Update submodules to use volesti's develop and make use of git sparse…

…-checkout

.github/workflows/R-CMD-check-macOS.yml

@@ -39,6 +39,9 @@ jobs:
 
       - name: Fetch and update submodule
         run: git submodule update --init --recursive
+             cd src/volesti
+             git sparse-checkout set include external
+             git checkout
 
       - name: Install dependencies
         run: Rscript -e "install.packages(c('devtools', dependencies=TRUE))" -e "install.packages(c('rcmdcheck', 'devtools', 'Rcpp', 'RcppEigen', 'BH', 'testthat', 'downloader', 'xfun'))";

.github/workflows/R-CMD-check-ubuntu.yml

@@ -41,6 +41,9 @@ jobs:
 
       - name: Fetch and update submodule
         run: git submodule update --init --recursive
+             cd src/volesti
+             git sparse-checkout set include external
+             git checkout
 
       - name: Install dependencies
         run: Rscript -e "install.packages(c('testthat', 'pkgload', 'rcmdcheck', 'devtools', 'Rcpp', 'RcppEigen', 'BH', 'downloader', 'xfun', dependencies=TRUE))";

.github/workflows/R-CMD-check-windows.yml

@@ -38,6 +38,9 @@ jobs:
 
       - name: Fetch and update submodule
         run: git submodule update --init --recursive
+             cd src/volesti
+             git sparse-checkout set include external
+             git checkout
 
       - name: Install dependencies
         run: Rscript -e "install.packages(c('devtools', dependencies=TRUE))" -e "install.packages(c('rcmdcheck', 'devtools', 'Rcpp', 'RcppEigen', 'BH', 'testthat', 'downloader', 'xfun'))"

.gitmodules

@@ -1,4 +1,3 @@
-[submodule "volesti_cran_include"]
-	path = src/include
+[submodule "src/volesti"]
+	path = src/volesti
 	url = https://github.com/GeomScale/volesti.git
-	branch = cran_include

R/RcppExports.R

@@ -202,7 +202,9 @@ load_sdpa_format_file <- function(input_file = NULL) {
 #' @return A list which contains elements "x_1", ..., "x_n" representing each derivative results. Each "x_i" corresponds to a d x n matrix where each column represents a certain timestep of the solver.
 #'
 #' @examples
-#' # Please visit the examples directory on examples demonstrating usage of the ODE solvers.
+#' F <- function (x) (-x)
+#' initial_conditions <- list("x_1" = c(0), "x_2" = c(1))
+#' states <- ode_solve(dimension=1, n=1000, F=F, initial_time=0, step_size=0.01, order=2, method="leapfrog", initial_conditions=initial_conditions, domains = list())
 #'
 #' @export
 ode_solve <- function(n, step_size, order, dimension, initial_time, F, method, domains = NULL, initial_conditions = NULL) {

src/Makevars

@@ -1,16 +1,16 @@
-PKG_CPPFLAGS=-Iexternal -Iexternal/lpsolve/headers/run_headers -Iexternal/minimum_ellipsoid -Iinclude -Iinclude/convex_bodies/spectrahedra
+PKG_CPPFLAGS=-Ivolesti/external -Ilpsolve/headers/run_headers -Ivolesti/external/minimum_ellipsoid -Ivolesti/include -Ivolesti/include/convex_bodies/spectrahedra
 PKG_CXXFLAGS= -DBOOST_NO_AUTO_PTR -DDISABLE_NLP_ORACLES
 
-PKG_LIBS=-Lexternal/lpsolve/build/lp_solve -llp_solve -Lexternal/PackedCSparse/qd -lqd $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_LIBS=-Llpsolve/build/lp_solve -llp_solve -Lvolesti/external/PackedCSparse/qd -lqd $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
 
-$(SHLIB): external/lpsolve/build/lp_solve/liblp_solve.a external/PackedCSparse/qd/libqd.a
+$(SHLIB): lpsolve/build/lp_solve/liblp_solve.a volesti/external/PackedCSparse/qd/libqd.a
 
-external/lpsolve/build/lp_solve/liblp_solve.a:
-	@(cd external/lpsolve/build/lp_solve && $(MAKE) liblp_solve.a \
+lpsolve/build/lp_solve/liblp_solve.a:
+	@(cd lpsolve/build/lp_solve && $(MAKE) liblp_solve.a \
     CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
     CPICFLAGS="$(CPICFLAGS)" AR="$(AR)" RANLIB="$(RANLIB)")
 
-external/PackedCSparse/qd/libqd.a:
-	@(cd external/PackedCSparse/qd && $(MAKE) libqd.a \
+volesti/external/PackedCSparse/qd/libqd.a:
+	@(cd volesti/external/PackedCSparse/qd && $(MAKE) libqd.a \
 		CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
 		CPICFLAGS="$(CPICFLAGS)" AR="$(AR)")

src/Makevars.win

@@ -1,17 +1,17 @@
-PKG_CPPFLAGS=-Iexternal -Iexternal/lpsolve/headers/run_headers -Iexternal/minimum_ellipsoid -Iinclude -Iinclude/convex_bodies/spectrahedra
+PKG_CPPFLAGS=-Ivolesti/external -Ilpsolve/headers/run_headers -Ivolesti/external/minimum_ellipsoid -Ivolesti/include -Ivolesti/include/convex_bodies/spectrahedra
 PKG_CXXFLAGS= -lm -ldl -DBOOST_NO_AUTO_PTR -DDISABLE_NLP_ORACLES
 
-PKG_LIBS=-Lexternal/lpsolve/build/lp_solve -llp_solve -Lexternal/PackedCSparse/qd -lqd $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_LIBS=-Llpsolve/build/lp_solve -llp_solve -Lvolesti/external/PackedCSparse/qd -lqd $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
 
-$(SHLIB): external/lpsolve/build/lp_solve/liblp_solve.a external/PackedCSparse/qd/libqd.a
+$(SHLIB): lpsolve/build/lp_solve/liblp_solve.a volesti/external/PackedCSparse/qd/libqd.a
 
-external/lpsolve/build/lp_solve/liblp_solve.a:
-	@(cd external/lpsolve/build/lp_solve && $(MAKE) liblp_solve.a \
+lpsolve/build/lp_solve/liblp_solve.a:
+	@(cd lpsolve/build/lp_solve && $(MAKE) liblp_solve.a \
     CC="$(CC)" CPPFLAGS="$(CPPFLAGS) -DUSRDLL -DINLINE=static" \
     CFLAGS="$(CFLAGS)" CPICFLAGS="$(CPICFLAGS)" AR="$(AR)" \
     RANLIB="$(RANLIB)")
 
-external/PackedCSparse/qd/libqd.a:
-	@(cd external/PackedCSparse/qd && $(MAKE) libqd.a \
+volesti/external/PackedCSparse/qd/libqd.a:
+	@(cd volesti/external/PackedCSparse/qd && $(MAKE) libqd.a \
 		CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
 		CPICFLAGS="$(CPICFLAGS)" AR="$(AR)")