git subrepo clone --branch=ee2e0d2189e047558c8dc1a1d8fc171446ec4203 -…

…-force git@github.com:dweindl/AMICI.git deps/AMICI subrepo: subdir: "deps/AMICI" merged: "ee2e0d21" upstream: origin: "git@github.com:dweindl/AMICI.git" branch: "ee2e0d2189e047558c8dc1a1d8fc171446ec4203" commit: "ee2e0d21" git-subrepo: version: "0.4.6" origin: "https://github.com/ingydotnet/git-subrepo" commit: "110b9eb"
ICB-DCM · Oct 16, 2024 · 741dbcf · 741dbcf
1 parent 5cdcd62
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diff --git a/deps/AMICI/.github/workflows/test_python_cplusplus.yml b/deps/AMICI/.github/workflows/test_python_cplusplus.yml
@@ -38,6 +38,11 @@ jobs:
     - name: Set up AMICI C++ libraries
       uses: ./.github/actions/setup-amici-cpp
 
+    - name: Install libsuitesparse-dev
+      # We don't need libsuitesparse-dev, but let's have it installed,
+      # to ensure that its presence does not break the build
+      run: sudo apt-get install -y libsuitesparse-dev
+
     - name: C++ tests
       run: scripts/run-cpp-tests.sh
 

diff --git a/deps/AMICI/.gitrepo b/deps/AMICI/.gitrepo
@@ -5,8 +5,8 @@
 ;
 [subrepo]
 	remote = git@github.com:ICB-DCM/AMICI.git
-	branch = c11c51ee1b2f8ed07677fcb47e81ac014e12855b
-	commit = c11c51ee1b2f8ed07677fcb47e81ac014e12855b
-	parent = d2b37e189980fa085cddcecf76fe93932f3f566a
+	branch = ee2e0d2189e047558c8dc1a1d8fc171446ec4203
+	commit = ee2e0d2189e047558c8dc1a1d8fc171446ec4203
+	parent = 5cdcd62f892854fa197f6513b0a520ec2c1cb0e6
 	cmdver = 0.4.6
 	method = merge
diff --git a/deps/AMICI/CMakeLists.txt b/deps/AMICI/CMakeLists.txt
@@ -269,23 +269,23 @@ target_link_libraries(
          SUNDIALS::sunmatrixband_static
          SUNDIALS::sunmatrixdense_static
          SUNDIALS::sunmatrixsparse_static
-         SUNDIALS::sunlinsolband_static
-         SUNDIALS::sunlinsoldense_static
-         SUNDIALS::sunlinsolpcg_static
          SUNDIALS::sunlinsolspbcgs_static
          SUNDIALS::sunlinsolspfgmr_static
          SUNDIALS::sunlinsolspgmr_static
          SUNDIALS::sunlinsolsptfqmr_static
-         SUNDIALS::sunlinsolklu_static
-         SUNDIALS::sunnonlinsolnewton_static
-         SUNDIALS::sunnonlinsolfixedpoint_static
          SUNDIALS::cvodes_static
          SUNDIALS::idas_static
          $<$<BOOL:${Boost_CHRONO_FOUND}>:Boost::chrono>
          $<$<BOOL:${OpenMP_FOUND}>:OpenMP::OpenMP_CXX>
          ${CMAKE_DL_LIBS}
   PRIVATE
     BLAS::BLAS
+    SUNDIALS::sunnonlinsolnewton_static
+    SUNDIALS::sunnonlinsolfixedpoint_static
+    SUNDIALS::sunlinsolklu_static
+    SUNDIALS::sunlinsolband_static
+    SUNDIALS::sunlinsoldense_static
+    SUNDIALS::sunlinsolpcg_static
     $<$<BOOL:${SUNDIALS_SUPERLUMT_ENABLE}>:SUNDIALS::sundials_sunlinsolsuperlumt>
 )
 

diff --git a/deps/AMICI/cmake/AmiciConfig.cmake.in b/deps/AMICI/cmake/AmiciConfig.cmake.in
@@ -4,6 +4,12 @@ include(CMakeFindDependencyMacro)
 
 find_package(OpenMP)
 
+# Current SUNDIALSConfig.cmake doesn't use KLU's FindKLU, but hardcodes paths,
+# and is not relocatable. This does not work with Python package installation in
+# tmpdirs.
+list(APPEND CMAKE_PREFIX_PATH
+     @CMAKE_SOURCE_DIR@/ThirdParty/SuiteSparse/install/)
+
 include("${CMAKE_CURRENT_LIST_DIR}/AmiciFindBLAS.cmake")
 
 find_dependency(SUNDIALS REQUIRED PATHS

diff --git a/deps/AMICI/include/amici/abstract_model.h b/deps/AMICI/include/amici/abstract_model.h
@@ -6,10 +6,6 @@
 #include "amici/sundials_matrix_wrapper.h"
 #include "amici/vector.h"
 
-#include <sunmatrix/sunmatrix_band.h>
-#include <sunmatrix/sunmatrix_dense.h>
-#include <sunmatrix/sunmatrix_sparse.h>
-
 #include <memory>
 
 namespace amici {

diff --git a/deps/AMICI/include/amici/forwardproblem.h b/deps/AMICI/include/amici/forwardproblem.h
@@ -5,9 +5,7 @@
 #include "amici/misc.h"
 #include "amici/model.h"
 #include "amici/vector.h"
-#include <amici/amici.h>
 
-#include <sundials/sundials_direct.h>
 #include <vector>
 
 namespace amici {

diff --git a/deps/AMICI/include/amici/misc.h b/deps/AMICI/include/amici/misc.h
@@ -4,7 +4,6 @@
 #include "amici/defines.h"
 #include "amici/exception.h"
 #include "amici/vector.h"
-#include <sunmatrix/sunmatrix_sparse.h> // SUNMatrixContent_Sparse
 
 #include <algorithm>
 #include <ctime>

diff --git a/deps/AMICI/include/amici/model_dae.h b/deps/AMICI/include/amici/model_dae.h
@@ -3,13 +3,9 @@
 
 #include "amici/model.h"
 
-#include <nvector/nvector_serial.h>
-
-#include <sunmatrix/sunmatrix_band.h>
-#include <sunmatrix/sunmatrix_dense.h>
-#include <sunmatrix/sunmatrix_sparse.h>
-
 #include <numeric>
+#include <sundials/sundials_matrix.h>
+#include <sundials/sundials_nvector.h>
 #include <vector>
 
 namespace amici {

diff --git a/deps/AMICI/include/amici/model_ode.h b/deps/AMICI/include/amici/model_ode.h
@@ -3,12 +3,8 @@
 
 #include "amici/model.h"
 
-#include <nvector/nvector_serial.h>
-
 #include <sundials/sundials_matrix.h>
-#include <sunmatrix/sunmatrix_band.h>
-#include <sunmatrix/sunmatrix_dense.h>
-#include <sunmatrix/sunmatrix_sparse.h>
+#include <sundials/sundials_nvector.h>
 
 #include <vector>
 

diff --git a/deps/AMICI/include/amici/newton_solver.h b/deps/AMICI/include/amici/newton_solver.h
@@ -1,7 +1,8 @@
 #ifndef amici_newton_solver_h
 #define amici_newton_solver_h
 
-#include "amici/solver.h"
+#include "amici/defines.h"
+#include "amici/sundials_linsol_wrapper.h"
 #include "amici/vector.h"
 
 namespace amici {

diff --git a/deps/AMICI/include/amici/solver_cvodes.h b/deps/AMICI/include/amici/solver_cvodes.h
@@ -5,8 +5,6 @@
 #include "amici/solver.h"
 #include "amici/vector.h"
 
-#include <sundials/sundials_matrix.h>
-
 namespace amici {
 class ExpData;
 class ReturnData;

diff --git a/deps/AMICI/include/amici/solver_idas.h b/deps/AMICI/include/amici/solver_idas.h
@@ -3,8 +3,6 @@
 
 #include "amici/solver.h"
 
-#include <sundials/sundials_matrix.h>
-
 namespace amici {
 class ExpData;
 class ReturnData;

diff --git a/deps/AMICI/include/amici/steadystateproblem.h b/deps/AMICI/include/amici/steadystateproblem.h
@@ -6,15 +6,14 @@
 #include <amici/newton_solver.h>
 #include <amici/vector.h>
 
-#include <nvector/nvector_serial.h>
-
 #include <memory>
 
 namespace amici {
 
 class ExpData;
 class Solver;
 class Model;
+class BackwardProblem;
 
 /**
  * @brief The SteadystateProblem class solves a steady-state problem using

diff --git a/deps/AMICI/include/amici/sundials_linsol_wrapper.h b/deps/AMICI/include/amici/sundials_linsol_wrapper.h
@@ -5,19 +5,12 @@
 #include "amici/vector.h"
 
 #include <sundials/sundials_config.h>
-#include <sunlinsol/sunlinsol_band.h>
-#include <sunlinsol/sunlinsol_dense.h>
-#include <sunlinsol/sunlinsol_klu.h>
-#include <sunlinsol/sunlinsol_pcg.h>
+#include <sundials/sundials_iterative.h>
+#include <sundials/sundials_nonlinearsolver.h>
 #include <sunlinsol/sunlinsol_spbcgs.h>
 #include <sunlinsol/sunlinsol_spfgmr.h>
 #include <sunlinsol/sunlinsol_spgmr.h>
 #include <sunlinsol/sunlinsol_sptfqmr.h>
-#ifdef SUNDIALS_SUPERLUMT
-#include <sunlinsol/sunlinsol_superlumt.h>
-#endif
-#include <sunnonlinsol/sunnonlinsol_fixedpoint.h>
-#include <sunnonlinsol/sunnonlinsol_newton.h>
 
 namespace amici {
 

diff --git a/deps/AMICI/src/solver_cvodes.cpp b/deps/AMICI/src/solver_cvodes.cpp
@@ -89,7 +89,7 @@ static_assert(
 static_assert(
     amici::AMICI_FIRST_QRHSFUNC_ERR == CV_FIRST_QRHSFUNC_ERR,
     "AMICI_FIRST_QRHSFUNC_ERR != CV_FIRST_QRHSFUNC_ERR"
-    );
+);
 
 /*
  * The following static members are callback function to CVODES.

diff --git a/deps/AMICI/src/sundials_linsol_wrapper.cpp b/deps/AMICI/src/sundials_linsol_wrapper.cpp
@@ -1,6 +1,15 @@
 #include <amici/sundials_linsol_wrapper.h>
 
 #include <amici/exception.h>
+#include <sunlinsol/sunlinsol_band.h>
+#include <sunlinsol/sunlinsol_dense.h>
+#include <sunlinsol/sunlinsol_klu.h>
+#include <sunlinsol/sunlinsol_pcg.h>
+#ifdef SUNDIALS_SUPERLUMT
+#include <sunlinsol/sunlinsol_superlumt.h>
+#endif
+#include <sunnonlinsol/sunnonlinsol_fixedpoint.h>
+#include <sunnonlinsol/sunnonlinsol_newton.h>
 
 #include <utility>