Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Bug fix: Optimizing branch lengths in NNI Engine via GP #484

Merged
merged 10 commits into from
Dec 19, 2023
Merged

Bug fix: Optimizing branch lengths in NNI Engine via GP #484

Changes from 1 commit
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
dfd8efe
Fixed GP branch length optimization.
davidrich27 Dec 12, 2023
f045cf5
cleanup.
davidrich27 Dec 12, 2023
3bc85b0
Remove return value from fully_connect.
chrisjenningsshaffer Dec 14, 2023
39c3a49
Remove return value of fully_connect.
chrisjenningsshaffer Dec 14, 2023
75a9896
cleanup resonse to comments.
davidrich27 Dec 18, 2023
86d70ab
Merge branch '483-nni-search-gp-branch-lengths-fix' of github.com:phy…
davidrich27 Dec 18, 2023
6b5b766
clean up.
davidrich27 Dec 18, 2023
974a49f
PR changes.
davidrich27 Dec 18, 2023
4db0445
PR changes.
davidrich27 Dec 18, 2023
493a27b
PR changes.
davidrich27 Dec 19, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
30 changes: 28 additions & 2 deletions src/pybito.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -824,8 +824,9 @@ PYBIND11_MODULE(bito, m) {
"Add parent/child subsplit pair to DAG.")
.def("add_nodes", &GPDAG::AddNodes)
.def("add_edges", &GPDAG::AddEdges)
.def("fully_connect", &GPDAG::FullyConnect,
"Adds all valid edges with present nodes to the DAG.")
.def(
"fully_connect", [](GPDAG &self) { self.FullyConnect(); },
"Adds all valid edges with present nodes to the DAG.")
// ** I/O
Copy link
Collaborator

Choose a reason for hiding this comment

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

Python complains with this version because it doesn't know about the return type. I've removed the return value, since we don't need it on the python side and that's less work than exposing it here.

Copy link
Collaborator Author

Choose a reason for hiding this comment

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

It looks like you made these changes.

.def("tree_to_newick_topology", &GPDAG::TreeToNewickTopology)
.def("tree_to_newick_tree", &GPDAG::TreeToNewickTree)
Expand Down Expand Up @@ -1060,6 +1061,31 @@ PYBIND11_MODULE(bito, m) {
"Set whether to re-evaluate NNIs rejected by a previous iteration.")
.def("set_rescore_rejected_nnis", &NNIEngine::SetRescoreRejectedNNIs,
"Set whether to re-score NNIs rejected by a previous iteration.")
////////////////////////////////
.def(
"is_optimize_on_init",
[](NNIEngine &self) { return self.GetEvalEngine().IsOptimizeOnInit(); },
"...")
.def(
"is_optimize_new_edges",
[](NNIEngine &self) { return self.GetEvalEngine().IsOptimizeNewEdges(); },
"...")
.def(
"is_copy_new_edges",
[](NNIEngine &self) { return self.GetEvalEngine().IsCopyNewEdges(); }, "...")
.def(
"GetOptimizationMaxIteration",
[](NNIEngine &self) {
return self.GetEvalEngine().GetOptimizationMaxIteration();
},
"...")
.def(
"set_optimize_new_edges",
[](NNIEngine &self, const bool optimize) {
self.GetEvalEngine().SetOptimizeNewEdges(optimize);
},
"...")
/////////////////////////////////
// Scoring
.def("get_score_by_nni", &NNIEngine::GetScoreByNNI, "Get score by NNI.")
.def("get_score_by_edge", &NNIEngine::GetScoreByEdge, "Get score by EdgeId.");
Expand Down