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https://github.com/tierra-colada/h5gt
HDF5 C++17 wrapper and includes python bindings. Aimed at developers who uses HDF5 in C++ and python project
https://github.com/tierra-colada/h5gt
cpp hdf5 header-only python
Last synced: 4 days ago
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HDF5 C++17 wrapper and includes python bindings. Aimed at developers who uses HDF5 in C++ and python project
- Host: GitHub
- URL: https://github.com/tierra-colada/h5gt
- Owner: tierra-colada
- License: bsl-1.0
- Created: 2021-03-09T22:13:02.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2024-05-12T10:09:14.000Z (9 months ago)
- Last Synced: 2024-11-19T07:22:50.409Z (2 months ago)
- Topics: cpp, hdf5, header-only, python
- Language: C++
- Homepage:
- Size: 2.6 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
[![][build-img]][build-status]
[![][docs-dev-img]][docs-dev-status]
C++ wrapper of [HDF5](https://www.hdfgroup.org/solutions/hdf5/) library based on [HighFive](https://github.com/BlueBrain/HighFive.git) project. It also includes python bindings **h5gtpy** that you can install with cmake.
**h5gtpy** doesn't provide `pip install` as it is inteded to be used only for projects that run on both C++ and python sides.
***h5gtpy** uses [pybind11](https://github.com/pybind/pybind11) to make python bindings and there may be some perfomance penalty when copying matrices from C++ `Eigen3` matrices to `numpy` (or `std::vector` to `py::list`). No perfomance testing were done.*
***This project is aimed at developers who uses C++ along with python. If you only need python HDF5 API you should better refer to [h5py](https://github.com/h5py/h5py) project.
That is why **h5gtpy** doesn't provide `pip install`***
## Documentation
Common documentation: [h5gt.readthedocs.io](https://h5gt.readthedocs.io/)
C++ API documentation: [tierra-colada.github.io/h5gt](https://tierra-colada.github.io/h5gt/)
## Building h5gt
As **h5gt** is header only library you don't need to buid it (but of course you can do that). See `src/examples` and `tests/unit` for usage examples.
## Building h5gtpy
To build with python support you need:
* set `H5GT_BUILD_h5gtpy` to `ON`
* provide python to cmake (I do it with `PYTHON_EXECUTABLE=/path/to/python.exe`)
* enable Eigen3 support `H5GT_USE_EIGEN=ON` (`Eigen3_ROOT` is enough to find eigen)
* specify `HDF5_RUNTIME_DIRS` containing HDF5-runtime (probably it is enough to have it in `PATH` env)
* **build HDF5 as SHARED C library**
i.e. configure it with:
```cmake
mkdir build
cd build
cmake ..
-DH5GT_BUILD_h5gtpy=ON
-DPYTHON_EXECUTABLE=/path/to/python.exe
-DH5GT_USE_EIGEN=ON
-DEigen3_ROOT=/path/to/eigen3
-DHDF5_DIR=/path/to/hdf5-config.cmake
-DHDF5_RUNTIME_DIRS=/path/to/hdf5-runtime
-DZLIB_RUNTIME_DIRS=/path/to/zlib-runtime
-DH5GTPY_COPY_RUNTIME_DEPS=OFF
cmake --build .
```
If your HDF5 depends on ZLIB or MPI you may also need to add it.
To run **h5gtpy** python must know where HDF5-runtime is. You may choose whether to copy HDF5-runtime to `site-packages/h5gtpy` dir or add this dir to path env (done automatically at installation step when `H5GTPY_COPY_RUNTIME_DEPS=OFF`).
## Installation h5gtpy
`h5gtpy` installation is done the same way one usually installs cmake project:
```cmake
cmake --install . --prefix /some/path --config Release`
```
Then you can find **h5gtpy** in `site-packages` of your python env.
**NOTE:** cmake tries to find runtime dependencies at `install` step. If there are unresolved or conflict dependencies then you need to modify `PATH` env, rerun `cmake ..` and `cmake --install . --prefix /some/path --config Release`. **You don't have to rebuild the project!**
## Usage
Importing is done via:
```python
from h5gtpy import h5gt
```
A test is also given in `site-packages/h5gtpy`.
To run test:
```python
python -m unittest discover h5gtpy.tests
```
## Integrating with VS Code
There is stub file `h5gtpy/h5gt.pyi`. You need to set VS Code setting `"python.analysis.stubPath": "some/relative/path/to/stub-storage"`: where `stub-storage` is supposed to contain folder `h5gtpy` with `h5gt.pyi` file.
I'm some kind of a uncomfortable to distribute stub file, so to be sure that stub file is updated you can generate your own stub file:
```shell
pip install pybind11-stubgen
pybind11-stubgen --no-setup-py h5gtpy._h5gt
```
## Integrating with PyCharm
You don't need to provide stub file to PyCharm as it handles this by its own.
## Supported HDF5 versions
1.10, 1.12 (recommended)
## Supported platforms
Windows 10, Linux, OSX
[build-img]:https://img.shields.io/travis/com/tierra-colada/h5gt?style=plastic
[build-status]:https://app.travis-ci.com/tierra-colada/h5gt
[docs-dev-img]:https://img.shields.io/badge/docs-dev-blue.svg?style=plastic
[docs-dev-status]:https://h5gt.readthedocs.io/en/latest/?badge=latest