Improve `Geometry` class by yguclu · Pull Request #527 · pyccel/psydac

yguclu · 2025-10-07T13:17:21Z

Add new factory class method from_file
Use __init__ method in all factory class methods (from_file, from_discrete_mapping, and from_topological_domain)
Discourage direct use of __init__ (factory class methods should be preferred)
Add mandatory pdim parameter (number of dimensions of physical domain) to __init__
Clean up and document (with docstrings) the factory class methods
Add Pytest mark @pytest.mark.xdist_group('h5py') to all tests in psydac.cad.tests.test_geometry, because h5py is not thread-safe

Moreover:

Use SymPDE version 0.20.0
Always provide interface orientation to the join constructor of Domain objects (from sympde.topology.domain)
Add interface orientation to multipatch geometry files (in the folder psydac/cad/mesh/multipatch)
Use ubuntu_installations action in documentation workflow
Fix module name in documentation sources: cmd.mesh >> cmd.psydac_mesh

TO DO:

In from_file, make sure that the domain argument (an instance of sympde.topology.Domain) is compatible with the topological domain defined in the .yml section of the HDF5 file.
Update unit tests in cad.tests.test_geometry:
- Add some 1D unit tests
- Add proper asserts statements to test_geometry_2d_1 and test_geometry_2d_2
- Remove obsolete test function test_geometry_1
- Test functions from cad.cad in new module cad.tests.test_cad
After release of SymPDE version 0.20.0, update pyproject.toml and run all unit tests once again on all platforms
Mention SymPDE 0.20.0 in PR description
Mention SymPDE 0.20.0 in CHANGELOG.md

- Write 3D geometry in parallel without `mpi_dims_mask` - Read 3D geometry in parallel with `mpi_dims_mask` - Verify correct distribution of domain for any number of MPI processes

Add parameter `mpi_dims_mask` to class method `from_discrete_mapping` and bound method `read`.

Use new variable for dictionary with number of cells for each patch.

test methods from_discrete_mapping and from_topological_domain with mpi_dims_mask

- Add new constructor Geometry.from_file - Remove `filename` from __init__ parameters

commit ccbd6e3 Author: Yaman Güçlü <yaman.guclu@gmail.com> Date: Wed Oct 1 06:25:42 2025 +0200 Allow `mpi_dims_mask` with geometry file (#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 <alisa.kirkinskaia@tum.de> Co-authored-by: Alisa Kirkinskaia <alisa.kirkinsk@gmail.com>

… constructor

- Add function `get_available_mappings` - Clean up function `discrete_mapping` and add docstring to it

Use the custom action `ubuntu_install` for installing non-Python dependencies, like in the `testing` workflow. Add a separate step to install the packages `graphviz` and `pandoc` required for documentation.

campospinto · 2026-02-12T15:02:13Z

+    The Geometry object can be created in four ways:
+    - case 0 : providing a `Domain` to `__init__` with detailed parameters for each patch.
+    - case 1 : passing the path to a geometry file to `from_file`.
+    - case 2 : passing a `SplineMapping` to `from_discrete_mapping` (single patch).
+    - case 3 : passing a `Domain`, ncells, and periodicity to `from_topological_domain` (single or multi-patch).



It's very nice to list these cases!
Maybe we should also specify here which cases should be suggested to users ?
My feeling is that case 0 should only be used "internally", i.e. called by existing functions

edit 1: ok I see now that this is also explained in the PR description. then I suggest to specify it in this docstring as well.

edit2: it would be useful to indicate also here that case 1 and 3 are called by the discretize_domain interface (or just discretize called on a SymPDE Domain)

In particular, I would suggest to remove or rewrite the direct constructions of Geometry objects in cad/cad.py, to avoid giving bad ideas

Do you mean the script-like code on the bottom of cad/cad.py? I believe that code does not work right now, so we could either remove it or try to create a unit test out of it

yes, I guess I was referring to these calls to the Geometry constructor. Since these are not advised the best is probably to remove them

Excluding some unit tests (which naturally have to test also the __init__ function), I can find those calls only at the bottom of cad/cad.py. That is why I was asking

campospinto · 2026-02-12T15:12:15Z

    #--------------------------------------------------------------------------
    @classmethod
    def from_topological_domain(cls, domain, ncells, *, periodic=None, comm=None, mpi_dims_mask=None):
        interior = domain.interior


here I suggest checking that domain is of correct type (a symPDE Domain I guess)

Done in 349eee8

campospinto · 2026-02-12T15:20:14Z

+        return Geometry.from_file(filename, comm=comm, mpi_dims_mask=mpi_dims_mask)



codacy-production · 2026-04-21T14:24:13Z

Up to standards ✅

🟢 Issues 0 issues

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🟢 Metrics 18 complexity · 0 duplication

Metric Results

Complexity 18

Duplication 0

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🟢 Coverage 81.91% diff coverage

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Diff coverage ✅ 81.91% diff coverage

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Head commit (2cb2971) 49506 32929 66.52%

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yguclu and others added 28 commits September 18, 2025 15:27

Allow mpi_dims_mask with geometry file

461ae4e

unit test for mpi_dims_mask

1e46072

Update test_geometry.py

3376e31

- Write 3D geometry in parallel without `mpi_dims_mask` - Read 3D geometry in parallel with `mpi_dims_mask` - Verify correct distribution of domain for any number of MPI processes

Update geometry.py

2704716

Add parameter `mpi_dims_mask` to class method `from_discrete_mapping` and bound method `read`.

Update test_geometry.py

e1a13f8

Use new variable for dictionary with number of cells for each patch.

new tests for class Geometry

51a32da

test methods from_discrete_mapping and from_topological_domain with mpi_dims_mask

run only my tests

505db31

run only my tests

39c51a4

run only my tests

34e42e6

run only my tests

90553f9

run only my tests

243d2b1

run only my tests

9bfda59

fixed failing tests due to deleting file in parallel

f75df55

revert files

2a7bb4d

Merge branch 'devel' into yguclu-fix-mpi_dims_mask

659831d

Avoid function check_decomposition in tests

e7b6bfb

Fix typo in test_geometry.py

f6afb54

Improve Geometry class:

81b1c6d

- Add new constructor Geometry.from_file - Remove `filename` from __init__ parameters

Update Geometry unit tests

e3c30db

Do not create __psydac__ directory in parallel

7111b8e

Use Geometry.from_file in discretize_domain

cc097a3

Use correct parameter name (periods) in MultiPatchDomainDecomposition…

cd925fb

… constructor

Add mandatory parameter pdim to Geometry.__init__

f1b6bb1

Clean up Geometry.read()

2716065

Remove unused property is_parallel from Geometry

818be2a

Merge branch 'devel' into yguclu-improve-Geometry

31fbb37

Clean up module psydac.mapping.discrete_gallery:

cb8ccb5

- Add function `get_available_mappings` - Clean up function `discrete_mapping` and add docstring to it

campospinto mentioned this pull request Oct 17, 2025

Fix method plot_2d_decomposition of TensorFemSpace #529

Merged

3 tasks

yguclu mentioned this pull request Oct 17, 2025

Make plot_2d_decomposition use Geometry instead of TensorFemSpace #532

Open

yguclu added 4 commits February 10, 2026 14:15

Use SymPDE branch clean-multipatch-domain

a06a7d3

Provide interface orientation to Domain.join

e968bc5

Add interface orientation to multipatch geometry files

a31e07a

Merge branch 'devel' into yguclu-improve-Geometry

29e82cf

yguclu marked this pull request as ready for review February 11, 2026 10:50

yguclu added 3 commits February 12, 2026 11:32

Use ubuntu_install action in documentation workflow

326952b

Use the custom action `ubuntu_install` for installing non-Python dependencies, like in the `testing` workflow. Add a separate step to install the packages `graphviz` and `pandoc` required for documentation.

Clone the latest release of PETSc (see PR #539)

800e506

Install mpi4py >= 4.0.0 in parallel_h5py action

9f092d3

campospinto reviewed Feb 12, 2026

View reviewed changes

yguclu mentioned this pull request Feb 23, 2026

Rework some tests for shorter CI runs #575

Merged

Merge branch 'devel' into yguclu-improve-Geometry

e41f301

yguclu added 7 commits April 21, 2026 17:12

Add missing orientation (-1 or +1) to connectivity in test_plot_field

3702e70

Minor cleanup

d91b2ba

Avoid deprecation warning about scipy.odr

0b426e2

Check input domain type in Geometry.from_topological_domain

349eee8

Add docstring to translate() in psydac.cad.cad

a84e24d

Merge branch 'devel' into yguclu-improve-Geometry

e291f2a

Test SymPDE version 0.20.0 (from GitHub)

b403819

yguclu marked this pull request as draft September 9, 2026 13:31

yguclu marked this pull request as ready for review September 9, 2026 13:32

yguclu added 2 commits September 11, 2026 18:18

Fix wrong action filename in docs workflow

ca148d0

Give name to checkout step in testing workflow

43082ab

yguclu marked this pull request as draft September 11, 2026 16:22

yguclu marked this pull request as ready for review September 11, 2026 16:22

Fix module name in documentation: cmd.mesh >> cmd.psydac_mesh

2cb2971

yguclu marked this pull request as draft September 11, 2026 16:36

yguclu marked this pull request as ready for review September 11, 2026 16:36

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Improve `Geometry` class - #527

Improve `Geometry` class#527
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		return Geometry.from_file(filename, comm=comm, mpi_dims_mask=mpi_dims_mask)

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yguclu commented Oct 7, 2025 •

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