Update an option for checking the strong connectivity of connectivity matrix.

[isacdaavid]

It looks good to me. Thoughts @wmayner ?

snippet at work:

import pyphi
import numpy as np

node_labels = ("A", "B", "C")

tpm = np.array(
    [
        [1, 0, 0],
        [0, 1, 0],
        [1, 1, 1],
        [0, 1, 1],
        [0, 0, 0],
        [1, 1, 0],
        [0, 0, 1],
        [1, 0, 1],
    ]
)

connectivity_matrix = np.array([
    [1, 1, 0,],
    [0, 1, 0,],
    [0, 0, 1,],
])

network = pyphi.Network(tpm, cm=connectivity_matrix, node_labels=node_labels)

state = (1, 0, 0)

subsystem_backward = pyphi.Subsystem(
    network,
    state,
    nodes=node_labels,
    backward_tpm=True
)

subsystem_forward = pyphi.Subsystem(
    network,
    state,
    nodes=node_labels
)

pyphi.backwards.sia(subsystem_backward, subsystem_forward)

┌──────────────────────────────────┐
│ NullSystemIrreducibilityAnalysis │
│     ━━━━━━━━━━━━━━━━━━━━━━━      │
│        Subsystem:  A,B,C         │
│                Φ: 0.0            │
│            CAUSE:  (0,0,0)       │
│             II_c: 0.25           │
│           EFFECT:  (0,1,0)       │
│             II_e: 0.25           │
└──────────────────────────────────┘

Tests:

Before: 97 failed, 581 passed, 32 skipped, 22 deselected, 2 xfailed, 22 errors in 1441.59s (0:24:01)

After: 97 failed, 581 passed, 32 skipped, 22 deselected, 2 xfailed, 22 errors in 1343.88s (0:22:23)

[wmayner]

This is a good idea, but we should integrate the logic into the existing system for checking short-circuit conditions rather than copy-pasting from the 3.0 code path.

This would mean adding another function like the one on this line.

@Astrocytes120 , would you be willing to update the PR accordingly? Then we can review and approve.

[Astrocytes120]

Yes, I think that is a valid point. I would check the line you pointed out.

Thanks, Myeongjin Jeong.

12/14/23 오후 10:49, William Mayner @.***> 작성:

This is a good idea, but we should integrate the logic into the existing system for checking short-circuit conditions rather than copy-pasting from the 3.0 code path.

This would mean adding another function like the one on this line https://github.com/wmayner/pyphi/pull/111/files#diff-26742afb055ef4973f0411d53fff2bc986969e5fbd3afc80a1ee4b32eecb20ccR360.

@Astrocytes120 https://github.com/Astrocytes120 , would you be willing to update the PR accordingly? Then we can review and approve.

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