Minor changes to fix build and install problems.

No changes to functionality.

Author: Wolfgang Kastaun

README renamed to README.rst

@@ -26,30 +26,30 @@ installed via Python's pip. For more info, see
 https://mesonbuild.com
 
 
-To build the library, 
+To build the library::
+
+  $> cd <repository>
+  $> meson mbuild --buildtype=release
+  $> cd mbuild
+  $> ninja
 
-$> cd <repository>
-$> meson mbuild --buildtype=release
-$> cd mbuild
-$> ninja
-   
 This will compile with optimization and without debug symbols. Other
-possibilities are --buildtype=debug and --buildtype=debugoptimized
+possibilities are `--buildtype=debug` and `--buildtype=debugoptimized`
 To use a different compiler, e.g. clang, prefix the meson command
-with CC=clang CXX=clang++.
+with `CC=clang CXX=clang++`.
 See https://mesonbuild.com/Running-Meson.html for general Meson usage.
 
 
 Installing
 ----------
 
-To install the library systemwide,
+To install the library systemwide::
+
+  $> ninja install
 
-$> ninja install
-   
-To install in a user-defined location
+To install in a user-defined location::
 
-$> DESTDIR=<prefix absolute path> ninja install
+  $> DESTDIR=<prefix absolute path> ninja install
 
 
 Using the Library
@@ -63,65 +63,62 @@ with `libRePrimAnd`.
 Creating Documentation
 ----------------------
 
-To just build the documentation, use the target `documentation`.
+To just build the documentation, use the target `documentation`::
 
-$> ninja documentation
+  $> ninja documentation
 
 The resulting pages can be found in the build directory under
-docsrc/sphinx/index.html
+`docsrc/sphinx/index.html`
 When installing the library, the documentation is installed as well
-by default, to <prefix>/usr/local/share/doc/libreprimand/index.html
+by default, to `<prefix>/usr/local/share/doc/libreprimand/index.html`
 
 The building of the documentation requires sphinx with the breathe 
 extension as well as doxygen. To disable building documentation and 
-remove the corresponding dependencies, use the build option
+remove the corresponding dependencies, use the build option::
 
-$> cd <repository>/mbuild
-$> meson configure -Dbuild_documentation=false
+  $> cd <repository>/mbuild
+  $> meson configure -Dbuild_documentation=false
 
 
 Running Tests
 -------------
 
 Please also take a minute to run the unit tests to ensure 
-correct compilation
+correct compilation::
+
+  $> ninja test
 
-$> ninja test
-   
 
 Benchmarks
 ----------
 
 The repository contains code to map the efficiency and accuracy of
 the primitive recovery, producing the plots shown in the 
-article. To recreate the data and plots,
+article. To recreate the data and plots::
 
+  $> ninja benchplots
+  $> ninja accuracyplots
 
-$> ninja benchplots
-$> ninja accuracyplots
-   
 The resulting pdf figures are placed in the build directory under
 tests/benchmarks
 
 This requires Python+matplotlib. To disable building benchmarking and 
-remove the corresponding dependencies, use the build option
-
-$> cd <repository>/mbuild
-$> meson configure -Dbuild_benchmarks=false
+remove the corresponding dependencies, use the build option::
 
+  $> cd <repository>/mbuild
+  $> meson configure -Dbuild_benchmarks=false
 
 Visualizing Master Function
 ---------------------------
 
 In addition, there is code to sample the primitive recovery master
 function (the central ingredient of the scheme) for various cases,
-as shown in the paper.
+as shown in the paper::
 
+  $> ninja srootdata
 
-$> ninja srootdata
-  
 The resulting data files are placed in the build directory under 
-tests/sample_root/
+`tests/sample_root/`
 
 
 

library/BasicStuff/include/meson.build

@@ -3,6 +3,6 @@ include_basic_stuff = include_directories('.')
 
 headers_basic_stuff = files('config.h','interpol.h', 'intervals.h',
                             'unitconv.h', 'smtensor.h', 
-                            'global_registry.h')
+                            'global_registry.h', 'hdf5imple.h')
 
 install_headers(headers_basic_stuff, subdir : project_headers_dest)

library/Con2Prim_IMHD/con2prim_imhd.cc

@@ -337,7 +337,7 @@ void con2prim_mhd::operator()(prim_vars_mhd& pv, cons_vars_mhd& cv,
   froot::cache sol{};
   froot f{eos, ye, d, q, rsqr, rbsqr, bsqr, sol}; 
 
-  auto bracket { f.initial_bracket(errs) };
+  auto bracket = f.initial_bracket(errs);
 
   if (errs.failed()) {
     set_to_nan(pv, cv);

library/EOS_Barotropic/eos_barotr_file.cc

@@ -11,7 +11,7 @@ eos_barotr detail::load_eos_barotr(const h5grp& g, const units& u)
 
   h5grp g2(g, std::string("eos_")+spec);
 
-  auto& r {implementations::registry_reader_eos_barotr::get(spec)};
+  auto& r = implementations::registry_reader_eos_barotr::get(spec);
   return r.load(g2,u);  
 }
 

library/EOS_Barotropic/eos_barotr_gpoly.cc

@@ -1,6 +1,7 @@
 #include "eos_barotr_gpoly.h"
 #include "eos_barotr_gpoly_impl.h"
 #include <cmath>
+#include <stdexcept>
 
 using namespace std;
 using namespace EOS_Toolkit;

library/EOS_Barotropic/eos_barotr_poly.cc

@@ -1,6 +1,7 @@
 #include "eos_barotr_poly.h"
 #include "eos_barotr_poly_impl.h"
 #include <cmath>
+#include <stdexcept>
 
 using namespace std;
 using namespace EOS_Toolkit;

library/EOS_Thermal/eos_thermal_file.cc

@@ -11,7 +11,7 @@ eos_thermal detail::load_eos_thermal(const h5grp& g, const units& u)
 
   h5grp g2(g, std::string("eos_")+spec);
 
-  auto& r {implementations::registry_reader_eos_thermal::get(spec)};
+  auto& r = implementations::registry_reader_eos_thermal::get(spec);
   return r.load(g2,u);  
 }
 

tests/sample_root/src/froot_samp.cc

@@ -77,7 +77,7 @@ void sample_froot(const eos_thermal eos,
   detail::froot f(eos, ye0, d, q, rsqr, rbsqr, bsqr, sol); 
 
   con2prim_mhd::report errs;
-  auto bracket{ f.initial_bracket(errs)};  
+  auto bracket = f.initial_bracket(errs);  
 
   ofstream os(path + "/" + p.name.c_str() + ".dat"); 
   os << setprecision(15);

tests/src/meson.build

@@ -4,7 +4,7 @@ configure_file(input : 'test_config.h.in',
                output : 'test_config.h',
                configuration : conf_tests)
 
-dep_utf = dependency('boost', modules : ['unit_test_framework'])
+dep_utf = dependency('boost', static : false, modules : ['unit_test_framework'])
 
 src_tst_c2p = ['test_con2prim_mhd.cc', 'test_utils.cc']
 

tests/src/test_con2prim_mhd.cc

@@ -613,7 +613,7 @@ BOOST_AUTO_TEST_CASE( c2p_mhd_basic )
 
   env_idealgas par{1e6, 100., 1e-11, 1e-6, 10.0, 10.0, 4e-8};
 
-  const auto tst{make_env(par)};
+  const auto tst = make_env(par);
 
   const real_t ye_fixed{0.25};
   const real_t rho{1e-5};
@@ -674,7 +674,7 @@ BOOST_AUTO_TEST_CASE( c2p_mhd_fail )
 
   env_idealgas par{1e-3, 10., 1e-12, 1e-6, 10.0, 10.0, 4e-8};
 
-  const auto tst{make_env(par)};
+  const auto tst = make_env(par);
 
   cons_vars_mhd cv1{2e-3, 1e-4, 1e-3, {0.,0.,0.}, {0.,0.,0.}};    
   hope(tst.chk_fail_rho(cv1),
@@ -694,7 +694,7 @@ BOOST_AUTO_TEST_CASE( test_con2prim_phys_igas )
 
   env_idealgas par{1e6, 51., 1e-11, 1e-6, 1.0, 2e3, 1e-8};
 
-  const auto tst{make_env(par)};  
+  const auto tst = make_env(par);  
 
   const real_t max_z{ 1e3 };
   const real_t min_z{ 1e-2 };
@@ -729,7 +729,7 @@ BOOST_AUTO_TEST_CASE( test_con2prim_phys_hybr )
 
   env_hybrideos par{1e-12, 1.0, 2e3, 1e-8};
 
-  const auto tst{make_env(par)};             
+  const auto tst = make_env(par);             
 
   real_t max_z{ 1e3};
   real_t min_z{ 1e-2};