From f73f2f1b07a71f90e7fe041bc1d1e94d1ba4c8e6 Mon Sep 17 00:00:00 2001
From: "Malte S. Kurz" <malte.s.kurz@gmail.com>
Date: Fri, 22 Dec 2023 15:38:10 +0100
Subject: [PATCH] since rpy2 3.5.12 invisible r objects are no longer returned

---
 vineknockoffs/_utils_kde1d.py                    | 12 ++++++------
 vineknockoffs/_utils_knockoffs.py                |  2 +-
 vineknockoffs/_utils_vine_copulas.py             |  4 ++--
 vineknockoffs/tests/_utils_py_vs_r_vinecopula.py |  2 +-
 4 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/vineknockoffs/_utils_kde1d.py b/vineknockoffs/_utils_kde1d.py
index f09aa62..466949e 100644
--- a/vineknockoffs/_utils_kde1d.py
+++ b/vineknockoffs/_utils_kde1d.py
@@ -12,39 +12,39 @@
 
 
 r_kde1d_fit = robjects.r('''
-        kde_fit <- function(x) {
+        function(x) {
           return(kde1d::kde1d(x))
         }
         ''')
 
 r_kde1d_discrete_fit = robjects.r('''
-        kde_fit <- function(x, levels) {
+        function(x, levels) {
           x <- ordered(x, levels=levels)
           return(kde1d::kde1d(x))
         }
         ''')
 
 r_kde1d_cdf_eval = robjects.r('''
-        cdf_eval <- function(kde_fit, x) {
+        function(kde_fit, x) {
           return(kde1d::pkde1d(x, kde_fit))
         }
         ''')
 
 r_kde1d_invcdf_eval = robjects.r('''
-        invcdf_eval <- function(kde_fit, x) {
+        function(kde_fit, x) {
           return(kde1d::qkde1d(x, kde_fit))
         }
         ''')
 
 r_kde1d_discrete_invcdf_eval = robjects.r('''
-        invcdf_eval <- function(kde_fit, x) {
+        function(kde_fit, x) {
           res <- kde1d::qkde1d(x, kde_fit)
           return(as.numeric(levels(res)[res]))
         }
         ''')
 
 r_kde1d_pdf_eval = robjects.r('''
-        pdf_eval <- function(kde_fit, x) {
+        function(kde_fit, x) {
           return(kde1d::dkde1d(x, kde_fit))
         }
         ''')
diff --git a/vineknockoffs/_utils_knockoffs.py b/vineknockoffs/_utils_knockoffs.py
index fc194b8..536e6b5 100644
--- a/vineknockoffs/_utils_knockoffs.py
+++ b/vineknockoffs/_utils_knockoffs.py
@@ -12,7 +12,7 @@
 
 
 cv_glmnet_r = robjects.r('''
-        cv_glmnet <- function(x, y, s) {
+        function(x, y, s) {
           fit <- glmnet::cv.glmnet(x, y)
           return(as.numeric(coef(fit, s=s)))
         }
diff --git a/vineknockoffs/_utils_vine_copulas.py b/vineknockoffs/_utils_vine_copulas.py
index e74a35e..9581fd9 100644
--- a/vineknockoffs/_utils_vine_copulas.py
+++ b/vineknockoffs/_utils_vine_copulas.py
@@ -12,7 +12,7 @@
 if _has_rpy2:
     _has_r_tsp = robjects.r('library("TSP", quietly=TRUE, logical.return=TRUE)')[0]
     r_solve_tsp = robjects.r('''
-            solve_tsp <- function(one_m_tau_mat) {
+            function(one_m_tau_mat) {
                 hamilton = TSP::insert_dummy(TSP::TSP(one_m_tau_mat), label = "cut")
                 sol = TSP::solve_TSP(hamilton, method = "repetitive_nn")
                 order = TSP::cut_tour(sol, "cut")
@@ -53,7 +53,7 @@ def d_vine_structure_select(u, tsp_method='r_tsp'):
         if not (_has_rpy2 and _has_r_tsp):
             raise ImportError('To determine the D-vine structure with method r_tsp the python package rpy2 and the R '
                               'package TSP are required.')
-        permutation = r_solve_tsp(tau_mat)-1
+        permutation = np.array(r_solve_tsp(tau_mat))-1
     else:
         assert tsp_method == 'py_tsp'
         permutation, _ = solve_tsp_dynamic_programming(tau_mat)
diff --git a/vineknockoffs/tests/_utils_py_vs_r_vinecopula.py b/vineknockoffs/tests/_utils_py_vs_r_vinecopula.py
index 98d800c..a6c01a8 100644
--- a/vineknockoffs/tests/_utils_py_vs_r_vinecopula.py
+++ b/vineknockoffs/tests/_utils_py_vs_r_vinecopula.py
@@ -28,7 +28,7 @@ def py_copula_funs_eval(data, cop_obj, fun_type):
 
 r_copula_funs_eval = robjects.r('''
         library(VineCopula)
-        copula_funs_eval <- function(u, v, family, par, type) {
+        function(u, v, family, par, type) {
 
           if (type == 'cdf'){
             res = BiCopCDF(u, v, family, par)