Remove model name prefix in generated model files (#2015)

Helps to avoid issues with too long paths on Windows 💩

Author: dweindl

documentation/cpp_interface.rst

@@ -29,12 +29,13 @@ The content of a model source directory looks something like this (given
 
    CMakeLists.txt
    main.cpp
-   model_steadystate_deltaqB.cpp
-   model_steadystate_deltaqB.h
-   [... many more files model_steadystate_*.(cpp|h|md5|o) ]
+   deltaqB.cpp
+   deltaqB.h
+   [... many more files *.(cpp|h|md5|o) ]
    wrapfunctions.cpp
    wrapfunctions.h
    model_steadystate.h
+   model_steadystate.cpp
 
 These files provide the implementation of a model-specific subclass of
 :cpp:class:`amici::Model`. The ``CMakeLists.txt`` file can be used to build the

matlab/@amimodel/compileAndLinkModel.m

@@ -20,10 +20,12 @@ function compileAndLinkModel(modelname, modelSourceFolder, coptim, debug, funs,
     % if no list provided, try to determine relevant files from model
     % folder
     if(isempty(funs))
-        ls = dir(fullfile(modelSourceFolder, [modelname '_*.cpp']));
+        ls = dir(fullfile(modelSourceFolder, '*.cpp'));
+        % wrapfunctions is handled separately
         ls = {ls.name};
+        ls = ls(cellfun(@(x) ~strcmp(x, "wrapfunctions.cpp"), ls));
         % extract funs from filename (strip of modelname_ and .cpp
-        funs = cellfun(@(x) x((length(modelname)+2):(length(x)-4)), ls, 'UniformOutput', false);
+        funs = cellfun(@(x) x(1:(length(x)-4)), ls, 'UniformOutput', false);
     end
 
     objectFileSuffix = '.o';
@@ -74,7 +76,7 @@ function compileAndLinkModel(modelname, modelSourceFolder, coptim, debug, funs,
 
     %% Model-specific files
     for j=1:length(funs)
-        baseFileName = [modelname '_' strrep(funs{j}, 'sigma_', 'sigma')];
+        baseFileName = strrep(funs{j}, 'sigma_', 'sigma');
         cfun(1).(funs{j}) = sourceNeedsRecompilation(modelSourceFolder, modelObjectFolder, baseFileName, objectFileSuffix);
     end
 
@@ -124,7 +126,7 @@ function compileAndLinkModel(modelname, modelSourceFolder, coptim, debug, funs,
     if(numel(funsForRecompile))
         fprintf('ffuns | ');
 
-        sources = cellfun(@(x) ['"' fullfile(modelSourceFolder,[modelname '_' x '.cpp']) '"'],funsForRecompile,'UniformOutput',false);
+        sources = cellfun(@(x) ['"' fullfile(modelSourceFolder,[x '.cpp']) '"'],funsForRecompile,'UniformOutput',false);
         sources = strjoin(sources,' ');
 
         cmd = ['mex ' DEBUG COPT ...
@@ -136,15 +138,14 @@ function compileAndLinkModel(modelname, modelSourceFolder, coptim, debug, funs,
             disp(cmd);
             rethrow(ME);
         end
-        cellfun(@(x) updateFileHashSource(modelSourceFolder, modelObjectFolder, [modelname '_' x]),funsForRecompile,'UniformOutput',false);
+        cellfun(@(x) updateFileHashSource(modelSourceFolder, modelObjectFolder, x),funsForRecompile,'UniformOutput',false);
     end
 
     % append model object files
     for j=1:length(funs)
-        filename = fullfile(modelObjectFolder, [modelname '_' strrep(funs{j}, 'sigma_', 'sigma') objectFileSuffix]);
+        filename = fullfile(modelObjectFolder, [strrep(funs{j}, 'sigma_', 'sigma') objectFileSuffix]);
         if(exist(filename,'file'))
-            objectsstr = strcat(objectsstr,...
-                ' "',filename,'"');
+            objectsstr = strcat(objectsstr, ' "',filename,'"');
         end
     end
 

matlab/@amimodel/generateC.m

@@ -26,7 +26,7 @@ function generateC(this)
 
         if(bodyNotEmpty)
             fprintf([ifun{1} ' | ']);
-            fid = fopen(fullfile(this.wrap_path,'models',this.modelname,[this.modelname '_' cppFunctionName '.cpp']),'w');
+            fid = fopen(fullfile(this.wrap_path,'models',this.modelname,[ cppFunctionName '.cpp']),'w');
             fprintf(fid,'\n');
             fprintf(fid,'#include "amici/symbolic_functions.h"\n');
             fprintf(fid,'#include "amici/defines.h" //realtype definition\n');
@@ -267,7 +267,7 @@ function generateCMakeFile(this)
         funcName = this.funs{j};
         if(checkIfFunctionBodyIsNonEmpty(this,funcName))
             cppFunctionName = strrep(funcName, 'sigma_', 'sigma');
-            sourceStr = [ sourceStr, sprintf('${MODEL_DIR}/%s_%s.cpp\n', this.modelname, cppFunctionName) ];
+            sourceStr = [ sourceStr, sprintf('${MODEL_DIR}/%s.cpp\n', cppFunctionName) ];
         end
     end
 
@@ -315,5 +315,5 @@ function generateMainC(this)
     % if we don't have symbolic variables, it might have been generated before and symbolic expressions were simply not
     % regenerated. any() for empty (no generated) variables is always false.
     cppFunctionName = strrep(ifun, 'sigma_', 'sigma');
-    nonempty = or(exist(fullfile(this.wrap_path,'models',this.modelname,[this.modelname '_' cppFunctionName '.cpp']),'file'),any(this.fun.(ifun).sym(:)~=0));
+    nonempty = or(exist(fullfile(this.wrap_path,'models',this.modelname,[cppFunctionName '.cpp']),'file'),any(this.fun.(ifun).sym(:)~=0));
 end

models/model_calvetti/CMakeLists.txt

@@ -1,15 +1,4 @@
-cmake_minimum_required(VERSION 3.3)
-
-if(POLICY CMP0060)
-  cmake_policy(SET CMP0060 NEW)
-endif(POLICY CMP0060)
-if(POLICY CMP0065)
-  cmake_policy(SET CMP0065 NEW)
-endif(POLICY CMP0065)
-if(POLICY CMP0074)
-  # Use package_ROOT environment variables
-  cmake_policy(SET CMP0074 NEW)
-endif(POLICY CMP0074)
+cmake_minimum_required(VERSION 3.15)
 
 project(model_calvetti)
 
@@ -30,24 +19,24 @@ foreach(FLAG ${MY_CXX_FLAGS})
     endif()
 endforeach(FLAG)
 
-find_package(Amici  HINTS ${CMAKE_CURRENT_LIST_DIR}/../../build)
+find_package(Amici  REQUIRED HINTS ${CMAKE_CURRENT_LIST_DIR}/../../build)
 message(STATUS "Found AMICI ${Amici_DIR}")
 
 set(MODEL_DIR ${CMAKE_CURRENT_LIST_DIR})
 
-set(SRC_LIST_LIB ${MODEL_DIR}/model_calvetti_JSparse.cpp
-${MODEL_DIR}/model_calvetti_Jy.cpp
-${MODEL_DIR}/model_calvetti_M.cpp
-${MODEL_DIR}/model_calvetti_dJydsigma.cpp
-${MODEL_DIR}/model_calvetti_dJydy.cpp
-${MODEL_DIR}/model_calvetti_dwdx.cpp
-${MODEL_DIR}/model_calvetti_dydx.cpp
-${MODEL_DIR}/model_calvetti_root.cpp
-${MODEL_DIR}/model_calvetti_sigmay.cpp
-${MODEL_DIR}/model_calvetti_w.cpp
-${MODEL_DIR}/model_calvetti_x0.cpp
-${MODEL_DIR}/model_calvetti_xdot.cpp
-${MODEL_DIR}/model_calvetti_y.cpp
+set(SRC_LIST_LIB ${MODEL_DIR}/JSparse.cpp
+${MODEL_DIR}/Jy.cpp
+${MODEL_DIR}/M.cpp
+${MODEL_DIR}/dJydsigma.cpp
+${MODEL_DIR}/dJydy.cpp
+${MODEL_DIR}/dwdx.cpp
+${MODEL_DIR}/dydx.cpp
+${MODEL_DIR}/root.cpp
+${MODEL_DIR}/sigmay.cpp
+${MODEL_DIR}/w.cpp
+${MODEL_DIR}/x0.cpp
+${MODEL_DIR}/xdot.cpp
+${MODEL_DIR}/y.cpp
 
 ${MODEL_DIR}/wrapfunctions.cpp
 )