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Fix HDF5 OSX intermediate group creation errors #1741

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merged 3 commits into from
Mar 25, 2022
Merged

Fix HDF5 OSX intermediate group creation errors #1741

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cf88bcf
Fix HDF5 OSX intermediate group creation errors
dweindl Mar 25, 2022
40137f4
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dweindl Mar 25, 2022
177e804
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dweindl Mar 25, 2022
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7 changes: 2 additions & 5 deletions .github/workflows/test_pypi.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -31,11 +31,8 @@ jobs:
- name: homebrew
run: |
if [[ ${{ matrix.os }} == macos* ]] ; then \
brew install hdf5@1.10 swig gcc libomp \
&& echo "/usr/local/opt/hdf5@1.10/bin" >> $GITHUB_PATH \
&& echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/opt/hdf5@1.10/lib" >> $GITHUB_ENV \
&& echo CPPFLAGS="-I/usr/local/opt/hdf5@1.10/include" >> $GITHUB_ENV \
&& echo HDF5_BASE="/usr/local/opt/hdf5@1.10/" >> $GITHUB_ENV
brew install hdf5 swig gcc libomp \
&& echo LDFLAGS="-L/usr/local/lib/" >> $GITHUB_ENV
fi
- name: Set up Python ${{ matrix.python-version }}
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8 changes: 3 additions & 5 deletions .github/workflows/test_python_cplusplus.yml
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Expand Up @@ -152,13 +152,11 @@ jobs:
# install amici dependencies
- name: homebrew
run: |
brew install hdf5@1.10 swig gcc cppcheck libomp boost \
brew install hdf5 swig gcc cppcheck libomp boost \
&& brew ls -v boost \
&& brew ls -v libomp \
&& echo "/usr/local/opt/hdf5@1.10/bin" >> $GITHUB_PATH \
&& echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/opt/hdf5@1.10/lib -L/usr/local/Cellar/boost/1.78.0_1/lib/" >> $GITHUB_ENV \
&& echo CPPFLAGS="-I/usr/local/opt/hdf5@1.10/include -I/usr/local/Cellar/boost/1.78.0_1/include/" >> $GITHUB_ENV \
&& echo HDF5_BASE="/usr/local/opt/hdf5@1.10/" >> $GITHUB_ENV
&& echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/Cellar/boost/1.78.0_1/lib/" >> $GITHUB_ENV \
&& echo CPPFLAGS="-I/usr/local/Cellar/boost/1.78.0_1/include/" >> $GITHUB_ENV
- name: Build AMICI
run: |
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7 changes: 6 additions & 1 deletion src/hdf5.cpp
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Expand Up @@ -84,7 +84,11 @@ void checkEventDimensionsCompatible(hsize_t m, hsize_t n, Model const& model) {
void createGroup(H5::H5File const& file,
std::string const& groupPath,
bool recursively) {

#if H5_VERSION_GE(1, 10, 6)
H5::LinkCreatPropList lcpl;
lcpl.setCreateIntermediateGroup(recursively);
file.createGroup(groupPath.c_str(), lcpl);
#else
auto groupCreationPropertyList = H5P_DEFAULT;

if (recursively) {
Expand All @@ -101,6 +105,7 @@ void createGroup(H5::H5File const& file,
throw(AmiException("Failed to create group in hdf5CreateGroup: %s",
groupPath.c_str()));
H5Gclose(group);
#endif
}

std::unique_ptr<ExpData> readSimulationExpData(std::string const& hdf5Filename,
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