Merge branch 'next' into uuid-run-id

.github/workflows/tests.yml

@@ -10,7 +10,7 @@ jobs:
     name: ${{ matrix.config.name }}
     runs-on: ${{ matrix.config.os }}
     env:
-      BOUT_TEST_TIMEOUT: "5m"
+      BOUT_TEST_TIMEOUT: "6m"
       PETSC_DIR: /usr/lib/petscdir/3.7.7/x86_64-linux-gnu-real
       PETSC_ARCH: ""
       SLEPC_DIR: /usr/lib/slepcdir/3.7.4/x86_64-linux-gnu-real

.gitmodules

@@ -10,3 +10,9 @@
 [submodule "externalpackages/fmt"]
 	path = externalpackages/fmt
 	url = https://github.com/fmtlib/fmt.git
+[submodule "externalpackages/boutdata"]
+	path = externalpackages/boutdata
+	url = https://github.com/boutproject/boutdata.git
+[submodule "externalpackages/boututils"]
+	path = externalpackages/boututils
+	url = https://github.com/boutproject/boututils.git

CHANGELOG.md

@@ -43,6 +43,9 @@
 - The `LaplaceShoot` Laplacian implementation was removed. There are
   very few cases, if any, where this implementation actually
   works. [\#2177](https://github.com/boutproject/BOUT-dev/pull/2177)
+- `PhysicsModel` expects the options `datadir` and `dump_format` to
+  have been set; this is only a problem if you don't call
+  `BoutInitialise`. [\#2062](https://github.com/boutproject/BOUT-dev/pull/2062)
 
 
 ## [v4.3.2](https://github.com/boutproject/BOUT-dev/tree/v4.3.2) (2020-10-19)

README.md

@@ -25,10 +25,10 @@ equations appearing in a readable form.
 For example, the following set of equations for magnetohydrodynamics
 (MHD):
 
-![ddt_rho](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20%5Crho%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%5Crho%20-%20%5Crho%5Cnabla%5Ccdot%5Cmathbf%7Bv%7D)  
-![ddt_p](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20p%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%20p%20-%20%5Cgamma%20p%5Cnabla%5Ccdot%5Cmathbf%7Bv%7D)  
-![ddt_v](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20%5Cmathbf%7Bv%7D%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%5Cmathbf%7Bv%7D%20+%20%5Cfrac%7B1%7D%7B%5Crho%7D%28-%5Cnabla%20p%20+%20%28%5Cnabla%5Ctimes%5Cmathbf%7BB%7D%29%5Ctimes%5Cmathbf%7BB%7D%29)  
-![ddt_B](http://latex.codecogs.com/png.latex?%7B%7B%5Cfrac%7B%5Cpartial%20%5Cmathbf%7BB%7D%7D%7B%5Cpartial%20t%7D%7D%7D%20%3D%20%5Cnabla%5Ctimes%28%5Cmathbf%7Bv%7D%5Ctimes%5Cmathbf%7BB%7D%29)  
+![ddt_rho](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20%5Crho%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%5Crho%20-%20%5Crho%5Cnabla%5Ccdot%5Cmathbf%7Bv%7D)
+![ddt_p](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20p%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%20p%20-%20%5Cgamma%20p%5Cnabla%5Ccdot%5Cmathbf%7Bv%7D)
+![ddt_v](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20%5Cmathbf%7Bv%7D%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%5Cmathbf%7Bv%7D%20+%20%5Cfrac%7B1%7D%7B%5Crho%7D%28-%5Cnabla%20p%20+%20%28%5Cnabla%5Ctimes%5Cmathbf%7BB%7D%29%5Ctimes%5Cmathbf%7BB%7D%29)
+![ddt_B](http://latex.codecogs.com/png.latex?%7B%7B%5Cfrac%7B%5Cpartial%20%5Cmathbf%7BB%7D%7D%7B%5Cpartial%20t%7D%7D%7D%20%3D%20%5Cnabla%5Ctimes%28%5Cmathbf%7Bv%7D%5Ctimes%5Cmathbf%7BB%7D%29)
 
 can be written simply as:
 
@@ -138,7 +138,6 @@ This directory contains
 
     * **boutdata**        Routines to simplify accessing BOUT++ output
     * **boututils**       Some useful routines for accessing and plotting data
-    * **bout_runners**    A python wrapper to submit several runs at once (either on a normal computer, or through a PBS system)
     * **post_bout**       Routines for post processing in BOUT++
 
   * **slab**              IDL routine for grid generation of a slab
@@ -185,3 +184,4 @@ BOUT++ links by default with some GPL licensed libraries. Thus if you
 compile BOUT++ with any of them, BOUT++ will automatically be licensed
 as GPL. Thus if you want to use BOUT++ with GPL non-compatible code,
 make sure to compile without GPLed code.
+

autoconf_build_defines.hxx.in

@@ -24,6 +24,9 @@
 /* LAPACK support */
 #undef BOUT_HAS_LAPACK
 
+/* NETCDF support */
+#undef BOUT_HAS_LEGACY_NETCDF
+
 /* NETCDF support */
 #undef BOUT_HAS_NETCDF
 

bin/bout-config.in

@@ -29,6 +29,7 @@ idlpath="@IDLCONFIGPATH@"
 pythonpath="@PYTHONCONFIGPATH@"
 
 has_netcdf="@BOUT_HAS_NETCDF@"
+has_legacy_netcdf="@BOUT_HAS_LEGACY_NETCDF@"
 has_pnetcdf="@BOUT_HAS_PNETCDF@"
 has_hdf5="@BOUT_HAS_HDF5@"
 has_pvode="@BOUT_HAS_PVODE@"
@@ -68,6 +69,7 @@ Available values for OPTION include:
   --python       Python path
 
   --has-netcdf  NetCDF file support
+  --has-legacy-netcdf  Legacy NetCDF file support
   --has-pnetcdf Parallel NetCDF file support
   --has-hdf5    HDF5 file support
   --has-pvode   PVODE solver support
@@ -103,6 +105,7 @@ all()
         echo "  --python      -> $pythonpath"
         echo
         echo "  --has-netcdf  -> $has_netcdf"
+        echo "  --has-legacy-netcdf  -> $has_legacy_netcdf"
         echo "  --has-pnetcdf -> $has_pnetcdf"
         echo "  --has-hdf5    -> $has_hdf5"
         echo "  --has-pvode   -> $has_pvode"
@@ -189,6 +192,10 @@ while test $# -gt 0; do
         echo $has_netcdf
         ;;
 
+    --has-legacy-netcdf)
+        echo $has_legacy_netcdf
+        ;;
+
     --has-pnetcdf)
         echo $has_pnetcdf
         ;;

bin/bout-pylib-cmd-to-bin

@@ -250,7 +250,6 @@ if __name__ == "__main__":
         print("Please wait, scanning modules ...")
         x=boutmodules(["boutcore",
                        "boutdata",
-                       "bout_runners",
                        "boututils",
                        "post_bout",
                        "zoidberg"])
@@ -292,3 +291,4 @@ if __name__ == "__main__":
         print("Creating failed. To rerun and overwrite the file without asking run:")
         print("%s %s %s %s -f"%(sys.argv[0],mod,fun,name))
         raise
+

bin/bout-v5-macro-upgrader.py

@@ -131,6 +131,13 @@
         "macro": True,
         "always_defined": True,
     },
+    {
+        "old": "NCDF",
+        "new": "BOUT_HAS_LEGACY_NETCDF",
+        "headers": "bout/build_config.hxx",
+        "macro": True,
+        "always_defined": True,
+    },
     {
         "old": "HDF5",
         "new": "BOUT_HAS_HDF5",
@@ -274,14 +281,14 @@ def fix_ifdefs(old, source):
 def fix_always_defined_macros(old, new, source):
     """Fix '#ifdef's that should become plain '#if'
     """
-    new_source = re.sub(r"#ifdef\s+{}".format(old), r"#if {}".format(new), source)
-    return re.sub(r"#ifndef\s+{}".format(old), r"#if !{}".format(new), new_source)
+    new_source = re.sub(r"#ifdef\s+{}\b".format(old), r"#if {}".format(new), source)
+    return re.sub(r"#ifndef\s+{}\b".format(old), r"#if !{}".format(new), new_source)
 
 
 def fix_replacement(old, new, source):
     """Straight replacements
     """
-    return re.sub(r'([^"])\b{}\b([^"])'.format(old), r"\1{}\2".format(new), source)
+    return re.sub(r'([^"_])\b{}\b([^"_])'.format(old), r"\1{}\2".format(new), source)
 
 
 def apply_fixes(replacements, source):

cmake_build_defines.hxx.in

@@ -27,4 +27,7 @@
 #cmakedefine01 BOUT_USE_SIGNAL
 #cmakedefine01 BOUT_USE_TRACK
 
+// CMake build does not support legacy interface
+#define BOUT_HAS_LEGACY_NETCDF 0
+
 #endif // BOUT_BUILD_CONFIG_HXX

configure

@@ -643,6 +643,7 @@ BOUT_HAS_PVODE
 BOUT_HAS_PRETTY_FUNCTION
 BOUT_HAS_PNETCDF
 BOUT_HAS_PETSC
+BOUT_HAS_LEGACY_NETCDF
 BOUT_HAS_NETCDF
 BOUT_HAS_LAPACK
 BOUT_HAS_IDA
@@ -6631,6 +6632,8 @@ fi
 
 NCCONF="" # Configuration script
 
+BOUT_HAS_NETCDF=no
+BOUT_HAS_LEGACY_NETCDF=no
 if test "x$with_netcdf" != "xno"; then :
 
   ##########################################
@@ -6784,7 +6787,9 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
         LIBS=$save_LIBS
         LDFLAGS=$save_LDFLAGS
-        CXXFLAGS="$save_CXXFLAGS -DNCDF"
+        CXXFLAGS="$save_CXXFLAGS"
+        BOUT_HAS_NETCDF=yes
+        BOUT_HAS_LEGACY_NETCDF=yes
 
 fi
       EXTRA_LIBS="$EXTRA_LIBS $NCLIB"
@@ -7197,7 +7202,8 @@ fi
          { $as_echo "$as_me:${as_lineno-$LINENO}:  -> Legacy NetCDF support enabled" >&5
 $as_echo "$as_me:  -> Legacy NetCDF support enabled" >&6;}
          NCPATH="found"
-         CXXFLAGS="$CXXFLAGS -DNCDF"
+         BOUT_HAS_NETCDF=yes
+         BOUT_HAS_LEGACY_NETCDF=yes
 
 fi
 
@@ -16368,6 +16374,18 @@ fi
 
 
 
+if test "x$BOUT_HAS_LEGACY_NETCDF" = "xyes"; then :
+
+$as_echo "#define BOUT_HAS_LEGACY_NETCDF 1" >>confdefs.h
+
+else
+
+$as_echo "#define BOUT_HAS_LEGACY_NETCDF 0" >>confdefs.h
+
+fi
+
+
+
 if test "x$BOUT_HAS_PETSC" = "xyes"; then :
 
 $as_echo "#define BOUT_HAS_PETSC 1" >>confdefs.h
@@ -18047,8 +18065,8 @@ $as_echo "$as_me:   CVODE support           : $BOUT_HAS_CVODE" >&6;}
 $as_echo "$as_me:   ARKODE support          : $BOUT_HAS_ARKODE" >&6;}
 { $as_echo "$as_me:${as_lineno-$LINENO}:   FFTW support            : $BOUT_HAS_FFTW" >&5
 $as_echo "$as_me:   FFTW support            : $BOUT_HAS_FFTW" >&6;}
-{ $as_echo "$as_me:${as_lineno-$LINENO}:   NetCDF support          : $BOUT_HAS_NETCDF" >&5
-$as_echo "$as_me:   NetCDF support          : $BOUT_HAS_NETCDF" >&6;}
+{ $as_echo "$as_me:${as_lineno-$LINENO}:   NetCDF support          : $BOUT_HAS_NETCDF (legacy: $BOUT_HAS_LEGACY_NETCDF)" >&5
+$as_echo "$as_me:   NetCDF support          : $BOUT_HAS_NETCDF (legacy: $BOUT_HAS_LEGACY_NETCDF)" >&6;}
 { $as_echo "$as_me:${as_lineno-$LINENO}:   Parallel-NetCDF support : $BOUT_HAS_PNETCDF" >&5
 $as_echo "$as_me:   Parallel-NetCDF support : $BOUT_HAS_PNETCDF" >&6;}
 { $as_echo "$as_me:${as_lineno-$LINENO}:   HDF5 support            : $BOUT_HAS_HDF5 (parallel: $BOUT_HAS_PHDF5)" >&5

configure.ac

@@ -488,6 +488,8 @@ BOUT_HAS_FFTW="no"
 
 NCCONF="" # Configuration script
 
+BOUT_HAS_NETCDF=no
+BOUT_HAS_LEGACY_NETCDF=no
 AS_IF([test "x$with_netcdf" != "xno"],
 [
   ##########################################
@@ -553,7 +555,9 @@ AS_IF([test "x$with_netcdf" != "xno"],
         AC_LANG_POP([C++])
         LIBS=$save_LIBS
         LDFLAGS=$save_LDFLAGS
-        CXXFLAGS="$save_CXXFLAGS -DNCDF"
+        CXXFLAGS="$save_CXXFLAGS"
+        BOUT_HAS_NETCDF=yes
+        BOUT_HAS_LEGACY_NETCDF=yes
        ])
       EXTRA_LIBS="$EXTRA_LIBS $NCLIB"
 
@@ -574,7 +578,8 @@ AS_IF([test "x$with_netcdf" != "xno"],
          file_formats="$file_formats netCDF"
          AC_MSG_NOTICE([ -> Legacy NetCDF support enabled])
          NCPATH="found"
-         CXXFLAGS="$CXXFLAGS -DNCDF"
+         BOUT_HAS_NETCDF=yes
+         BOUT_HAS_LEGACY_NETCDF=yes
         ], [])
   ])
 
@@ -1342,6 +1347,7 @@ BOUT_DEFINE_SUBST(BOUT_HAS_HDF5, [HDF5 support])
 BOUT_DEFINE_SUBST(BOUT_HAS_IDA, [IDA support])
 BOUT_DEFINE_SUBST(BOUT_HAS_LAPACK, [LAPACK support])
 BOUT_DEFINE_SUBST(BOUT_HAS_NETCDF, [NETCDF support])
+BOUT_DEFINE_SUBST(BOUT_HAS_LEGACY_NETCDF, [NETCDF support])
 BOUT_DEFINE_SUBST(BOUT_HAS_PETSC, [PETSc support])
 BOUT_DEFINE_SUBST(BOUT_HAS_PNETCDF, [PNETCDF support])
 BOUT_DEFINE_SUBST(BOUT_HAS_PRETTY_FUNCTION, [Compiler PRETTYFUNCTION support])
@@ -1389,7 +1395,7 @@ AC_MSG_NOTICE([  IDA support             : $BOUT_HAS_IDA])
 AC_MSG_NOTICE([  CVODE support           : $BOUT_HAS_CVODE])
 AC_MSG_NOTICE([  ARKODE support          : $BOUT_HAS_ARKODE])
 AC_MSG_NOTICE([  FFTW support            : $BOUT_HAS_FFTW])
-AC_MSG_NOTICE([  NetCDF support          : $BOUT_HAS_NETCDF])
+AC_MSG_NOTICE([  NetCDF support          : $BOUT_HAS_NETCDF (legacy: $BOUT_HAS_LEGACY_NETCDF)])
 AC_MSG_NOTICE([  Parallel-NetCDF support : $BOUT_HAS_PNETCDF])
 AC_MSG_NOTICE([  HDF5 support            : $BOUT_HAS_HDF5 (parallel: $BOUT_HAS_PHDF5)])
 AC_MSG_NOTICE([  Lapack support          : $BOUT_HAS_LAPACK])