Setup PR tests #5
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Add code to generate the docs. Additionally markdown files are added to the new `docs/` folder to provide more context to the development. Tests are added to the CI to ensure that future code is documented. Tests fail if a file is modified but does not have correct documentation, or if a new file is added to a folder which does not have a `README.md` file. GitHub action files are updated to use docker more intuitively. An additional action is added to build and push the docs to the documentation branch whenever something is pushed to the main branch of the GitHub repo. This will then be located here: https://gyselax.github.io/gyselalibxx/
In this PR a stage is added to the documentation compilation to call the script `ci_tools/readme_to_doxygen.py` which converts from GitHub/GitLab markdown syntax to Doxygen syntax. The page tags are generated automatically from the paths and inserted into Markdown references. This makes both the docs and the READMEs legible. It also removes the need for `About.md` which duplicated `README.md`. Additionally sub-sections are now correctly marked which fixes the indexing on the pages generated by Doxygen.
Add analytical invertible mapping class to access to the inverse mapping function and add inverse jacobian matrix in the Curvilinear2DToCartesian class.
Add `constexpr` functions which determine whether the points should be uniform or non-uniform. This allows the type of `IDimX` etc to be determined without the use of the `InterpPoints` class. This type is renamed to `SplineInterpPoints` to reflect the fact that it should be used to initialise the interpolation points when splines are used. When other methods (e.g. Lagrange) are used `IDimX` can be initialised using `ddc::init_discrete_space` with arguments describing the initialisation of the sampling.
Only generate subpage if folder is below referenced page in the hierarchy
Generalise `Quadrature` class to accept N dimensions. Add a helper function `quadrature_coeffs_nd` to return N-D coefficients from 1D functions defining the quadrature along each of the dimensions.
Now that the splines have been migrated to DDC, DDC's tests are quite slow. Gysela is the only place where these tests are run so they should not be removed completely, however currently DDC's tests are slowing down the pipeline dramatically. The following is an example of the times currently taken by an example pipeline: - cmake_tests : 13m - cmake_tests_Release : 16m - cmake_tests_Release_OMP : 19m - cmake_tests_Release_GPU : 38m This PR treats DDC in a similar way to SLL and the Polar Poisson solver and only runs these tests if the contents of the associated folder have been modified See merge request gysela-developpers/gyselalibxx!561 --------------------------------------------
Closes #270 See merge request gysela-developpers/gyselalibxx!559 --------------------------------------------
Adds realistic calculations for the reactions rates of neutrals for three processes: charge exchange, recombination and ionization. See merge request gysela-developpers/gyselalibxx!503 -------------------------------------------- Co-authored-by: Emily Bourne <[email protected]> Co-authored-by: Thomas Padioleau <[email protected]> Co-authored-by: Baptiste LEGOUIX <[email protected]>
An index is incorrectly named as though it were a discrete dimension See merge request gysela-developpers/gyselalibxx!560 --------------------------------------------
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