Improve Geometry class

.github/actions/install_h5py/action.yml

@@ -21,6 +21,7 @@ runs:
       run: |
         export CC="mpicc"
         export HDF5_MPI="ON"
+        pip install 'mpi4py>=4.0.0'
         pip install h5py --no-cache-dir --no-binary h5py
         pip list
 

.github/workflows/documentation.yml

@@ -23,9 +23,11 @@ permissions:
 jobs:
   build_docs:
     runs-on: ubuntu-latest
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN}}
       OMP_NUM_THREADS: 2
+
     steps:
     - name: Checkout
       uses: actions/checkout@v6
@@ -38,17 +40,7 @@ jobs:
         python-version: '3.10'
 
     - name: Install non-Python dependencies on Ubuntu
-      uses: awalsh128/cache-apt-pkgs-action@latest
-      with:
-        packages: gfortran openmpi-bin libopenmpi-dev libhdf5-openmpi-dev
-        version: 1.0
-        execute_install_scripts: true
-
-    - name: Reconfigure non-Python dependencies on Ubuntu
-      run: |
-        sudo apt-get update
-        sudo apt-get install --reinstall openmpi-bin libhdf5-openmpi-dev liblapack-dev libblas-dev
-        sudo apt install graphviz pandoc
+      uses: ./.github/actions/ubuntu_installations
 
     - name: Print information on MPI and HDF5 libraries
       run: |
@@ -70,6 +62,10 @@ jobs:
         pip install .[test]
         pip freeze
 
+    - name: Install non-Python dependencies for Documentation
+      run: |
+        sudo apt install graphviz pandoc
+
     - name: Install Python dependencies for Documentation
       run: |
         pip install -r docs/requirements.txt

.github/workflows/testing.yml

@@ -40,7 +40,8 @@ jobs:
       OMP_NUM_THREADS: 2
 
     steps:
-      - uses: actions/checkout@v6
+      - name: Checkout
+        uses: actions/checkout@v6
         with:
           submodules: true
 
@@ -125,17 +126,17 @@ jobs:
         if: matrix.os == 'macos-14'
         working-directory: ./scratch
         run: |
-          coverage report --ignore-errors --show-missing --sort=cover
+          psydac test --mod psydac.mapping -x -v
 
       - name: Run MPI tests with Pytest
         working-directory: ./scratch
         run: |
-          psydac test --mpi
+          psydac test --mod psydac.fem -x -v
 
       - name: Run single-process PETSc tests with Pytest
         working-directory: ./scratch
         run: |
-          psydac test --petsc
+          psydac test --mod psydac.feec -x -v
 
       - name: Run MPI PETSc tests with Pytest
         working-directory: ./scratch

CHANGELOG.md

@@ -11,19 +11,23 @@ All notable changes to this project will be documented in this file.
 -   #576 : Add module `psydac.utilities.parallel_utils` for parallel execution and gathering variable-length arrays
 -   #576 : Add module `psydac.utilities.operators` with class `Laplacian` used in some old examples
 -   #577 : Add an installation configuration option to choose the backend language
+-   #567 : Improve `psydac test` command (with several new features)
+-   #565 : Expand editable install info in `README.md`
 -   [DEVELOPER] Create action `install_petsc4py` to install PETSc & `petsc4py` w/ complex support
+-   [DEVELOPER] Configure Pylint in `pyproject.toml`
+-   [DEVELOPER] Add `CLAUDE.md` with developer rules
 
 ### Fixed
 
--   #576 : Fix bug in `TensorFemSpace.eval_field` caused by round-off at MPI subdomain boundaries
+-   #527 : Require `sympde==0.20.0` which changes how multipatch interfaces are defined
 -   #576 : Require `sympde==0.19.3` which fixes a bug in the linearity checks
 -   #579 : Require `h5py>=3.16` which installs correctly with `setuptools>=81.0`
+-   #576 : Fix bug in `TensorFemSpace.eval_field` caused by round-off at MPI subdomain boundaries
 -   #579 : Don't run postprocessing unit tests with `pytest-xdist` because `h5py` is not thread-safe
 -   #579 : Return error code on failure of the `psydac test` and `psydac compile` commands
 -   #577 : Fix installation following release of Pyccel 2.2
 -   #571 : Fix correct application of the sum factorization algorithm
--   #570 : Optimize PSYDAC logo
--   #565 : Expand editable install info in `README.md`
+-   #567 : Fix parallel creation of folder `__psydac__` in `psydac.api.fem_bilinear_form`
 -   #566 : Fix command `psydac test --mpi` on Ubuntu machines
 -   [DEVELOPER] Add missing 'description' properties (required!) to our GitHub actions
 -   [DEVELOPER] Update CI installation of `petsc4py` after release of `setuptools` 81.0
@@ -32,13 +36,15 @@ All notable changes to this project will be documented in this file.
 
 ### Changed
 
+-   #527 : Improve `Geometry` class in module `psydac.cad.geometry`
 -   #576 : Use latest version of Igakit (commit dalcinl/igakit@92ee097 of 2026/07/24) which supports NumPy >= 2.4
 -   #595 : Use PETSc 3.25.5 whose Python bindings `petsc4py` are built correctly with `cython>=3`
 -   #580 : Use PETSc 3.25.0 whose Python bindings `petsc4py` install correctly with `setuptools>=81.0`
 -   #579 : Require `pyccel>=2.2.3` which can compile all kernels with C
 -   #579 : Require `numpy>=2.1` to support Python >= 3.10
 -   #579 : Require `pytest>=9.0` and use `pytest.toml` instead of `pytest.ini` for Pytest configuration
 -   #579 : Move coverage configuration from `pyproject.toml` to `psydac/pytest.toml`
+-   #570 : Optimize PSYDAC logo
 -   [DEVELOPER] Update GitHub Actions for repository checkout and Python setup
 -   [DEVELOPER] Rename actions: `macos/ubuntu_install` -> `macos/ubuntu_installations`
 -   [DEVELOPER] Do not check file changes to trigger testing workflow on PRs

CLAUDE.md

@@ -0,0 +1,74 @@
+# Project: PSYDAC
+
+## Overview
+Python 3 library for isogeometric analysis (IGA). Solve general systems of partial
+differential equations (PDEs) in weak form, defined using the domain-specific
+language provided by SymPDE. Supports finite element exterior calculus (FEEC)
+with tensor-product spline spaces. Handles multi-patch geometries in various ways;
+usually broken-FEEC a.k.a. CONGA (conforming/non-conforming Galerkin).
+Python code is automatically generated for the assembly of user-defined functionals,
+linear forms, and bilinear forms. This Python code is then accelerated to C/Fortran
+speed using Pyccel. The library enables large parallel computations on distributed-
+memory supercomputers using MPI and OpenMP.
+
+## Tech stack
+- Python 3.10+, type hints required everywhere
+- meson-python + mesonpy for building
+- pip with submodules (for igakit)
+- pytest + pytest-cov + pytest-mpi + pytest-xdist for testing
+- sympde for symbolic definition of weak formulations
+- pyccel for translation of Python kernels to Fortran or C
+- mpi4py for MPI parallelization
+- h5py for parallel I/O
+- petsc4py for direct linear solvers (optional install)
+
+## Code standards
+- Follow PEP 8 style guide whenever possible
+- Docstrings of public functions and classes follow Numpydoc conventions
+- pylint + black + isort for linting/typing
+- Computational kernels to be accelerated with Pyccel named as `<module>_kernels.py`
+- Minimize code duplication. Never add code that already exists
+- Strive for concise, clean, and human-readable code. Avoid useless verbosity
+- Self-explanatory names for variables, functions, and classes
+- Do not reassign value to an existing variable, especially if the type changes
+- Use short comments (one-liners or inline) to explain "why" rather than "what" or "how"
+
+## Testing conventions
+- Each library subpackage contains a `tests/` folder with an `__init__.py` file
+- Unit tests are part of the library and shipped with it
+- Unit tests can be run with `psydac test` CLI command (see `README.md`)
+- Test file names follow `test_<module>.py`
+- Test function names follow `test_<function>` or `test_<class>_<method>`
+- Parametrize unit tests with `@pytest.parametrize` to minimize code duplication
+- Keep run time of tests at a minimum
+- Aim for 100% coverage on newly committed code
+
+## File structure
+- psydac/api - high-level Python interface
+- psydac/cad - computer-aided design (CAD) functionality
+- psydac/cmd - command-line interface (CLI) commands
+- psydac/core - splines functionality
+- psydac/ddm - MPI decomposition of domain, vectors of spline coefficients, and matrices
+- psydac/feec - finite element exterior calculus (FEEC)
+- psydac/fem - "finite element method" middle-level Python interface (spaces and fields)
+- psydac/linalg - "linear algebra" low-level Python interface (vectors, linear operators, iterative solvers)
+- psydac/polar - implementation of polar splines for H1 spaces
+- psydac/pyccel - distillation of an old version of Pyccel for Python code generation (to be removed)
+- psydac/utilities - various generic functions used across the library
+- docs - Sphinx documentation
+- examples - Various examples of library usage (mostly Jupyter notebooks)
+- scripts - Various scripts for library maintenance
+- subprojects - Git submodules
+
+## Always do
+- Before claiming done:
+  . Run `python -m black --check $(git ls-files "*.py")`
+  . Run `python -m isort --check $(git ls-files "*.py" | grep -v "FOUND_DUPLICATED_IMPORT.py")`
+  . Run `pylint --disable=all --enable=unused-import ./psydac --ignore-paths="__pyccel*" --ignore-paths="__epyccel*"`
+- Unless specified differently, assume process with `rank=0` in MPI communicator is root
+- Use root MPI process to perform serial operations (e.g. open/save image)
+
+## Never do
+- Commit secrets or `.env` files
+- Add new dependencies without team discussion
+- Use `eval` function together with `input`

psydac/api/discretization.py

@@ -578,7 +578,7 @@ def discretize_domain(domain, *, filename=None, ncells=None, periodic=None, comm
         raise ValueError("Cannot provide both 'filename' and 'ncells'")
 
     elif filename:
-        return Geometry(filename=filename, comm=comm, mpi_dims_mask=mpi_dims_mask)
+        return Geometry.from_file(filename, comm=comm, mpi_dims_mask=mpi_dims_mask)
 
     elif ncells:
         return Geometry.from_topological_domain(domain, ncells, periodic=periodic, comm=comm, mpi_dims_mask=mpi_dims_mask)

psydac/api/tests/test_2d_complex.py

@@ -363,7 +363,7 @@ def test_complex_poisson_2d_multipatch():
     A = Square('A',bounds1=(0, 0.5), bounds2=(0, 1))
     B = Square('B',bounds1=(0.5, 1.), bounds2=(0, 1))
 
-    domain = Domain.join([A, B], [((0, 0, 1), (1, 0, -1))], 'domain')
+    domain = Domain.join([A, B], [((0, 0, 1), (1, 0, -1), 1)], 'domain')
 
     x, y = domain.coordinates
 

psydac/api/tests/test_2d_multipatch_mapping_maxwell.py

@@ -7,25 +7,22 @@
 from pathlib import Path
 
 import pytest
-import numpy as np
 from mpi4py import MPI
 from sympy  import pi, sin, cos, Tuple, Matrix
 
-from sympde.calculus      import grad, dot, curl, cross
+from sympde.calculus      import dot, curl, cross
 from sympde.calculus      import minus, plus
 from sympde.topology      import VectorFunctionSpace
 from sympde.topology      import elements_of
 from sympde.topology      import NormalVector
-from sympde.topology      import Square, Domain
-from sympde.topology      import IdentityMapping, PolarMapping
+from sympde.topology      import Domain
 from sympde.expr.expr     import LinearForm, BilinearForm
 from sympde.expr.expr     import integral
 from sympde.expr.expr     import Norm
-from sympde.expr.equation import find, EssentialBC
+from sympde.expr.equation import find
 
 from psydac.api.discretization       import discretize
 from psydac.api.tests.build_domain   import build_11_patch_pretzel, build_2_patch_annulus
-from psydac.fem.basic                import FemField
 from psydac.api.settings             import PSYDAC_BACKEND_GPYCCEL
 from psydac.feec.pull_push           import pull_2d_hcurl
 
@@ -204,10 +201,10 @@ def teardown_function():
 
 if __name__ == '__main__':
 
-    from collections                               import OrderedDict
-    from sympy                                     import lambdify
+    from collections                     import OrderedDict
+    from sympy                           import lambdify
     from psydac.fem.plotting_utilities   import get_plotting_grid, get_grid_vals
-    from psydac.fem.plotting_utilities   import get_patch_knots_gridlines, my_small_plot
+    from psydac.fem.plotting_utilities   import my_small_plot
 
     domain    = build_11_patch_pretzel()
     x,y       = domain.coordinates

psydac/api/tests/test_2d_multipatch_mapping_poisson.py

@@ -15,7 +15,7 @@
 from sympde.calculus      import minus, plus
 from sympde.topology      import ScalarFunctionSpace
 from sympde.topology      import elements_of
-from sympde.topology      import NormalVector, Union
+from sympde.topology      import NormalVector
 from sympde.topology      import Square, Domain
 from sympde.topology      import IdentityMapping, PolarMapping, AffineMapping
 from sympde.expr.expr     import LinearForm, BilinearForm
@@ -141,12 +141,12 @@ def test_poisson_2d_3_patches_dirichlet_2():
     B = Square('B',bounds1=(0.5, 1.), bounds2=(0, np.pi))
     C = Square('C',bounds1=(0.5, 1.), bounds2=(np.pi-0.5, np.pi + 1))
 
-    D1     = mapping_1(A)
-    D2     = mapping_2(B)
-    D3     = mapping_3(C)
+    D1 = mapping_1(A)
+    D2 = mapping_2(B)
+    D3 = mapping_3(C)
 
-    connectivity = [((0,1,1),(1,1,-1)), ((1,1,1),(2,1,-1))]
     patches = [D1, D2, D3]
+    connectivity = [((0, 1, 1), (1, 1,-1), 1), ((1, 1, 1), (2, 1,-1), 1)]
     domain = Domain.join(patches, connectivity, 'domain')
 
     x,y       = domain.coordinates
@@ -252,8 +252,11 @@ def test_poisson_2d_4_patch_dirichlet_0():
     D3     = mapping_3(C)
     D4     = mapping_4(D)
 
-    connectivity = [((0,1,1),(1,1,-1)), ((2,1,1),(3,1,-1)), ((0,0,1),(2,0,-1)),((1,0,1),(3,0,-1))]
     patches = [D1, D2, D3, D4]
+    connectivity = [((0, 1, 1), (1, 1,-1), 1),
+                    ((2, 1, 1), (3, 1,-1), 1),
+                    ((0, 0, 1), (2, 0,-1), 1),
+                    ((1, 0, 1), (3, 0,-1), 1)]
     domain = Domain.join(patches, connectivity, 'domain')
 
     x,y       = domain.coordinates

psydac/api/tests/test_2d_multipatch_poisson.py

@@ -78,8 +78,8 @@ def test_poisson_2d_2_patch_dirichlet_0():
     A = Square('A', bounds1=(0, 0.5), bounds2=(0, 1))
     B = Square('B', bounds1=(0.5, 1), bounds2=(0, 1))
 
-    connectivity = [((0,0,1), (1,0,-1), 1)]
     patches = [A, B]
+    connectivity = [((0, 0, 1), (1, 0,-1), 1)]
     domain = Domain.join(patches, connectivity, 'domain')
 
     x,y = domain.coordinates
@@ -100,8 +100,8 @@ def test_poisson_2d_2_patch_dirichlet_1():
     A = Square('A', bounds1=(0, 0.5), bounds2=(0, 1))
     B = Square('B', bounds1=(0.5, 1), bounds2=(0, 1))
 
-    connectivity = [((0,0,1), (1,0,-1), 1)]
     patches = [A, B]
+    connectivity = [((0, 0, 1), (1, 0,-1), 1)]
     domain = Domain.join(patches, connectivity, 'domain')
 
     x,y = domain.coordinates
@@ -121,8 +121,8 @@ def test_poisson_2d_2_patch_dirichlet_2():
     A = Square('A', bounds1=(0, 0.5), bounds2=(0, 1))
     B = Square('B', bounds1=(0.5, 1), bounds2=(0, 1))
 
-    connectivity = [((0,0,1), (1,0,-1), 1)]
     patches = [A, B]
+    connectivity = [((0, 0, 1), (1, 0,-1), 1)]
     domain = Domain.join(patches, connectivity, 'domain')
 
     x,y = domain.coordinates
@@ -150,8 +150,8 @@ def test_poisson_2d_2_patch_dirichlet_3():
     D1 = M1(A)
     D2 = M2(B)
 
-    connectivity = [((0,0,1), (1,0,1), 1)]
     patches = [D1, D2]
+    connectivity = [((0, 0, 1), (1, 0, 1), 1)]
     domain = Domain.join(patches, connectivity, 'domain')
 
     x,y = domain.coordinates
@@ -182,8 +182,8 @@ def test_poisson_2d_2_patch_dirichlet_4():
     D1 = M1(A)
     D2 = M2(B)
 
-    connectivity = [((0,0,-1), (1,0,-1), 1)]
-    patches = [D1,D2]
+    patches = [D1, D2]
+    connectivity = [((0, 0, -1), (1, 0, -1), 1)]
     domain = Domain.join(patches, connectivity, 'domain')
 
     x,y = domain.coordinates

psydac/api/tests/test_postprocessing.py

@@ -57,7 +57,7 @@ def build_2_mapped_squares():
     D2     = mapping_2(B)
 
     patches = [D1, D2]
-    connectivity = [((0,1,1),(1,1,-1))]
+    connectivity = [((0, 1, 1), (1, 1,-1), 1)]
     return Domain.join(patches, connectivity, 'domain')
 
 
@@ -66,7 +66,7 @@ def build_2_squares():
     B = Square('B',bounds1=(0.5, 1.), bounds2=(np.pi/2, np.pi))
 
     patches = [A, B]
-    connectivity = [((0,1,1),(1,1,-1))]
+    connectivity = [((0, 1, 1), (1, 1,-1), 1)]
     return Domain.join(patches, connectivity, 'domain')
 
 
@@ -75,10 +75,9 @@ def build_2_cubes():
     B = Cube('B',bounds1=(0.5, 1.), bounds2=(np.pi/2, np.pi), bounds3=(0, 1))
 
     patches = [A, B]
-    connectivity = [((0,1,1),(1,1,-1))]
+    connectivity = [((0, 1, 1), (1, 1,-1), (1, 1, 1))]
     return Domain.join(patches, connectivity, 'domain')
 
-
 ###############################################################################
 #                            Output Manager tests                             #
 ###############################################################################
@@ -538,8 +537,8 @@ def test_reconstruct_multipatch(dtype):
     A = Square('A',bounds1=bounds1, bounds2=bounds2_A)
     B = Square('B',bounds1=bounds1, bounds2=bounds2_B)
 
-    connectivity = [((0,1,1),(1,1,-1))]
-    patches = [A,B]
+    patches = [A, B]
+    connectivity = [((0, 1, 1), (1, 1,-1), 1)]
     domain = Domain.join(patches, connectivity, 'domain')
 
     Va = ScalarFunctionSpace('Va', A)