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Merged
AndiMajore merged 2 commits into from
Jun 22, 2026
Merged

Add fixes and features #24

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e241978
persist seed of clustering in task parameters always
lspindler2509 Jun 9, 2026
b2fb3df
fix for added self loops in first neighbor task
lspindler2509 Jun 9, 2026
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4 changes: 4 additions & 0 deletions tasks/first_neighbor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,7 @@ def first_neighbor(task_hook: TaskHook):
custom_edges = task_hook.parameters.get("custom_edges", False)

no_default_edges = task_hook.parameters.get("exclude_drugstone_ppi_edges", False)
allow_self_references = task_hook.parameters["config"].get("selfReferences", False)


# Set number of threads if OpenMP support is enabled.
Expand Down Expand Up @@ -214,6 +215,9 @@ def first_neighbor(task_hook: TaskHook):
}
edges.append(edge)

if not allow_self_references:
edges = [edge for edge in edges if edge["from"] != edge["to"]]

# Filter nodes to keep only upstream regulators if parameter is set
only_upstream_regulators = task_hook.parameters.get("only_upstream_regulators", False)
is_omnipath = ppi_dataset["name"] == "OmniPath"
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2 changes: 1 addition & 1 deletion tasks/leiden_clustering.py
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Expand Up @@ -158,7 +158,7 @@ def leiden_clustering(task_hook: TaskHook):
# If seed is not set, generate a random seed.
if seed is None:
seed = random.randint(1, 10000)
task_hook.parameters["seed"] = seed
task_hook.parameters["seed"] = seed

# Parsing input file.
task_hook.set_progress(1 / 4.0, "Parsing input.")
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2 changes: 1 addition & 1 deletion tasks/louvain_clustering.py
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Expand Up @@ -157,7 +157,7 @@ def louvain_clustering(task_hook: TaskHook):
# If seed is not set, generate a random seed.
if seed is None:
seed = random.randint(1, 10000)
task_hook.parameters["seed"] = seed
task_hook.parameters["seed"] = seed

# Parsing input file.
task_hook.set_progress(1 / 4.0, "Parsing input.")
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