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test: mv algorithm tests to subfolder #391

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06a211e
chore: mv
tristan-f-r Oct 14, 2025
bcb219b
fix: paths
tristan-f-r Oct 14, 2025
8a7490c
test(ln): correct path
tristan-f-r Oct 14, 2025
20fa21d
chore: manually update test_duration paths
tristan-f-r Oct 14, 2025
ef6c7e7
test(rn): fix path
tristan-f-r Oct 14, 2025
3bce801
test(pathlinker): correct path
tristan-f-r Oct 14, 2025
56fa440
test(ln): correct path
tristan-f-r Oct 14, 2025
4caa8cf
test(domino): fix path
tristan-f-r Oct 14, 2025
ca7c230
Merge branch 'umain' into test-alg-move
tristan-f-r Oct 17, 2025
0ab7a18
Merge branch 'main' into test-alg-move
tristan-f-r Oct 25, 2025
fa1db4d
Merge branch 'main' into test-alg-move
tristan-f-r Oct 25, 2025
0e5aed9
Merge branch 'main' into test-alg-move
tristan-f-r Nov 18, 2025
1095771
Merge branch 'main' into test-alg-move
tristan-f-r Jan 10, 2026
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142 changes: 71 additions & 71 deletions .test_durations
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Original file line number Diff line number Diff line change
@@ -1,75 +1,75 @@
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2 changes: 1 addition & 1 deletion test/AllPairs/test_ap.py → test/algorithms/AllPairs/test_ap.py
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Expand Up @@ -13,7 +13,7 @@
# like setting hash length behaviors, container registries, etc.
config.init_from_file("config/config.yaml")

TEST_DIR = Path('test/AllPairs/')
TEST_DIR = Path('test/algorithms/AllPairs/')
OUT_DIR = TEST_DIR / 'output'
EXPECTED_DIR = TEST_DIR / 'expected'

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config.init_from_file("config/config.yaml")

TEST_DIR = Path('test', 'BowTieBuilder/')
TEST_DIR = Path('test', 'algorithms', 'BowTieBuilder/')
OUT_FILE_DEFAULT = Path(TEST_DIR, 'output', 'raw-pathway.txt')


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config.init_from_file("config/config.yaml")

TEST_DIR = Path('test', 'DOMINO')
TEST_DIR = Path('test', 'algorithms', 'DOMINO')
OUT_FILE_DEFAULT = TEST_DIR / 'output' / 'domino-output.txt'
OUT_FILE_OPTIONAL = TEST_DIR / 'output' / 'domino-output-thresholds.txt'

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# TODO consider refactoring to simplify the import
# Modify the path because of the - in the directory
SPRAS_ROOT = Path(__file__).parent.parent.parent.absolute()
SPRAS_ROOT = Path(__file__).parent.parent.parent.parent.absolute()
sys.path.append(str(Path(SPRAS_ROOT, 'docker-wrappers', 'LocalNeighborhood')))
from local_neighborhood_alg import local_neighborhood

TEST_DIR = Path('test', 'LocalNeighborhood/')
TEST_DIR = Path('test', 'algorithms', 'LocalNeighborhood/')
OUT_FILE = Path(TEST_DIR, 'output', 'ln-output.txt')


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config.init_from_file("config/config.yaml")

TEST_DIR = 'test/MEO/'
TEST_DIR = 'test/algorithms/MEO/'
OUT_FILE = TEST_DIR + 'output/edges.txt'


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config.init_from_file("config/config.yaml")

TEST_DIR = 'test/MinCostFlow/'
TEST_DIR = 'test/algorithms/MinCostFlow/'
OUT_FILE = TEST_DIR + 'output/mincostflow-output.txt'


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config.init_from_file("config/config.yaml")

TEST_DIR = 'test/OmicsIntegrator1/'
TEST_DIR = 'test/algorithms/OmicsIntegrator1/'
OUT_FILE = TEST_DIR+'output/test_optimalForest.sif'


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config.init_from_file("config/config.yaml")

TEST_DIR = Path('test', 'OmicsIntegrator2')
TEST_DIR = Path('test', 'algorithms', 'OmicsIntegrator2')
OUT_FILE = TEST_DIR / 'output' / 'test.tsv'

EDGE_FILE = TEST_DIR / 'input' / 'simple' / 'oi2-edges.txt'
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config.init_from_file("config/config.yaml")

TEST_DIR = 'test/PathLinker/'
TEST_DIR = 'test/algorithms/PathLinker/'
OUT_FILE_DEFAULT = TEST_DIR+'output/pathlinker-ranked-edges.txt'
OUT_FILE_100 = TEST_DIR+'output/pathlinker-ranked-edges-k100.txt'

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config.init_from_file("config/config.yaml")

TEST_DIR = Path('test', 'RWR/')
TEST_DIR = Path('test', 'algorithms', 'RWR/')
OUT_FILE = Path(TEST_DIR, 'output', 'rwr-output.txt')


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config.init_from_file("config/config.yaml")

TEST_DIR = Path('test', 'ResponseNet')
TEST_DIR = Path('test', 'algorithms', 'ResponseNet')
OUT_FILE = TEST_DIR / 'output' / 'rn-output.txt'
EXPECTED_FILE = TEST_DIR / 'expected' / 'rn-expected.txt'
EXPECTED_FILE_OPTIONAL = TEST_DIR / 'expected' / 'rn-expected-optional.txt'
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config.init_from_file("config/config.yaml")

TEST_DIR = Path('test', 'ST_RWR')
TEST_DIR = Path('test', 'algorithms', 'ST_RWR')
OUT_FILE = Path(TEST_DIR, 'output', 'strwr-output.txt')
EXPECTED_OUTPUT = Path(TEST_DIR, 'expected_output', 'strwr-output.txt')

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