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The pylint warnings, comments and remarks were deactivated to prevent pylint errors in MRs which hadn't changed Python files. This was occurring because pylint was updated and the new version added new patterns and removed old patterns (resulting in the configuration file raising warnings). This MR fixes that by pinning pylint to the most recent version (1.17.4). It also fixes the pylint errors which are newly flagged or have been introduced since the pylint warnings were hidden.
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/
Closes #251 See merge request gysela-developpers/gyselalibxx!530 --------------------------------------------
In order to handle patches derivatives will be needed at the boundaries of the domain. This MR introduces a structure to link values and derivatives of a field in one structure which fixes #224. DDC does not provide a sub-domain type. Such a type is important as `DiscreteElement`s are linked to coordinates and we want values on the same grid. This MR therefore implements a sub-domain type and stores data internally on mdspans instead of `ddc::Chunk`s. See merge request gysela-developpers/gyselalibxx!484 --------------------------------------------
Related to #229 See merge request gysela-developpers/gyselalibxx!533 --------------------------------------------
Related to #229 See merge request gysela-developpers/gyselalibxx!532 --------------------------------------------
Add LAPACKE to the docker generated by github. Necessary for the CI of !531 See merge request gysela-developpers/gyselalibxx!534 --------------------------------------------
Add an advection operator which can solve the following equation :
$\\partial_t f + A \\partial\_{x_i} f = 0$
The advection direction can be spatial or along the velocity dimension. We need to provide an advection field. The function \\( f \\) can be only on a full domain (with Species, Space and Velocity), on a space/velocity domain (Space and Velocity) or on a space domain (Space).
See merge request gysela-developpers/gyselalibxx!481
--------------------------------------------
Co-authored-by: Pauline Vidal <[email protected]>
Closes #255 See merge request gysela-developpers/gyselalibxx!538 --------------------------------------------
Fixes #207 See merge request gysela-developpers/gyselalibxx!539 --------------------------------------------
Closes #219 Add a guiding center in XY geometry for further tests on multipatch geometry. Any new operator to implement, only the simulation. Implementation on CPU in this branch. Maybe an update to GPU or it will be made in another branch. **New comment:** * Add a guiding center simulation on XY geometry with Kelvin-Helmholtz test case. * KelvinHelmholtzInstabilityInitialisation, PredCorrRK2XY operators implemented. * Add a geometryXY folder in source. * Simulation runs on CPU and GPU. * Add some python scripts for the diagnosis in a geometryXY/ folder. See merge request gysela-developpers/gyselalibxx!467 -------------------------------------------- Co-authored-by: Pauline Vidal <[email protected]>
Closes #261. * Add the option to use `device_t` on `VectorField` and `VectorFieldSpan` too. * Add a test `device_host_t.cpp` which tests `device_t` and `host_t` on Chunk, ChunkSpan, VectorField and VectorFieldSpan. * Fix a compilation error due to redeclaration of `deepcopy` in `vector_field_common.hpp` and `derivative_field.hpp`. See merge request gysela-developpers/gyselalibxx!542 -------------------------------------------- Co-authored-by: Pauline Vidal <[email protected]>
Unitary tests were not discovered by gtest and thus not run by the CI. The `neumann` test is also fixed as it was using the wrong memory and execution space for the spline builder. See merge request gysela-developpers/gyselalibxx!556 --------------------------------------------
Fixes #265 See merge request gysela-developpers/gyselalibxx!554 --------------------------------------------
There were a few minor issues in the READMEs making the docs harder to read. While fixing #267 I have cleaned these up. The issues were: - READMEs that were not linked to as described here: https://gyselax.github.io/gyselalibxx/docs_Adding_docs.html#docs_Adding_docs__Documentation_describing_general_methods leading to a large number of sections in the index tab - Fixes #267 - a bad link when an apostrophe is used in the section header - Bad links to classes only defined via template specialisation. This is fixed through the use of anchors - Python syntax used to comment markdown code in the collision documentation See merge request gysela-developpers/gyselalibxx!555 --------------------------------------------
- Add README in /geometryRTheta/geometry/ - Clean geometry file. - Use aliases for VectorFieldSpan. - Remove depencies on species_info.hpp. - Reorder some #include in advection test folder. See merge request gysela-developpers/gyselalibxx!558 -------------------------------------------- Co-authored-by: Pauline Vidal <[email protected]>
`fluid_masses` was defined on wrong domain in `species_init` See merge request gysela-developpers/gyselalibxx!557 --------------------------------------------
Add a spline builder on multipatch geometry. This builder calls the builders on each patch. It uses std::tuple. See merge request gysela-developpers/gyselalibxx!549 -------------------------------------------- Co-authored-by: Pauline Vidal <[email protected]>
* Splines LAPACK backend * `ddc::parallel_for_each` now can take a label! Usefull for profiling. * Align `UniformBSplines` API to `NonUniformBSplines` API * Change terminology in splines (ie. `spline_domain` -\> `batched_spline_domain`... complete list: CExA-project/ddc#382) * Ginkgo throws error in case of non-convergency. * Bsplines API is based on `mdspan` in place of `std::array`. * Deprecate `nbe_xmin` and `nbe_xmax` in splines (it is redundant with `nbc_xmin`and `nbc_xmax` for all boundary conditions except NATURAL which has been removed because unused). * Update supposedly-ddc-internal SplinesLinearProblem API (which is used by quadrature). * Lot of minor internal changes. See merge request gysela-developpers/gyselalibxx!548 -------------------------------------------- Co-authored-by: Emily Bourne <[email protected]>
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 --------------------------------------------
Test job on persee runner
add source .bash_profile
redirect output for module av
add the configured deployment environment to the runner
EmilyBourne
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Test job on persee runner