Ingmar Schoegl
7630316c7e
[base] Remove HighFive headers from Storage.h
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
417dcc9632
[base] Simplify SolutionArray data structure
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
f6cdcbc3dc
Address review comments
2023-01-12 14:05:37 -05:00
Ray Speth
f550faa477
[Python] Defer import of h5py until time of use
...
This avoids potential conflicts between the versions of libhdf5 linked
to the Cantera library and h5py, which could occur when a C++ main
application made use of the Python ExtensibleRate class.
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
0aca5f7004
[CI] Test HighFive installation routes
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
9ac0f05695
[UnitTest] Skip PythonExtensibleRate if HDF5 is used
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
90cb10802b
[samples] Remove Sim1D.write_hdf from Python samples
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
df3d6f96fc
[Python] Deprecate Sim1D.write_hdf
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
85efbc1bdd
Ensure HDF5 can be read by SolutionArray.read_hdf
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
f5dc973ee5
Implement HDF5 compression
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
c6aa334830
Refine HDF5 support infrastructure
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
54ee85742a
Isolate HighFive to Storage.h
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
4962c924f4
[samples] Update diffusion_flame_batch.py
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
3e48d46912
[UnitTest] Add test for restoring from HDF
...
Also test for backward compatibility for legacy implementations
and formats.
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
2d97dafbd9
Mark new features
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
88c306b472
Fix SolutionArray serialization for Boundary1D
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
84de1cf1d1
[base] Create Storage class to handle HDF files
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
169aa7e1a9
[SCons] Install HighFive submodule on demand
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
d9c576016c
[Python] Add methods to test pre-existing YAML converters
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
57e114128f
[base] Streamline SolutionArray
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
0df1f97f6a
[AnyMap] Add AnyMap::keys
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
8891d271cd
[oneD] Update properties for StFlow::restore
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
4c140a8625
[Base] Implement SolutionArray::writeEntry
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
bdfcbcf077
[OneD] Implement Domain::asArray converter
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
06a0436fa3
[base] Add SolutionArray::setState
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
7edf7c36f2
[base] Create hdfUtils.h
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
c64fd048e1
[OneD] Add alternative formats to Sim1D::save
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
d6ad4ec54f
[base] Implement SolutionArray::writeHeader
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
240f9bba19
[Python] Add utility to query HDF support
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
0d79adbfa6
[SCons] Add CPPDEFINE for HighFive on Windows
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
29fc674b6c
[OneD] Convert legacy HDF header to meta data
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
30d396649a
[base] Add SolutionArray::readHeader
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
b6950992c5
[OneD] integrate SolutionArray into Sim1D::restore
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
8a01efe3d7
[base] Augment C++ SolutionArray API
...
- Add setters/getters to SolutionArray
- Also remove unnecessary code stubs
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
6f9561f0d1
[base] Implement import of SolutionArray from HDF
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
74cba84658
[base] Implement import of SolutionArray from yaml
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
d8cbc41b05
[base] Add initial C++ SolutionArray implementation
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
23c2ada862
[base] Add tokenizePath utility
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
f51fb653c8
[OneD] Check groups and data size in HDF import file
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
6550238337
[CI] Add highfive HDF to workflows
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
a5327f37ca
Add basic C++ HighFive HDF infrastructure
2023-01-12 14:05:37 -05:00
Ingmar Schoegl
957dd2414b
[yaml2ck] Fix explicit third body reaction output
...
Prior to this fix, third body efficiencies were erroneously specified
for third body reactions with explicit collision partners (see #1415 ).
2023-01-04 09:07:29 -05:00
ssun30
2ce92eac2e
Fixed Matlab legacy examples and added missing blank lines.
...
Added Su Sun to AUTHORS.
2022-12-15 07:16:04 +01:00
ssun30
6042429d9f
Removed redundant error checks.
2022-12-10 06:53:36 -06:00
Ray Speth
7d86e26112
[CI] Make h5py optional for some builds
...
PyPI packages are not always available for the most recent Python version
on all platforms.
2022-11-21 09:00:30 -06:00
Ray Speth
e43cf38940
[CI] Use correct Python version on macOS
...
Linking to libpython with GitHub's Python 3.8 and 3.10 requires linking
to libintl, but no compatible version of this library is present in
the GitHub actions images (the Homebrew one has the wrong "macOS deployment
target"). This problem is fixed in GitHub's build of Python 3.11.
Scons 4.4.0 (and maybe other versions) can't be pip installed for the
Homebrew Python, since it tries to write man pages into an incorrect,
read-only directory.
The Homebrew-installed Python was never actually being used. All macOS
builds are done using Python cached in the GitHub actions image.
2022-11-21 09:00:30 -06:00
Ray Speth
b0932bb446
[CI] Test with Sundials 6.4.1
2022-11-21 09:00:30 -06:00
Ray Speth
fbe7e71b30
Resolve rename of Sundials bandGBTRF/S
...
The functions 'bandGBTRF' and 'bandGBTRS' were renamed in Sundials 6.0,
with the old names deprecated and slated for removal in Sundials 7.0. The
new names are 'SUNDlsMat_bandGBTRF' and 'SUNDlsMat_bandGBTRS'.
2022-11-21 09:00:30 -06:00
Ray Speth
f04d482223
Eliminate use of deprecated Py_SetProgramName function
2022-11-21 09:00:30 -06:00
Ray Speth
d5068c7f55
[CI] Test with Python 3.11
2022-11-21 09:00:30 -06:00
