Fix adaptive refinement by FilippoOlivo · Pull Request #571 · mathLab/PINA

FilippoOlivo · 2025-05-08T10:12:45Z

Description

This PR fixes #539

Checklist

Code follows the project’s Code Style Guidelines
Tests have been added or updated
Documentation has been updated if necessary
Pull request is linked to an open issue

github-actions · 2025-05-13T12:54:08Z

Code Coverage Summary

Filename                                                   Stmts    Miss  Cover    Missing
-------------------------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------
__init__.py                                                    7       0  100.00%
collector.py                                                  39       1  97.44%   46
graph.py                                                     114      11  90.35%   99-100, 112, 124, 126, 142, 144, 166, 169, 182, 271
label_tensor.py                                              251      32  87.25%   81, 121, 144-148, 165, 177, 182, 188-193, 273, 280, 332, 334, 348, 444-447, 490, 537, 629, 649-651, 664-673, 688, 710
operator.py                                                   68       5  92.65%   250-268, 457
operators.py                                                   6       6  0.00%    3-12
plotter.py                                                     1       1  0.00%    3
trainer.py                                                    75       6  92.00%   195-204, 293, 314, 318, 322
utils.py                                                      56       8  85.71%   113, 150, 153, 156, 192-195
adaptive_function/__init__.py                                  3       0  100.00%
adaptive_function/adaptive_function.py                        55       0  100.00%
adaptive_function/adaptive_function_interface.py              51       6  88.24%   98, 141, 148-151
adaptive_functions/__init__.py                                 6       6  0.00%    3-12
callback/__init__.py                                           5       0  100.00%
callback/linear_weight_update_callback.py                     28       1  96.43%   63
callback/optimizer_callback.py                                22       1  95.45%   34
callback/processing_callback.py                               49       5  89.80%   42-43, 73, 168, 171
callback/refinement/__init__.py                                3       0  100.00%
callback/refinement/r3_refinement.py                          28       1  96.43%   88
callback/refinement/refinement_interface.py                   50       5  90.00%   32, 59, 67, 72, 78
callbacks/__init__.py                                          6       6  0.00%    3-12
condition/__init__.py                                          7       0  100.00%
condition/condition.py                                        35       8  77.14%   23, 127-128, 131-132, 135-136, 151
condition/condition_interface.py                              37       4  89.19%   31, 76, 100, 122
condition/data_condition.py                                   26       1  96.15%   56
condition/domain_equation_condition.py                        19       0  100.00%
condition/input_equation_condition.py                         44       1  97.73%   129
condition/input_target_condition.py                           44       1  97.73%   125
data/__init__.py                                               3       0  100.00%
data/data_module.py                                          204      22  89.22%   42-53, 133, 173, 194, 233, 314-318, 324-328, 400, 467, 547, 638, 640
data/dataset.py                                               85       7  91.76%   42, 123-126, 256, 307
domain/__init__.py                                            10       0  100.00%
domain/cartesian.py                                          112      10  91.07%   37, 47, 75-76, 92, 97, 103, 246, 256, 264
domain/difference_domain.py                                   25       2  92.00%   54, 87
domain/domain_interface.py                                    20       5  75.00%   37-41
domain/ellipsoid.py                                          104      24  76.92%   52, 56, 127, 250-257, 269-282, 286-287, 290, 295
domain/exclusion_domain.py                                    28       1  96.43%   86
domain/intersection_domain.py                                 28       1  96.43%   85
domain/operation_interface.py                                 26       1  96.15%   88
domain/simplex.py                                             72      14  80.56%   62, 207-225, 246-247, 251, 256
domain/union_domain.py                                        25       2  92.00%   43, 114
equation/__init__.py                                           4       0  100.00%
equation/equation.py                                          11       0  100.00%
equation/equation_factory.py                                  24      10  58.33%   37, 62-75, 97-110, 132-145
equation/equation_interface.py                                 4       0  100.00%
equation/system_equation.py                                   22       0  100.00%
geometry/__init__.py                                           7       7  0.00%    3-15
loss/__init__.py                                               7       0  100.00%
loss/loss_interface.py                                        17       2  88.24%   45, 51
loss/lp_loss.py                                               15       0  100.00%
loss/ntk_weighting.py                                         26       0  100.00%
loss/power_loss.py                                            15       0  100.00%
loss/scalar_weighting.py                                      16       0  100.00%
loss/weighting_interface.py                                    6       0  100.00%
model/__init__.py                                             10       0  100.00%
model/average_neural_operator.py                              31       2  93.55%   73, 82
model/deeponet.py                                             93      13  86.02%   187-190, 209, 240, 283, 293, 303, 313, 323, 333, 488, 498
model/feed_forward.py                                         89      11  87.64%   58, 195, 200, 278-292
model/fourier_neural_operator.py                              78      10  87.18%   96-100, 110, 155-159, 218, 220, 242, 342
model/graph_neural_operator.py                                40       2  95.00%   58, 60
model/kernel_neural_operator.py                               34       6  82.35%   83-84, 103-104, 123-124
model/low_rank_neural_operator.py                             27       2  92.59%   89, 98
model/multi_feed_forward.py                                   12       5  58.33%   25-31
model/spline.py                                               89      37  58.43%   30, 41-66, 69, 128-132, 135, 159-177, 180
model/block/__init__.py                                       12       0  100.00%
model/block/average_neural_operator_block.py                  12       0  100.00%
model/block/convolution.py                                    64      13  79.69%   77, 81, 85, 91, 97, 111, 114, 151, 161, 171, 181, 191, 201
model/block/convolution_2d.py                                146      27  81.51%   155, 162, 282, 314, 379-433, 456
model/block/embedding.py                                      48       7  85.42%   93, 143-146, 155, 168
model/block/fourier_block.py                                  31       0  100.00%
model/block/gno_block.py                                      22       4  81.82%   73-77, 87
model/block/integral.py                                       18       4  77.78%   22-25, 71
model/block/low_rank_block.py                                 24       0  100.00%
model/block/orthogonal.py                                     37       0  100.00%
model/block/pod_block.py                                      73      10  86.30%   55-58, 70, 83, 113, 148-153, 187, 212
model/block/rbf_block.py                                     179      25  86.03%   18, 42, 53, 64, 75, 86, 97, 223, 280, 282, 298, 301, 329, 335, 363, 367, 511-524
model/block/residual.py                                       46       0  100.00%
model/block/spectral.py                                       83       4  95.18%   132, 140, 262, 270
model/block/stride.py                                         28       7  75.00%   55, 58, 61, 67, 72-74
model/block/utils_convolution.py                              22       3  86.36%   58-60
model/layers/__init__.py                                       6       6  0.00%    3-12
optim/__init__.py                                              5       0  100.00%
optim/optimizer_interface.py                                   7       0  100.00%
optim/scheduler_interface.py                                   7       0  100.00%
optim/torch_optimizer.py                                      14       0  100.00%
optim/torch_scheduler.py                                      19       2  89.47%   5-6
problem/__init__.py                                            6       0  100.00%
problem/abstract_problem.py                                  104      14  86.54%   52, 61, 101-106, 135, 147, 165, 239, 243, 272
problem/inverse_problem.py                                    22       0  100.00%
problem/parametric_problem.py                                  8       1  87.50%   29
problem/spatial_problem.py                                     8       0  100.00%
problem/time_dependent_problem.py                              8       0  100.00%
problem/zoo/__init__.py                                        8       0  100.00%
problem/zoo/advection.py                                      33       7  78.79%   36-38, 52, 108-110
problem/zoo/allen_cahn.py                                     20       6  70.00%   20-22, 34-36
problem/zoo/diffusion_reaction.py                             29       5  82.76%   94-104
problem/zoo/helmholtz.py                                      30       6  80.00%   36-42, 103-107
problem/zoo/inverse_poisson_2d_square.py                      31       0  100.00%
problem/zoo/poisson_2d_square.py                              19       3  84.21%   65-70
problem/zoo/supervised_problem.py                             11       0  100.00%
solver/__init__.py                                             6       0  100.00%
solver/garom.py                                              107       2  98.13%   129-130
solver/solver.py                                             188      10  94.68%   192, 215, 287, 290-291, 350, 432, 515, 556, 562
solver/ensemble_solver/__init__.py                             4       0  100.00%
solver/ensemble_solver/ensemble_pinn.py                       23       1  95.65%   104
solver/ensemble_solver/ensemble_solver_interface.py           27       0  100.00%
solver/ensemble_solver/ensemble_supervised.py                  9       0  100.00%
solver/physics_informed_solver/__init__.py                     8       0  100.00%
solver/physics_informed_solver/causal_pinn.py                 47       3  93.62%   157, 166-167
solver/physics_informed_solver/competitive_pinn.py            58       0  100.00%
solver/physics_informed_solver/gradient_pinn.py               17       0  100.00%
solver/physics_informed_solver/pinn.py                        18       0  100.00%
solver/physics_informed_solver/pinn_interface.py              47       1  97.87%   130
solver/physics_informed_solver/rba_pinn.py                    35       3  91.43%   155-158
solver/physics_informed_solver/self_adaptive_pinn.py          90       3  96.67%   315-318
solver/supervised_solver/__init__.py                           4       0  100.00%
solver/supervised_solver/reduced_order_model.py               24       1  95.83%   137
solver/supervised_solver/supervised.py                         7       0  100.00%
solver/supervised_solver/supervised_solver_interface.py       25       0  100.00%
solvers/__init__.py                                            6       6  0.00%    3-12
solvers/pinns/__init__.py                                      6       6  0.00%    3-12
TOTAL                                                       4550     502  88.97%

Results for commit: 2a316a8

Minimum allowed coverage is 80.123%

♻️ This comment has been updated with latest results

Copilot

Pull Request Overview

This PR fixes issue #539 by refactoring the adaptive refinement functionality and updating the related tests and documentation. Key changes include the migration of the R3Refinement callback to a new module structure, the removal of the deprecated adaptive_refinement_callback, and an addition of a dataset update method to support the new refinement logic.

Reviewed Changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tests/test_callback/test_adaptive_refinement_callback.py	Updated imports and test functions for the new R3Refinement callback, including a keyword change from "callback" to "callbacks".
pina/data/dataset.py	Added update_data() method to enable dataset updates with new conditions.
pina/callback/refinement/refinement_interface.py	Introduced the new refinement interface with adaptive point updating logic.
pina/callback/refinement/r3_refinement.py	Implemented the R3Refinement callback for adaptive point sampling.
pina/callback/adaptive_refinement_callback.py	Removed the deprecated adaptive refinement callback implementation.
pina/callback/init.py	Updated callback exports to reflect the new module structure.
docs	Revised documentation to reference updated module paths for refinement callbacks.

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

FilippoOlivo · 2025-05-14T13:47:49Z

@dario-coscia I fixed codacy warnings in your code! Let me know if the changes are ok!

dario-coscia · 2025-05-14T13:59:55Z

@dario-coscia I fixed codacy warnings in your code! Let me know if the changes are ok!

Great! Code-wise and test, I think we are ready to go. Would you mind adjusting the docstrings ?

FilippoOlivo · 2025-05-14T16:09:46Z

@dario-coscia Done!

dario-coscia · 2025-05-15T08:48:56Z

For me is good to go, @GiovanniCanali what do you think?

GiovanniCanali

Very nice update! I left few comments to address before merging.

GiovanniCanali · 2025-05-15T09:40:05Z

+        parameter.
+
+        :param dict new_conditions_dict: Dictionary containing the new data.
+        :type new_conditions_dict: dict


Please, remove :type new_conditions_dict: dict, as type is already specified in the previous line.

GiovanniCanali · 2025-05-15T09:49:29Z

+        :param ~lightning.pytorch.trainer.trainer.Trainer: The trainer object.
+        :param PINNInterface solver: The solver object.
+        """
+        if trainer.current_epoch % self.sample_every == 0:


I would modify this control as follows:

if (trainer.current_epoch % self.sample_every == 0) and (trainer.current_epoch != 0)

This is done to avoid resampling after the first epoch.

GiovanniCanali · 2025-05-15T09:52:27Z

+        :param solver: The solver object.
+        :return: New points sampled based on the R3 strategy.
+        :rtype: LabelTensor
+        """


Please, add parameters' type to this docstring.

* Fix adaptive refinement (#571) --------- Co-authored-by: Dario Coscia <93731561+dario-coscia@users.noreply.github.com> * Remove collector * Fixes * Fixes * rm unnecessary comment * fix advection (#581) * Fix tutorial .html link (#580) * fix problem data collection for v0.1 (#584) * Message Passing Module (#516) * add deep tensor network block * add interaction network block * add radial field network block * add schnet block * add equivariant network block * fix + tests + doc files * fix egnn + equivariance/invariance tests Co-authored-by: Dario Coscia <dariocos99@gmail.com> --------- Co-authored-by: giovanni <giovanni.canali98@yahoo.it> Co-authored-by: AleDinve <giuseppealessio.d@student.unisi.it> * add type checker (#527) --------- Co-authored-by: Filippo Olivo <filippo@filippoolivo.com> Co-authored-by: Giovanni Canali <115086358+GiovanniCanali@users.noreply.github.com> Co-authored-by: giovanni <giovanni.canali98@yahoo.it> Co-authored-by: AleDinve <giuseppealessio.d@student.unisi.it>

* Fix adaptive refinement (mathLab#571) --------- Co-authored-by: Dario Coscia <93731561+dario-coscia@users.noreply.github.com> * Remove collector * Fixes * Fixes * rm unnecessary comment * fix advection (mathLab#581) * Fix tutorial .html link (mathLab#580) * fix problem data collection for v0.1 (mathLab#584) * Message Passing Module (mathLab#516) * add deep tensor network block * add interaction network block * add radial field network block * add schnet block * add equivariant network block * fix + tests + doc files * fix egnn + equivariance/invariance tests Co-authored-by: Dario Coscia <dariocos99@gmail.com> --------- Co-authored-by: giovanni <giovanni.canali98@yahoo.it> Co-authored-by: AleDinve <giuseppealessio.d@student.unisi.it> * add type checker (mathLab#527) --------- Co-authored-by: Filippo Olivo <filippo@filippoolivo.com> Co-authored-by: Giovanni Canali <115086358+GiovanniCanali@users.noreply.github.com> Co-authored-by: giovanni <giovanni.canali98@yahoo.it> Co-authored-by: AleDinve <giuseppealessio.d@student.unisi.it>

FilippoOlivo force-pushed the refinement branch from 03a8f31 to e9f47c8 Compare May 8, 2025 10:14

FilippoOlivo linked an issue May 8, 2025 that may be closed by this pull request

Updating Refinement classes #539

Closed

FilippoOlivo self-assigned this May 8, 2025

FilippoOlivo added enhancement New feature or request pr-to-fix Label for PR that needs modification labels May 8, 2025

FilippoOlivo changed the title ~~Refinement~~ Fix adaptive refinement May 8, 2025

dario-coscia force-pushed the dev branch from e88aafa to 6b355b4 Compare May 13, 2025 09:25

Fix adaptive refinement

90701f6

FilippoOlivo force-pushed the refinement branch 4 times, most recently from 5e9ccc6 to ca57ef0 Compare May 13, 2025 12:48

FilippoOlivo added 2 commits May 13, 2025 15:02

Reimplement refinement

eb18138

Fix doc

518264d

FilippoOlivo force-pushed the refinement branch from ca57ef0 to 518264d Compare May 13, 2025 13:03

FilippoOlivo requested a review from Copilot May 13, 2025 13:34

Copilot AI reviewed May 13, 2025

View reviewed changes

Comment thread tests/test_callback/test_adaptive_refinement_callback.py Outdated

Comment thread pina/data/dataset.py Outdated

Comment thread pina/callback/refinement/refinement_interface.py Outdated

FilippoOlivo and others added 3 commits May 13, 2025 15:37

Fix doc

1a05642

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Fix test

abb8718

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

clean code

1e9e920

dario-coscia force-pushed the refinement branch from 1a05f38 to 1e9e920 Compare May 14, 2025 11:58

Monthly Tag bot and others added 2 commits May 14, 2025 14:43

fix tests

360943e

Fix codacy

36d4924

FilippoOlivo marked this pull request as ready for review May 14, 2025 13:47

FilippoOlivo marked this pull request as draft May 14, 2025 13:47

dario-coscia force-pushed the refinement branch from 36d4924 to b76b5a5 Compare May 14, 2025 13:56

Fix docstring

0666cf4

FilippoOlivo force-pushed the refinement branch from b76b5a5 to 0666cf4 Compare May 14, 2025 16:08

dario-coscia added 2 commits May 14, 2025 18:54

add white space

9e69796

update doc

eb0b17c

dario-coscia approved these changes May 14, 2025

View reviewed changes

dario-coscia marked this pull request as ready for review May 14, 2025 16:57

dario-coscia requested a review from GiovanniCanali May 14, 2025 16:57

dario-coscia added pr-to-review Label for PR that are ready to been reviewed and removed pr-to-fix Label for PR that needs modification labels May 14, 2025

GiovanniCanali requested changes May 15, 2025

View reviewed changes

Fixes

2a316a8

FilippoOlivo requested a review from GiovanniCanali May 15, 2025 12:30

GiovanniCanali approved these changes May 16, 2025

View reviewed changes

FilippoOlivo merged commit ac0437b into dev May 16, 2025
19 checks passed

FilippoOlivo deleted the refinement branch May 16, 2025 12:45

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Fix adaptive refinement#571

Fix adaptive refinement#571
FilippoOlivo merged 12 commits into
devfrom
refinement

FilippoOlivo commented May 8, 2025 •

edited by dario-coscia

Loading

Uh oh!

github-actions Bot commented May 13, 2025 •

edited

Loading

Uh oh!

Copilot AI left a comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

FilippoOlivo commented May 14, 2025

Uh oh!

dario-coscia commented May 14, 2025

Uh oh!

FilippoOlivo commented May 14, 2025

Uh oh!

dario-coscia commented May 15, 2025

Uh oh!

GiovanniCanali left a comment

Uh oh!

GiovanniCanali May 15, 2025

Uh oh!

Uh oh!

GiovanniCanali May 15, 2025

Uh oh!

GiovanniCanali May 15, 2025

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Conversation

FilippoOlivo commented May 8, 2025 • edited by dario-coscia Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Description

Checklist

Uh oh!

github-actions Bot commented May 13, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Code Coverage Summary

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull Request Overview

Reviewed Changes

Uh oh!

Uh oh!

Uh oh!

Uh oh!

FilippoOlivo commented May 14, 2025

Uh oh!

dario-coscia commented May 14, 2025

Uh oh!

FilippoOlivo commented May 14, 2025

Uh oh!

dario-coscia commented May 15, 2025

Uh oh!

GiovanniCanali left a comment

Choose a reason for hiding this comment

Uh oh!

GiovanniCanali May 15, 2025

Choose a reason for hiding this comment

Uh oh!

Uh oh!

GiovanniCanali May 15, 2025

Choose a reason for hiding this comment

Uh oh!

GiovanniCanali May 15, 2025

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

FilippoOlivo commented May 8, 2025 •

edited by dario-coscia

Loading

github-actions Bot commented May 13, 2025 •

edited

Loading