Skip to content

Commit

Permalink
reconciling #71 and #73 for #69
Browse files Browse the repository at this point in the history
  • Loading branch information
jcrozum committed Jul 25, 2023
1 parent a810dc0 commit 45269e0
Show file tree
Hide file tree
Showing 25 changed files with 1,741 additions and 723 deletions.
26 changes: 18 additions & 8 deletions conftest.py
Original file line number Diff line number Diff line change
@@ -1,17 +1,27 @@
# type: ignore
import os
from biodivine_aeon import BooleanNetwork # type: ignore
# The purpose of this file is to detect tests with `network_file` as input and
# then supply these tests with networks from `bbm-bnet-inputs-true` up to a certain
# network size. This network size can be configured using `--networksize` and
# its default value is 20.

from biodivine_aeon import BooleanNetwork

# The purpose of this file is to detect tests with `network_file` as input and
# then supply these tests with networks from `bbm-bnet-inputs-true` up to a
# certain network size. This network size can be configured using
# `--networksize` and its default value is 20.

# We intentionally test on the `-inputs-true` models as opposed to `-inputs-identity`,
# as having fixed inputs ensures there are not too many trap spaces, fixed points, etc.


def pytest_addoption(parser):
parser.addoption("--networksize", action="store", default="20", help="Only check networks up to this size.")
parser.addoption(
"--networksize",
action="store",
default="20",
help="Only check networks up to this size.",
)


def pytest_generate_tests(metafunc):
def pytest_generate_tests(metafunc):
if "network_file" in metafunc.fixturenames:
size = int(metafunc.config.getoption("networksize"))
models = []
Expand All @@ -24,4 +34,4 @@ def pytest_generate_tests(metafunc):
if bn.num_vars() > size:
continue
models.append(path)
metafunc.parametrize("network_file", models)
metafunc.parametrize("network_file", models)
434 changes: 239 additions & 195 deletions nfvsmotifs/SuccessionDiagram.py

Large diffs are not rendered by default.

19 changes: 10 additions & 9 deletions nfvsmotifs/_sd_algorithms/__init__.py
Original file line number Diff line number Diff line change
@@ -1,11 +1,12 @@
"""
This is an internal module which contains the implementations of the more involved
algorithms related to `SuccessionDiagram` construction and manipulation. The idea
is that any implementation that requires some helper methods or data structures
should be present here instead of `SuccessionDiagram.py` to avoid mixing of code
used by different algorithms and bloating the core succession diagram implementation.
This is an internal module which contains the implementations of the more
involved algorithms related to `SuccessionDiagram` construction and
manipulation. The idea is that any implementation that requires some helper
methods or data structures should be present here instead of
`SuccessionDiagram.py` to avoid mixing of code used by different algorithms and
bloating the core succession diagram implementation.
The algorithms within this module here should only use the public API of
the `SuccessionDiagram` to avoid violating its invariants. The actual algorithms
are then "re-exported" as a public methods of the `SuccessionDiagram` class.
"""
The algorithms within this module here should only use the public API of the
`SuccessionDiagram` to avoid violating its invariants. The actual algorithms are
then "re-exported" as a public methods of the `SuccessionDiagram` class.
"""
33 changes: 20 additions & 13 deletions nfvsmotifs/_sd_algorithms/compute_attractor_seeds.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,21 +5,27 @@
if TYPE_CHECKING:
from nfvsmotifs.SuccessionDiagram import SuccessionDiagram

from nfvsmotifs.motif_avoidant import detect_motif_avoidant_attractors, make_retained_set
from nfvsmotifs.terminal_restriction_space import get_terminal_restriction_space
from nfvsmotifs.trappist_core import compute_fixed_point_reduced_STG, trappist
import nfvsmotifs
import nfvsmotifs.SuccessionDiagram
from nfvsmotifs.motif_avoidant import (
detect_motif_avoidant_attractors,
make_retained_set,
)
from nfvsmotifs.terminal_restriction_space import get_terminal_restriction_space
from nfvsmotifs.trappist_core import compute_fixed_point_reduced_STG


def compute_attractor_seeds(
sd: SuccessionDiagram,
node_id: int,
) -> list[dict[str, int]]:
"""
Compute the list of vertices such that each attractor within the subspace of the given `node_id` is covered by
exactly one vertex.
Compute the list of vertices such that each attractor within the subspace of
the given `node_id` is covered by exactly one vertex.
If the node is a stub, the result covers the whole subspace. If the node is expanded, the result only covers
the "immediate" subspace without the subspaces of the child nodes.
If the node is a stub, the result covers the whole subspace. If the node is
expanded, the result only covers the "immediate" subspace without the
subspaces of the child nodes.
"""

if nfvsmotifs.SuccessionDiagram.DEBUG:
Expand All @@ -28,13 +34,14 @@ def compute_attractor_seeds(
node_space = sd.node_space(node_id)

if len(node_space) == sd.network.num_vars():
# This node is a fixed-point.
# This node is a fixed-point.
return [node_space]

# Compute the list of child spaces if the node is expanded. Otherwise "pretend" that there are no children.
# Compute the list of child spaces if the node is expanded. Otherwise
# "pretend" that there are no children.
child_spaces = []
if sd.node_is_expanded(node_id):
child_spaces = [ sd.node_space(s) for s in sd.node_successors(node_id) ]
child_spaces = [sd.node_space(s) for s in sd.node_successors(node_id)]

# Fix everything in the NFVS to zero, as long as
# it isn't already fixed by our `node_space`.
Expand All @@ -43,7 +50,7 @@ def compute_attractor_seeds(
# the space is a trap and this will remove the corresponding unnecessary
# Petri net transitions.
retained_set = make_retained_set(sd.network, sd.nfvs, node_space, child_spaces)

if len(retained_set) == sd.network.num_vars() and len(child_spaces) == 0:
# There is only a single attractor remaining here,
# and its "seed" is the retained set.
Expand All @@ -62,7 +69,7 @@ def compute_attractor_seeds(
retained_set,
ensure_subspace=node_space,
avoid_subspaces=child_spaces,
)
)

if nfvsmotifs.SuccessionDiagram.DEBUG:
print(f"[{node_id}] Found {len(candidate_seeds)} seed candidates.")
Expand All @@ -78,7 +85,7 @@ def compute_attractor_seeds(
candidate_seeds,
terminal_restriction_space,
max_iterations=1000,
is_in_an_mts=len(child_spaces)==0
is_in_an_mts=len(child_spaces) == 0,
)

return attractors
59 changes: 35 additions & 24 deletions nfvsmotifs/_sd_algorithms/expand_attractor_seeds.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,24 +5,29 @@
if TYPE_CHECKING:
from nfvsmotifs.SuccessionDiagram import SuccessionDiagram

from nfvsmotifs.trappist_core import compute_fixed_point_reduced_STG
import nfvsmotifs
import nfvsmotifs.SuccessionDiagram
from nfvsmotifs.motif_avoidant import make_retained_set
from nfvsmotifs.space_utils import intersect
import nfvsmotifs
from nfvsmotifs.trappist_core import compute_fixed_point_reduced_STG


def expand_attractor_seeds(sd: SuccessionDiagram, size_limit: int | None = None):
"""
See `SuccessionDiagram.expand_attractor_seeds` for documentation.
"""

# First, expand the succession diagram such that all minimal trap spaces are found.
# This reduces the amount of work performed in this algorithm, because for every attractor
# in a minimal trap space, we already have the closest trap space, now we just need to
# do the same for (potential) motif-avoidant attractors.
# First, expand the succession diagram such that all minimal trap spaces are
# found. This reduces the amount of work performed in this algorithm,
# because for every attractor in a minimal trap space, we already have the
# closest trap space, now we just need to do the same for (potential)
# motif-avoidant attractors.
sd.expand_minimal_spaces(size_limit)

if nfvsmotifs.SuccessionDiagram.DEBUG:
print("Minimal trap space expansion finished. Proceeding to attractor expansion.")
print(
"Minimal trap space expansion finished. Proceeding to attractor expansion."
)

root = sd.root()
seen = set([root])
Expand All @@ -37,21 +42,23 @@ def expand_attractor_seeds(sd: SuccessionDiagram, size_limit: int | None = None)
return False

successors = sd.node_successors(node, compute=True)
successors = sorted(successors, reverse=True) # For determinism!
successors = sorted(successors, reverse=True) # For determinism!
# (reversed because we explore the list from the back)

node_space = sd.node_space(node)

# Retrieve the stable motifs of children that are already expanded.
expanded_children = [ x for x in sd.node_successors(node) if sd.node_is_expanded(x) ]
expanded_motifs = [ sd.edge_stable_motif(node, child) for child in expanded_children ]

# Now, we skip all successors that are either already seen, or that
expanded_children = [
x for x in sd.node_successors(node) if sd.node_is_expanded(x)
]
expanded_motifs = [
sd.edge_stable_motif(node, child) for child in expanded_children
]

# Now, we skip all successors that are either already seen, or that
# do not contain any candidate states for motif-avoidant attractors.
while len(successors) > 0:
if successors[-1] in seen:
# The next node was already seen on stack. We can thus skip it and continue
# to the next one.
# The next node was already seen on stack. We can thus skip it
# and continue to the next one.
successors.pop()
continue
if sd.node_is_expanded(successors[-1]):
Expand All @@ -65,8 +72,10 @@ def expand_attractor_seeds(sd: SuccessionDiagram, size_limit: int | None = None)
successor_space = sd.node_space(successors[-1])
retained_set = make_retained_set(sd.network, sd.nfvs, successor_space)

avoid_or_none = [ intersect(successor_space, child) for child in expanded_motifs ]
avoid = [ x for x in avoid_or_none if x is not None ]
avoid_or_none = [
intersect(successor_space, child) for child in expanded_motifs
]
avoid = [x for x in avoid_or_none if x is not None]

successor_seeds = compute_fixed_point_reduced_STG(
sd.petri_net,
Expand All @@ -77,14 +86,16 @@ def expand_attractor_seeds(sd: SuccessionDiagram, size_limit: int | None = None)
)

if len(successor_seeds) == 0:
# At this point, we know that this successor is not expanded and there are either
# no candidate states in it, or all candidate states are already covered by some
# other expanded successor.
# At this point, we know that this successor is not expanded and
# there are either no candidate states in it, or all candidate
# states are already covered by some other expanded successor.
successors.pop()
continue

if nfvsmotifs.SuccessionDiagram.DEBUG:
print(f"[{node}] Found successor with new attractor candidate seeds. Expand node {successors[-1]}.")
print(
f"[{node}] Found successor with new attractor candidate seeds. Expand node {successors[-1]}."
)

break

Expand All @@ -100,5 +111,5 @@ def expand_attractor_seeds(sd: SuccessionDiagram, size_limit: int | None = None)
stack.append((node, successors))
# Push the successor onto the stack.
stack.append((s, None))
return True

return True
17 changes: 9 additions & 8 deletions nfvsmotifs/_sd_algorithms/expand_bfs.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,12 @@
if TYPE_CHECKING:
from nfvsmotifs.SuccessionDiagram import SuccessionDiagram


def expand_bfs(
sd: SuccessionDiagram,
node_id: int | None = None,
bfs_level_limit: int | None = None,
size_limit: int | None = None
sd: SuccessionDiagram,
node_id: int | None = None,
bfs_level_limit: int | None = None,
size_limit: int | None = None,
) -> bool:
"""
See `SuccessionDiagram.expand_bfs` for documentation.
Expand All @@ -18,12 +19,12 @@ def expand_bfs(
if node_id is None:
node_id = sd.root()

seen = set()
seen: set[int] = set()
seen.add(node_id)

level_id = 0
current_level = [node_id]
next_level = []
next_level: list[int] = []

while len(current_level) > 0:
for node in current_level:
Expand All @@ -42,9 +43,9 @@ def expand_bfs(
if s not in seen:
seen.add(s)
next_level.append(s)

# The level is explored. Check if this exceeds the level limit.
if (bfs_level_limit is not None) and (level_id >= bfs_level_limit):
if (bfs_level_limit is not None) and (level_id >= bfs_level_limit):
# Level limit reached.
return False

Expand Down
13 changes: 7 additions & 6 deletions nfvsmotifs/_sd_algorithms/expand_dfs.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
if TYPE_CHECKING:
from nfvsmotifs.SuccessionDiagram import SuccessionDiagram


def expand_dfs(
sd: SuccessionDiagram,
node_id: int | None = None,
Expand All @@ -18,7 +19,7 @@ def expand_dfs(
if node_id is None:
node_id = sd.root()

seen = set()
seen: set[int] = set()
seen.add(node_id)

stack: list[tuple[int, list[int] | None]] = [(node_id, None)]
Expand All @@ -32,9 +33,9 @@ def expand_dfs(
if (size_limit is not None) and (len(sd) >= size_limit):
# Size limit reached.
return False

successors = sd.node_successors(node, compute=True)
successors = sorted(successors, reverse=True) # For determinism!
successors = sorted(successors, reverse=True) # For determinism!
# (reversed because we explore the list from the back)

# Remove all immediate successors that are already visited.
Expand All @@ -48,7 +49,7 @@ def expand_dfs(
if (dfs_stack_limit is not None) and (len(stack) >= dfs_stack_limit):
# We cannot push any successor nodes because it would exceed
# the stack limit. As such, we can just continue with the next
# item on the stack. however, we must remember that we skipped
# item on the stack. however, we must remember that we skipped
# some nodes and the result is thus incomplete.
result_is_complete = False
continue
Expand All @@ -58,6 +59,6 @@ def expand_dfs(
# Push the node back with the remaining successors.
stack.append((node, successors))
# Push the successor onto the stack.
stack.append((s, None))
stack.append((s, None))

return result_is_complete
return result_is_complete
Loading

1 comment on commit 45269e0

@github-actions
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Coverage

Coverage Report
FileStmtsMissCoverMissing
nfvsmotifs
   SuccessionDiagram.py154497%6–7, 208, 452
   control.py1221389%47, 56, 60, 66, 80, 89–105, 324, 339
   interaction_graph_utils.py142894%6–9, 57, 70, 95–96
   motif_avoidant.py163696%23–24, 130, 147, 184, 309
   petri_net_translation.py84693%23–24, 52, 63–64, 94
   pyeda_utils.py953464%12, 56–66, 90, 95, 98–112, 140–144
   space_utils.py118596%15–16, 198, 213, 270
   state_utils.py681282%15, 55–66, 98, 105, 114
   terminal_restriction_space.py44393%6–7, 80
   trappist_core.py1862089%10–11, 39, 41, 81, 127, 192, 194, 196, 231–233, 259, 317, 319, 349, 389, 391, 422, 451
nfvsmotifs/FVSpython3
   FVS.py481079%90–91, 97, 133, 183–189
   FVS_localsearch_10_python.py90199%179
nfvsmotifs/_sd_algorithms
   compute_attractor_seeds.py29197%6
   expand_attractor_seeds.py51492%6, 95–100
   expand_bfs.py28196%6
   expand_dfs.py30197%6
   expand_minimal_spaces.py37197%6
   expand_to_target.py30390%6, 37, 42
TOTAL161613392% 

Tests Skipped Failures Errors Time
360 0 💤 0 ❌ 0 🔥 4m 0s ⏱️

Please sign in to comment.