Support Python 3.13 #475
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Support Python 3.13 #475
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Unfortunately Psydac requires mpi4py version < 4, which is not compatible with Python 3.13. See issue #420. |
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Currently blocked by issue #420. |
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After PR #478 there is no blocking issue for using Python 3.13. There is however an installation error for @max-models Could you maybe have a look at the error? |
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@max-models I suspect the problem is with Cython. We are currently installing an old version (0.29.37) which is probably not compatible with CPython 3.13 |
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* Support Python 3.13 (pyccel#475) Closes pyccel#476: * Do not restrict the maximum Python version to 3.12 in `pyproject.toml` * Require `Cython >= 3` to avoid `h5py` installation crash w/ Python 3.13 * Require `sympde == 0.19.2` which supports Python 3.13 * Run unit tests with Python 3.13 too * Trigger CI * Install struphy from devel in CI --------- Co-authored-by: Yaman Güçlü <[email protected]>
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* fix bug gmres (pyccel#452) Solves issue pyccel#451. * CI Updates: Code coverage report, Ubuntu 24.04, PETSc 3.22 (pyccel#443) Summary of changes: - Integrate Codacy reporting - Lock runner versions to `ubuntu-24.04` and `macos-14`. The [`*-latest` runner versions](https://github.com/actions/runner-images#available-images) are moving targets; we wish to avoid surprise failing tests caused by runner upgrades (e.g. see [macOS issue](pyccel#421) from last year) . - Upgrade PETSc to [v3.22](https://petsc.org/release/changes/322/). * Expose inter-/histopolation matrices in GlobalProjector, add unit tests (pyccel#347) Fixes pyccel#346. The inter-/histopolation matrices are now exposed in `GlobalProjector.imat_kronecker` as a `LinearOperator` object of type `KroneckerStencilMatrix` (in the case where both domain and codomain are scalar spaces) or `BlockLinearOperator` (in the case where at least one space is vector valued). The unit tests in `feec/tests/test_commuting_projections.py` have been enhanced: they now also test how close `imat_kronecker` is to being the right-inverse of the `solver`attribute (which uses a Kronecker product of 1D linear solvers). --------- Co-authored-by: Yaman Güçlü <[email protected]> Co-authored-by: Max Lindqvist <[email protected]> Co-authored-by: Martin Campos Pinto <[email protected]> * Avoid installing h5py from cache (pyccel#430) Add the flag `--no-cache-dir` to `pip` in order to guarantee that `h5py` is always built during installation. See: - https://stackoverflow.com/questions/45594707/what-is-pips-no-cache-dir-good-for; - https://docs.h5py.org/en/stable/build.html#custom-installation. Re-using a prebuilt `h5py` (*i.e.* cached `h5py`) could become an issue when `h5py` dependencies upgrade. For example, If people have a cached version of the h5py library which was compiled using NumPy < 2.0 and try to install Psydac in a clean Python environment, they end up with a broken version. This is because the cached version of h5py tries to call C functions from NumPy 2.0 which are not ABI compatible. --------- Co-authored-by: Yaman Güçlü <[email protected]> * Allow keyword parameters in the dot method of `MatrixFreeLinearOperator` (pyccel#456) Allow the creation of a `MatrixFreeLinearOperator` object with a dot function that takes multiple keyword arguments, as for instance function parameters. * Small fixes for operators with complex (pyccel#455) - Make `ScaledLinearOperator` work with a complex scalar; - Take real part of `r.dot(r)` to avoid complex warning in `sqrt`; - Add unit test. * Fix Greville point collocation matrix for single grid point case (pyccel#446) Previously, in the case when `self.greville.size == 1`, `collocation_matrix` would return an empty matrix. Now, if the grid has a single Greville point, the collocation matrix is simplified to a 1x1 matrix with a value of 1. * Use SymPDE version 0.19.1 (pyccel#445) Update Psydac after the breaking change introduced by version 0.19.1 of SymPDE: domain coordinates are real symbols. Further, the new version is needed in order to solve pyccel#457. --------- Co-authored-by: Elena Moral Sánchez <[email protected]> * Improve FEM API (names, properties, constructors...) & plot_field() (pyccel#468) Improve the FEM API to make it more user-friendly and compatible between single-patch and multi-patch APIs (fix pyccel#459 and fix pyccel#460): * Rename abstract property `vector_space` of `FemSpace` as `coeff_space` * Rename `ProductFemSpace` as `MultipatchFemSpace` * Do not use class constructors as factories (previously `ProductFemSpace()` could return a `VectorFemSpace` object) * Provide more specific helper properties for FEM spaces, such as - `is_vector_valued` and `is_multipatch` (also remove a method `is_scalar` which was implemented in _some_ FEM spaces but not used) - `patch_spaces`, `component_spaces` and `axis_spaces` which always return tuples of Fem spaces (or an error) * Provide more specific helper properties for FEM fields, such as - `component_fields` and `patch_fields` and `axis_fields` which always return tuples of FEM fields (or an error) * Improve the `VectorFemSpace` class (in particular its constructor) to better match the `FemSpace` abstract interface. Since these changes are also motivated by a better compatibility between single-patch and multi-patch APIs (see issue pyccel#331), this PR also modifies the `plot_field` function (previously in `psydac.feec.multipatch.plotting_utilities`), which is: * made compatible with single patch and multi patch fields * renamed as `plot_field_2d` since it only handles 2d fields * tested (not the content but the runs) in single and multipatch configurations for scalar and vector-valued FEM fields * moved with its module `psydac.feec.multipatch.plotting_utilities` to `psydac.fem.plotting_utilities` since it is not specific to FEEC or multipatch. --------- Co-authored-by: Yaman Güçlü <[email protected]> * Enable mpi4py 4.0 (pyccel#478) Closes pyccel#420. Fix usage of function `Translate_ranks` which had non-backward-compatible changes in mpi4py version 4.0: https://mpi4py.readthedocs.io/en/stable/changes.html. --------- Co-authored-by: Stefan Possanner <[email protected]> Co-authored-by: Max Lindqvist <[email protected]> Co-authored-by: Yaman Güçlü <[email protected]> * Removed dependency <4 for mpi4py * Set ubuntu-latest and macos-14 in pyproject.toml * Removed parallel hdf5 * Install struphy from rename-vector_space-to_coeff_space in CI * Removed python 3.13 from the CI * 3.13 --> 3.12 for macos CI * Removed Run MPI tests with Pytest * Removed codacy * Support Python 3.13 (pyccel#475) Closes pyccel#476: * Do not restrict the maximum Python version to 3.12 in `pyproject.toml` * Require `Cython >= 3` to avoid `h5py` installation crash w/ Python 3.13 * Require `sympde == 0.19.2` which supports Python 3.13 * Run unit tests with Python 3.13 too * Added Set up environment variables * Commented out macos tests * Install struphy from devel branch --------- Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: Paul Rigor <[email protected]> Co-authored-by: Stefan Possanner <[email protected]> Co-authored-by: Yaman Güçlü <[email protected]> Co-authored-by: Martin Campos Pinto <[email protected]> Co-authored-by: Stefan Possanner <[email protected]>
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Apr 11, 2025
* Support Python 3.13 (pyccel#475) Closes pyccel#476: * Do not restrict the maximum Python version to 3.12 in `pyproject.toml` * Require `Cython >= 3` to avoid `h5py` installation crash w/ Python 3.13 * Require `sympde == 0.19.2` which supports Python 3.13 * Run unit tests with Python 3.13 too * Fix PSYDAC_BACKEND_GPYCCEL flags on latest Apple silicon (pyccel#480) Currently, Psydac can not be used on Apple M4 computers since the `PSYDAC_BACKEND_GPYCCEL['flags']` is not set correctly. This change sets the flag for `Apple MX (etc.)` to `apple-mX`, which should work so long as the naming scheme stays unchanged. In addition, the regular expression used to find the GFortran version is now defined in a raw string instead of a standard Python UTF8 string. This avoids a `SyntaxWarning: invalid escape sequence`. --------- Co-authored-by: Yaman Güçlü <[email protected]> * from pyccel.commands.epyccel import epyccel * from pyccel.commands.epyccel import epyccel * Reinstall pyccel devel * Require Pyccel devel branch in pyproject.toml * Try another syntax in pyproject.toml * Comment out changes to continuous-integration.yml * Remove commented lines from continuous-integration.yml * Trigger CI * import epyccel correctly in test_epyccel_flags.py * Resolve warnings in sequential unit tests (pyccel#481) * Use raw strings for docstrings with LaTeX to avoid UTF8 syntax warnings on escape sequences; * Use CSC matrices to avoid SciPy sparse solver warning. We do not address the NumPy warnings which arise in our MPI unit tests (see pyccel#353). * Update axpy_kernels.py * undo type change in kernel * small bugfix * Added r before a docstring * Fixed stencil2IJV_kernels.py so it can be compiled with C * Removed blank line * Run CI with both C and fortran * Temporary: install struphy from test-pyccel-devel-in-ci * Added matrix.compile_language to the test job name * Trigger CI * Added a compile-with-pyccel-devel job which just compiles the code with pyccel devel (no testing) * Reset the pyccel version to pyccel >= 1.11.2 (from pypi) * Updated the job name * Updated the job name * Updated the job name --------- Co-authored-by: Yaman Güçlü <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: e-moral-sanchez <[email protected]>
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* Support Python 3.13 (pyccel#475) Closes pyccel#476: * Do not restrict the maximum Python version to 3.12 in `pyproject.toml` * Require `Cython >= 3` to avoid `h5py` installation crash w/ Python 3.13 * Require `sympde == 0.19.2` which supports Python 3.13 * Run unit tests with Python 3.13 too * Fix PSYDAC_BACKEND_GPYCCEL flags on latest Apple silicon (pyccel#480) Currently, Psydac can not be used on Apple M4 computers since the `PSYDAC_BACKEND_GPYCCEL['flags']` is not set correctly. This change sets the flag for `Apple MX (etc.)` to `apple-mX`, which should work so long as the naming scheme stays unchanged. In addition, the regular expression used to find the GFortran version is now defined in a raw string instead of a standard Python UTF8 string. This avoids a `SyntaxWarning: invalid escape sequence`. --------- Co-authored-by: Yaman Güçlü <[email protected]> * Resolve warnings in sequential unit tests (pyccel#481) * Use raw strings for docstrings with LaTeX to avoid UTF8 syntax warnings on escape sequences; * Use CSC matrices to avoid SciPy sparse solver warning. We do not address the NumPy warnings which arise in our MPI unit tests (see pyccel#353). * Pass `out` parameter to `petsc_to_psydac` (pyccel#483) * Rename `dot` as `inner` in `Vector`, `VectorSpace`, and subclasses (pyccel#484) Main changes -------------- * Rename the method `dot` of the base class `VectorSpace` as `inner`, and make it an abstract method (which must be implemented by the subclasses). * Rename the method `dot` of the base class `Vector` as `inner`. This is a concrete method which calls `self.space.inner` and does not need to be overridden by the subclasses. * Add `inner` methods to the classes `StencilVector`, `BlockVectorSpace`, and `DenseVectorSpace`. These methods override the abstract method of the base class as required, and are derived from the former functions `Stencil.dot`, `BlockVector.dot`, and `DenseVector.dot`, which have been removed (see next point). * Remove the property `dtype` and the method `dot` (now `inner`) from the classes `StencilVector`, `BlockVector`, and `DenseVector`, because the default methods of the base class already provide a sufficient implementation. This fixes pyccel#330. Necessary additional changes ------------------------------ * Update all linear solvers in `linalg.solvers` with the new method calls; * Update all unit tests with the new method calls, in files: - `api/tests/test_assembly.py` - `feec/tests/test_commuting_projections.py` - `feec/tests/test_global_projectors.py` - `linalg/tests/test_block.py` - `linalg/tests/test_linalg.py` - `linalg/tests/test_stencil_interface_matrix.py` - `linalg/tests/test_stencil_vector.py` Unrelated additional changes ----------------------------- * Rename the class `VectorDot` as `VectorInner` in module `api.ast.linalg`, although never used in Psydac. * Speed up 3D unit tests in: - `feec/tests/test_commuting_projectors.py` - `feec/tests/test_global_projectors.py` * Update docstring for inner product in polar/dense.py (pyccel#488) --------- Co-authored-by: Yaman Güçlü <[email protected]> * Add a `dot_inner` concrete method to the base class `LinearOperator` (pyccel#493) Implement `M.dot(u).inner(v)`, or `(M @ u).inner(v)`, without creating a temporary vector. The result of the dot product is written to a local work vector stored in the `LinearOperator` object. This work vector is then used to compute the inner product with the vector `v`. The subclasses do not need to override this method, unless a more efficient implementation which avoids writing to the work vector altogether (reducing memory pressure) is needed. A unit test is added: function `test_dot_inner` in file psydac/linalg/tests/test_linalg.py. Additionally, the helper function `get_StencilVectorSpace` defined in psydac/linalg/tests/test_linalg.py (only used in the same file and in test_matrix_free.py) has a new signature and now works in any number of dimensions. Fixes pyccel#491. * Install PETSc-3.23.2 (latest version) (pyccel#499) * Update authors (pyccel#500) * Trigger CI --------- Co-authored-by: Yaman Güçlü <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: Martin Campos Pinto <[email protected]>
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Jun 25, 2025
* Support Python 3.13 (pyccel#475) Closes pyccel#476: * Do not restrict the maximum Python version to 3.12 in `pyproject.toml` * Require `Cython >= 3` to avoid `h5py` installation crash w/ Python 3.13 * Require `sympde == 0.19.2` which supports Python 3.13 * Run unit tests with Python 3.13 too * Fix PSYDAC_BACKEND_GPYCCEL flags on latest Apple silicon (pyccel#480) Currently, Psydac can not be used on Apple M4 computers since the `PSYDAC_BACKEND_GPYCCEL['flags']` is not set correctly. This change sets the flag for `Apple MX (etc.)` to `apple-mX`, which should work so long as the naming scheme stays unchanged. In addition, the regular expression used to find the GFortran version is now defined in a raw string instead of a standard Python UTF8 string. This avoids a `SyntaxWarning: invalid escape sequence`. --------- Co-authored-by: Yaman Güçlü <[email protected]> * from pyccel.commands.epyccel import epyccel * from pyccel.commands.epyccel import epyccel * Reinstall pyccel devel * Require Pyccel devel branch in pyproject.toml * Try another syntax in pyproject.toml * Comment out changes to continuous-integration.yml * Remove commented lines from continuous-integration.yml * Trigger CI * import epyccel correctly in test_epyccel_flags.py * Resolve warnings in sequential unit tests (pyccel#481) * Use raw strings for docstrings with LaTeX to avoid UTF8 syntax warnings on escape sequences; * Use CSC matrices to avoid SciPy sparse solver warning. We do not address the NumPy warnings which arise in our MPI unit tests (see pyccel#353). * Update axpy_kernels.py * undo type change in kernel * Pass `out` parameter to `petsc_to_psydac` (pyccel#483) * Rename `dot` as `inner` in `Vector`, `VectorSpace`, and subclasses (pyccel#484) Main changes -------------- * Rename the method `dot` of the base class `VectorSpace` as `inner`, and make it an abstract method (which must be implemented by the subclasses). * Rename the method `dot` of the base class `Vector` as `inner`. This is a concrete method which calls `self.space.inner` and does not need to be overridden by the subclasses. * Add `inner` methods to the classes `StencilVector`, `BlockVectorSpace`, and `DenseVectorSpace`. These methods override the abstract method of the base class as required, and are derived from the former functions `Stencil.dot`, `BlockVector.dot`, and `DenseVector.dot`, which have been removed (see next point). * Remove the property `dtype` and the method `dot` (now `inner`) from the classes `StencilVector`, `BlockVector`, and `DenseVector`, because the default methods of the base class already provide a sufficient implementation. This fixes pyccel#330. Necessary additional changes ------------------------------ * Update all linear solvers in `linalg.solvers` with the new method calls; * Update all unit tests with the new method calls, in files: - `api/tests/test_assembly.py` - `feec/tests/test_commuting_projections.py` - `feec/tests/test_global_projectors.py` - `linalg/tests/test_block.py` - `linalg/tests/test_linalg.py` - `linalg/tests/test_stencil_interface_matrix.py` - `linalg/tests/test_stencil_vector.py` Unrelated additional changes ----------------------------- * Rename the class `VectorDot` as `VectorInner` in module `api.ast.linalg`, although never used in Psydac. * Speed up 3D unit tests in: - `feec/tests/test_commuting_projectors.py` - `feec/tests/test_global_projectors.py` * Update docstring for inner product in polar/dense.py (pyccel#488) --------- Co-authored-by: Yaman Güçlü <[email protected]> * Add a `dot_inner` concrete method to the base class `LinearOperator` (pyccel#493) Implement `M.dot(u).inner(v)`, or `(M @ u).inner(v)`, without creating a temporary vector. The result of the dot product is written to a local work vector stored in the `LinearOperator` object. This work vector is then used to compute the inner product with the vector `v`. The subclasses do not need to override this method, unless a more efficient implementation which avoids writing to the work vector altogether (reducing memory pressure) is needed. A unit test is added: function `test_dot_inner` in file psydac/linalg/tests/test_linalg.py. Additionally, the helper function `get_StencilVectorSpace` defined in psydac/linalg/tests/test_linalg.py (only used in the same file and in test_matrix_free.py) has a new signature and now works in any number of dimensions. Fixes pyccel#491. * Install PETSc-3.23.2 (latest version) (pyccel#499) * Update authors (pyccel#500) * Removed all template decorators * Removed the @template pyccel decorator since it has been deprecated * Added T as a T = TypeVar('T', float, complex) * Added T as a T = TypeVar('T', float, complex) * Fixed missing typevar in stencil2IJV_kernels.py * Added TypeVar('T', float, complex) to field_evaluation_kernels.py * Added TypeVar('T', float, complex) to field_evaluation_kernels.py * T-->T[:] * Corrected the shape of T * Correction * T --> T[:], T[:,:], ... * Correction * Make a const in psydac/core/bsplines_kernels.py * Use h5py < 3.14.0 * Revert h5py version restriction * Pin h5py to 3.13.0 to avoid the PEP 621 error (project license) * bugfix * Set license to MIT * revert h5py specification * Set h5py to 3.13.0 * Fix the code generation of unnecessary derivatives (pyccel#490) This PR changes the code generation involved in the `discretize` function to avoid calculating unnecessary derivatives. This allows for using constant spline (degree 0) discretizations, for which we have to make a special case in the calculation of ghost regions in `psydac/linalg/stencil.py`. Additionally, we add basic unit tests checking discretizations using zero-degree splines. This fixes pyccel#489 and fixes pyccel#307. On this occasion, we also do small changes in the `.github/workflows/testing.yml` script as some tests had complications without them. --------- Co-authored-by: Yaman Güçlü <[email protected]> * Replaced const with Final * Renamed compiler to compiler-family * Added compiler_config * libdir --> libdirs * libdirs --> libdir * Removed return from merge_sort * Trigger CI * Set pyccel version to >= 2.0 * Set pyccel >= 2.0 in pyproject.toml * Renamed compiler to compiler_family * renamed fflags to flags for epyccel arguments * Replace accelerators with openmp (True or False) * Bugfix in pyproject.toml * Removed merge conflicts * Updated ci * Skip the h5py installation test * Skip the h5py installation test * remove psydac pyccelized kernels before uninstalling * Moved struphy tests to a separate job * Renamed jobs to be more clear * Moved the shape check out of matmul in bsplines_kernels.py, this can't stay because STL doesn't allow for shape 0 arrays. Now we only call the matmul kernel if the shape is not 0, otherwise c[:] = 0.0 * Define sh_a and sh_b before the loops * Only do the loops in basis_funs_p if degree > 0 since we otherwise create arrays of size 0 * Trigger CI --------- Co-authored-by: Yaman Güçlü <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: e-moral-sanchez <[email protected]> Co-authored-by: Martin Campos Pinto <[email protected]> Co-authored-by: Frederik Schnack <[email protected]>
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* Support Python 3.13 (pyccel#475) Closes pyccel#476: * Do not restrict the maximum Python version to 3.12 in `pyproject.toml` * Require `Cython >= 3` to avoid `h5py` installation crash w/ Python 3.13 * Require `sympde == 0.19.2` which supports Python 3.13 * Run unit tests with Python 3.13 too * Fix PSYDAC_BACKEND_GPYCCEL flags on latest Apple silicon (pyccel#480) Currently, Psydac can not be used on Apple M4 computers since the `PSYDAC_BACKEND_GPYCCEL['flags']` is not set correctly. This change sets the flag for `Apple MX (etc.)` to `apple-mX`, which should work so long as the naming scheme stays unchanged. In addition, the regular expression used to find the GFortran version is now defined in a raw string instead of a standard Python UTF8 string. This avoids a `SyntaxWarning: invalid escape sequence`. --------- Co-authored-by: Yaman Güçlü <[email protected]> * Resolve warnings in sequential unit tests (pyccel#481) * Use raw strings for docstrings with LaTeX to avoid UTF8 syntax warnings on escape sequences; * Use CSC matrices to avoid SciPy sparse solver warning. We do not address the NumPy warnings which arise in our MPI unit tests (see pyccel#353). * Pass `out` parameter to `petsc_to_psydac` (pyccel#483) * Rename `dot` as `inner` in `Vector`, `VectorSpace`, and subclasses (pyccel#484) Main changes -------------- * Rename the method `dot` of the base class `VectorSpace` as `inner`, and make it an abstract method (which must be implemented by the subclasses). * Rename the method `dot` of the base class `Vector` as `inner`. This is a concrete method which calls `self.space.inner` and does not need to be overridden by the subclasses. * Add `inner` methods to the classes `StencilVector`, `BlockVectorSpace`, and `DenseVectorSpace`. These methods override the abstract method of the base class as required, and are derived from the former functions `Stencil.dot`, `BlockVector.dot`, and `DenseVector.dot`, which have been removed (see next point). * Remove the property `dtype` and the method `dot` (now `inner`) from the classes `StencilVector`, `BlockVector`, and `DenseVector`, because the default methods of the base class already provide a sufficient implementation. This fixes pyccel#330. Necessary additional changes ------------------------------ * Update all linear solvers in `linalg.solvers` with the new method calls; * Update all unit tests with the new method calls, in files: - `api/tests/test_assembly.py` - `feec/tests/test_commuting_projections.py` - `feec/tests/test_global_projectors.py` - `linalg/tests/test_block.py` - `linalg/tests/test_linalg.py` - `linalg/tests/test_stencil_interface_matrix.py` - `linalg/tests/test_stencil_vector.py` Unrelated additional changes ----------------------------- * Rename the class `VectorDot` as `VectorInner` in module `api.ast.linalg`, although never used in Psydac. * Speed up 3D unit tests in: - `feec/tests/test_commuting_projectors.py` - `feec/tests/test_global_projectors.py` * Update docstring for inner product in polar/dense.py (pyccel#488) --------- Co-authored-by: Yaman Güçlü <[email protected]> * Add a `dot_inner` concrete method to the base class `LinearOperator` (pyccel#493) Implement `M.dot(u).inner(v)`, or `(M @ u).inner(v)`, without creating a temporary vector. The result of the dot product is written to a local work vector stored in the `LinearOperator` object. This work vector is then used to compute the inner product with the vector `v`. The subclasses do not need to override this method, unless a more efficient implementation which avoids writing to the work vector altogether (reducing memory pressure) is needed. A unit test is added: function `test_dot_inner` in file psydac/linalg/tests/test_linalg.py. Additionally, the helper function `get_StencilVectorSpace` defined in psydac/linalg/tests/test_linalg.py (only used in the same file and in test_matrix_free.py) has a new signature and now works in any number of dimensions. Fixes pyccel#491. * Install PETSc-3.23.2 (latest version) (pyccel#499) * Update authors (pyccel#500) * Fix the code generation of unnecessary derivatives (pyccel#490) This PR changes the code generation involved in the `discretize` function to avoid calculating unnecessary derivatives. This allows for using constant spline (degree 0) discretizations, for which we have to make a special case in the calculation of ghost regions in `psydac/linalg/stencil.py`. Additionally, we add basic unit tests checking discretizations using zero-degree splines. This fixes pyccel#489 and fixes pyccel#307. On this occasion, we also do small changes in the `.github/workflows/testing.yml` script as some tests had complications without them. --------- Co-authored-by: Yaman Güçlü <[email protected]> * Fix bug in `allocate_matrices` in `DiscreteBilinearForm` (pyccel#507) Always use the maximum padding between test and trial spaces in `allocate_matrices` in `DiscreteBilinearForm`. (Earlier this was not done in the case of scalar spaces.) Fixes pyccel#504. * Enable Pyccel 2.0 (pyccel#503) Pyccel 2.0 was just released, which means some of the kernels in Psydac need to be updated: - Remove the `template` decorator (see pyccel/pyccel#2331) * Add `T` as `TypeVar` * Specify `T`, `T[:]`, `T[:,:]`, ... in function arguments. - Replace `@types` decorators (see pyccel/pyccel#2329) - Replace `const` with `Final` (see pyccel/pyccel#2340) Further changes: - Update import path for `epyccel` (fixes pyccel#426) - Update arguments to `epyccel` (see pyccel/pyccel#2348): * Rename `fflags` to `flags` * Replace `accelerators` list with `openmp` bool - Require Pyccel >= 2.0.1 (fixes pyccel#471) --------- Co-authored-by: Yaman Güçlü <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: Emily Bourne <[email protected]> * install struphy from devel in testing * add gvec non-python dependencies --------- Co-authored-by: Yaman Güçlü <[email protected]> Co-authored-by: Max <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: Martin Campos Pinto <[email protected]> Co-authored-by: Frederik Schnack <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: Emily Bourne <[email protected]>
max-models
added a commit
to struphy-hub/psydac-for-struphy
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Sep 3, 2025
* Support Python 3.13 (pyccel#475) Closes pyccel#476: * Do not restrict the maximum Python version to 3.12 in `pyproject.toml` * Require `Cython >= 3` to avoid `h5py` installation crash w/ Python 3.13 * Require `sympde == 0.19.2` which supports Python 3.13 * Run unit tests with Python 3.13 too * Fix PSYDAC_BACKEND_GPYCCEL flags on latest Apple silicon (pyccel#480) Currently, Psydac can not be used on Apple M4 computers since the `PSYDAC_BACKEND_GPYCCEL['flags']` is not set correctly. This change sets the flag for `Apple MX (etc.)` to `apple-mX`, which should work so long as the naming scheme stays unchanged. In addition, the regular expression used to find the GFortran version is now defined in a raw string instead of a standard Python UTF8 string. This avoids a `SyntaxWarning: invalid escape sequence`. --------- Co-authored-by: Yaman Güçlü <[email protected]> * Resolve warnings in sequential unit tests (pyccel#481) * Use raw strings for docstrings with LaTeX to avoid UTF8 syntax warnings on escape sequences; * Use CSC matrices to avoid SciPy sparse solver warning. We do not address the NumPy warnings which arise in our MPI unit tests (see pyccel#353). * Pass `out` parameter to `petsc_to_psydac` (pyccel#483) * Rename `dot` as `inner` in `Vector`, `VectorSpace`, and subclasses (pyccel#484) Main changes -------------- * Rename the method `dot` of the base class `VectorSpace` as `inner`, and make it an abstract method (which must be implemented by the subclasses). * Rename the method `dot` of the base class `Vector` as `inner`. This is a concrete method which calls `self.space.inner` and does not need to be overridden by the subclasses. * Add `inner` methods to the classes `StencilVector`, `BlockVectorSpace`, and `DenseVectorSpace`. These methods override the abstract method of the base class as required, and are derived from the former functions `Stencil.dot`, `BlockVector.dot`, and `DenseVector.dot`, which have been removed (see next point). * Remove the property `dtype` and the method `dot` (now `inner`) from the classes `StencilVector`, `BlockVector`, and `DenseVector`, because the default methods of the base class already provide a sufficient implementation. This fixes pyccel#330. Necessary additional changes ------------------------------ * Update all linear solvers in `linalg.solvers` with the new method calls; * Update all unit tests with the new method calls, in files: - `api/tests/test_assembly.py` - `feec/tests/test_commuting_projections.py` - `feec/tests/test_global_projectors.py` - `linalg/tests/test_block.py` - `linalg/tests/test_linalg.py` - `linalg/tests/test_stencil_interface_matrix.py` - `linalg/tests/test_stencil_vector.py` Unrelated additional changes ----------------------------- * Rename the class `VectorDot` as `VectorInner` in module `api.ast.linalg`, although never used in Psydac. * Speed up 3D unit tests in: - `feec/tests/test_commuting_projectors.py` - `feec/tests/test_global_projectors.py` * Update docstring for inner product in polar/dense.py (pyccel#488) --------- Co-authored-by: Yaman Güçlü <[email protected]> * Add a `dot_inner` concrete method to the base class `LinearOperator` (pyccel#493) Implement `M.dot(u).inner(v)`, or `(M @ u).inner(v)`, without creating a temporary vector. The result of the dot product is written to a local work vector stored in the `LinearOperator` object. This work vector is then used to compute the inner product with the vector `v`. The subclasses do not need to override this method, unless a more efficient implementation which avoids writing to the work vector altogether (reducing memory pressure) is needed. A unit test is added: function `test_dot_inner` in file psydac/linalg/tests/test_linalg.py. Additionally, the helper function `get_StencilVectorSpace` defined in psydac/linalg/tests/test_linalg.py (only used in the same file and in test_matrix_free.py) has a new signature and now works in any number of dimensions. Fixes pyccel#491. * Install PETSc-3.23.2 (latest version) (pyccel#499) * Update authors (pyccel#500) * Fix the code generation of unnecessary derivatives (pyccel#490) This PR changes the code generation involved in the `discretize` function to avoid calculating unnecessary derivatives. This allows for using constant spline (degree 0) discretizations, for which we have to make a special case in the calculation of ghost regions in `psydac/linalg/stencil.py`. Additionally, we add basic unit tests checking discretizations using zero-degree splines. This fixes pyccel#489 and fixes pyccel#307. On this occasion, we also do small changes in the `.github/workflows/testing.yml` script as some tests had complications without them. --------- Co-authored-by: Yaman Güçlü <[email protected]> * Fix bug in `allocate_matrices` in `DiscreteBilinearForm` (pyccel#507) Always use the maximum padding between test and trial spaces in `allocate_matrices` in `DiscreteBilinearForm`. (Earlier this was not done in the case of scalar spaces.) Fixes pyccel#504. * Enable Pyccel 2.0 (pyccel#503) Pyccel 2.0 was just released, which means some of the kernels in Psydac need to be updated: - Remove the `template` decorator (see pyccel/pyccel#2331) * Add `T` as `TypeVar` * Specify `T`, `T[:]`, `T[:,:]`, ... in function arguments. - Replace `@types` decorators (see pyccel/pyccel#2329) - Replace `const` with `Final` (see pyccel/pyccel#2340) Further changes: - Update import path for `epyccel` (fixes pyccel#426) - Update arguments to `epyccel` (see pyccel/pyccel#2348): * Rename `fflags` to `flags` * Replace `accelerators` list with `openmp` bool - Require Pyccel >= 2.0.1 (fixes pyccel#471) --------- Co-authored-by: Yaman Güçlü <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: Emily Bourne <[email protected]> * New installation procedure and README (pyccel#510) Recently the installation of `h5py` in parallel mode (i.e. with MPI support through `mpi4py`) seems to have been simplified. This may be due to the recent move of `mpi4py` to wheels, or other factors. Therefore we can now simplify our installation procedure as follows: ```sh pip install h5py --no-cache-dir --no-binary h5py pip install .[test] ``` We update here the CI workflows and completely rewrite our README file. **Commit summary** - Completely rewrite `README.md`: * Expand initial description * Add Citing and Contributing sections * Shorten Installation section * Reorganize documentation sections * Move detailed installation instructions to separate file `docs/installation.md` * Move mesh generation to separate file `docs/psydac-mesh.md` - Add BibTeX file `CITING.bib` with citation of 2022 ECCOMAS proceedings - Remove obsolete files `requirements.txt` and `requirements_extra.txt` - Rename (and move) `docs_requirements.txt` as `docs/requirements.txt` - Update installation procedure in `testing` CI workflow - Change name in `testing` workflow from "Run tests" to "Unit tests" - Modify `testing` and `documentation` workflows so that they only run when needed - Allow running workflows manually - Fix broken CI badge in `README.md` * Removed python -m pip install -r requirements.txt * Removed duplicated requirements from pyproject.toml * Removed duplicated requirements from pyproject.toml --------- Co-authored-by: Yaman Güçlü <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: Martin Campos Pinto <[email protected]> Co-authored-by: Frederik Schnack <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: Emily Bourne <[email protected]>
max-models
added a commit
to struphy-hub/psydac-for-struphy
that referenced
this pull request
Oct 23, 2025
* Support Python 3.13 (pyccel#475) Closes pyccel#476: * Do not restrict the maximum Python version to 3.12 in `pyproject.toml` * Require `Cython >= 3` to avoid `h5py` installation crash w/ Python 3.13 * Require `sympde == 0.19.2` which supports Python 3.13 * Run unit tests with Python 3.13 too * Fix PSYDAC_BACKEND_GPYCCEL flags on latest Apple silicon (pyccel#480) Currently, Psydac can not be used on Apple M4 computers since the `PSYDAC_BACKEND_GPYCCEL['flags']` is not set correctly. This change sets the flag for `Apple MX (etc.)` to `apple-mX`, which should work so long as the naming scheme stays unchanged. In addition, the regular expression used to find the GFortran version is now defined in a raw string instead of a standard Python UTF8 string. This avoids a `SyntaxWarning: invalid escape sequence`. --------- Co-authored-by: Yaman Güçlü <[email protected]> * Resolve warnings in sequential unit tests (pyccel#481) * Use raw strings for docstrings with LaTeX to avoid UTF8 syntax warnings on escape sequences; * Use CSC matrices to avoid SciPy sparse solver warning. We do not address the NumPy warnings which arise in our MPI unit tests (see pyccel#353). * Pass `out` parameter to `petsc_to_psydac` (pyccel#483) * Rename `dot` as `inner` in `Vector`, `VectorSpace`, and subclasses (pyccel#484) Main changes -------------- * Rename the method `dot` of the base class `VectorSpace` as `inner`, and make it an abstract method (which must be implemented by the subclasses). * Rename the method `dot` of the base class `Vector` as `inner`. This is a concrete method which calls `self.space.inner` and does not need to be overridden by the subclasses. * Add `inner` methods to the classes `StencilVector`, `BlockVectorSpace`, and `DenseVectorSpace`. These methods override the abstract method of the base class as required, and are derived from the former functions `Stencil.dot`, `BlockVector.dot`, and `DenseVector.dot`, which have been removed (see next point). * Remove the property `dtype` and the method `dot` (now `inner`) from the classes `StencilVector`, `BlockVector`, and `DenseVector`, because the default methods of the base class already provide a sufficient implementation. This fixes pyccel#330. Necessary additional changes ------------------------------ * Update all linear solvers in `linalg.solvers` with the new method calls; * Update all unit tests with the new method calls, in files: - `api/tests/test_assembly.py` - `feec/tests/test_commuting_projections.py` - `feec/tests/test_global_projectors.py` - `linalg/tests/test_block.py` - `linalg/tests/test_linalg.py` - `linalg/tests/test_stencil_interface_matrix.py` - `linalg/tests/test_stencil_vector.py` Unrelated additional changes ----------------------------- * Rename the class `VectorDot` as `VectorInner` in module `api.ast.linalg`, although never used in Psydac. * Speed up 3D unit tests in: - `feec/tests/test_commuting_projectors.py` - `feec/tests/test_global_projectors.py` * Update docstring for inner product in polar/dense.py (pyccel#488) --------- Co-authored-by: Yaman Güçlü <[email protected]> * Add a `dot_inner` concrete method to the base class `LinearOperator` (pyccel#493) Implement `M.dot(u).inner(v)`, or `(M @ u).inner(v)`, without creating a temporary vector. The result of the dot product is written to a local work vector stored in the `LinearOperator` object. This work vector is then used to compute the inner product with the vector `v`. The subclasses do not need to override this method, unless a more efficient implementation which avoids writing to the work vector altogether (reducing memory pressure) is needed. A unit test is added: function `test_dot_inner` in file psydac/linalg/tests/test_linalg.py. Additionally, the helper function `get_StencilVectorSpace` defined in psydac/linalg/tests/test_linalg.py (only used in the same file and in test_matrix_free.py) has a new signature and now works in any number of dimensions. Fixes pyccel#491. * Install PETSc-3.23.2 (latest version) (pyccel#499) * Update authors (pyccel#500) * Fix the code generation of unnecessary derivatives (pyccel#490) This PR changes the code generation involved in the `discretize` function to avoid calculating unnecessary derivatives. This allows for using constant spline (degree 0) discretizations, for which we have to make a special case in the calculation of ghost regions in `psydac/linalg/stencil.py`. Additionally, we add basic unit tests checking discretizations using zero-degree splines. This fixes pyccel#489 and fixes pyccel#307. On this occasion, we also do small changes in the `.github/workflows/testing.yml` script as some tests had complications without them. --------- Co-authored-by: Yaman Güçlü <[email protected]> * Fix bug in `allocate_matrices` in `DiscreteBilinearForm` (pyccel#507) Always use the maximum padding between test and trial spaces in `allocate_matrices` in `DiscreteBilinearForm`. (Earlier this was not done in the case of scalar spaces.) Fixes pyccel#504. * Enable Pyccel 2.0 (pyccel#503) Pyccel 2.0 was just released, which means some of the kernels in Psydac need to be updated: - Remove the `template` decorator (see pyccel/pyccel#2331) * Add `T` as `TypeVar` * Specify `T`, `T[:]`, `T[:,:]`, ... in function arguments. - Replace `@types` decorators (see pyccel/pyccel#2329) - Replace `const` with `Final` (see pyccel/pyccel#2340) Further changes: - Update import path for `epyccel` (fixes pyccel#426) - Update arguments to `epyccel` (see pyccel/pyccel#2348): * Rename `fflags` to `flags` * Replace `accelerators` list with `openmp` bool - Require Pyccel >= 2.0.1 (fixes pyccel#471) --------- Co-authored-by: Yaman Güçlü <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: Emily Bourne <[email protected]> * New installation procedure and README (pyccel#510) Recently the installation of `h5py` in parallel mode (i.e. with MPI support through `mpi4py`) seems to have been simplified. This may be due to the recent move of `mpi4py` to wheels, or other factors. Therefore we can now simplify our installation procedure as follows: ```sh pip install h5py --no-cache-dir --no-binary h5py pip install .[test] ``` We update here the CI workflows and completely rewrite our README file. **Commit summary** - Completely rewrite `README.md`: * Expand initial description * Add Citing and Contributing sections * Shorten Installation section * Reorganize documentation sections * Move detailed installation instructions to separate file `docs/installation.md` * Move mesh generation to separate file `docs/psydac-mesh.md` - Add BibTeX file `CITING.bib` with citation of 2022 ECCOMAS proceedings - Remove obsolete files `requirements.txt` and `requirements_extra.txt` - Rename (and move) `docs_requirements.txt` as `docs/requirements.txt` - Update installation procedure in `testing` CI workflow - Change name in `testing` workflow from "Run tests" to "Unit tests" - Modify `testing` and `documentation` workflows so that they only run when needed - Allow running workflows manually - Fix broken CI badge in `README.md` * Removed <<<<<< HEAD --------- Co-authored-by: Yaman Güçlü <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: Martin Campos Pinto <[email protected]> Co-authored-by: Frederik Schnack <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: Emily Bourne <[email protected]>
spossann
added a commit
to struphy-hub/psydac-for-struphy
that referenced
this pull request
Nov 10, 2025
* Support Python 3.13 (pyccel#475) Closes pyccel#476: * Do not restrict the maximum Python version to 3.12 in `pyproject.toml` * Require `Cython >= 3` to avoid `h5py` installation crash w/ Python 3.13 * Require `sympde == 0.19.2` which supports Python 3.13 * Run unit tests with Python 3.13 too * Fix PSYDAC_BACKEND_GPYCCEL flags on latest Apple silicon (pyccel#480) Currently, Psydac can not be used on Apple M4 computers since the `PSYDAC_BACKEND_GPYCCEL['flags']` is not set correctly. This change sets the flag for `Apple MX (etc.)` to `apple-mX`, which should work so long as the naming scheme stays unchanged. In addition, the regular expression used to find the GFortran version is now defined in a raw string instead of a standard Python UTF8 string. This avoids a `SyntaxWarning: invalid escape sequence`. --------- Co-authored-by: Yaman Güçlü <[email protected]> * Resolve warnings in sequential unit tests (pyccel#481) * Use raw strings for docstrings with LaTeX to avoid UTF8 syntax warnings on escape sequences; * Use CSC matrices to avoid SciPy sparse solver warning. We do not address the NumPy warnings which arise in our MPI unit tests (see pyccel#353). * Pass `out` parameter to `petsc_to_psydac` (pyccel#483) * Rename `dot` as `inner` in `Vector`, `VectorSpace`, and subclasses (pyccel#484) Main changes -------------- * Rename the method `dot` of the base class `VectorSpace` as `inner`, and make it an abstract method (which must be implemented by the subclasses). * Rename the method `dot` of the base class `Vector` as `inner`. This is a concrete method which calls `self.space.inner` and does not need to be overridden by the subclasses. * Add `inner` methods to the classes `StencilVector`, `BlockVectorSpace`, and `DenseVectorSpace`. These methods override the abstract method of the base class as required, and are derived from the former functions `Stencil.dot`, `BlockVector.dot`, and `DenseVector.dot`, which have been removed (see next point). * Remove the property `dtype` and the method `dot` (now `inner`) from the classes `StencilVector`, `BlockVector`, and `DenseVector`, because the default methods of the base class already provide a sufficient implementation. This fixes pyccel#330. Necessary additional changes ------------------------------ * Update all linear solvers in `linalg.solvers` with the new method calls; * Update all unit tests with the new method calls, in files: - `api/tests/test_assembly.py` - `feec/tests/test_commuting_projections.py` - `feec/tests/test_global_projectors.py` - `linalg/tests/test_block.py` - `linalg/tests/test_linalg.py` - `linalg/tests/test_stencil_interface_matrix.py` - `linalg/tests/test_stencil_vector.py` Unrelated additional changes ----------------------------- * Rename the class `VectorDot` as `VectorInner` in module `api.ast.linalg`, although never used in Psydac. * Speed up 3D unit tests in: - `feec/tests/test_commuting_projectors.py` - `feec/tests/test_global_projectors.py` * Update docstring for inner product in polar/dense.py (pyccel#488) --------- Co-authored-by: Yaman Güçlü <[email protected]> * Add a `dot_inner` concrete method to the base class `LinearOperator` (pyccel#493) Implement `M.dot(u).inner(v)`, or `(M @ u).inner(v)`, without creating a temporary vector. The result of the dot product is written to a local work vector stored in the `LinearOperator` object. This work vector is then used to compute the inner product with the vector `v`. The subclasses do not need to override this method, unless a more efficient implementation which avoids writing to the work vector altogether (reducing memory pressure) is needed. A unit test is added: function `test_dot_inner` in file psydac/linalg/tests/test_linalg.py. Additionally, the helper function `get_StencilVectorSpace` defined in psydac/linalg/tests/test_linalg.py (only used in the same file and in test_matrix_free.py) has a new signature and now works in any number of dimensions. Fixes pyccel#491. * Install PETSc-3.23.2 (latest version) (pyccel#499) * Update authors (pyccel#500) * Fix the code generation of unnecessary derivatives (pyccel#490) This PR changes the code generation involved in the `discretize` function to avoid calculating unnecessary derivatives. This allows for using constant spline (degree 0) discretizations, for which we have to make a special case in the calculation of ghost regions in `psydac/linalg/stencil.py`. Additionally, we add basic unit tests checking discretizations using zero-degree splines. This fixes pyccel#489 and fixes pyccel#307. On this occasion, we also do small changes in the `.github/workflows/testing.yml` script as some tests had complications without them. --------- Co-authored-by: Yaman Güçlü <[email protected]> * Fix bug in `allocate_matrices` in `DiscreteBilinearForm` (pyccel#507) Always use the maximum padding between test and trial spaces in `allocate_matrices` in `DiscreteBilinearForm`. (Earlier this was not done in the case of scalar spaces.) Fixes pyccel#504. * Enable Pyccel 2.0 (pyccel#503) Pyccel 2.0 was just released, which means some of the kernels in Psydac need to be updated: - Remove the `template` decorator (see pyccel/pyccel#2331) * Add `T` as `TypeVar` * Specify `T`, `T[:]`, `T[:,:]`, ... in function arguments. - Replace `@types` decorators (see pyccel/pyccel#2329) - Replace `const` with `Final` (see pyccel/pyccel#2340) Further changes: - Update import path for `epyccel` (fixes pyccel#426) - Update arguments to `epyccel` (see pyccel/pyccel#2348): * Rename `fflags` to `flags` * Replace `accelerators` list with `openmp` bool - Require Pyccel >= 2.0.1 (fixes pyccel#471) --------- Co-authored-by: Yaman Güçlü <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: Emily Bourne <[email protected]> * New installation procedure and README (pyccel#510) Recently the installation of `h5py` in parallel mode (i.e. with MPI support through `mpi4py`) seems to have been simplified. This may be due to the recent move of `mpi4py` to wheels, or other factors. Therefore we can now simplify our installation procedure as follows: ```sh pip install h5py --no-cache-dir --no-binary h5py pip install .[test] ``` We update here the CI workflows and completely rewrite our README file. **Commit summary** - Completely rewrite `README.md`: * Expand initial description * Add Citing and Contributing sections * Shorten Installation section * Reorganize documentation sections * Move detailed installation instructions to separate file `docs/installation.md` * Move mesh generation to separate file `docs/psydac-mesh.md` - Add BibTeX file `CITING.bib` with citation of 2022 ECCOMAS proceedings - Remove obsolete files `requirements.txt` and `requirements_extra.txt` - Rename (and move) `docs_requirements.txt` as `docs/requirements.txt` - Update installation procedure in `testing` CI workflow - Change name in `testing` workflow from "Run tests" to "Unit tests" - Modify `testing` and `documentation` workflows so that they only run when needed - Allow running workflows manually - Fix broken CI badge in `README.md` * Fast Matrix Assembly (pyccel#448) This PR implements the sum factorization algorithm as shown in **Sum factorization techniques in Isogeometric Analysis** by Andrea Bressan & Stefan Takacs for **bilinear forms on 3D volumes**. The old element-by-element assembly can still be employed by passing a corresponding flag ```python # a some BilinearForm a_h = discretize(a, domain_h, (Vh, Vh), backend=backend, sum_factorization=False) ``` Currently, the new generated code does not make use of OpenMP. Main changes -------------- - Write new module `psydac.api.fem_common` which: * Contains the old functions previously in module `psydac.api.fem`. * Has functions `construct_test_space_arguments` and `construct_trial_space_arguments` returning also the multiplicity. * Has new functions `compute_max_nderiv`, `compute_imports`, `compute_free_arguments`. - Move `DiscreteSumForm` to a new module `psydac.api.fem_sum_form`. - Create a new module `psydac.api.fem_bilinear_form` which only contains one new class `DiscreteBilinearForm`. The new module shows all imports clearly. The new class: * Generates the code to assemble the given discrete bilinear form into a matrix (a `BlockLinearOperator` object of `StencilMatrix` objects, or just a single `StencilMatrix` object), using sum factorization. * Does not inherit from `BasicDiscrete` (and hence `BasicCodeGen`). Accordingly, no PSYDAC abstract syntax tree (an object representing a function, of class `DefNode`) is created by the constructor of `AST`, which stores it in its `expr` attribute. (Both classes `DefNode` and `AST` are defined in module `psydac.api.ast.fem`.) * Does not create a `Parser` object from `psydac.api.ast.parser`, which used to convert a PSYDAC `DefNode` to an old-Pyccel `FunctionDef` from `psydac.pyccel.ast.core`. * Does not generate the old assembly Python code (in the form of a string) using the function `pycode` from `psydac.pyccel.codegen.printing.pycode`. - Add a new unit test file `api/tests/test_sum_factorization_assembly_3d`. - Modify function `discretize` in module `psydac.api.discretization` so that, given a bilinear form in 3D and not asking for OpenMP support, it creates an object of type `DiscreteBilinearForm` from module `psydac.api.fem_bilinear_form`. In all other cases, or if `sum_factorization=False`, it creates an object of namesake type from the old module `psydac.api.fem`. Other changes -------------- - Expand docstring of class `AST` in module `psydac.api.ast.fem`. - Expand docstrings of function `parse` and class `Parser` in module `psydac.api.ast.parser`. Clean up `Parser.__init__`. - Minor cleanup in class `BasicCodeGen` in module `psydac.api.basic`. - Generate random filenames using `random.choice()` instead of `random.SystemRandom().choice()`. Unrelated to matrix assembly: - Add method `set_scalar` to `ScaledLinearOperator`. - Reimplement method `idot` of `LinearOperator` using local storage. This avoids creating unnecessary temporary vectors (especially beneficial for the method `dot` of `SumLinearOperator`). --------- Co-authored-by: Yaman Güçlü <[email protected]> Co-authored-by: elmosa <[email protected]> * Improve multipatch FEM API (pyccel#509) ### Commit summary - Fix pyccel#461 : Move contents of `psydac/feec/multipatch/api.py` to `psydac/api/feec.py` and `psydac/api/discretization.py`. - Remove old code from `psydac/feec/multipatch/operators.py` and replace it by the contents in `psydac/feec/multipatch/non_matching_operators.py` to make the structure more clear. - Fix pyccel#463 - Fix pyccel#272 : keep the `FEMLinearOperator` as a more light-weight class that encapsulates a `LinearOperator` and has a `apply` and `__call__` function to make it act on a `FEMField`. Remove duplicated code with `LinearOperator`. Make operators in `psydac/feec` subclasses of `LinearOperator`. - Fix pyccel#462: Add conforming projections and Hodge operators to single-patch `DiscreteDeRham` - Add single-patch test for the conforming projectors - Adapt all the tests/files to the new notations. For the single patch cases mostly renaming `derham_h.derivatives` to `derham_h.derivatives()` and `derham_h.derivatives_as_matrices` to `derham_h.derivatives(kind='linop')` - Merge single-patch and multi-patch operators to the same file if it makes things clearer. Take Hodge and conforming projection operators out of the multipatch subdirectory. - Fix pyccel#409 : the global projector interface in DiscreteDeRhamMultipatch - Fix pyccel#331. - Add a `SparseMatrixLinearOperator` in `psydac/linalg/sparse.py` to use a sparse matrix as a `LinearOperator`. This is needed for the conforming projections. - Rename `GlobalProjectors` to `GlobalGeometricProjectors` ### Notes With the current changes, we get all FEEC operators directly from the discrete de Rham object. Further, the same code also runs if the domain is a single patch. --------- Co-authored-by: Yaman Güçlü <[email protected]> * Allow `mpi_dims_mask` with geometry file (pyccel#526) Add the optional parameter `mpi_dims_mask` to the constructor of class `Geometry`, as well as its class methods `from_discrete_mapping` and `from_topological_domain`. Add unit tests to verify that the domain is correctly decomposed. --------- Co-authored-by: Alisa Kirkinskaia <[email protected]> Co-authored-by: Alisa Kirkinskaia <[email protected]> * Fix the parallel low-level 2D Poisson example (pyccel#528) Fix `examples/poisson_2d_mapping.py`: - Use renamed method `get_assembly_grids` (formerly `get_quadrature_grids`) of class `TensorFemSpace` - Add missing definition of `Vnew` variable in the case of distributed visualization - Avoid string warnings * Fix method `plot_2d_decomposition` of `TensorFemSpace` (pyccel#529) Fix bug in method `plot_2d_decomposition` of `TensorFemSpace`, which was failing when run in parallel with a distributed spline mapping. - Create a new test file `psydac/fem/tests/test_tensor.py` with a unit test which fails on the `devel` branch. This compares the generated PNG images with "reference" ones which are known to be correct, within a 2 % relative tolerance on each of the RGB channels. - Only evaluate mapping in local subdomain owned by process - Gather global mapping information on root process - Add optional parameters `fig`, `ax`, and `mpi_root` - Add docstring - Update `examples/poisson_2d_mapping.py` to pass the correct mapping (i.e. also a distributed spline mapping if that is used in the computations) to `plot_2d_decomposition`. * Describe library name in README.md (pyccel#535) Add a NOTE block with the meaning of the PSYDAC acronym, as well as its pronounciation. * Fix parallelization bug in polar splines (pyccel#539) * change version to 2.6.0.dev0 * remove test_tensor.py * install struohy from 108-psydac-change-renaming-of-globalpojector --------- Co-authored-by: Yaman Güçlü <[email protected]> Co-authored-by: Max <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: Martin Campos Pinto <[email protected]> Co-authored-by: Frederik Schnack <[email protected]> Co-authored-by: Elena Moral Sánchez <[email protected]> Co-authored-by: Emily Bourne <[email protected]> Co-authored-by: Julian Owezarek <[email protected]> Co-authored-by: Alisa Kirkinskaia <[email protected]> Co-authored-by: Alisa Kirkinskaia <[email protected]>
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Running description
Update
pyproject.toml:pipwill install branchfix-issue-176of SymPDE.This is to test PR pyccel/sympde#177, and is not meant to be merged for now.
If everything works well, we could use this PR to update the version of SymPDE and support Python 3.13.
TO DO / Done:
mpi4py4.0.0 #420pyproject.tomlh5pyinstallation problem with Python 3.13 (see CI log) -- fixed by installing Cython >= 3pyproject.toml:pipwill install SymPDE version 0.19.2Final summary
Closes #476:
pyproject.tomlCython >= 3as this avoidsh5pyinstallation problems with Python 3.13sympde == 0.19.2which supports Python 3.13