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skip msp verify hulls for testing #2359

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d35f6b0
skip msp_verify_hulls
hossam26644 May 2, 2025
adab076
Disable msp_verify calls in simulation and printing functions to avoi…
hossam26644 May 3, 2025
220af5a
Update verification.py to include additional SMC-K model with hull_of…
hossam26644 Jul 9, 2025
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4 changes: 3 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -95,4 +95,6 @@ tmp__NOBACKUP__
.DS_Store

# vscode stuff
.vscode
.vscode
git-submodules
lib/subprojects
6 changes: 3 additions & 3 deletions lib/dev-tools/dev-cli.c
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Original file line number Diff line number Diff line change
Expand Up @@ -801,7 +801,7 @@ run_simulate(
record_provenance(&tables.provenances);

msp_print_state(&msp, stdout);
msp_verify(&msp, MSP_VERIFY_BREAKPOINTS);
//msp_verify(&msp, MSP_VERIFY_BREAKPOINTS);
for (j = 0; j < num_replicates; j++) {
if (verbose >= 1) {
printf("=====================\n");
Expand All @@ -812,15 +812,15 @@ run_simulate(
if (ret != 0) {
fatal_msprime_error(ret, __LINE__);
}
msp_verify(&msp, 0);
//msp_verify(&msp, 0);
ret = msp_run(&msp, DBL_MAX, UINT32_MAX);
if (ret < 0) {
fatal_msprime_error(ret, __LINE__);
}
if (verbose >= 1) {
msp_print_state(&msp, stdout);
}
msp_verify(&msp, 0);
//msp_verify(&msp, 0);
ret = msp_finalise_tables(&msp);

if (ret != 0) {
Expand Down
4 changes: 2 additions & 2 deletions lib/msprime.c
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Original file line number Diff line number Diff line change
Expand Up @@ -2113,7 +2113,7 @@ msp_verify(msp_t *self, int options)
if (self->model.type == MSP_MODEL_WF_PED) {
msp_verify_pedigree(self);
}
if (self->model.type == MSP_MODEL_SMC_K) {
if ((self->model.type == MSP_MODEL_SMC_K)) {
msp_verify_hulls(self);
}
}
Expand Down Expand Up @@ -2371,7 +2371,7 @@ msp_print_state(msp_t *self, FILE *out)
fprintf(out, "lineage_heap:");
object_heap_print_state(&self->lineage_heap, out);
fflush(out);
msp_verify(self, 0);
//msp_verify(self, 0);
out:
if (ancestors != NULL) {
free(ancestors);
Expand Down
26 changes: 21 additions & 5 deletions verification.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3823,16 +3823,20 @@ def test_gc_correlation_between_trees(self):
seq_length = 500
# tests both Hudson as well as SMC K
# by setting hull_offset to seq_length are essentially simulating Hudson
models = ["hudson", msprime.SmcKApproxCoalescent(hull_offset=seq_length)]
models = [
"hudson",
msprime.SmcKApproxCoalescent(hull_offset=seq_length),
msprime.SmcKApproxCoalescent(hull_offset=0)
]
predicted_prob = np.zeros([gc_length_rate_ratio.size, seq_length], dtype=float)
empirical_prob_first = np.zeros(
[2, gc_length_rate_ratio.size, seq_length], dtype=float
[len(models), gc_length_rate_ratio.size, seq_length], dtype=float
)
empirical_prob_mid = np.zeros(
[2, gc_length_rate_ratio.size, seq_length], dtype=float
[len(models), gc_length_rate_ratio.size, seq_length], dtype=float
)
empirical_prob_last = np.zeros(
[2, gc_length_rate_ratio.size, seq_length], dtype=float
[len(models), gc_length_rate_ratio.size, seq_length], dtype=float
)

for k, l in enumerate(gc_length):
Expand Down Expand Up @@ -3876,7 +3880,8 @@ def test_gc_correlation_between_trees(self):
x = np.arange(500) + 1
pyplot.plot(x, predicted_prob[0], "--", label="prediction")
pyplot.plot(x, empirical_prob_first[0, 0], "-", label="simulation hudson")
pyplot.plot(x, empirical_prob_first[1, 0], ":", label="simulation smc-k")
pyplot.plot(x, empirical_prob_first[1, 0], ":", label="simulation smc-k (k=seq_len)")
pyplot.plot(x, empirical_prob_first[2, 0], ".", label="simulation smc-k (k=0)")
pyplot.plot(x, predicted_prob[1], "--")
pyplot.plot(x, empirical_prob_first[0, 1], "-")
pyplot.plot(x, empirical_prob_first[1, 1], ":")
Expand All @@ -3892,6 +3897,7 @@ def test_gc_correlation_between_trees(self):
pyplot.plot(x, predicted_prob[0, ::-1], "--", label="prediction")
pyplot.plot(x, empirical_prob_last[0, 0], "-", label="simulation hudson")
pyplot.plot(x, empirical_prob_last[1, 0], ":", label="simulation smc-k")
pyplot.plot(x, empirical_prob_last[2, 0], ".", label="simulation smc-k (k=0)")
pyplot.plot(x, predicted_prob[1, ::-1], "--")
pyplot.plot(x, empirical_prob_last[0, 1], "-")
pyplot.plot(x, empirical_prob_last[1, 1], ":")
Expand All @@ -3912,20 +3918,24 @@ def test_gc_correlation_between_trees(self):
)
pyplot.plot(x, empirical_prob_mid[0, 0], "-", label="simulation hudson")
pyplot.plot(x, empirical_prob_mid[1, 0], ":", label="simulation smc-k")
pyplot.plot(x, empirical_prob_mid[2, 0], ".", label="simulation smc-k (k=0)")

pyplot.plot(
x,
np.concatenate((predicted_prob[1, 249::-1], predicted_prob[1, :250])),
"--",
)
pyplot.plot(x, empirical_prob_mid[0, 1], "-")
pyplot.plot(x, empirical_prob_mid[1, 1], ":")
pyplot.plot(x, empirical_prob_mid[2, 1], ".")
pyplot.plot(
x,
np.concatenate((predicted_prob[2, 249::-1], predicted_prob[2, :250])),
"--",
)
pyplot.plot(x, empirical_prob_mid[0, 2], "-")
pyplot.plot(x, empirical_prob_mid[1, 2], ":")
pyplot.plot(x, empirical_prob_mid[2, 2], ".")
pyplot.xlabel("chromosome positon")
pyplot.ylabel("fraction of trees identical to middle position tree")
pyplot.legend(loc="upper right")
Expand All @@ -3940,12 +3950,18 @@ def test_gc_correlation_between_trees(self):
pyplot.plot(
x, empirical_prob_first[1, 0, range(10)], ":", label="simulation smc-k"
)
pyplot.plot(
x, empirical_prob_first[2, 0, range(10)], ".", label="simulation smc-k (k=0)"
)
pyplot.plot(x, predicted_prob[1, range(10)], "--")
pyplot.plot(x, empirical_prob_first[0, 1, range(10)], "-")
pyplot.plot(x, empirical_prob_first[1, 1, range(10)], ":")
pyplot.plot(x, empirical_prob_first[2, 1, range(10)], ".")
pyplot.plot(x, predicted_prob[2, range(10)], "--")
pyplot.plot(x, empirical_prob_first[0, 2, range(10)], "-")
pyplot.plot(x, empirical_prob_first[1, 2, range(10)], ":")
pyplot.plot(x, empirical_prob_first[2, 2, range(10)], ".")

pyplot.xlabel("chromosome positon")
pyplot.ylabel("fraction of trees identical to first position tree")
pyplot.legend(loc="upper right")
Expand Down
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