Merge branch 'master' into oblate_coord_rot

buildscripts/build_dependencies.sh

@@ -41,6 +41,11 @@ if ! command -v ninja &> /dev/null; then
     fi
 fi
 
+# Get the OpenMP Libraries
+if [ $OS = "MacOSX" ]; then
+    ${SCRIPT_DIR}/get_lomp.sh ${ARGS}
+fi
+
 ${SCRIPT_DIR}/build_zlib.sh ${ARGS}
 ${SCRIPT_DIR}/build_hdf5.sh ${ARGS}
 ${SCRIPT_DIR}/build_netcdf-c.sh ${ARGS}

buildscripts/build_hdf5.sh

@@ -12,18 +12,14 @@
 # If not, see: https://www.gnu.org/licenses. 
 
 HDF5_VER="1_14_2"
-PLUGIN_VER="1.14.0"
 ZLIB_VER="1.3"
 
 SCRIPT_DIR=$(realpath $(dirname $0))
 set -a
 ARGS=$@
 . ${SCRIPT_DIR}/_build_getopts.sh ${ARGS}
 . ${SCRIPT_DIR}/set_compilers.sh
-# Get the OpenMP Libraries
-if [ $OS = "MacOSX" ]; then
-    ${SCRIPT_DIR}/get_lomp.sh ${ARGS}
-fi
+
 
 NPROC=$(nproc)
 
@@ -54,7 +50,6 @@ fi
 if [ ! -d ${DEPENDENCY_DIR}/hdfsrc ]; then
     curl -s -L https://github.com/HDFGroup/hdf5/releases/download/hdf5-${HDF5_VER}/hdf5-${HDF5_VER}.tar.gz | tar xvz -C ${DEPENDENCY_DIR}
 fi
-
 printf "\n"
 printf "*********************************************************\n"
 printf "*               BUILDING HDF5 LIBRARY                   *\n"
@@ -68,9 +63,6 @@ printf "LDFLAGS: ${LDFLAGS}\n"
 printf "*********************************************************\n"
 
 cd ${DEPENDENCY_DIR}/hdfsrc
-ZLIB_TGZ_NAME="zlib-${ZLIB_VER}.tar.gz"
-ZLIB_TGZ_ORIGPATH="https://github.com/madler/zlib/releases/download/v${ZLIB_VER}/"
-curl -L "https://github.com/HDFGroup/hdf5_plugins/archive/refs/tags/${PLUGIN_VER}.tar.gz" -o hdf5_plugins.tar.gz
 
 HDF5_ROOT=${PREFIX}
 ZLIB_ROOT=${PREFIX}
@@ -108,18 +100,6 @@ else
     sudo cmake --install build 
 fi
 
-# tar xvzf hdf5_plugins.tar.gz
-# PLUGIN_SOURCE=hdf5_plugins-${PLUGIN_VER}
-
-# BUILD_OPTIONS="-DTGZPATH:PATH=${PLUGIN_SOURCE}/libs -DH5PL_ALLOW_EXTERNAL_SUPPORT:STRING=\"TGZ\""
-# cmake -B ${PLUGIN_SOURCE}/build -C ${PLUGIN_SOURCE}/config/cmake/cacheinit.cmake -DCMAKE_BUILD_TYPE:STRING=Release ${BUILD_OPTIONS} -G Ninja ${PLUGIN_SOURCE}
-# cmake --build ${PLUGIN_SOURCE}/build -j${NPROC} --config Release
-# if [ -w ${PREFIX} ]; then
-#     cmake --install ${PLUGIN_SOURCE}/build 
-# else
-#     sudo cmake --install ${PLUGIN_SOURCE}/build 
-# fi
-
 if [ $? -ne 0 ]; then
    printf "hdf5 could not be compiled.\n"
    exit 1

buildscripts/build_netcdf-c.sh

@@ -15,10 +15,6 @@ set -a
 ARGS=$@
 . ${SCRIPT_DIR}/_build_getopts.sh ${ARGS}
 . ${SCRIPT_DIR}/set_compilers.sh
-# Get the OpenMP Libraries
-if [ $OS = "MacOSX" ]; then
-    ${SCRIPT_DIR}/get_lomp.sh ${ARGS}
-fi
 
 NPROC=$(nproc)
 

buildscripts/build_netcdf-fortran.sh

@@ -15,10 +15,6 @@ set -a
 ARGS=$@
 . ${SCRIPT_DIR}/_build_getopts.sh ${ARGS}
 . ${SCRIPT_DIR}/set_compilers.sh
-# Get the OpenMP Libraries
-if [ $OS = "MacOSX" ]; then
-    ${SCRIPT_DIR}/get_lomp.sh ${ARGS}
-fi
 
 NPROC=$(nproc)
 

buildscripts/build_zlib.sh

@@ -15,10 +15,6 @@ set -a
 ARGS=$@
 . ${SCRIPT_DIR}/_build_getopts.sh ${ARGS}
 . ${SCRIPT_DIR}/set_compilers.sh
-# Get the OpenMP Libraries
-if [ $OS = "MacOSX" ]; then
-    ${SCRIPT_DIR}/get_lomp.sh ${ARGS}
-fi
 
 NPROC=$(nproc)
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "swiftest"
-version = "2023.9.4"
+version = "2023.10.0"
 authors=[
     {name = 'David A. Minton', email='daminton@purdue.edu'},
     {name = 'Carlisle Wishard'},
@@ -30,8 +30,9 @@ dependencies = [
     'dask>=2022.1',
     'distributed>=2022.1',
     'bottleneck>=1.3.5',
-    'h5netcdf>=1.0.2',
-    'netcdf4>=1.6.2',
+    'h5netcdf',
+    'h5py',
+    'netcdf4',
     'matplotlib>=3.7.1',
     'astropy>=5.1',
     'astroquery>=0.4.6',
@@ -103,7 +104,7 @@ before-all = [
 ]
 
 [tool.cibuildwheel.linux]
-skip = "cp312-*"
+skip = "cp312-* pp* -manylinux_i686* *-musllinux*"
 before-all = [
     "yum install doxygen libxml2-devel libcurl-devel fftw-devel blas-devel lapack-devel -y",
     "buildscripts/build_dependencies.sh -p /usr/local"

src/globals/globals_module.f90

@@ -48,7 +48,7 @@ module globals
    integer(I4B), parameter :: UPPERCASE_OFFSET = iachar('A') - iachar('a') !! ASCII character set parameter for lower to upper 
                                                                            !! conversion - offset between upper and lower
 
-   character(*), parameter :: VERSION = "2023.9.4" !! Swiftest version
+   character(*), parameter :: VERSION = "2023.10.0" !! Swiftest version
 
    !> Symbolic name for integrator types
    character(*), parameter :: UNKNOWN_INTEGRATOR = "UKNOWN INTEGRATOR"

swiftest/simulation_class.py

@@ -412,15 +412,16 @@ def run(self,dask: bool = False, **kwargs):
         if len(kwargs) > 0:
             self.set_parameter(**kwargs)
 
-        # Write out the current parameter set before executing run
-        self.write_param()
-
         if self.codename != "Swiftest":
             warnings.warn(f"Running an integration is not yet supported for {self.codename}",stacklevel=2)
             return
 
+        # Save initial conditions
         if not self.restart:
             self.clean()
+
+        # Write out the current parameter set before executing run
+        self.write_param(verbose=False,**kwargs)
 
         print(f"Running a {self.codename} {self.integrator} run from tstart={self.param['TSTART']} {self.TU_name} to tstop={self.param['TSTOP']} {self.TU_name}")
 
@@ -2176,10 +2177,8 @@ def add_solar_system_body(self,
         dsnew = init_cond.vec2xr(self.param,**kwargs)
 
         dsnew = self._combine_and_fix_dsnew(dsnew)
-        if dsnew['npl'] > 0 or dsnew['ntp'] > 0:
+        if dsnew['id'].max(dim='name') > 0 and dsnew['name'].size > 0:
            self.save(verbose=False)
-
-
 
         self.init_cond = self.data.copy(deep=True)