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The usual siphon of Development into Main - #8
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The environment.yml file was link to the one in the obsolete .binder folder that we removed when we moved to a separate launch repository (for efficiency reasons) but we do need the file so ... it's back.
- environment.yml need numpy<2 - setup.cfg calls auto version label, half loading uw3 - remove for now. MUST pip install with '--no-build-isolation' argument for now.
Expressions need some simplification but first debugging the complicated version
We need to be careful to retain the original expression objects in solver F0 and F1 otherwise we lose the lazy evaluation property. This is for Stokes bodyforce and Stokes F0. Others have not been checked.
This is now a SW-NE specified box on the sphere. Clearly this needs some more work to be complete, particularly in coordinate transformations
It just seems inevitable that we have to have different builds for different machines at this point
Update petsc_generic_snes_solvers.pyx Fixes#277 to is not yet optimised. More work to come on that.
Adding function to collect data to kdtree points or from kdtree points in the RBF interpolator functionality. We tend to use both depending on the way we want to map between point clouds and so both ways need a general interface.
update two files - test_1130_IndexSwarmVariable.py Test IndexSwarmVariable in getting the right value on the Symmetrical Points. - Ex_IndexSwarmVariable.ipynb Vis the errors in the original code uw.swarm.IndexSwarmVariable._update(), and provide two methods to fix that. - MaterialA: the original code - MaterialB: assign the particles to the nearest mesh_levelset nodes, and calculate the material property value on mesh_levelset nodes from them. - MaterialC: calculate the material property value on mesh_levelset nodes from the nearest N particles directly. The values on mesh_levelset nodes (for M_0 indicated by red, P=10.0, for M_1 indicated by blue, P=1.0)  The particles used to calculate the value on nodes 6 (blue) and 7 (red) (nodes 6 & 7 are the points in the middle of the left and right wall)  Need a further review of these two methods. They work fine for the structured box, but not well in the unstructured_irregular box. ###
* set CC env variable Fixes issues with finding mpi * Gather the CC used by PETSc for UW3 extensions. Hopefully this is a fix for effiectively getting mpicc. Need to test using conda next. --------- Co-authored-by: Julian Giordani <julesghub@users.noreply.github.com>
1. Add version information back to install, it went missing in recent changes. 2. Remove git revision in utils.auditor - this can be done better when we move to pyproject.toml 3. Update setup.cfg to be numpy<2
Bug fixes: - expressions not evaluating when nested - Solvers: F0, F1 as expressions should not be recreated on assignment (or the lazy evaluation breaks) change this to be reassignment of the internal expression Changes: - Regional spherical mesh - changed the interface to work on geographical coordinates (more work required for coordinate transformations to be user-friendly but it is functional)
1. adding a minus sign to the solver._u_f0 (bodyforce term) 2. fix small bugs in meshing.BoxInternalBoundary
* Added pytest for vector advection with semi-Lagrangian * Modified vector advection pytest --------- Co-authored-by: Juan Carlos Graciosa <juan.graciosa@monash.edu>
…on. (#290) * Added parallel test for checking if particles are lost during nodal swarm advection in SLCN. * Changed test description. --------- Co-authored-by: Juan Carlos Graciosa <juan.graciosa@monash.edu>
* Attempt to align the 2 conda environments. More testing to come. * more tweaks to environment.yaml * Unifying conda environments for mac and intel * Removing `environment-macos.yml` * Adding Lior's packages * Comment on memory leak in parallel test (to revisit) * Moving as many packages from pip -> conda * Align codespaces to the new conda environment * Create UW3 docker using micromamba --------- Co-authored-by: Ben Knight <55677727+bknight1@users.noreply.github.com>
* Adding pyproject.toml for PEP518-ness. Now we can explore this more. * Adding a compile.sh. With pyproject.toml we always need --no-build-isolation on * compile.sh always outputs to `compile.log` * `compile.log` is gitignored
* Section on installation is update. * Added a section on uninstallation. * Added a `pip install -e` to build_api_docs.sh - that must be done otherwise pdoc fails.
* Added fix to mesh2mesh_meshVariable() * Added get_dof_partition() function for getting DOFs in each processor * Added option of not saving DOF viewer outputs in a file. --------- Co-authored-by: Juan Carlos Graciosa <juan.graciosa@monash.edu>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
do not return from within a context manager
Joss submission branch - bring changes into dev.
Swarm rework dev merged - pull all development branch changes back into the swarm rework for synchronisation and testing.
Some small corrections to PR #2
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Pull Request Overview
This PR merges development branch changes into main to keep up with PETSc compatibility and includes updates for JOSS submission requirements. The changes span multiple areas including test improvements, API updates, and visualization enhancements.
- Updates function evaluation API from
evalfto standardizedevaluatewithevalfparameter - Adds new test files for various functionality including swarm variables, semi-Lagrangian methods, and geometry tools
- Enhances visualization capabilities with direct PyVista mesh creation and improved function evaluation
Reviewed Changes
Copilot reviewed 81 out of 92 changed files in this pull request and generated 6 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/test_1130_IndexSwarmVariable.py | New test for IndexSwarmVariable functionality with symmetrical point validation |
| tests/test_1100_SLVectorCartesian.py | New test for semi-Lagrangian vector field advection |
| tests/test_1100_AdvDiffCartesian.py | Updated advection-diffusion test with analytical solutions |
| tests/test_0505_rbf_swarm_mesh.py | Simplified RBF interpolation test with analytic field validation |
| tests/test_0504_projections.py | Updated function calls from evalf to evaluate with evalf=True |
| tests/test_0503_evaluate2.py | New comprehensive function evaluation test suite |
| tests/test_0503_evaluate.py | Streamlined evaluation tests with API updates |
| tests/test_0101_kdtree.py | Updated KDTree tests to use new API and improved assertions |
| tests/test_0050_utils.py | Minor visualization and test utility updates |
| tests/test_0004_pointwise_fns.py | Updated string matching for JIT processing output |
| tests/test_0002_swarm.py | Added test for addNPoints functionality |
| tests/parallel/ptest_004_nodal_swarm_advection.py | New parallel test for nodal swarm advection |
| tests/parallel/ptest_002_projection.py | Added memory usage warning comment |
| tests/dont_test_0005_check_xdmf.py | New XDMF/HDF5 validation test (disabled) |
| test.sh | Enhanced test runner with better error handling and status reporting |
| src/underworld3/visualisation.py | Major refactor with direct PyVista mesh creation and API updates |
| src/underworld3/utilities/geometry_tools.py | New geometry utility functions for spatial operations |
| src/underworld3/utilities/create_dmplex_from_medit.py | Optimized MEDIT file processing with caching and efficiency improvements |
| src/underworld3/utilities/_utils.py | Added PostHog telemetry functionality and code cleanup |
| src/underworld3/utilities/init.py | Added imports for new geometry tools and PostHog |
| src/underworld3/systems/solvers.py | Extensive solver updates with new expression handling and DDT integrations |
| src/underworld3/systems/ddt.py | New time integration classes (Symbolic, Eulerian) and API improvements |
| src/underworld3/systems/init.py | Added imports for new solver and DDT classes |
Comments suppressed due to low confidence (1)
src/underworld3/utilities/_utils.py:257
- Function name 'postHog' doesn't follow Python naming conventions. It should be 'post_hog' or 'send_posthog_event' to be more descriptive and follow snake_case convention.
def postHog( event_name, ev_dict ):
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
lmoresi
commented
Jul 28, 2025
MemberAuthor
In person review with @jcgraciosa - will merge when you are ok with the changes. |
jcgraciosa
commented
Jul 28, 2025
Contributor
@lmoresi, I am okay with the changes. These can be merged. |
lmoresi
commented
Jul 28, 2025
MemberAuthor
Thanks, JC. |
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We need to do this to keep up with the PETSc changes (main currently does not build in the CI phase, dev does).
Also, JOSS submission needs to be completed and the auto builds / PETSc layers need to be part of this.