Merge pull request #184 from ThrunGroup/hotfixes

BanditPAM `v3.0.4`

.github/workflows/run_style_checks.yml

@@ -30,4 +30,4 @@ jobs:
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=79 --statistics --exclude headers/carma
       - name: Lint with cpplint
         run: |
-          cpplint --exclude=headers/carma --exclude=build --filter=-legal/copyright,-build/c++11 --recursive .
+          cpplint --exclude=headers/carma --exclude=build --filter=-legal/copyright,-build/c++11,-build/include_subdir --recursive .

setup.py

@@ -8,7 +8,7 @@
 import distutils.sysconfig
 import distutils.spawn
 
-__version__ = "3.0.3"
+__version__ = "3.0.4"
 
 # TODO(@motiwari): Move this to a separate file
 GHA = 'GITHUB_ACTIONS'

src/algorithms/kmedoids_algorithm.cpp

@@ -280,9 +280,8 @@ float KMedoids::LINF(
 float KMedoids::cos(const arma::fmat& data,
   const size_t i,
   const size_t j) const {
-  return arma::dot(
-    data.col(i),
-    data.col(j)) / (arma::norm(data.col(i))* arma::norm(data.col(j)));
+  return 1 - (arma::dot(data.col(i), data.col(j))
+    / (arma::norm(data.col(i)) * arma::norm(data.col(j))));
 }
 
 float KMedoids::manhattan(const arma::fmat& data,

src/python_bindings/kmedoids_pywrapper.cpp

@@ -17,10 +17,6 @@
 namespace km {
 PYBIND11_MODULE(banditpam, m) {
   m.doc() = "BanditPAM Python library, implemented in C++";
-  m.def("get_max_threads",  // TODO(@motiwari): change to get_num_threads
-    &omp_get_max_threads, "Returns max number of threads");
-  m.def("set_num_threads",
-    &omp_set_num_threads, "Set the maximum number of threads");
   pybind11::class_<KMedoidsWrapper> cls(m, "KMedoids");
   cls.def(pybind11::init<int, std::string, int, int, int>(),
           pybind11::arg("n_medoids") = NULL,