Merge branch 'main' of https://github.com/jcrozum/nfvs-motifs into ba…

…sic_analysis
jcrozum · Sep 13, 2023 · 56f0237 · 56f0237 · github-actions · Sep 13, 2023
2 parents a50d75f + 4c616ca
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diff --git a/conftest.py b/conftest.py
@@ -25,11 +25,11 @@ def pytest_generate_tests(metafunc):
     if "network_file" in metafunc.fixturenames:
         size = int(metafunc.config.getoption("networksize"))
         models = []
-        for model in os.listdir("./bbm-bnet-inputs-true"):
+        for model in os.listdir("./models/bbm-bnet-inputs-true"):
             if not model.endswith(".bnet"):
                 # Just in case there are some other files there.
                 continue
-            path = f"./bbm-bnet-inputs-true/{model}"
+            path = f"./models/bbm-bnet-inputs-true/{model}"
             bn = BooleanNetwork.from_file(path)
             if bn.num_vars() > size:
                 continue

diff --git a/models/.gitignore b/models/.gitignore
@@ -0,0 +1 @@
+bbm-bnet-inputs-random-128
diff --git a/PyBoolNet-repo/arellano_rootstem.bnet → models/PyBoolNet-repo/arellano_rootstem.bnet b/PyBoolNet-repo/arellano_rootstem.bnet → models/PyBoolNet-repo/arellano_rootstem.bnet
diff --git a/PyBoolNet-repo/calzone_cellfate.bnet → models/PyBoolNet-repo/calzone_cellfate.bnet b/PyBoolNet-repo/calzone_cellfate.bnet → models/PyBoolNet-repo/calzone_cellfate.bnet
diff --git a/PyBoolNet-repo/dahlhaus_neuroplastoma.bnet → ...yBoolNet-repo/dahlhaus_neuroplastoma.bnet b/PyBoolNet-repo/dahlhaus_neuroplastoma.bnet → ...yBoolNet-repo/dahlhaus_neuroplastoma.bnet
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diff --git a/PyBoolNet-repo/tournier_apoptosis.bnet → ...ls/PyBoolNet-repo/tournier_apoptosis.bnet b/PyBoolNet-repo/tournier_apoptosis.bnet → ...ls/PyBoolNet-repo/tournier_apoptosis.bnet
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diff --git a/bbm-bnet-inputs-identity/README.md → models/bbm-bnet-inputs-identity/README.md b/bbm-bnet-inputs-identity/README.md → models/bbm-bnet-inputs-identity/README.md
diff --git a/bbm-bnet-inputs-identity/metadata.json → ...ls/bbm-bnet-inputs-identity/metadata.json b/bbm-bnet-inputs-identity/metadata.json → ...ls/bbm-bnet-inputs-identity/metadata.json
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diff --git a/models/bbm-bnet-inputs-random-128.zip b/models/bbm-bnet-inputs-random-128.zip
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diff --git a/bbm-bnet-inputs-true/053.bnet → models/bbm-bnet-inputs-true/053.bnet b/bbm-bnet-inputs-true/053.bnet → models/bbm-bnet-inputs-true/053.bnet
File	Stmts	Miss	Cover	Missing
nfvsmotifs
SuccessionDiagram.py	154	4	97%	6–7, 208, 452
control.py	120	13	89%	47, 56, 60, 66, 80, 89–105, 319, 334
interaction_graph_utils.py	142	8	94%	6–9, 57, 70, 95–96
motif_avoidant.py	163	6	96%	23–24, 130, 147, 184, 309
petri_net_translation.py	84	6	93%	23–24, 52, 63–64, 94
pyeda_utils.py	95	34	64%	12, 56–66, 90, 95, 98–112, 140–144
space_utils.py	118	5	96%	15–16, 198, 213, 270
state_utils.py	68	12	82%	15, 55–66, 98, 105, 114
terminal_restriction_space.py	44	3	93%	6–7, 80
trappist_core.py	186	20	89%	10–11, 39, 41, 81, 127, 192, 194, 196, 231–233, 259, 317, 319, 349, 389, 391, 422, 451
nfvsmotifs/FVSpython3
FVS.py	48	10	79%	90–91, 97, 133, 183–189
FVS_localsearch_10_python.py	90	1	99%	179
nfvsmotifs/_sd_algorithms
compute_attractor_seeds.py	29	1	97%	6
expand_attractor_seeds.py	51	4	92%	6, 95–100
expand_bfs.py	28	1	96%	6
expand_dfs.py	30	1	97%	6
expand_minimal_spaces.py	37	1	97%	6
expand_to_target.py	30	3	90%	6, 37, 42
TOTAL	1614	133	92%