Removing scons and adding an error message

apps/texttest/weekly/MeshConvert/Tutorial.wiki

@@ -15,19 +15,6 @@ our special binary version of the Triangle/Tetgen format.
  to containing element indices.  The presence of this file cuts the calculation cost at mesh load time.
  * If a Chaste format fibre file (.axi or .ortho) is associated with the mesh then this will also be converted to our binary format.
 
-=== Making the executable(s) ===
-
-It is assumed that as you are running on a parallel cluster or supercomputer you have access to the Chaste 
-source code.  You can produce all executables (including the standalone Chaste program) using:
-{{{
-#!sh
-scons chaste_libs=1 compile_only=1 exe=1 build=GccOpt apps
-}}}
-Binaries {{{Chaste, MeshConvert...}}} are made in {{{apps/src}}}.
-
-You may get a speed improvement from using a "no debug" build-type like {{{build=GccOpt_ndebug}}}, but
-this is at the expense of doing less error checking.
-
 === Running the converter ===
 
 You may want to download and save the attached file [attachment:MeshConvert.tgz MeshConvert.tgz] and 

chaste-lucid.supp

@@ -6,12 +6,7 @@
 #############################################################
 
 #################################################
-# Note if memory leaks depend on the context (e.g. 
-# CHASTE_TEST_OUTPUT it may be advisable for Scons
-# to produce suppressions automatically:
-#       python/BuildTypes.py
-#       -    #_valgrind_flags +=" --gen-suppressions=all"
-#       +    _valgrind_flags +=" --gen-suppressions=all"
+# Note if memory leaks depend on the context
 #################################################
 
 # HDF5

chaste.supp

@@ -2,12 +2,7 @@
 # valgrind --tool=memcheck --track-fds=yes --leak-check=yes --num-callers=50 --suppressions=chaste.supp --gen-suppressions=yes io/build/debug/TestSpiralParametersReaderRunner
 
 #################################################
-# Note if memory leaks depend on the context (e.g. 
-# CHASTE_TEST_OUTPUT it may be advisable for Scons
-# to produce suppressions automatically:
-#       python/BuildTypes.py
-#       -    #_valgrind_flags +=" --gen-suppressions=all"
-#       +    _valgrind_flags +=" --gen-suppressions=all"
+# Note if memory leaks depend on the context
 #################################################
 
 

crypt/test/simulation/TestArchiveFormat.hpp

@@ -87,9 +87,6 @@ class TestArchiveFormat : public CxxTest::TestSuite
      *  ctest -R TestGenerateSteadyStateCrypt
      *  cp /tmp/$USER/testoutput/SteadyStateCrypt/archive/?*_150.* ../crypt/test/data/SteadyStateCrypt/archive/
      *
-     * OR to produce archives in CMake:
-     *  scons build=GccOpt_hostconfig,boost=1-58,use-cvode=0 test_suite=crypt/test/simulation/TestGenerateSteadyStateCrypt.hpp
-     *  cp /tmp/$USER/testoutput/SteadyStateCrypt/archive/?*_150.* crypt/test/data/SteadyStateCrypt/archive/
      *
      */
     void TestLoadArchive()

eclipse_settings/Compile and run the currently opened test.launch

@@ -2,6 +2,5 @@
 <launchConfiguration type="org.eclipse.ui.externaltools.ProgramLaunchConfigurationType">
 <stringAttribute key="org.eclipse.ui.externaltools.ATTR_TOOL_ARGUMENTS" value="test_suite=${resource_loc}"/>
 <stringAttribute key="org.eclipse.ui.externaltools.ATTR_WORKING_DIRECTORY" value="${project_loc}"/>
-<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="/usr/bin/scons"/>
 <booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
 </launchConfiguration>

eclipse_settings/preferences.epf

@@ -28,7 +28,6 @@ file_export_version=3.0
 /instance/org.eclipse.core.resources/encoding=ISO-8859-1
 /instance/org.eclipse.core.resources/version=1
 /instance/org.eclipse.core.runtime/content-types/org.eclipse.cdt.core.cxxSource/file-names=*.cpp.in
-/instance/org.eclipse.core.runtime/content-types/org.python.pydev.pythonfile/file-names=SConscript
 /instance/org.eclipse.debug.ui/org.eclipse.debug.ui.build_before_launch=false
 /instance/org.eclipse.team.svn.ui/preference.decoration.icon.modified=true
 /instance/org.eclipse.team.svn.ui/preference.history.connectToCompareWith=false
@@ -40,7 +39,6 @@ file_export_version=3.0
 /instance/org.eclipse.ui.editors/spacesForTabs=true
 /instance/org.eclipse.ui.ide/EXIT_PROMPT_ON_CLOSE_LAST_WINDOW=false
 /instance/org.eclipse.ui.workbench/perspectives=<C/C++>
-/instance/org.eclipse.ui.workbench/resourcetypes=<?xml version\="1.0" encoding\="UTF-8"?>\n<editors version\="3.1">\n<info extension\="" name\="SConstruct">\n<editor id\="org.python.pydev.editor.PythonEditor"/>\n<defaultEditor id\="org.python.pydev.editor.PythonEditor"/>\n</info>\n<info extension\="" name\="SConscript">\n<editor id\="org.python.pydev.editor.PythonEditor"/>\n<defaultEditor id\="org.python.pydev.editor.PythonEditor"/>\n</info>\n</editors>
 /instance/org.python.pydev/COMMENT_COLOR=128,128,128
 /instance/org.python.pydev/DOCSTRING\ CHARACTER="
 /instance/org.python.pydev/DONT_GENERATE_TYPETAGS_PREFIXES=sz\u0000n\u0000f\u0000

global/src/OutputFileHandler.cpp

@@ -164,7 +164,7 @@ std::string OutputFileHandler::GetChasteTestOutputDirectory()
     FileFinder directory_root;
     if (chaste_test_output == nullptr || *chaste_test_output == 0)
     {
-        // Mimic the old SCons behaviour of setting CHASTE_TEST_OUTPUT: /tmp/'+os.environ['USER']+'/testoutput/
+        // Mimic the old behaviour of setting CHASTE_TEST_OUTPUT: /tmp/'+os.environ['USER']+'/testoutput/
         std::stringstream  tmp_directory;
         if (getenv("USER")!=NULL)
         {

global/src/Version.cpp.in

@@ -38,7 +38,6 @@ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  * 
  * This is a template file for generating the Version.cpp source on the fly.
  * Content of the form %(example)s is replaced by suitable values.
- * See the function GetVersionCpp in python/SConsTools.py for more details.
  */
 
 #include "Version.hpp"

global/src/Version_cmake.cpp.in

@@ -38,7 +38,6 @@ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  * 
  * This is a template file for generating the Version.cpp source on the fly.
  * Content of the form ${example} is replaced by suitable values.
- * See the function GetVersionCpp in python/SConsTools.py for more details.
  */
 
 #include "Version.hpp"

global/test/TestCommandLineArguments.hpp

@@ -54,13 +54,6 @@ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *
  *
  *
- *  For example:
- *  scons co=1 projects/you/TestBlah.hpp
- *  ./projects/you/build/debug/TestBlahRunner -myparam 10.4
- *
- *  Alternatively, you can add the arguments to SCons so that you can compile and run in one go:
- *  scons run_time_flags="--verbose true" global/test/TestCommandLineArguments.hpp
- *  This should produce "You have successfully set --verbose to take the value 1." for this test suite.
  *
  * Note: error messages such as
  *   WARNING! There are options you set that were not used!

global/test/TestFileFinder.hpp

@@ -226,7 +226,6 @@ class TestFileFinder : public CxxTest::TestSuite
 
         // We can also compute relative paths
         TS_ASSERT_EQUALS(child.GetRelativePath(dir), "src/");
-        TS_ASSERT_EQUALS(FileFinder("SConscript", dir).GetRelativePath(dir), "SConscript");
         TS_ASSERT_THROWS_CONTAINS(child.GetRelativePath(new_dir), "' is not relative to '");
     }
 

heart/src/io/ChasteParameters_2017_1.xsd

@@ -261,8 +261,7 @@
       <xs:documentation xml:lang="en"> An attribute for path_type elements that describes how to
         interpret the path value. It can be relative to the current working directory, relative to
         $CHASTE_TEST_OUTPUT, relative to the parameters file, relative to the Chaste source
-        code root, relative to the directory Chaste was built in (which for SCons builds is the same
-        as the source root, but may differ for CMake builds), or an absolute path. It can also be
+        code root, relative to the directory Chaste was built in, or an absolute path. It can also be
         specified as a path relative to the XML configuration file. </xs:documentation>
     </xs:annotation>
     <xs:restriction base="xs:string">

heart/src/io/ChasteParameters_3_4.xsd

@@ -261,8 +261,7 @@
       <xs:documentation xml:lang="en"> An attribute for path_type elements that describes how to
         interpret the path value. It can be relative to the current working directory, relative to
         $CHASTE_TEST_OUTPUT, relative to the parameters file, relative to the Chaste source
-        code root, relative to the directory Chaste was built in (which for SCons builds is the same
-        as the source root, but may differ for CMake builds), or an absolute path. It can also be
+        code root, relative to the directory Chaste was built in, or an absolute path. It can also be
         specified as a path relative to the XML configuration file. </xs:documentation>
     </xs:annotation>
     <xs:restriction base="xs:string">

heart/src/odes/CellMLToSharedLibraryConverter.cpp

@@ -196,7 +196,6 @@ void CellMLToSharedLibraryConverter::ConvertCellmlToSo(const std::string& rCellm
                 r_cellml_file.CopyTo(tmp_folder);
             }
 
-#ifdef CHASTE_CMAKE
             std::string cmake_lists_filename = tmp_folder.GetAbsolutePath() + "/CMakeLists.txt";
             std::ofstream cmake_lists_filestream(cmake_lists_filename.c_str());
             cmake_lists_filestream << "cmake_minimum_required(VERSION 2.8.12)\n" <<
@@ -219,25 +218,6 @@ void CellMLToSharedLibraryConverter::ConvertCellmlToSo(const std::string& rCellm
             EXPECT0(chdir, tmp_folder.GetAbsolutePath());
             EXPECT0(system, "cmake" + cmake_args + " .");
             EXPECT0(system, "cmake --build . --config " + ChasteBuildType());
-#else
-            // Change to Chaste source folder
-            EXPECT0(chdir, chaste_root.GetAbsolutePath());
-
-            // Run scons to generate C++ code and compile it to a .so
-            EXPECT0(system, "scons --warn=no-all dyn_libs_only=1 chaste_libs=1 --codegen_args=\""+codegen_args+"\" --codegen_base_folder=" + chaste_source.GetAbsolutePath() + " build=" + ChasteBuildType() + " " + tmp_folder.GetAbsolutePath());
-            if (mPreserveGeneratedSources)
-            {
-                // Copy the generated source (.hpp and .cpp) to the same place as the .so file is going.
-                // NB. CMake does this by default
-                FileFinder destination_folder_for_sources(rCellmlFolder, RelativeTo::Absolute);
-                // Copy generated source code as well
-                std::vector<FileFinder> generated_files = build_folder.FindMatches("*.?pp");
-                BOOST_FOREACH(const FileFinder& r_generated_file, generated_files)
-                {
-                    r_generated_file.CopyTo(destination_folder_for_sources);
-                }
-            }
-#endif
 
             FileFinder so_file(tmp_folder.GetAbsolutePath() + "/lib" + cellml_leaf_name + "." + msSoSuffix, RelativeTo::Absolute);
 std::cout<< "so file: "<< tmp_folder.GetAbsolutePath() + "/lib" + cellml_leaf_name + "." + msSoSuffix <<std::endl;

heart/test/TestCardiacSimulation.hpp

@@ -438,15 +438,6 @@ class TestCardiacSimulation : public CxxTest::TestSuite
     /**
      * Note: from Chaste release 3.1 onward we no longer support Boost 1.33.
      * The earliest version of Boost supported is 1.34
-     * Run TestCardiacSimulationArchiveBidomain on 4 processors to create the archive for this test,
-     * and copy it to the repository using:
-     *
-       scons build=GccOpt_hostconfig,boost=1-34_4 test_suite=heart/test/TestCardiacSimulation.hpp
-       cp -r /tmp/$USER/testoutput/SaveBidomainShort_checkpoints/0.2ms heart/test/data/checkpoint_migration_via_xml/
-       rm -f heart/test/data/checkpoint_migration_via_xml/0.2ms/SaveBidomainShort/progress_status.txt
-       rm -f heart/test/data/checkpoint_migration_via_xml/0.2ms/SaveBidomainShort_0.2ms/mesh.ncl
-       rm -f heart/test/data/checkpoint_migration_via_xml/0.2ms/SaveBidomainShort_0.2ms/ChasteParameters_?_?xsd
-       rm -rf heart/test/data/checkpoint_migration_via_xml/0.2ms/SaveBidomainShort/output
      */
     void TestCardiacSimulationResumeMigration()
     {