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test/algorithms/AllPairs/expected/correctness-expected.txt diff --git a/test/AllPairs/expected/directed-expected.txt b/test/algorithms/AllPairs/expected/directed-expected.txt similarity index 100% rename from test/AllPairs/expected/directed-expected.txt rename to test/algorithms/AllPairs/expected/directed-expected.txt diff --git a/test/AllPairs/expected/sample-out-expected.txt b/test/algorithms/AllPairs/expected/sample-out-expected.txt similarity index 100% rename from test/AllPairs/expected/sample-out-expected.txt rename to test/algorithms/AllPairs/expected/sample-out-expected.txt diff --git a/test/AllPairs/expected/zero-length-expected.txt b/test/algorithms/AllPairs/expected/zero-length-expected.txt similarity index 100% rename from test/AllPairs/expected/zero-length-expected.txt rename to test/algorithms/AllPairs/expected/zero-length-expected.txt diff --git a/test/AllPairs/input/correctness-network.txt b/test/algorithms/AllPairs/input/correctness-network.txt similarity index 100% rename from test/AllPairs/input/correctness-network.txt rename to test/algorithms/AllPairs/input/correctness-network.txt diff --git a/test/AllPairs/input/correctness-nodetypes.txt b/test/algorithms/AllPairs/input/correctness-nodetypes.txt similarity index 100% rename from test/AllPairs/input/correctness-nodetypes.txt rename to test/algorithms/AllPairs/input/correctness-nodetypes.txt diff --git a/test/AllPairs/input/directed-flag-false.txt b/test/algorithms/AllPairs/input/directed-flag-false.txt similarity index 100% rename from test/AllPairs/input/directed-flag-false.txt rename to test/algorithms/AllPairs/input/directed-flag-false.txt diff --git a/test/AllPairs/input/directed-flag-true.txt b/test/algorithms/AllPairs/input/directed-flag-true.txt similarity index 100% rename from test/AllPairs/input/directed-flag-true.txt rename to test/algorithms/AllPairs/input/directed-flag-true.txt diff --git a/test/AllPairs/input/directed-network.txt b/test/algorithms/AllPairs/input/directed-network.txt similarity index 100% rename from test/AllPairs/input/directed-network.txt rename to test/algorithms/AllPairs/input/directed-network.txt diff --git a/test/AllPairs/input/directed-nodetypes.txt b/test/algorithms/AllPairs/input/directed-nodetypes.txt similarity index 100% rename from test/AllPairs/input/directed-nodetypes.txt rename to test/algorithms/AllPairs/input/directed-nodetypes.txt diff --git a/test/AllPairs/input/sample-in-net.txt b/test/algorithms/AllPairs/input/sample-in-net.txt similarity index 100% rename from test/AllPairs/input/sample-in-net.txt rename to test/algorithms/AllPairs/input/sample-in-net.txt diff --git a/test/AllPairs/input/sample-in-nodetypes.txt b/test/algorithms/AllPairs/input/sample-in-nodetypes.txt similarity index 100% rename from test/AllPairs/input/sample-in-nodetypes.txt rename to test/algorithms/AllPairs/input/sample-in-nodetypes.txt diff --git a/test/AllPairs/input/zero-length-network.txt b/test/algorithms/AllPairs/input/zero-length-network.txt similarity index 100% rename from test/AllPairs/input/zero-length-network.txt rename to test/algorithms/AllPairs/input/zero-length-network.txt diff --git a/test/AllPairs/input/zero-length-nodetypes.txt b/test/algorithms/AllPairs/input/zero-length-nodetypes.txt similarity index 100% rename from test/AllPairs/input/zero-length-nodetypes.txt rename to test/algorithms/AllPairs/input/zero-length-nodetypes.txt diff --git a/test/AllPairs/test_ap.py b/test/algorithms/AllPairs/test_ap.py similarity index 99% rename from test/AllPairs/test_ap.py rename to test/algorithms/AllPairs/test_ap.py index e9e8a8e37..0f83feaff 100644 --- a/test/AllPairs/test_ap.py +++ b/test/algorithms/AllPairs/test_ap.py @@ -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' diff --git a/test/BowTieBuilder/__init__.py b/test/algorithms/BowTieBuilder/__init__.py similarity index 100% rename from test/BowTieBuilder/__init__.py rename to test/algorithms/BowTieBuilder/__init__.py diff --git a/test/BowTieBuilder/expected/bidirectional-output.txt b/test/algorithms/BowTieBuilder/expected/bidirectional-output.txt similarity index 100% rename from test/BowTieBuilder/expected/bidirectional-output.txt rename to test/algorithms/BowTieBuilder/expected/bidirectional-output.txt diff --git a/test/BowTieBuilder/expected/btb-output.txt b/test/algorithms/BowTieBuilder/expected/btb-output.txt similarity index 100% rename from test/BowTieBuilder/expected/btb-output.txt rename to test/algorithms/BowTieBuilder/expected/btb-output.txt diff --git a/test/BowTieBuilder/expected/disjoint-output.txt b/test/algorithms/BowTieBuilder/expected/disjoint-output.txt similarity index 100% rename from test/BowTieBuilder/expected/disjoint-output.txt rename to test/algorithms/BowTieBuilder/expected/disjoint-output.txt diff --git a/test/BowTieBuilder/expected/empty-output.txt b/test/algorithms/BowTieBuilder/expected/empty-output.txt similarity index 100% rename from test/BowTieBuilder/expected/empty-output.txt rename to test/algorithms/BowTieBuilder/expected/empty-output.txt diff --git a/test/BowTieBuilder/expected/loop-output.txt b/test/algorithms/BowTieBuilder/expected/loop-output.txt similarity index 100% rename from test/BowTieBuilder/expected/loop-output.txt rename to test/algorithms/BowTieBuilder/expected/loop-output.txt diff --git a/test/BowTieBuilder/expected/source-to-source-disjoint-output.txt b/test/algorithms/BowTieBuilder/expected/source-to-source-disjoint-output.txt similarity index 100% rename from test/BowTieBuilder/expected/source-to-source-disjoint-output.txt rename to test/algorithms/BowTieBuilder/expected/source-to-source-disjoint-output.txt diff --git a/test/BowTieBuilder/expected/source-to-source-output.txt b/test/algorithms/BowTieBuilder/expected/source-to-source-output.txt similarity index 100% rename from test/BowTieBuilder/expected/source-to-source-output.txt rename to test/algorithms/BowTieBuilder/expected/source-to-source-output.txt diff --git a/test/BowTieBuilder/expected/source-to-source2-output.txt b/test/algorithms/BowTieBuilder/expected/source-to-source2-output.txt similarity index 100% rename from test/BowTieBuilder/expected/source-to-source2-output.txt rename to test/algorithms/BowTieBuilder/expected/source-to-source2-output.txt diff --git a/test/BowTieBuilder/expected/weighted-output.txt b/test/algorithms/BowTieBuilder/expected/weighted-output.txt similarity index 100% rename from test/BowTieBuilder/expected/weighted-output.txt rename to test/algorithms/BowTieBuilder/expected/weighted-output.txt diff --git a/test/BowTieBuilder/input/bad-edges.txt b/test/algorithms/BowTieBuilder/input/bad-edges.txt similarity index 100% rename from test/BowTieBuilder/input/bad-edges.txt rename to test/algorithms/BowTieBuilder/input/bad-edges.txt diff --git a/test/BowTieBuilder/input/bidirectional-edges.txt b/test/algorithms/BowTieBuilder/input/bidirectional-edges.txt similarity index 100% rename from test/BowTieBuilder/input/bidirectional-edges.txt rename to test/algorithms/BowTieBuilder/input/bidirectional-edges.txt diff --git a/test/BowTieBuilder/input/btb-bad-edges.txt b/test/algorithms/BowTieBuilder/input/btb-bad-edges.txt similarity index 100% rename from test/BowTieBuilder/input/btb-bad-edges.txt rename to test/algorithms/BowTieBuilder/input/btb-bad-edges.txt diff --git a/test/BowTieBuilder/input/btb-edges.txt b/test/algorithms/BowTieBuilder/input/btb-edges.txt similarity index 100% rename from test/BowTieBuilder/input/btb-edges.txt rename to test/algorithms/BowTieBuilder/input/btb-edges.txt diff --git a/test/BowTieBuilder/input/btb-sources.txt b/test/algorithms/BowTieBuilder/input/btb-sources.txt similarity index 100% rename from test/BowTieBuilder/input/btb-sources.txt rename to test/algorithms/BowTieBuilder/input/btb-sources.txt diff --git a/test/BowTieBuilder/input/btb-targets.txt b/test/algorithms/BowTieBuilder/input/btb-targets.txt similarity index 100% rename from test/BowTieBuilder/input/btb-targets.txt rename to test/algorithms/BowTieBuilder/input/btb-targets.txt diff --git a/test/BowTieBuilder/input/disjoint-edges.txt b/test/algorithms/BowTieBuilder/input/disjoint-edges.txt similarity index 100% rename from test/BowTieBuilder/input/disjoint-edges.txt rename to test/algorithms/BowTieBuilder/input/disjoint-edges.txt diff --git a/test/BowTieBuilder/input/disjoint-sources.txt b/test/algorithms/BowTieBuilder/input/disjoint-sources.txt similarity index 100% rename from test/BowTieBuilder/input/disjoint-sources.txt rename to test/algorithms/BowTieBuilder/input/disjoint-sources.txt diff --git a/test/BowTieBuilder/input/disjoint-targets.txt b/test/algorithms/BowTieBuilder/input/disjoint-targets.txt similarity index 100% rename from test/BowTieBuilder/input/disjoint-targets.txt rename to test/algorithms/BowTieBuilder/input/disjoint-targets.txt diff --git a/test/BowTieBuilder/input/disjoint2-edges.txt b/test/algorithms/BowTieBuilder/input/disjoint2-edges.txt similarity index 100% rename from test/BowTieBuilder/input/disjoint2-edges.txt rename to test/algorithms/BowTieBuilder/input/disjoint2-edges.txt diff --git a/test/BowTieBuilder/input/edges1.txt b/test/algorithms/BowTieBuilder/input/edges1.txt similarity index 100% rename from test/BowTieBuilder/input/edges1.txt rename to test/algorithms/BowTieBuilder/input/edges1.txt diff --git a/test/BowTieBuilder/input/loop-edges.txt b/test/algorithms/BowTieBuilder/input/loop-edges.txt similarity index 100% rename from test/BowTieBuilder/input/loop-edges.txt rename to test/algorithms/BowTieBuilder/input/loop-edges.txt diff --git a/test/BowTieBuilder/input/source-to-source-disjoint-edges.txt b/test/algorithms/BowTieBuilder/input/source-to-source-disjoint-edges.txt similarity index 100% rename from test/BowTieBuilder/input/source-to-source-disjoint-edges.txt rename to test/algorithms/BowTieBuilder/input/source-to-source-disjoint-edges.txt diff --git a/test/BowTieBuilder/input/source-to-source-edges.txt b/test/algorithms/BowTieBuilder/input/source-to-source-edges.txt similarity index 100% rename from test/BowTieBuilder/input/source-to-source-edges.txt rename to test/algorithms/BowTieBuilder/input/source-to-source-edges.txt diff --git a/test/BowTieBuilder/input/source-to-source2-edges.txt b/test/algorithms/BowTieBuilder/input/source-to-source2-edges.txt similarity index 100% rename from test/BowTieBuilder/input/source-to-source2-edges.txt rename to test/algorithms/BowTieBuilder/input/source-to-source2-edges.txt diff --git a/test/BowTieBuilder/input/source1.txt b/test/algorithms/BowTieBuilder/input/source1.txt similarity index 100% rename from test/BowTieBuilder/input/source1.txt rename to test/algorithms/BowTieBuilder/input/source1.txt diff --git a/test/BowTieBuilder/input/target-to-source-edges.txt b/test/algorithms/BowTieBuilder/input/target-to-source-edges.txt similarity index 100% rename from test/BowTieBuilder/input/target-to-source-edges.txt rename to test/algorithms/BowTieBuilder/input/target-to-source-edges.txt diff --git a/test/BowTieBuilder/input/target1.txt b/test/algorithms/BowTieBuilder/input/target1.txt similarity index 100% rename from test/BowTieBuilder/input/target1.txt rename to test/algorithms/BowTieBuilder/input/target1.txt diff --git a/test/BowTieBuilder/input/weight-one-edges.txt b/test/algorithms/BowTieBuilder/input/weight-one-edges.txt similarity index 100% rename from test/BowTieBuilder/input/weight-one-edges.txt rename to test/algorithms/BowTieBuilder/input/weight-one-edges.txt diff --git a/test/BowTieBuilder/input/weighted-edges.txt b/test/algorithms/BowTieBuilder/input/weighted-edges.txt similarity index 100% rename from test/BowTieBuilder/input/weighted-edges.txt rename to test/algorithms/BowTieBuilder/input/weighted-edges.txt diff --git a/test/BowTieBuilder/test_btb.py b/test/algorithms/BowTieBuilder/test_btb.py similarity index 99% rename from test/BowTieBuilder/test_btb.py rename to test/algorithms/BowTieBuilder/test_btb.py index 18279ddae..6558b90a5 100644 --- a/test/BowTieBuilder/test_btb.py +++ b/test/algorithms/BowTieBuilder/test_btb.py @@ -9,7 +9,7 @@ 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') diff --git a/test/DOMINO/__init__.py b/test/algorithms/DOMINO/__init__.py similarity index 100% rename from test/DOMINO/__init__.py rename to test/algorithms/DOMINO/__init__.py diff --git a/test/DOMINO/input/empty/domino-active-genes.txt b/test/algorithms/DOMINO/input/empty/domino-active-genes.txt similarity index 100% rename from test/DOMINO/input/empty/domino-active-genes.txt rename to test/algorithms/DOMINO/input/empty/domino-active-genes.txt diff --git a/test/DOMINO/input/empty/domino-network.txt b/test/algorithms/DOMINO/input/empty/domino-network.txt similarity index 100% rename from test/DOMINO/input/empty/domino-network.txt rename to test/algorithms/DOMINO/input/empty/domino-network.txt diff --git a/test/DOMINO/input/simple/domino-active-genes.txt b/test/algorithms/DOMINO/input/simple/domino-active-genes.txt similarity index 100% rename from test/DOMINO/input/simple/domino-active-genes.txt rename to test/algorithms/DOMINO/input/simple/domino-active-genes.txt diff --git a/test/DOMINO/input/simple/domino-network.txt b/test/algorithms/DOMINO/input/simple/domino-network.txt similarity index 100% rename from test/DOMINO/input/simple/domino-network.txt rename to test/algorithms/DOMINO/input/simple/domino-network.txt diff --git a/test/DOMINO/test_domino.py b/test/algorithms/DOMINO/test_domino.py similarity index 98% rename from test/DOMINO/test_domino.py rename to test/algorithms/DOMINO/test_domino.py index 2f88e4c03..558144eae 100644 --- a/test/DOMINO/test_domino.py +++ b/test/algorithms/DOMINO/test_domino.py @@ -14,7 +14,7 @@ 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' diff --git a/test/LocalNeighborhood/__init__.py b/test/algorithms/LocalNeighborhood/__init__.py similarity index 100% rename from test/LocalNeighborhood/__init__.py rename to test/algorithms/LocalNeighborhood/__init__.py diff --git a/test/LocalNeighborhood/expected_output/ln-output.txt b/test/algorithms/LocalNeighborhood/expected_output/ln-output.txt similarity index 100% rename from test/LocalNeighborhood/expected_output/ln-output.txt rename to test/algorithms/LocalNeighborhood/expected_output/ln-output.txt diff --git a/test/LocalNeighborhood/input/ln-bad-network.txt b/test/algorithms/LocalNeighborhood/input/ln-bad-network.txt similarity index 100% rename from test/LocalNeighborhood/input/ln-bad-network.txt rename to test/algorithms/LocalNeighborhood/input/ln-bad-network.txt diff --git a/test/LocalNeighborhood/input/ln-network.txt b/test/algorithms/LocalNeighborhood/input/ln-network.txt similarity index 100% rename from test/LocalNeighborhood/input/ln-network.txt rename to test/algorithms/LocalNeighborhood/input/ln-network.txt diff --git a/test/LocalNeighborhood/input/ln-nodes.txt b/test/algorithms/LocalNeighborhood/input/ln-nodes.txt similarity index 100% rename from test/LocalNeighborhood/input/ln-nodes.txt rename to test/algorithms/LocalNeighborhood/input/ln-nodes.txt diff --git a/test/LocalNeighborhood/test_ln.py b/test/algorithms/LocalNeighborhood/test_ln.py similarity index 94% rename from test/LocalNeighborhood/test_ln.py rename to test/algorithms/LocalNeighborhood/test_ln.py index 9093efc68..8781df6c9 100644 --- a/test/LocalNeighborhood/test_ln.py +++ b/test/algorithms/LocalNeighborhood/test_ln.py @@ -10,11 +10,11 @@ # 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') diff --git a/test/MEO/__init__.py b/test/algorithms/MEO/__init__.py similarity index 100% rename from test/MEO/__init__.py rename to test/algorithms/MEO/__init__.py diff --git a/test/MEO/input/meo-edges.txt b/test/algorithms/MEO/input/meo-edges.txt similarity index 100% rename from test/MEO/input/meo-edges.txt rename to test/algorithms/MEO/input/meo-edges.txt diff --git a/test/MEO/input/meo-sources.txt b/test/algorithms/MEO/input/meo-sources.txt similarity index 100% rename from test/MEO/input/meo-sources.txt rename to test/algorithms/MEO/input/meo-sources.txt diff --git a/test/MEO/input/meo-targets.txt b/test/algorithms/MEO/input/meo-targets.txt similarity index 100% rename from test/MEO/input/meo-targets.txt rename to test/algorithms/MEO/input/meo-targets.txt diff --git a/test/MEO/test_meo.py b/test/algorithms/MEO/test_meo.py similarity index 98% rename from test/MEO/test_meo.py rename to test/algorithms/MEO/test_meo.py index 7322bf003..6e5e25029 100644 --- a/test/MEO/test_meo.py +++ b/test/algorithms/MEO/test_meo.py @@ -9,7 +9,7 @@ config.init_from_file("config/config.yaml") -TEST_DIR = 'test/MEO/' +TEST_DIR = 'test/algorithms/MEO/' OUT_FILE = TEST_DIR + 'output/edges.txt' diff --git a/test/MinCostFlow/__init__.py b/test/algorithms/MinCostFlow/__init__.py similarity index 100% rename from test/MinCostFlow/__init__.py rename to test/algorithms/MinCostFlow/__init__.py diff --git a/test/MinCostFlow/expected/graph1/graph1_flow1_c1.0.sif b/test/algorithms/MinCostFlow/expected/graph1/graph1_flow1_c1.0.sif similarity index 100% rename from test/MinCostFlow/expected/graph1/graph1_flow1_c1.0.sif rename to test/algorithms/MinCostFlow/expected/graph1/graph1_flow1_c1.0.sif diff --git a/test/MinCostFlow/expected/graph1/graph1_flow2_c1.0.sif b/test/algorithms/MinCostFlow/expected/graph1/graph1_flow2_c1.0.sif similarity index 100% rename from test/MinCostFlow/expected/graph1/graph1_flow2_c1.0.sif rename to test/algorithms/MinCostFlow/expected/graph1/graph1_flow2_c1.0.sif diff --git a/test/MinCostFlow/expected/graph2/graph2_flow1_c1.0.sif b/test/algorithms/MinCostFlow/expected/graph2/graph2_flow1_c1.0.sif similarity index 100% rename from test/MinCostFlow/expected/graph2/graph2_flow1_c1.0.sif rename to test/algorithms/MinCostFlow/expected/graph2/graph2_flow1_c1.0.sif diff --git a/test/MinCostFlow/expected/graph2/graph2_flow2_c1.0.sif b/test/algorithms/MinCostFlow/expected/graph2/graph2_flow2_c1.0.sif similarity index 100% rename from test/MinCostFlow/expected/graph2/graph2_flow2_c1.0.sif rename to test/algorithms/MinCostFlow/expected/graph2/graph2_flow2_c1.0.sif diff --git a/test/MinCostFlow/expected/graph2/graph2_flow3_c1.0.sif b/test/algorithms/MinCostFlow/expected/graph2/graph2_flow3_c1.0.sif similarity index 100% rename from test/MinCostFlow/expected/graph2/graph2_flow3_c1.0.sif rename to test/algorithms/MinCostFlow/expected/graph2/graph2_flow3_c1.0.sif diff --git a/test/MinCostFlow/expected/graph3/graph3_flow1_c1.0.sif b/test/algorithms/MinCostFlow/expected/graph3/graph3_flow1_c1.0.sif similarity index 100% rename from test/MinCostFlow/expected/graph3/graph3_flow1_c1.0.sif rename to test/algorithms/MinCostFlow/expected/graph3/graph3_flow1_c1.0.sif diff --git a/test/MinCostFlow/expected/graph3/graph3_flow2_c1.0.sif b/test/algorithms/MinCostFlow/expected/graph3/graph3_flow2_c1.0.sif similarity index 100% rename from test/MinCostFlow/expected/graph3/graph3_flow2_c1.0.sif rename to test/algorithms/MinCostFlow/expected/graph3/graph3_flow2_c1.0.sif diff --git a/test/MinCostFlow/expected/graph4/graph4_flow1_c1.0.sif b/test/algorithms/MinCostFlow/expected/graph4/graph4_flow1_c1.0.sif similarity index 100% rename from test/MinCostFlow/expected/graph4/graph4_flow1_c1.0.sif rename to test/algorithms/MinCostFlow/expected/graph4/graph4_flow1_c1.0.sif diff --git a/test/MinCostFlow/expected/graph4/graph4_flow2_c1.0.sif b/test/algorithms/MinCostFlow/expected/graph4/graph4_flow2_c1.0.sif similarity index 100% rename from test/MinCostFlow/expected/graph4/graph4_flow2_c1.0.sif rename to test/algorithms/MinCostFlow/expected/graph4/graph4_flow2_c1.0.sif diff --git a/test/MinCostFlow/input/graph1/edges.txt b/test/algorithms/MinCostFlow/input/graph1/edges.txt similarity index 100% rename from test/MinCostFlow/input/graph1/edges.txt rename to test/algorithms/MinCostFlow/input/graph1/edges.txt diff --git a/test/MinCostFlow/input/graph1/sources.txt b/test/algorithms/MinCostFlow/input/graph1/sources.txt similarity index 100% rename from test/MinCostFlow/input/graph1/sources.txt rename to test/algorithms/MinCostFlow/input/graph1/sources.txt diff --git a/test/MinCostFlow/input/graph1/targets.txt b/test/algorithms/MinCostFlow/input/graph1/targets.txt similarity index 100% rename from test/MinCostFlow/input/graph1/targets.txt rename to test/algorithms/MinCostFlow/input/graph1/targets.txt diff --git a/test/MinCostFlow/input/graph2/edges.txt b/test/algorithms/MinCostFlow/input/graph2/edges.txt similarity index 100% rename from test/MinCostFlow/input/graph2/edges.txt rename to test/algorithms/MinCostFlow/input/graph2/edges.txt diff --git a/test/MinCostFlow/input/graph2/sources.txt b/test/algorithms/MinCostFlow/input/graph2/sources.txt similarity index 100% rename from test/MinCostFlow/input/graph2/sources.txt rename to test/algorithms/MinCostFlow/input/graph2/sources.txt diff --git a/test/MinCostFlow/input/graph2/targets.txt b/test/algorithms/MinCostFlow/input/graph2/targets.txt similarity index 100% rename from test/MinCostFlow/input/graph2/targets.txt rename to test/algorithms/MinCostFlow/input/graph2/targets.txt diff --git a/test/MinCostFlow/input/graph3/edges.txt b/test/algorithms/MinCostFlow/input/graph3/edges.txt similarity index 100% rename from test/MinCostFlow/input/graph3/edges.txt rename to test/algorithms/MinCostFlow/input/graph3/edges.txt diff --git a/test/MinCostFlow/input/graph3/sources.txt b/test/algorithms/MinCostFlow/input/graph3/sources.txt similarity index 100% rename from test/MinCostFlow/input/graph3/sources.txt rename to test/algorithms/MinCostFlow/input/graph3/sources.txt diff --git a/test/MinCostFlow/input/graph3/targets.txt b/test/algorithms/MinCostFlow/input/graph3/targets.txt similarity index 100% rename from test/MinCostFlow/input/graph3/targets.txt rename to test/algorithms/MinCostFlow/input/graph3/targets.txt diff --git a/test/MinCostFlow/input/graph4/edges.txt b/test/algorithms/MinCostFlow/input/graph4/edges.txt similarity index 100% rename from test/MinCostFlow/input/graph4/edges.txt rename to test/algorithms/MinCostFlow/input/graph4/edges.txt diff --git a/test/MinCostFlow/input/graph4/sources.txt b/test/algorithms/MinCostFlow/input/graph4/sources.txt similarity index 100% rename from test/MinCostFlow/input/graph4/sources.txt rename to test/algorithms/MinCostFlow/input/graph4/sources.txt diff --git a/test/MinCostFlow/input/graph4/targets.txt b/test/algorithms/MinCostFlow/input/graph4/targets.txt similarity index 100% rename from test/MinCostFlow/input/graph4/targets.txt rename to test/algorithms/MinCostFlow/input/graph4/targets.txt diff --git a/test/MinCostFlow/test_mcf.py b/test/algorithms/MinCostFlow/test_mcf.py similarity index 99% rename from test/MinCostFlow/test_mcf.py rename to test/algorithms/MinCostFlow/test_mcf.py index 23e597175..5863c3889 100644 --- a/test/MinCostFlow/test_mcf.py +++ b/test/algorithms/MinCostFlow/test_mcf.py @@ -9,7 +9,7 @@ config.init_from_file("config/config.yaml") -TEST_DIR = 'test/MinCostFlow/' +TEST_DIR = 'test/algorithms/MinCostFlow/' OUT_FILE = TEST_DIR + 'output/mincostflow-output.txt' diff --git a/test/OmicsIntegrator1/__init__.py b/test/algorithms/OmicsIntegrator1/__init__.py similarity index 100% rename from test/OmicsIntegrator1/__init__.py rename to test/algorithms/OmicsIntegrator1/__init__.py diff --git a/test/OmicsIntegrator1/input/oi1-dummy.txt b/test/algorithms/OmicsIntegrator1/input/oi1-dummy.txt similarity index 100% rename from test/OmicsIntegrator1/input/oi1-dummy.txt rename to test/algorithms/OmicsIntegrator1/input/oi1-dummy.txt diff --git a/test/OmicsIntegrator1/input/oi1-edges.txt b/test/algorithms/OmicsIntegrator1/input/oi1-edges.txt similarity index 100% rename from test/OmicsIntegrator1/input/oi1-edges.txt rename to test/algorithms/OmicsIntegrator1/input/oi1-edges.txt diff --git a/test/OmicsIntegrator1/input/oi1-prizes.txt b/test/algorithms/OmicsIntegrator1/input/oi1-prizes.txt similarity index 100% rename from test/OmicsIntegrator1/input/oi1-prizes.txt rename to test/algorithms/OmicsIntegrator1/input/oi1-prizes.txt diff --git a/test/OmicsIntegrator1/test_oi1.py b/test/algorithms/OmicsIntegrator1/test_oi1.py similarity index 99% rename from test/OmicsIntegrator1/test_oi1.py rename to test/algorithms/OmicsIntegrator1/test_oi1.py index c0fa19914..d2809d815 100644 --- a/test/OmicsIntegrator1/test_oi1.py +++ b/test/algorithms/OmicsIntegrator1/test_oi1.py @@ -14,7 +14,7 @@ config.init_from_file("config/config.yaml") -TEST_DIR = 'test/OmicsIntegrator1/' +TEST_DIR = 'test/algorithms/OmicsIntegrator1/' OUT_FILE = TEST_DIR+'output/test_optimalForest.sif' diff --git a/test/OmicsIntegrator2/__init__.py b/test/algorithms/OmicsIntegrator2/__init__.py similarity index 100% rename from test/OmicsIntegrator2/__init__.py rename to test/algorithms/OmicsIntegrator2/__init__.py diff --git a/test/OmicsIntegrator2/input/simple/oi2-edges.txt b/test/algorithms/OmicsIntegrator2/input/simple/oi2-edges.txt similarity index 100% rename from test/OmicsIntegrator2/input/simple/oi2-edges.txt rename to test/algorithms/OmicsIntegrator2/input/simple/oi2-edges.txt diff --git a/test/OmicsIntegrator2/input/simple/oi2-prizes.txt b/test/algorithms/OmicsIntegrator2/input/simple/oi2-prizes.txt similarity index 100% rename from test/OmicsIntegrator2/input/simple/oi2-prizes.txt rename to test/algorithms/OmicsIntegrator2/input/simple/oi2-prizes.txt diff --git a/test/OmicsIntegrator2/test_oi2.py b/test/algorithms/OmicsIntegrator2/test_oi2.py similarity index 97% rename from test/OmicsIntegrator2/test_oi2.py rename to test/algorithms/OmicsIntegrator2/test_oi2.py index 3638587e8..99e79a5ed 100644 --- a/test/OmicsIntegrator2/test_oi2.py +++ b/test/algorithms/OmicsIntegrator2/test_oi2.py @@ -9,7 +9,7 @@ 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' diff --git a/test/PathLinker/__init__.py b/test/algorithms/PathLinker/__init__.py similarity index 100% rename from test/PathLinker/__init__.py rename to test/algorithms/PathLinker/__init__.py diff --git a/test/PathLinker/input/sample-in-net.txt b/test/algorithms/PathLinker/input/sample-in-net.txt similarity index 100% rename from test/PathLinker/input/sample-in-net.txt rename to test/algorithms/PathLinker/input/sample-in-net.txt diff --git a/test/PathLinker/input/sample-in-nodetypes.txt b/test/algorithms/PathLinker/input/sample-in-nodetypes.txt similarity index 100% rename from test/PathLinker/input/sample-in-nodetypes.txt rename to test/algorithms/PathLinker/input/sample-in-nodetypes.txt diff --git a/test/PathLinker/test_pathlinker.py b/test/algorithms/PathLinker/test_pathlinker.py similarity index 98% rename from test/PathLinker/test_pathlinker.py rename to test/algorithms/PathLinker/test_pathlinker.py index e2d3e6fae..fd92c38f2 100644 --- a/test/PathLinker/test_pathlinker.py +++ b/test/algorithms/PathLinker/test_pathlinker.py @@ -9,7 +9,7 @@ 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' diff --git a/test/RWR/__init__.py b/test/algorithms/RWR/__init__.py similarity index 100% rename from test/RWR/__init__.py rename to test/algorithms/RWR/__init__.py diff --git a/test/RWR/expected_output/rwr-output.txt b/test/algorithms/RWR/expected_output/rwr-output.txt similarity index 100% rename from test/RWR/expected_output/rwr-output.txt rename to test/algorithms/RWR/expected_output/rwr-output.txt diff --git a/test/RWR/input/rwr-bad-network.txt b/test/algorithms/RWR/input/rwr-bad-network.txt similarity index 100% rename from test/RWR/input/rwr-bad-network.txt rename to test/algorithms/RWR/input/rwr-bad-network.txt diff --git a/test/RWR/input/rwr-network.txt b/test/algorithms/RWR/input/rwr-network.txt similarity index 100% rename from test/RWR/input/rwr-network.txt rename to test/algorithms/RWR/input/rwr-network.txt diff --git a/test/RWR/input/rwr-nodes.txt b/test/algorithms/RWR/input/rwr-nodes.txt similarity index 100% rename from test/RWR/input/rwr-nodes.txt rename to test/algorithms/RWR/input/rwr-nodes.txt diff --git a/test/RWR/test_RWR.py b/test/algorithms/RWR/test_RWR.py similarity index 98% rename from test/RWR/test_RWR.py rename to test/algorithms/RWR/test_RWR.py index fa3ca96f1..4f9b07fc8 100644 --- a/test/RWR/test_RWR.py +++ b/test/algorithms/RWR/test_RWR.py @@ -10,7 +10,7 @@ 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') diff --git a/test/ResponseNet/expected/rn-expected-optional.txt b/test/algorithms/ResponseNet/expected/rn-expected-optional.txt similarity index 100% rename from test/ResponseNet/expected/rn-expected-optional.txt rename to test/algorithms/ResponseNet/expected/rn-expected-optional.txt diff --git a/test/ResponseNet/expected/rn-expected.txt b/test/algorithms/ResponseNet/expected/rn-expected.txt similarity index 100% rename from test/ResponseNet/expected/rn-expected.txt rename to test/algorithms/ResponseNet/expected/rn-expected.txt diff --git a/test/ResponseNet/input/rn-edges.txt b/test/algorithms/ResponseNet/input/rn-edges.txt similarity index 100% rename from test/ResponseNet/input/rn-edges.txt rename to test/algorithms/ResponseNet/input/rn-edges.txt diff --git a/test/ResponseNet/input/rn-sources.txt b/test/algorithms/ResponseNet/input/rn-sources.txt similarity index 100% rename from test/ResponseNet/input/rn-sources.txt rename to test/algorithms/ResponseNet/input/rn-sources.txt diff --git a/test/ResponseNet/input/rn-targets.txt b/test/algorithms/ResponseNet/input/rn-targets.txt similarity index 100% rename from test/ResponseNet/input/rn-targets.txt rename to test/algorithms/ResponseNet/input/rn-targets.txt diff --git a/test/ResponseNet/test_rn.py b/test/algorithms/ResponseNet/test_rn.py similarity index 98% rename from test/ResponseNet/test_rn.py rename to test/algorithms/ResponseNet/test_rn.py index 9d3c1cbaa..e6a4ba85e 100644 --- a/test/ResponseNet/test_rn.py +++ b/test/algorithms/ResponseNet/test_rn.py @@ -10,7 +10,7 @@ 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' diff --git a/test/ST_RWR/__init__.py b/test/algorithms/ST_RWR/__init__.py similarity index 100% rename from test/ST_RWR/__init__.py rename to test/algorithms/ST_RWR/__init__.py diff --git a/test/ST_RWR/expected_output/strwr-output.txt b/test/algorithms/ST_RWR/expected_output/strwr-output.txt similarity index 100% rename from test/ST_RWR/expected_output/strwr-output.txt rename to test/algorithms/ST_RWR/expected_output/strwr-output.txt diff --git a/test/ST_RWR/input/strwr-bad-network.txt b/test/algorithms/ST_RWR/input/strwr-bad-network.txt similarity index 100% rename from test/ST_RWR/input/strwr-bad-network.txt rename to test/algorithms/ST_RWR/input/strwr-bad-network.txt diff --git a/test/ST_RWR/input/strwr-network.txt b/test/algorithms/ST_RWR/input/strwr-network.txt similarity index 100% rename from test/ST_RWR/input/strwr-network.txt rename to test/algorithms/ST_RWR/input/strwr-network.txt diff --git a/test/ST_RWR/input/strwr-sources.txt b/test/algorithms/ST_RWR/input/strwr-sources.txt similarity index 100% rename from test/ST_RWR/input/strwr-sources.txt rename to test/algorithms/ST_RWR/input/strwr-sources.txt diff --git a/test/ST_RWR/input/strwr-targets.txt b/test/algorithms/ST_RWR/input/strwr-targets.txt similarity index 100% rename from test/ST_RWR/input/strwr-targets.txt rename to test/algorithms/ST_RWR/input/strwr-targets.txt diff --git a/test/ST_RWR/test_STRWR.py b/test/algorithms/ST_RWR/test_STRWR.py similarity index 98% rename from test/ST_RWR/test_STRWR.py rename to test/algorithms/ST_RWR/test_STRWR.py index be5a7c20c..57e57bc56 100644 --- a/test/ST_RWR/test_STRWR.py +++ b/test/algorithms/ST_RWR/test_STRWR.py @@ -10,7 +10,7 @@ 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')