Change geosx to geos in macros, include guards, namespace... (#2392)

This patch aims at shrinking `GEOSX` into `GEOS`. - The `geosx` namespace is renamed `geos`. - All the `GEOSX_ASSERT`, `GEOSX_LOG`, … are renamed `GEOS_…` - All the include guards are modified. - All the paths to the old `http://gihub.com/GEOSX/GEOSX` are renamed appropriately - Mention to `GEOSX` in the text of the documentation is changed to `GEOS` Meanwhile, `GEOSX` is kept for the following cases - The executable is still named `geosx`, the examples in the doc still reflect the current naming. - All the tools named after `geosx` kept their `geosx` (_e.g._ `pygeox`, `geosx_xml_tools`) - All the `cmake` configuration flags (_e.g._ `GEOSX_TPL_DIR`, `GEOSX_USE_CUDA`) are unchanged. - The `host-config` files are not changed. - The variables names, classes or files containing `GEOSX` are not modified.
GEOS-DEV · Apr 15, 2023 · 478ff4e · 478ff4e
1 parent 51bbcc0
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diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -15,11 +15,11 @@ stages:
 .build_script:
   script:
     # Change submodule paths to absolute github paths (default is relative to GEOSX gitlab path)
-    - git submodule set-url src/coreComponents/LvArray https://github.com/GEOSX/LvArray.git
+    - git submodule set-url src/coreComponents/LvArray https://github.com/GEOS-DEV/LvArray.git
     - git submodule set-url src/cmake/blt https://github.com/LLNL/blt.git
-    - git submodule set-url src/coreComponents/constitutive/PVTPackage https://github.com/GEOSX/PVTPackage.git
+    - git submodule set-url src/coreComponents/constitutive/PVTPackage https://github.com/GEOS-DEV/PVTPackage.git
     - git submodule set-url integratedTests [email protected]:GEOSX/integratedTests.git
-    - git submodule set-url src/coreComponents/fileIO/coupling/hdf5_interface https://github.com/GEOSX/hdf5_interface.git
+    - git submodule set-url src/coreComponents/fileIO/coupling/hdf5_interface https://github.com/GEOS-DEV/hdf5_interface.git
 
     # Update submodules
     - git submodule update --init --recursive src/cmake/blt

diff --git a/CITATION.cff b/CITATION.cff
@@ -92,4 +92,4 @@ title: "GEOSX"
 version: 0.2.1
 doi: 10.5281/zenodo.7151032
 date-released: 2022-10-06
-url: "https://github.com/GEOSX/GEOSX"
+url: "https://github.com/GEOS-DEV/GEOS"
diff --git a/CONTRIBUTORS b/CONTRIBUTORS
@@ -3,4 +3,4 @@ CONTRIBUTORS
 A current list of individuals who have contributed source code to the 
 GEOSX project is available at:
 
-https://github.com/GEOSX/GEOSX/graphs/contributors
+https://github.com/GEOS-DEV/GEOS/graphs/contributors
diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -9,12 +9,12 @@
 [comment]: # (All right reserved)
 [comment]: # 
 [comment]: # (For more details see:)
-[comment]: # (  https://github.com/GEOSX/GEOSX/LICENSE)
-[comment]: # (  https://github.com/GEOSX/GEOSX/COPYRIGHT)
-[comment]: # (  https://github.com/GEOSX/GEOSX/CONTRIBUTORS)
-[comment]: # (  https://github.com/GEOSX/GEOSX/NOTICE)
-[comment]: # (  https://github.com/GEOSX/GEOSX/ACKNOWLEDGEMENTS)
-[comment]: # (  https://github.com/GEOSX/GEOSX/RELEASE)
+[comment]: # (  https://github.com/GEOS-DEV/GEOS/LICENSE)
+[comment]: # (  https://github.com/GEOS-DEV/GEOS/COPYRIGHT)
+[comment]: # (  https://github.com/GEOS-DEV/GEOS/CONTRIBUTORS)
+[comment]: # (  https://github.com/GEOS-DEV/GEOS/NOTICE)
+[comment]: # (  https://github.com/GEOS-DEV/GEOS/ACKNOWLEDGEMENTS)
+[comment]: # (  https://github.com/GEOS-DEV/GEOS/RELEASE)
 
 
 Version v0.2.0 -- Release date 2020-06-20

diff --git a/examples/ObjectCatalog/Base.hpp b/examples/ObjectCatalog/Base.hpp
@@ -26,14 +26,14 @@ class Parameter
   Parameter( Parameter const & source ):
     member( source.member )
   {
-    GEOSX_LOG( "called copy constructor for Parameter" );
+    GEOS_LOG( "called copy constructor for Parameter" );
   }
 
 #if ( __cplusplus >= 201103L )
   Parameter( Parameter && source ):
     member( std::move( source.member ))
   {
-    GEOSX_LOG( "called move constructor for Parameter" );
+    GEOS_LOG( "called move constructor for Parameter" );
   }
 #endif
 
@@ -47,12 +47,12 @@ class Base
 public:
   Base( int junk, double const & junk2, Parameter& pbv )
   {
-    GEOSX_LOG( "calling Base constructor with arguments (" << junk << " " << junk2 << ")" );
+    GEOS_LOG( "calling Base constructor with arguments (" << junk << " " << junk2 << ")" );
   }
 
   ~Base()
   {
-    GEOSX_LOG( "calling Base destructor" );
+    GEOS_LOG( "calling Base destructor" );
   }
 
   using CatalogInterface = dataRepository::CatalogInterface< Base, int, double const &, Parameter& >;

diff --git a/examples/ObjectCatalog/Derived1.cpp b/examples/ObjectCatalog/Derived1.cpp
@@ -18,12 +18,12 @@
 Derived1::Derived1( int junk, double const & junk2, Parameter& param ):
   Base( junk, junk2, param )
 {
-  GEOSX_LOG( "calling Derived1 constructor with arguments ("<<junk<<" "<<junk2<<")" );
+  GEOS_LOG( "calling Derived1 constructor with arguments ("<<junk<<" "<<junk2<<")" );
 }
 
 Derived1::~Derived1()
 {
-  GEOSX_LOG( "calling Derived1 destructor" );
+  GEOS_LOG( "calling Derived1 destructor" );
 }
 
 REGISTER_CATALOG_ENTRY( Base, Derived1, int, double const &, Parameter& )
diff --git a/examples/ObjectCatalog/Derived2.cpp b/examples/ObjectCatalog/Derived2.cpp
@@ -17,12 +17,12 @@
 Derived2::Derived2( int junk, double const & junk2, Parameter& param ):
   Base( junk, junk2, param )
 {
-  GEOSX_LOG( "calling Derived2 constructor with arguments ("<<junk<<" "<<junk2<<")" );
+  GEOS_LOG( "calling Derived2 constructor with arguments ("<<junk<<" "<<junk2<<")" );
 }
 
 Derived2::~Derived2()
 {
-  GEOSX_LOG( "calling Derived2 destructor" );
+  GEOS_LOG( "calling Derived2 destructor" );
 }
 
 REGISTER_CATALOG_ENTRY( Base, Derived2, int, double const &, Parameter& )
diff --git a/examples/ObjectCatalog/main.cpp b/examples/ObjectCatalog/main.cpp
@@ -22,18 +22,18 @@
 
 int main( int argc, char *argv[] )
 {
-  GEOSX_LOG( "EXECUTING MAIN" );
+  GEOS_LOG( "EXECUTING MAIN" );
   int junk = 1;
   double junk2 = 3.14;
   double junk3 = 2*3.14;
   Parameter param;
 
 
-  GEOSX_LOG( "Attempting to create a Derived1 object" );
+  GEOS_LOG( "Attempting to create a Derived1 object" );
   std::unique_ptr<Base> derived1 = Base::CatalogInterface::Factory( "derived1", junk, junk2, param );
-  GEOSX_LOG( "Attempting to create a Derived2 object" );
+  GEOS_LOG( "Attempting to create a Derived2 object" );
   std::unique_ptr<Base> derived2 = Base::CatalogInterface::Factory( "derived2", junk, junk3, param );
 
   Base::CatalogInterface::catalog_cast<Derived1>( *(derived2.get()));
-  GEOSX_LOG( "EXITING MAIN" );
+  GEOS_LOG( "EXITING MAIN" );
 }
diff --git a/ide_files/clion_codestyle.xml b/ide_files/clion_codestyle.xml
@@ -1,4 +1,4 @@
-<code_scheme name="GEOSX" version="173">
+<code_scheme name="GEOS" version="173">
   <Objective-C>
     <option name="INDENT_NAMESPACE_MEMBERS" value="0" />
     <option name="INDENT_C_STRUCT_MEMBERS" value="2" />

diff --git a/scripts/uberenv/packages/geosx/package.py b/scripts/uberenv/packages/geosx/package.py
@@ -52,8 +52,8 @@ def cmake_cache_option(name, boolean_value, comment=""):
 class Geosx(CMakePackage, CudaPackage):
     """GEOSX simulation framework."""
 
-    homepage = "https://github.com/GEOSX/GEOSX"
-    git = "https://github.com/GEOSX/GEOSX.git"
+    homepage = "https://github.com/GEOS-DEV/GEOS"
+    git = "https://github.com/GEOS-DEV/GEOS.git"
 
     version('develop', branch='develop', submodules='True')
 

diff --git a/src/coreComponents/LvArray b/src/coreComponents/LvArray
diff --git a/src/coreComponents/codingUtilities/EnumStrings.hpp b/src/coreComponents/codingUtilities/EnumStrings.hpp
@@ -21,8 +21,8 @@
  * of these strings, like stream insertion/extraction operators.
  */
 
-#ifndef GEOSX_CODINGUTILITIES_ENUMSTRINGS_HPP
-#define GEOSX_CODINGUTILITIES_ENUMSTRINGS_HPP
+#ifndef GEOS_CODINGUTILITIES_ENUMSTRINGS_HPP
+#define GEOS_CODINGUTILITIES_ENUMSTRINGS_HPP
 
 #include "StringUtilities.hpp"
 #include "common/DataTypes.hpp"
@@ -32,7 +32,7 @@
 #include <type_traits>
 #include <algorithm>
 
-namespace geosx
+namespace geos
 {
 
 namespace internal
@@ -135,9 +135,9 @@ struct EnumStrings
     auto const & strings = get();
     std::size_t size = std::distance( std::begin( strings ), std::end( strings ) );
     base_type const index = static_cast< base_type >( e );
-    GEOSX_THROW_IF( index >= LvArray::integerConversion< base_type >( size ),
-                    "Invalid value " << index << " of type " << TypeName< ENUM >::brief() << ". Valid range is 0.." << size - 1,
-                    InputError );
+    GEOS_THROW_IF( index >= LvArray::integerConversion< base_type >( size ),
+                   "Invalid value " << index << " of type " << TypeName< ENUM >::brief() << ". Valid range is 0.." << size - 1,
+                   InputError );
     return strings[ index ];
   }
 
@@ -150,9 +150,9 @@ struct EnumStrings
   {
     auto const & strings = get();
     auto const it = std::find( std::begin( strings ), std::end( strings ), s );
-    GEOSX_THROW_IF( it == std::end( strings ),
-                    "Invalid value '" << s << "' of type " << TypeName< enum_type >::brief() << ". Valid options are: " << concat( ", " ),
-                    InputError );
+    GEOS_THROW_IF( it == std::end( strings ),
+                   "Invalid value '" << s << "' of type " << TypeName< enum_type >::brief() << ". Valid options are: " << concat( ", " ),
+                   InputError );
     enum_type const e = static_cast< enum_type >( LvArray::integerConversion< base_type >( std::distance( std::begin( strings ), it ) ) );
     return e;
   }
@@ -179,6 +179,6 @@ struct TypeRegex< ENUM, std::enable_if_t< internal::HasEnumStrings< ENUM > > >
   }
 };
 
-} // namespace geosx
+} // namespace geos
 
-#endif //GEOSX_CODINGUTILITIES_ENUMSTRINGS_HPP
+#endif //GEOS_CODINGUTILITIES_ENUMSTRINGS_HPP
diff --git a/src/coreComponents/codingUtilities/Parsing.cpp b/src/coreComponents/codingUtilities/Parsing.cpp
@@ -20,7 +20,7 @@
 
 #include <cstdlib>
 
-namespace geosx
+namespace geos
 {
 
 namespace
@@ -83,4 +83,4 @@ INST_PARSEVALUE( long long );
 
 #undef INST_PARSEVALUE
 
-} // namespace geosx
+} // namespace geos
diff --git a/src/coreComponents/codingUtilities/Parsing.hpp b/src/coreComponents/codingUtilities/Parsing.hpp
@@ -16,14 +16,14 @@
  * @file Parsing.hpp
  */
 
-#ifndef GEOSX_CODINGUTILITIES_PARSING_HPP_
-#define GEOSX_CODINGUTILITIES_PARSING_HPP_
+#ifndef GEOS_CODINGUTILITIES_PARSING_HPP_
+#define GEOS_CODINGUTILITIES_PARSING_HPP_
 
 #include "common/DataTypes.hpp"
 
 #include <fstream>
 
-namespace geosx
+namespace geos
 {
 
 /**
@@ -129,18 +129,18 @@ void parseFile( string const & filename,
     if( ptr != end )
     {
       std::ptrdiff_t const left = std::distance( ptr, end );
-      GEOSX_THROW( GEOSX_FMT( "Unable to parse value in file {} at position {}: {}...",
-                              filename, static_cast< std::streamoff >( inputStream.tellg() ) - left,
-                              string( ptr, std::min( left, std::ptrdiff_t{32} ) ) ),
-                   std::runtime_error );
+      GEOS_THROW( GEOS_FMT( "Unable to parse value in file {} at position {}: {}...",
+                            filename, static_cast< std::streamoff >( inputStream.tellg() ) - left,
+                            string( ptr, std::min( left, std::ptrdiff_t{32} ) ) ),
+                  std::runtime_error );
     }
   }
 
-  GEOSX_THROW_IF( inputStream.fail() && !inputStream.eof(),
-                  GEOSX_FMT( "Error while reading file {}: {}", filename, std::strerror( errno ) ),
-                  std::runtime_error );
+  GEOS_THROW_IF( inputStream.fail() && !inputStream.eof(),
+                 GEOS_FMT( "Error while reading file {}: {}", filename, std::strerror( errno ) ),
+                 std::runtime_error );
 }
 
-} // namespace geosx
+} // namespace geos
 
-#endif //GEOSX_CODINGUTILITIES_PARSING_HPP_
+#endif //GEOS_CODINGUTILITIES_PARSING_HPP_
diff --git a/src/coreComponents/codingUtilities/SFINAE_Macros.hpp b/src/coreComponents/codingUtilities/SFINAE_Macros.hpp
@@ -16,8 +16,8 @@
  * @file SFINAE_Macros.hpp
  */
 
-#ifndef GEOSX_CODINGUTILITIES_SFINAE_MACROS_HPP_
-#define GEOSX_CODINGUTILITIES_SFINAE_MACROS_HPP_
+#ifndef GEOS_CODINGUTILITIES_SFINAE_MACROS_HPP_
+#define GEOS_CODINGUTILITIES_SFINAE_MACROS_HPP_
 
 #include "LvArray/src/Macros.hpp"
 #include "LvArray/src/typeManipulation.hpp"
@@ -59,4 +59,4 @@
   IS_VALID_EXPRESSION( HasAlias_ ## NAME, CLASS, !std::is_enum< typename CLASS::NAME >::value )
 
 
-#endif /* GEOSX_CODINGUTILITIES_SFINAE_MACROS_HPP_ */
+#endif /* GEOS_CODINGUTILITIES_SFINAE_MACROS_HPP_ */
diff --git a/src/coreComponents/codingUtilities/StringUtilities.cpp b/src/coreComponents/codingUtilities/StringUtilities.cpp
@@ -23,7 +23,7 @@
 #include <cstdlib>
 #include <cmath>
 
-namespace geosx
+namespace geos
 {
 namespace stringutilities
 {
@@ -89,8 +89,8 @@ string toMetricPrefixString( T const & value )
   snprintf( temp, 8, "%5.*f %c", p, scaledValue, prefixes[a+5] );
   rval = temp;
 
-  GEOSX_ERROR_IF( rval.empty(),
-                  GEOSX_FMT( "The value of {} was not able to be converted with a metric prefix", value ) );
+  GEOS_ERROR_IF( rval.empty(),
+                 GEOS_FMT( "The value of {} was not able to be converted with a metric prefix", value ) );
 
 
   return rval;

diff --git a/src/coreComponents/codingUtilities/StringUtilities.hpp b/src/coreComponents/codingUtilities/StringUtilities.hpp
@@ -16,15 +16,15 @@
  * @file StringUtilities.hpp
  */
 
-#ifndef GEOSX_CODINGUTILITIES_STRINGUTILITIES_HPP_
-#define GEOSX_CODINGUTILITIES_STRINGUTILITIES_HPP_
+#ifndef GEOS_CODINGUTILITIES_STRINGUTILITIES_HPP_
+#define GEOS_CODINGUTILITIES_STRINGUTILITIES_HPP_
 
 #include "common/DataTypes.hpp"
 
 #include <iomanip>
 #include <sstream>
 
-namespace geosx
+namespace geos
 {
 namespace stringutilities
 {
@@ -208,6 +208,6 @@ template< typename T >
 string toMetricPrefixString( T const & value );
 
 } // namespace stringutilities
-} // namespace geosx
+} // namespace geos
 
-#endif /* GEOSX_CODINGUTILITIES_STRINGUTILITIES_HPP_ */
+#endif /* GEOS_CODINGUTILITIES_STRINGUTILITIES_HPP_ */
diff --git a/src/coreComponents/codingUtilities/UnitTestUtilities.hpp b/src/coreComponents/codingUtilities/UnitTestUtilities.hpp
@@ -16,8 +16,8 @@
  * @file UnitTestUtilities.hpp
  */
 
-#ifndef GEOSX_CODINGUTILITIES_UNITTESTUTILITIES_HPP_
-#define GEOSX_CODINGUTILITIES_UNITTESTUTILITIES_HPP_
+#ifndef GEOS_CODINGUTILITIES_UNITTESTUTILITIES_HPP_
+#define GEOS_CODINGUTILITIES_UNITTESTUTILITIES_HPP_
 
 #include "common/DataTypes.hpp"
 
@@ -35,12 +35,12 @@
   } while( false )
 
 #define SKIP_TEST_IN_SERIAL( REASON ) \
-  SKIP_TEST_IF( geosx::MpiWrapper::commSize() == 1, REASON )
+  SKIP_TEST_IF( geos::MpiWrapper::commSize() == 1, REASON )
 
 #define SKIP_TEST_IN_PARALLEL( REASON ) \
-  SKIP_TEST_IF( geosx::MpiWrapper::commSize() != 1, REASON )
+  SKIP_TEST_IF( geos::MpiWrapper::commSize() != 1, REASON )
 
-namespace geosx
+namespace geos
 {
 
 namespace testing
@@ -70,7 +70,7 @@ T expected( T expectedSerial,
   }
   else
   {
-    GEOSX_ASSERT( expectedParallel.size() == std::size_t( mpiSize ) );
+    GEOS_ASSERT( expectedParallel.size() == std::size_t( mpiSize ) );
     std::vector< T > tmp( expectedParallel );
     return tmp[MpiWrapper::commRank( comm )];
   }
@@ -218,6 +218,6 @@ void compareLocalMatrices( CRSMatrixView< T const, COL_INDEX const > const & mat
 
 } // namespace testing
 
-} // namespace geosx
+} // namespace geos
 
-#endif //GEOSX_CODINGUTILITIES_UNITTESTUTILITIES_HPP_
+#endif //GEOS_CODINGUTILITIES_UNITTESTUTILITIES_HPP_
+3 −3		docs/sphinx/developmentAids.rst
+6 −0		src/Macros.hpp
+41 −24		src/input.hpp
+11 −11		unitTests/testInput.cpp