GEOPY-2910: reverting changes - introduced slowness#156
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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 <josephrcapriotti@gmail.com>
…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 <josephrcapriotti@gmail.com>
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 <josephrcapriotti@gmail.com>
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 <santisoler@fastmail.com>
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 <santisoler@fastmail.com>
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.
GEOPY-2884: Change data groups saved for MVI as requested by users
GEOPY-2898: Investigate edge cells recovered with DC2D inversions
GEOPY-2910: Reduce chunking of sensitivities for TEM inversions
GEOPY-2916: Investigate poor convergence of tipper with base station
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
GEOPY-2910: Reduce chunking of sensitivities for TEM inversions
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oops, wrong branch. cancel this PR |
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