Trapping 3-way merge #459
Open
Trapping 3-way merge #459
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…s into single file (and objective function), fixed some test errors, fixed issue where trapping algorithm Qijk piece was slightly off (and reran notebooks).
…lambda machine. Rerunning the 9 mode von karman example is too intensive for my computer.
…tial fix for Von Karman street
…so cleaned up the linting in trapping_sr3.py
…sindy into trapping_extended
…sindy into trapping_extended
…aping format needs to be fortran style. Added some of the examples from the dysts database, some of which dont seem to quite be behaving -- need to look closer at these. Importantly, added functionality in the code and in the example for including a bias (constant) term in the dynamical equations.
…sindy into trapping_extended
…sindy into trapping_extended
…ing the enstrophy in the trapping theorem and split up the dysts examples into a separate script to make things easier to use.
…sindy into trapping_extended
…ndy_examples/. Now includes four jupyter notebooks, for the local stability, for dysts and lid-cavity flow examples, for using the enstrophy with the trapping theorem, and for the original trapping SINDy paper notebook. Added all the mutual functions to the trapping_utils file.
…e system was added. More to add and polish in the future
…think we have some bugs left. The global version is still imposing the constraints on Q instead of on PQ. I think I fixed this for the local version but now not getting reasonably results, so probably there are bugs in both.
…tally symmetric part as well
This was referenced Jan 16, 2024
Merged
Closed
Comment on lines
+32
to
+38
| <<<<<<< HEAD | ||
| python-version: ["3.8", "3.10"] | ||
| ||||||| 5c6e9fd | ||
| python-version: [3.7, 3.8] | ||
| ======= | ||
| python-version: [3.7, 3.8, 3.9] | ||
| >>>>>>> origin/trapping_extended |
There was a problem hiding this comment.
So what happened here is that
- I bumped the minimum version to 3.8, as python 3.7 reached end of life
- I bumped the maximum version to the version of python to the max version in "security" maintenance support.
- I changed the type from numeric to string, because YAML be like that.
I didn't want to test intermediate versions for CI reasons, but maybe its better to. I could go either way.
This is a case where I'd recommend just going with HEAD. Thoughts?
Comment on lines
+319
to
+344
| <<<<<<< HEAD | ||
| def quadratic_library(): | ||
| ||||||| 5c6e9fd | ||
| def data_quadratic_library(): | ||
| ======= | ||
| def data_quadratic_library_with_bias(): | ||
| library_functions = [ | ||
| lambda x: x, | ||
| lambda x, y: x * y, | ||
| lambda x: x**2, | ||
| ] | ||
| function_names = [ | ||
| lambda x: str(x), | ||
| lambda x, y: "{} * {}".format(x, y), | ||
| lambda x: "{}^2".format(x), | ||
| ] | ||
| return CustomLibrary( | ||
| library_functions=library_functions, | ||
| function_names=function_names, | ||
| include_bias=True, | ||
| ) | ||
|
|
||
|
|
||
| @pytest.fixture | ||
| def data_quadratic_library(): | ||
| >>>>>>> origin/trapping_extended |
There was a problem hiding this comment.
Makes sense to add this 👍 . Couldn't we just use PolynomialLibrary though?
Comment on lines
+848
to
+853
| <<<<<<< HEAD:test/test_feature_library.py | ||
| differentiation_method=FiniteDifference(), | ||
| ||||||| 5c6e9fd:test/feature_library/test_feature_library.py | ||
| differentiation_method=FiniteDifference(drop_endpoints=True), | ||
| ======= | ||
| >>>>>>> origin/trapping_extended:test/feature_library/test_feature_library.py |
There was a problem hiding this comment.
LGTM, equivalent edits, prefer trapping_extended.
Comment on lines
+862
to
+867
| <<<<<<< HEAD:test/test_feature_library.py | ||
| differentiation_method=FiniteDifference(), | ||
| ||||||| 5c6e9fd:test/feature_library/test_feature_library.py | ||
| differentiation_method=FiniteDifference(drop_endpoints=True), | ||
| ======= | ||
| >>>>>>> origin/trapping_extended:test/feature_library/test_feature_library.py |
There was a problem hiding this comment.
LGTM, equivalent edits, prefer trapping_extended
Comment on lines
+123
to
+146
| @pytest.mark.parametrize( | ||
| "optimizer", | ||
| [ | ||
| STLSQ(), | ||
| SSR(), | ||
| SSR(criteria="model_residual"), | ||
| SR3(), | ||
| ConstrainedSR3(), | ||
| StableLinearSR3(), | ||
| TrappingSR3(), | ||
| Lasso(fit_intercept=False), | ||
| ElasticNet(fit_intercept=False), | ||
| MIOSR(), | ||
| ], | ||
| ) | ||
| def test_fit_2d(data_derivative_2d, optimizer): | ||
| x, x_dot = data_derivative_2d | ||
| opt = SINDyOptimizer(optimizer, unbias=False) | ||
| model = SINDy(optimizer=opt) | ||
| model.fit(x, x_dot=x_dot) | ||
|
|
||
| check_is_fitted(opt) | ||
| assert opt.complexity >= 0 | ||
| assert opt.coef_.shape == (2, 6) |
There was a problem hiding this comment.
I put a lot of work into cutting down test time, so sorry if I'm a bit particular here. For my thoughts on testing, see Kent Beck's test desiderata
- Did this test address a specific bug?
- Tests of optimizers shouldn't need to create a full
SINDymodel - I believe we've removed the
SINDyOptimizer(unbias passed directly to model) - Bugs in init are caused when this module is loaded, preventing running other tests. Could be mitigated with lazy fixture loading, construction inside test, or by following sklearn convention of a minimalistic
__init__. - Why test complexity? That the default parameters here find a solution for arbitrary 2D data seems iffy.
For context, here's the full commit that added these lines:
6178df9 2023-03-16 Added a fix to the soft constraints functionality. Issue was the reshaping format needs to be fortran style. Added some of the examples from the dysts database, some of which dont seem to quite be behaving -- need to look closer at these. Importantly, added functionality in the code and in the example for including a bias (constant) term in the dynamical equations. Alan Kaptanoglu
examples/17_trapping_inequality.ipynb | 1369 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++----------------
examples/8_trapping_sindy_paper_examples.ipynb | 186 ++++++++++----------
pysindy/optimizers/trapping_sr3.py | 101 +++++------
test/conftest.py | 19 +++
test/optimizers/test_optimizers.py | 147 +++++++++++-----
test/test_pysindy.py | 4 +-
Comment on lines
+240
to
+246
| <<<<<<< HEAD:test/test_optimizers.py | ||
| ||||||| 5c6e9fd:test/optimizers/test_optimizers.py | ||
| dict(inequality_constraints=True, evolve_w=False), | ||
| ======= | ||
| dict(inequality_constraints=True, evolve_w=False), | ||
| dict(inequality_constraints=True), | ||
| >>>>>>> origin/trapping_extended:test/optimizers/test_optimizers.py |
There was a problem hiding this comment.
I removed the evolve_w arg, you added the inequality constraints option. So both commits have some value. I'd recommend approving both removing the evolve_w param and adding your param without it.
Comment on lines
+529
to
+592
| @pytest.mark.parametrize( | ||
| "trapping_sr3_params", | ||
| [ | ||
| dict(), | ||
| dict(accel=True), | ||
| ], | ||
| ) | ||
| @pytest.mark.parametrize( | ||
| "params", | ||
| [ | ||
| dict(thresholder="l1", threshold=0), | ||
| dict(thresholder="l1", threshold=1e-5), | ||
| dict( | ||
| thresholder="weighted_l1", | ||
| thresholds=np.zeros((3, 10)), | ||
| eta=1e5, | ||
| alpha_m=1e4, | ||
| alpha_A=1e5, | ||
| ), | ||
| dict(thresholder="weighted_l1", thresholds=1e-5 * np.ones((3, 10))), | ||
| dict(thresholder="l2", threshold=0), | ||
| dict(thresholder="l2", threshold=1e-5), | ||
| dict(thresholder="weighted_l2", thresholds=np.zeros((3, 10))), | ||
| dict(thresholder="weighted_l2", thresholds=1e-5 * np.ones((3, 10))), | ||
| ], | ||
| ) | ||
| def test_trapping_sr3_quadratic_library_with_bias( | ||
| params, trapping_sr3_params, data_quadratic_library_with_bias | ||
| ): | ||
| np.random.seed(100) | ||
| x = np.random.standard_normal((100, 3)) | ||
|
|
||
| sindy_library = data_quadratic_library_with_bias | ||
| params.update(trapping_sr3_params) | ||
|
|
||
| opt = TrappingSR3(**params) | ||
| model = SINDy(optimizer=opt, feature_library=sindy_library) | ||
| model.fit(x) | ||
| assert opt.PL_unsym_.shape == (3, 3, 3, 10) | ||
| assert opt.PL_.shape == (3, 3, 3, 10) | ||
| assert opt.PQ_.shape == (3, 3, 3, 3, 10) | ||
| check_is_fitted(model) | ||
|
|
||
| # Rerun with identity constraints | ||
| r = 3 | ||
| N = 10 | ||
| p = r + r * (r - 1) + int(r * (r - 1) * (r - 2) / 6.0) | ||
| params["constraint_rhs"] = np.zeros(p) | ||
| params["constraint_lhs"] = np.eye(p, r * N) | ||
|
|
||
| opt = TrappingSR3(**params) | ||
| model = SINDy(optimizer=opt, feature_library=sindy_library) | ||
| model.fit(x) | ||
| assert opt.PL_unsym_.shape == (3, 3, 3, 10) | ||
| assert opt.PL_.shape == (3, 3, 3, 10) | ||
| assert opt.PQ_.shape == (3, 3, 3, 3, 10) | ||
| check_is_fitted(model) | ||
| # check is solve was infeasible first | ||
| if not np.allclose(opt.m_history_[-1], opt.m_history_[0]): | ||
| print(model.coefficients()) | ||
| zero_inds = [0, 1, 4, 7, 10, 13, 17, 20, 23, 26] | ||
| assert np.allclose((model.coefficients().flatten())[zero_inds], 0.0, atol=1e-5) | ||
|
|
||
|
|
There was a problem hiding this comment.
🏁🏁🏁🏁 for review later
We should see if this could be merely a parametrization of the test without bias. It uses different data and checks specific indices for zeros, but it's difficult to see why these terms are zero under all of the different weights and arguments in the signature.
Worse comes to worse we can add it (though def need to time this test, and maybe see if it's possible to shrink the size of the problem)
Comment on lines
+862
to
+872
| <<<<<<< HEAD:test/test_optimizers.py | ||
| x = x.reshape(-1, 1) | ||
| optimizer.max_iter = 0 # normally prohibited in constructor | ||
|
|
||
| ||||||| 5c6e9fd:test/optimizers/test_optimizers.py | ||
| x = x.reshape(-1, 1) | ||
|
|
||
| ======= | ||
| if len(x.shape) == 1: | ||
| x = x.reshape(-1, 1) | ||
| >>>>>>> origin/trapping_extended:test/optimizers/test_optimizers.py |
There was a problem hiding this comment.
How would we not know the shape of a test fixture?
Comment on lines
+877
to
+887
| <<<<<<< HEAD:test/test_optimizers.py | ||
| @pytest.mark.parametrize( | ||
| "optimizer", | ||
| [(ConstrainedSR3, {"max_iter": 80}), (TrappingSR3, {"max_iter": 100}), (MIOSR, {})], | ||
| ) | ||
| ||||||| 5c6e9fd:test/optimizers/test_optimizers.py | ||
| @pytest.mark.parametrize("optimizer", [ConstrainedSR3, TrappingSR3, MIOSR]) | ||
| ======= | ||
| # @pytest.mark.parametrize("optimizer", [ConstrainedSR3, TrappingSR3, MIOSR]) | ||
| @pytest.mark.parametrize("optimizer", [ConstrainedSR3, MIOSR]) | ||
| >>>>>>> origin/trapping_extended:test/optimizers/test_optimizers.py |
There was a problem hiding this comment.
🏁 🏁 🏁 🏁
tbh this was always a not-great test that does a whole lot of work in order to test whether it can accept row format constraints. And I want to get out of the business of two different constraint formats. So I'm happy to cut Trapping out of this list. But let's see if my change passes, once all is said and done.
Comment on lines
+336
to
+345
| <<<<<<< HEAD | ||
| def test_fit_multiple_trajectores(data_multiple_trajectories): | ||
| x, t = data_multiple_trajectories | ||
| ||||||| 5c6e9fd | ||
| def test_fit_multiple_trajectores(data_multiple_trajctories): | ||
| x, t = data_multiple_trajctories | ||
| ======= | ||
| def test_fit_multiple_trajectories(data_multiple_trajctories): | ||
| x, t = data_multiple_trajctories | ||
| >>>>>>> origin/trapping_extended |
There was a problem hiding this comment.
Good spelling catch :) yours is the right one here.
| dict(thresholder="l1", threshold=2, expected=2.5), | ||
| dict(thresholder="weighted_l1", thresholds=0.5 * np.ones((1, 2)), expected=1.0), | ||
| dict(thresholder="l2", threshold=2, expected=1.5), | ||
| dict( | ||
| thresholder="weighted_l2", thresholds=0.5 * np.ones((1, 2)), expected=0.75 | ||
| ), | ||
| ||||||| 5c6e9fd:test/optimizers/test_optimizers.py |
There was a problem hiding this comment.
🏁 🏁 🏁 🏁
This test almost deserves its own PR given the different directions we've gone with it. Just enumerating there to come back later:
- trapping_extended adds threshold=0 cases
- I shrunk size of problem from lorenz to mini
- You removed second test case
- I added testing for specific values equal to zero
But since I shifted the actual cvxpy work to ConsrainedSR3, it may make sense, if the point of this is just to check that inequality constraints are added, to remove this test?
This was referenced Apr 17, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Conflict resolution branch for @Jacob-Stevens-Haas @MPeng5 @akaptano.
We'll code review each merge conflict bit by bit, and as we resolve them, I'll push changes to this branch and backport them to a shadow branch to maintain testability.