复现graph-tool网络重建示例时collect_vertex_marginals函数传参报错

Let's work through this error you're facing—it boils down to a mismatch between the updated graph-tool documentation code and the older version of graph-tool running in your Docker container.

Why the Error Occurs #

The TypeError: collect_vertex_marginals() got an unexpected keyword argument 'b' happens because:

• Recent graph-tool updates changed the API: the new version requires the b parameter for collect_vertex_marginals, plus the gt.perfect_prop_hash call (your line 5) to handle block state hashing.
• But your Docker environment is running an older graph-tool version, where neither the b parameter nor that hash step existed.

Solution 1: Upgrade graph-tool in Docker #

The easiest fix is to pull the latest official graph-tool Docker image to align with the documentation code:

docker pull tiagopeixoto/graph-tool:latest

Restart your Docker container with this new image, and your original code should run without errors.

Solution 2: Adjust Code for Older graph-tool Versions #

If you need to keep your current environment, modify the code to match the older API by removing the new additions:

def collect_marginals(s):
    global pv, u, cs
    u = s.collect_marginal(u)
    bstate = s.get_block_state()
    # Remove the perfect_prop_hash line (line 5)
    pv = bstate.levels[0].collect_vertex_marginals(pv)  # Drop the b=b argument
    cs.append(gt.local_clustering(s.get_graph()).fa.mean())

This simplified version matches the older API that worked for you previously.

内容的提问来源于stack exchange，提问作者Marianna Demetriou