Use condition-specific parameter scales (#161)

* Use condition-specific parameter scales * Esnure preequilibration and simulation condition use same parameter scales * git subrepo clone --branch=update_petab_import --force [email protected]:ICB-DCM/AMICI.git deps/AMICI subrepo: subdir: "deps/AMICI" merged: "b42cc370" upstream: origin: "[email protected]:ICB-DCM/AMICI.git" branch: "update_petab_import" commit: "b42cc370" git-subrepo: version: "0.4.0" origin: "https://github.com/ingydotnet/git-subrepo" commit: "5d6aba9" * Install PEtab/develop from github
ICB-DCM · Apr 10, 2019 · c6694e2 · c6694e2
1 parent 99cecc8
commit c6694e2
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Showing 67 changed files with 3,920 additions and 644 deletions.
diff --git a/deps/AMICI/.gitrepo b/deps/AMICI/.gitrepo
@@ -5,8 +5,8 @@
 ;
 [subrepo]
 	remote = [email protected]:ICB-DCM/AMICI.git
-	branch = develop
-	commit = 3021af8cf9a67beca9de751a338e1944aeccb391
-	parent = 3fbdc8e249f8b51ca81ebed9354265f5a778528b
+	branch = update_petab_import
+	commit = b42cc370121c4b1a0376e144a3e1c6f6e31a704c
+	parent = 5fa74777520779b93632efe94c297e1883bacf31
 	cmdver = 0.4.0
 	method = merge
diff --git a/deps/AMICI/CMakeLists.txt b/deps/AMICI/CMakeLists.txt
@@ -2,6 +2,14 @@
 # Build AMICI library
 #
 cmake_minimum_required(VERSION 3.3)
+
+if(POLICY CMP0065)
+  cmake_policy(SET CMP0065 NEW)
+endif(POLICY CMP0065)
+if(POLICY CMP0077)
+  cmake_policy(SET CMP0077 NEW)
+endif(POLICY CMP0077)
+
 project(amici)
 
 set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake)
@@ -41,7 +49,7 @@ set(SUITESPARSE_LIBRARIES
     )
 
 set(SUNDIALS_LIB_DIR "${CMAKE_SOURCE_DIR}/ThirdParty/sundials/build/lib")
-set(SUNDIALS_LIBRARIES 
+set(SUNDIALS_LIBRARIES
     ${SUNDIALS_LIB_DIR}/libsundials_nvecserial${CMAKE_STATIC_LIBRARY_SUFFIX}
     ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolband${CMAKE_STATIC_LIBRARY_SUFFIX}
     ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolklu${CMAKE_STATIC_LIBRARY_SUFFIX}
@@ -58,6 +66,8 @@ set(SUNDIALS_LIBRARIES
     )
 set(SUNDIALS_INCLUDE_DIRS "${CMAKE_SOURCE_DIR}/ThirdParty/sundials/build/include")
 
+set(GSL_LITE_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/ThirdParty/gsl")
+
 # AMICI requires BLAS, currently Intel MKL, CBLAS or MATLAB BLAS can be used.
 # The latter is not supported via CMake yet.
 set(BLAS "CBLAS" CACHE STRING "BLAS library to use")
@@ -113,6 +123,7 @@ target_include_directories(${PROJECT_NAME}
     $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
     PUBLIC $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/include>
     PUBLIC swig
+    PUBLIC ${GSL_LITE_INCLUDE_DIR}
     PUBLIC ${SUNDIALS_INCLUDE_DIRS}
     PUBLIC ${SUITESPARSE_INCLUDE_DIRS}
     PUBLIC ${HDF5_INCLUDE_DIRS}
@@ -134,12 +145,12 @@ add_custom_target(matlabInterface SOURCES src/interface_matlab.cpp src/returndat
 add_custom_target(
     fileTemplates
     SOURCES
-    src/CMakeLists.template.txt
+    src/CMakeLists.template.cmake
     src/main.template.cpp
     src/model_header.ODE_template.h
     src/wrapfunctions.ODE_template.h
     src/wrapfunctions.template.cpp
-    swig/CMakeLists_model.txt
+    swig/CMakeLists_model.cmake
     swig/modelname.template.i
     )