merging changes

.github/workflows/continuous-integration.yml

@@ -58,6 +58,7 @@ jobs:
       - name: Set default MPI and HDF5 C compilers on Ubuntu
         if: matrix.os == 'ubuntu-latest'
         run: |
+          sudo apt-get update
           sudo apt-get install --reinstall openmpi-bin libhdf5-openmpi-dev
 
       - name: Install non-Python dependencies on macOS
@@ -159,9 +160,9 @@ jobs:
           python -m pip install .
           python -m pip freeze
 
-      - name: Test pyccel optimization flags
+      - name: Test Pyccel optimization flags
         run: |
-            pyccel --verbose ./psydac/linalg/kernels/axpy_kernels.py
+          pytest --pyargs psydac -m pyccel --capture=no
 
       - name: Initialize test directory
         run: |

.github/workflows/documentation.yml

@@ -18,9 +18,9 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN}}
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
     - name: Install non-Python dependencies on Ubuntu
@@ -37,9 +37,9 @@ jobs:
         make -C docs html
         python docs/update_links.py
     - name: Setup Pages
-      uses: actions/configure-pages@v3
+      uses: actions/configure-pages@v5
     - name: Upload artifact
-      uses: actions/upload-pages-artifact@v1
+      uses: actions/upload-pages-artifact@v3
       with:
         path: 'docs/build/html'
 
@@ -53,4 +53,4 @@ jobs:
     steps:
     - name: Deploy to GitHub Pages
       id: deployment
-      uses: actions/deploy-pages@v2
+      uses: actions/deploy-pages@v4

.gitignore

@@ -31,5 +31,5 @@ __test__/
 # pycharm directory
 .idea
 
-#macOs 
+# macOS
 */.DS_Store

README.md

@@ -186,7 +186,7 @@ python3 <PSYDAC-PATH>/mpi_tester.py --pyargs psydac -m "parallel and petsc"
 
 Many of Psydac's low-level Python functions can be translated to a compiled language using the [Pyccel](https://github.com/pyccel/pyccel) transpiler. Currently, all of those functions are collected in modules which follow the name pattern `[module]_kernels.py`.
 
-The classical installation translates all kernel files to Fortran without user intervention. This does not happen in the case of an editable install, but the command `psydac-accelerate` is made available to the user instead. This command applies Pyccel to all the kernel files in the source directory, and the C language may be selected instead of Fortran (which is the default).
+The classical installation translates all kernel files to Fortran without user intervention. This does not happen in the case of an editable install, but the command `psydac-accelerate` is made available to the user instead. This command applies Pyccel to all the kernel files in the source directory. The default language is currently Fortran, C should also be supported in a near future.
 
 -   **Only in development mode**:
     ```bash

psydac/api/ast/glt.py

@@ -31,7 +31,7 @@
 from sympde.topology             import LogicalExpr
 from sympde.topology             import SymbolicExpr
 from sympde.calculus.matrices    import SymbolicDeterminant
-from sympde.topology.analytic_mappings             import IdentityMapping
+from sympde.topology.analytic_mappings import IdentityMapping
 
 from sympde.expr.evaluation import TerminalExpr
 

psydac/api/settings.py

@@ -1,5 +1,8 @@
 # coding: utf-8
+import subprocess # nosec B404
 import platform
+import re
+from packaging.version import Version
 
 
 __all__ = ('PSYDAC_DEFAULT_FOLDER', 'PSYDAC_BACKENDS')
@@ -40,18 +43,26 @@
                        'openmp'  : False}
 # ...
 
+# Get gfortran version
+gfortran_version_output = subprocess.check_output(['gfortran', '--version']).decode('utf-8') # nosec B603, B607
+gfortran_version_string = re.search("(\d+\.\d+\.\d+)", gfortran_version_output).group()
+gfortran_version = Version(gfortran_version_string)
+
 # Platform-dependent flags
-if platform.system() == "Darwin" and platform.machine() == 'arm64':
+if platform.system() == "Darwin" and platform.machine() == 'arm64' and gfortran_version >= Version("14"):
+
     # Apple silicon requires architecture-specific flags (see https://github.com/pyccel/psydac/pull/411)
-    import subprocess # nosec B404
+    # which are only available on GCC version >= 14
     cpu_brand = subprocess.check_output(['sysctl','-n','machdep.cpu.brand_string']).decode('utf-8') # nosec B603, B607
-    if "Apple M1" in cpu_brand:
-        PSYDAC_BACKEND_GPYCCEL['flags'] += ' -mcpu=apple-m1'
+    if   "Apple M1" in cpu_brand: PSYDAC_BACKEND_GPYCCEL['flags'] += ' -mcpu=apple-m1'
+    elif "Apple M2" in cpu_brand: PSYDAC_BACKEND_GPYCCEL['flags'] += ' -mcpu=apple-m2'
+    elif "Apple M3" in cpu_brand: PSYDAC_BACKEND_GPYCCEL['flags'] += ' -mcpu=apple-m3'
     else:
         # TODO: Support later Apple CPU models. Perhaps the CPU naming scheme could be easily guessed
         # based on the output of 'sysctl -n machdep.cpu.brand_string', but I wouldn't rely on this
         # guess unless it has been manually verified. Loud errors are better than silent failures!
         raise SystemError(f"Unsupported Apple CPU '{cpu_brand}'.")
+
 else:
     # Default architecture flags
     PSYDAC_BACKEND_GPYCCEL['flags'] += ' -march=native -mtune=native'

psydac/api/tests/test_api_feec_2d.py

@@ -218,7 +218,7 @@ def run_maxwell_2d_TE(*, use_spline_mapping,
     from sympde.topology import Domain
     from sympde.topology import Square
 
-    from sympde.topology import CollelaMapping2D, BaseAnalyticMapping
+    from sympde.topology import BaseAnalyticMapping #, CollelaMapping2D
 
     from sympde.topology import Derham
     from sympde.topology import elements_of
@@ -280,6 +280,15 @@ def run_maxwell_2d_TE(*, use_spline_mapping,
     else:
         # Logical domain is unit square [0, 1] x [0, 1]
         logical_domain = Square('Omega')
+
+        # WARNING: this Collela mapping is not the same as in SymPDE
+        class CollelaMapping2D(BaseAnalyticMapping):
+
+            _ldim = 2
+            _pdim = 2
+            _expressions = {'x': 'a * (x1 + eps / (2*pi) * sin(2*pi*x1) * sin(2*pi*x2))',
+                            'y': 'b * (x2 + eps / (2*pi) * sin(2*pi*x1) * sin(2*pi*x2))'}
+
         mapping = CollelaMapping2D('M1', a=a, b=b, eps=eps)
         domain  = mapping(logical_domain)
 

psydac/api/tests/test_epyccel_flags.py

@@ -0,0 +1,35 @@
+import pytest
+
+
+@pytest.mark.pyccel
+def test_epyccel_flags():
+
+    from pyccel.epyccel import epyccel
+    from psydac.api.settings import PSYDAC_BACKEND_GPYCCEL as backend
+
+    kwargs = {'language'     : 'fortran',
+              'compiler'     : backend['compiler'],
+              'fflags'       : backend['flags'],
+              'accelerators' : ['openmp'] if backend['openmp'] else [],
+              'verbose'      : True,
+              }
+
+    # Function to be Pyccel-ized
+    def f(x : float):
+        return 3 * x
+
+    # Pyccel magic
+    # ------------
+    # Fortran code is generated and then compiled with the selected compiler.
+    # The compiled function is callable from Python through the C Python API.
+    # The necessary C wrapper functions are also generated by Pyccel.
+    fast_f = epyccel(f, **kwargs)
+
+    # Check output of pyccelized function
+    assert fast_f(3.5) == f(3.5)
+
+
+# Interactive usage
+if __name__ == '__main__':
+    test_epyccel_flags()
+    print('PASSED')

psydac/fem/tensor.py

@@ -456,7 +456,7 @@ def eval_fields(self, grid, *fields, weights=None, npts_per_cell=None, overlap=0
                 npts_per_cell = (npts_per_cell,) * self.ldim
             for i in range(self.ldim):
                 ncells_i = len(self.breaks[i]) - 1
-                grid[i] = np.reshape(grid[i], newshape=(ncells_i, npts_per_cell[i]))
+                grid[i] = np.reshape(grid[i], (ncells_i, npts_per_cell[i]))
             out_fields = self.eval_fields_regular_tensor_grid(grid, *fields, weights=weights, overlap=overlap)
             # return a list
             return [np.ascontiguousarray(out_fields[..., i]) for i in range(len(fields))]

psydac/mapping/discrete.py

@@ -295,7 +295,7 @@ def jac_mat_grid(self, grid, npts_per_cell=None, overlap=0):
                 npts_per_cell = (npts_per_cell,) * self.ldim
             for i in range(self.ldim):
                 ncells_i = len(self.space.breaks[i]) - 1
-                grid[i] = np.reshape(grid[i], newshape=(ncells_i, npts_per_cell[i]))
+                grid[i] = np.reshape(grid[i], (ncells_i, npts_per_cell[i]))
             jac_mats = self.jac_mat_regular_tensor_grid(grid, overlap=overlap)
             return jac_mats
 
@@ -465,7 +465,7 @@ def inv_jac_mat_grid(self, grid, npts_per_cell=None, overlap=0):
                 npts_per_cell = (npts_per_cell,) * self.ldim
             for i in range(self.ldim):
                 ncells_i = len(self.space.breaks[i]) - 1
-                grid[i] = np.reshape(grid[i], newshape=(ncells_i, npts_per_cell[i]))
+                grid[i] = np.reshape(grid[i], (ncells_i, npts_per_cell[i]))
             inv_jac_mats = self.inv_jac_mat_regular_tensor_grid(grid, overlap=overlap)
             return inv_jac_mats
 
@@ -636,7 +636,7 @@ def jac_det_grid(self, grid, npts_per_cell=None, overlap=0):
                 npts_per_cell = (npts_per_cell,) * self.ldim
             for i in range(self.ldim):
                 ncells_i = len(self.space.breaks[i]) - 1
-                grid[i] = np.reshape(grid[i], newshape=(ncells_i, npts_per_cell[i]))
+                grid[i] = np.reshape(grid[i], (ncells_i, npts_per_cell[i]))
             jac_dets = self.jac_det_regular_tensor_grid(grid, overlap=overlap)
             return jac_dets
 

pyproject.toml

@@ -33,7 +33,7 @@ dependencies = [
     'pyevtk',
 
     # Our packages from PyPi
-    'sympde == 0.19.0',
+    'sympde @ https://github.com/pyccel/sympde/archive/refs/heads/new-mapping-hierarchy-lagarrigue.zip',
     'pyccel >= 1.11.2',
     'gelato == 0.12',
 
@@ -49,15 +49,8 @@ dependencies = [
     # tracebacks, which allows mpi4py to broadcast exceptions
     'tblib',
 
-    # SYMPDE - development version
-    # 'sympde @ https://github.com/pyccel/sympde/archive/refs/heads/master.zip'
-
     # IGAKIT - not on PyPI
-
-    # !! WARNING !! Path to igakit below is from fork pyccel/igakit. This was done to
-    # quickly fix the numpy 2.0 issue. See https://github.com/dalcinl/igakit/pull/4
-    # !! WARNING !! commenting igakit to support python 3.12
-    # 'igakit @ https://github.com/pyccel/igakit/archive/refs/heads/bugfix-numpy2.0.zip'  
+    'igakit @ https://github.com/dalcinl/igakit/archive/refs/heads/master.zip'
 ]
 
 [project.urls]

pytest.ini

@@ -9,6 +9,7 @@ markers =
     serial: single-process test,
     parallel: test to be run using 'mpiexec',
     petsc: test requiring a working PETSc installation with petsc4py Python bindings
+    pyccel: test for checking Pyccel setup on machine
 
 python_files = test_*.py
 python_classes =