treats
output_id: DRUGBANK:DB01592
output_ids:
- DRUGBANK:DB01592
output_name: Iron (PUBCHEM)
expected_output: NeverShow
test_reference: https://github.com/NCATSTranslator/Feedback/issues/506
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14 changes: 14 additions & 0 deletions examples/Good-TestAsset-002.json
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@@ -0,0 +1,14 @@
{
"id": "example:TestAsset002",
"name": "TestAsset002",
"description": "Sirolimus treats Castleman disease",
"input_id": "MONDO:0015564",
"predicate_name": "treats",
"output_ids": ["PUBCHEM.COMPOUND:5284616", "CHEBI:9168"],
"output_name": "sirolimus",
"expected_output": "TopAnswer",
"test_runner_settings": ["inferred"],
"test_metadata": {
"id": "example:TestAsset002"
}
}
2 changes: 1 addition & 1 deletion examples/Good-TestCase-001.json
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Expand Up @@ -9,7 +9,7 @@
"description": "Fingolimod treats multiple sclerosis",
"input_id": "PUBCHEM.COMPOUND:107970",
"predicate_name": "treats",
"output_id": "MONDO:0005301",
"output_ids": ["MONDO:0005301"],
"expected_output": "Acceptable",
"test_runner_settings": ["inferred", "test"],
"test_metadata": {
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4 changes: 2 additions & 2 deletions examples/Good-TestCase-001.yaml
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Expand Up @@ -11,7 +11,6 @@
# TestCase, used to probe a particular test condition.
# is_a: TestEntity
# slots:
# - test_env
# - test_case_type
# - query_type
# - test_assets
Expand Down Expand Up @@ -41,7 +40,8 @@ test_assets:
name: TestAsset001
input_id: MONDO:0011426
predicate_name: treats
output_id: DRUGBANK:DB01592
output_ids:
- DRUGBANK:DB01592
expected_output: NeverShow
test_runner_settings:
- "inferred"
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4 changes: 2 additions & 2 deletions examples/SampleTestAssetList.json
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Expand Up @@ -5,7 +5,7 @@
"description": "Fingolimod treats multiple sclerosis",
"input_id": "PUBCHEM.COMPOUND:107970",
"predicate_name": "treats",
"output_id": "MONDO:0005301",
"output_ids": ["MONDO:0005301"],
"expected_output": "Acceptable",
"runner_settings": ["inferred", "test"],
"test_metadata": {
Expand All @@ -19,7 +19,7 @@
"description": "Carbamazepine treats Cerebral palsy",
"input_id": "PUBCHEM.COMPOUND:2554",
"predicate_name": "treats",
"output_id": "MONDO:0006497",
"output_ids": ["MONDO:0006497"],
"expected_output": "number_2_Acceptable",
"runner_settings": ["inferred", "test"],
"test_metadata": {
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