GEOPY-2522: Update simpeg fork to 0.25 #125
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Since zizmor is now available through conda-forge, we don't need to install it through `pip` when creating a conda environment from `environment.yml`.
Make `BaseDataMisfit.residual` to raise an error if the simulation returns an array with `nan`s and/or `inf`s after calling the `dpred` method. Add tests to check if the errors are correctly raised. Remove error in case `BaseDataMisfit.data` is `None`: the `data` setter method doesn't allow `BaseDataMisfit.data` to be `None`, therefore the error will never be raised.
Remove non-supported Python versions and add latest ones.
Use shell rendering in the runtime information required in the Bug Report Template.
Move some documentation pages like Getting Started, Examples and Tutorials inside the User Guide. Create a new `docs/content/user-guide` folder. Move Getting Started, Tutorials and Examples inside the new folder. Remove the `docs/content/user_guide.rst` and replace it by a `docs/content/user-guide/index.rst` file. Rename the `getting_started` folder into `getting-started` (to make a consistent use of the dash in urls). Update relevant index files, `docs/c onf.py`, `.gitignore` and `docs/Makefile`. Configure `sphinx-redirects` so Sphinx create dummy `.html` files for old locations of documentation pages that redirect to the new locations. Fix link to Octocat image.
Correctly use the "bug" label in the issue template for bug reports.
Fix the number of `../` should be pre-appended to the target link to generate the right redirect.
Assign the model before returning the Jacobian matrix. Don't use Numpy's `dot` function: it doesn't work propertly when mixing Numpy arrays and Scipy's sparse arrays. Use the matmul (`@`) operator instead. Add tests that catch the bug.
Fix manual redirect for the index page of the User Guide.
Add new `get_slice` and `get_all_slices` methods to `BaseSurvey` that mimics the behaviour of indexing `Data` objects. `get_slice` returns a `slice` object that can be used to slice flat arrays like data or uncertainty arrays. `get_all_slices` returns a dictionary with source-receiver pairs as keys, and their corresponding `slice` object as values. Optimize the implementation of these methods by working with slices rather than Numpy arrays with indices. Add tests for the new methods. Use `get_slice` in `Data`'s `__getitem__` and `__setitem__` instead of the `indexing_dictionary`. Add `typing_extensions` as a dependency for Python<3.13, and use the `deprecated` decorator to deprecate the `index_dictionary` property. --------- Co-authored-by: Joseph Capriotti <[email protected]>
…g#1622) Make the `G` property in the gravity survey to be either a 2D Numpy array, or a `scipy.sparse.LinearOperator` if `store_sensitivities` is set to `"forward_only"`. The `LinearOperator` is capable of performing operations like `G @ m` and `G.T @ v` without allocating the full `G` matrix on memory or disk. This allows `Jvec` and `Jtvec` to be called and not allocate the full `G` matrix. The `getJ` method also returns either a 2D Numpy array or a `LinearOperator` formed by the product between `G` and the `rhoDeriv` as a `LinearOperator` as well. Reimplement the `getJtJdiag` method: allow it to get the diagonal without building `G` if `"forward_only"`, optimize the computation of the diagonal when `G` is fully formed through `einsum`s, and fix the cache of `gtg_diagonal` by checking the hash of the `W` argument. Deprecate the public `gtg_diagonal` property. Extend docstrings of relevant methods. Add tests for all the new features. --------- Co-authored-by: Joseph Capriotti <[email protected]>
Increase maximum number of iterations in magnetic equivalent sources test.
#### Summary Allows multiple locations for EM1D receivers #### PR Checklist * [x] If this is a work in progress PR, set as a Draft PR * [x] Linted my code according to the [style guides](https://docs.simpeg.xyz/latest/content/getting_started/contributing/code-style.html). * [x] Added [tests](https://docs.simpeg.xyz/latest/content/getting_started/contributing/testing.html) to verify changes to the code. * [x] Added necessary documentation to any new functions/classes following the expect [style](https://docs.simpeg.xyz/latest/content/getting_started/contributing/documentation.html). * [x] Marked as ready for review (if this is was a draft PR), and converted to a Pull Request * [x] Tagged ``@simpeg/simpeg-developers`` when ready for review. #### Reference issue Closes simpeg#1629 #### What does this implement/fix? Allows for multiple locations in a single receiver for both 1D layered FDEM and TDEM simulations (and adds some simple testing to ensure it works).
Fix of the definition of `model` in J-related tests for the gravity simulation: use the inverse of the mapping to define the `model` based on the sample `densities`.
Fix typo, improve description of parameters and add some examples that can be tested.
Avoid using `dpred` in the gravity test that might lead to confusion. When the mapping is not a linear function, the `J @ m` is just a first order approximation of the forward model and not equal to the `dpred`.
Extend test of the `getJ` method of the gravity simulation: test the transpose of the `J` linear operator.
Add a new `.github/zizmor.yml` configuration file that allows zizmor to use tags to pin the two reviewdog actions we currently use: `reviewdog/action-flake8` and `reviewdog/action-black`.
Deprecate the `components` properties in potential field surveys. These properties weren't returning the expected output. Since receivers within the same survey can have different components, returning the components of the first receiver is misleading. --------- Co-authored-by: Joseph Capriotti <[email protected]>
Make use of `survey.nD` instead of just using the total number of receiver locations. Add the special case where `is_amplitude_data` is `True`. Add tests.
Use pytest's warning filter to make tests error when running a randomized discretize test that doesn't use a random seed.
Sets source list on potential fields receivers to the source field input (while ensuring their is only 1 item.
Make the `G` property in the magnetic survey to be either a 2D Numpy array, or a `scipy.sparse.LinearOperator` if `store_sensitivities` is set to `"forward_only"`. The `LinearOperator` is capable of performing operations like `G @ m` and `G.T @ v` without allocating the full `G` matrix on memory or disk. This allows `Jvec` and `Jtvec` to be called and not allocate the full `G` matrix. Overwrite the `getJ` method to return either a 2D Numpy array or a `LinearOperator` formed by the product between `G` and the `chiDeriv` as a `LinearOperator` as well. Reimplement the `getJtJdiag` method: allow it to get the diagonal without building `G` if `"forward_only"`, optimize the computation of the diagonal when `G` is fully formed through `einsum`s, and fix the cache of `gtg_diagonal` by checking the hash of the `W` argument. Raise `NotImplementedError`s in some methods when `is_amplitude_data` is `True`, specially the `"forward_only"` cases where we don't want to allocate the `G` matrix. Extend docstrings of relevant methods. Add tests for all the new features.
Use Numpy's RNG and ditch `unittest` in tests for depth weighting.
Overwrite the `getJ` method of the NSEM 1D finite volume simulations so they raise a `NotImplementedError`. Add tests for the new errors. First step towards addressing simpeg#1541.
) Make sure we set the model when calling getJ. This will ensure that if the model is changed, the sensitivity matrix is cleared (for nonlinear problems) and the sensitivity recomputed. This will close simpeg#1358 --------- Co-authored-by: Santiago Soler <[email protected]>
Standardize the `getJ` methods of TDEM and FDEM 1D simulations so they return a dense array instead of a dictionary with blocks of the `J` matrix. Make the old `getJ` method private by renaming it to `_getJ`. The new `getJ` method reuses the `_getJ` and builds the while `J` as a dense array before returning it. Update `Jvec` and `Jtvec` so they use the new private method. Add tests to check the behaviour of the new public method. --------- Co-authored-by: Santiago Soler <[email protected]>
Add release notes for SimPEG v0.24.0, and update the version switcher.
…peg#1665) Adds a description and units for gravity UV component in docstrings.
Standardize signature of `deriv` method across mappings: make sure they are all defined as `deriv(m, v=None)`. Implement the dot product between the derivative matrix and `v` if `v` is not `None`. Add tests for the modified methods. --------- Co-authored-by: Santiago Soler <[email protected]>
Update how mappings are being used in regularizations: regularize on `mapping(m) - mapping(m_ref)` instead of `mapping(m - m_ref)`. Update implementations and documentation of `Smallness`, `SmoothnessFirstOrder`, `SmoothnessSecondOrder`, and `SmoothnessFullGradient`: the `f_m` will compute difference of the mapped model and reference model, while the `f_m_deriv` will not make use of the reference model now, since it's not carried out in the derivative. Add tests to check this intended behaviour.
#### Fixes for pymatsolver 0.4.0 <!-- Add a summary of this Pull Request --> #### PR Checklist * [x] If this is a work in progress PR, set as a Draft PR * [x] Linted my code according to the [style guides](https://docs.simpeg.xyz/latest/content/getting_started/contributing/code-style.html). * [x] Added [tests](https://docs.simpeg.xyz/latest/content/getting_started/contributing/testing.html) to verify changes to the code. * [x] Added necessary documentation to any new functions/classes following the expect [style](https://docs.simpeg.xyz/latest/content/getting_started/contributing/documentation.html). * [x] Marked as ready for review (if this is was a draft PR), and converted to a Pull Request * [x] Tagged ``@simpeg/simpeg-developers`` when ready for review. #### What does this implement/fix? Squeeze these two locations in the SimulationDC operation (to be consistent on output of `__inner_mat_mul `operation) #### Additional information The `__inner_mat_mul` function will "squeeze" out single length second axes, so this fix causes it to be consistent for this operation in CG. This function had to perform this way because of the way pymatsoler previously handled single length array inputs.
Remove the duplicated current being multiplied when computing the `Mejs` in `LineCurrent`. Add a test that checks that the electric fields are linear in the current.
Apply some fixes to LaTeX equations in some regularization classes.
Make the `get_indices_block` function to always return an array of integers for the cells that belong to the specified block, instead of returning a tuple with just a single array. Improve its implementation. Fix it for 1D mesh since it wasn't working properly. Improve error messages: raise better errors than just `AssertError`s and improve messages. Avoid overwriting the `p0` and `p1` arrays in-place if they are not provided in the right order (west-south-bottom and then east-north-top). Add tests for the function. Update usage of the function across tests and examples. This introduces a backward incompatible change.
Remove the `Data.index_dictionary` property. Remove the `gtg_diagonal` property from gravity simulation. Remove the `components` property from gravity and magnetic surveys. Remove the `HasModel.deleteTheseOnModelUpdate` property.
Add new `shift_to_discrete_topography` function that shifts locations relative to discrete surface topography. Add also a new `get_discrete_topography` function that generates discrete topography locations out of a mesh and its active cells. We measure electric fields at the Earth's surface when performing MT surveys. Like DC/IP, the original measurement locations of the electric fields can end up in air cells when we define discrete surface topography. These functions allow the user to shift locations relative to discrete topography on Tensor and Tree meshes. For Airborne NSEM, they also allow the user to preserve the original flight heights. Deprecate the following functions: `gettopoCC`, `drapeTopotoLoc`, and `closestPointsGrid`. --------- Co-authored-by: Santiago Soler <[email protected]>
…g#1723) Deprecate the unused `force` and `topography` arguments of the method. Add tests to check the warnings are raised.
Fix a few LaTeX equations in `simpeg.potential_fields.magnetics.Simulation3DDifferential` that weren't rendering correctly.
Implement the B field computation from a closed-loop wire source in the TDEM code. We first compute the vector potential using the Biot-Savart Law (implemented in geoana) and then take the curl to get the initial B-field. Adds the computation of B with a step-off waveform using the B or H formulations. --------- Co-authored-by: Joseph Capriotti <[email protected]> Co-authored-by: Santiago Soler <[email protected]>
…mpeg#1714) Allow passing `ramp_start` and `ramp_end` to the `RampOffWaveform` TDEM source and fix issue with waveform being wrong at times before `-epsilon`. Deprecate the `off_time` argument.
Add changelog for next release of SimPEG: v0.25.0. Add the new version to the version switcher. --------- Co-authored-by: Joseph Capriotti <[email protected]> Co-authored-by: Lindsey Heagy <[email protected]>
Forgot to add the new release notes to the index, so they can show up in the website. Update the release date. Minor corrections to RST syntax.
Fix the name of the `threshold_value` argument in the docstring of the `UpdateSensitivityWeights` directive.
#### Summary Support complex permeability in forward 1D time-domain em simulations. #### PR Checklist * [x] If this is a work in progress PR, set as a Draft PR * [x] Linted my code according to the [style guides](https://docs.simpeg.xyz/latest/content/getting_started/contributing/code-style.html). * [x] Added [tests](https://docs.simpeg.xyz/latest/content/getting_started/contributing/testing.html) to verify changes to the code. * [x] Added necessary documentation to any new functions/classes following the expect [style](https://docs.simpeg.xyz/latest/content/getting_started/contributing/documentation.html). * [x] Marked as ready for review (if this is was a draft PR), and converted to a Pull Request * [x] Tagged ``@simpeg/simpeg-developers`` when ready for review. #### What does this implement/fix? removes cast to `real` #### Additional information `geoana` supports complex permeability in the kernel, so the cast to real is unnecessary.
#### Summary allows the sigmoid to map from `a` to `b` regardless of their respective order, only errors if they are equal. #### PR Checklist * [x] If this is a work in progress PR, set as a Draft PR * [x] Linted my code according to the [style guides](https://docs.simpeg.xyz/latest/content/getting_started/contributing/code-style.html). * [x] Added [tests](https://docs.simpeg.xyz/latest/content/getting_started/contributing/testing.html) to verify changes to the code. * [x] Added necessary documentation to any new functions/classes following the expect [style](https://docs.simpeg.xyz/latest/content/getting_started/contributing/documentation.html). * [x] Marked as ready for review (if this is was a draft PR), and converted to a Pull Request * [x] Tagged ``@simpeg/simpeg-developers`` when ready for review. #### What does this implement/fix? Allows the sigmoid map to go arbitrarily between two numbers `a` and `b`, #### Additional information having the sigmoid map the interval to [-5, 5] is just as valid as [5, -5]
Since sklearn 1.8.0, many methods of their `GaussianMixtureModel` take an extra `xp` parameter that's intended to be a module compatible with the array API. Methods like `fit` are passing that extra parameter to these methods, making SimPEG's GMMs to fail due to invalid argument. This PR patches SimPEG's GMMs to take that extra `xp` parameter, while raising a warning in case `xp` is not Numpy.
This PR is meant to fix a bug in the NSEM ApparentConductivity receiver class. The current implementation adds the fields for x and y polarizations before taking the absolute value. This is incorrect. As you can see, the anomalies do not align with 3D structures. This was missed in current pytesting since the forward simulation is being validated for a 1D model.
Improve the style of the docstrings of a few GMM classes used in PGI.
(cherry picked from commit a39f9b18c127505fd5e33cb8ccad9325b8521813)
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GEOPY-2522 - Update simpeg fork to 0.25