Add conversion of prisms or a prism layer to PyVista objects #291
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Create a new visualization module to host it.
The method returns a pyvista.Unstructured object that represents the layer.
Also improve the example
It needs pyvista and it's not always installed on CIs
There's no need for that example to exists, it's not a public function, so it's purpose was for testing. It's better to leave the testing functions inside tests.
Now the tests are run with and without optional dependencies.
Instead of generating each set of vertices per prism using a Python for loop, we have defined a new function that runs this conversion for a full set of prisms boundaries using Numpy for optimization. Only 24 for loops iterations are used, independently of the size of the prisms list.
Ditch the old requirements-optional.txt file.
santisoler
changed the title
Make prisms_to_pyvista public and available through harmonica.visualization module. Add visualization module to the API Reference.
The example uses the plot-pyvista directive to run the code when documentation builds and show the generated plot.
santisoler
commented
Apr 22, 2022
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I've made the |
santisoler
changed the title
santisoler
changed the title
santisoler
changed the title
santisoler
changed the title
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Merged even codecov was failing. We are missing the test in cases where |
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🎉 can't wait to see this in the docs! |
LL-Geo
added a commit
to LL-Geo/harmonica
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Jun 23, 2022
commit 54c3cbe52bd33a94ccbb5bb44f2958bb3afc9330
Author: LL-Geo <54405391+LL-Geo@users.noreply.github.com>
Date: Thu Jun 23 21:36:23 2022 +0800
Update filter
Add more filter
commit 4a5d6f1
Author: Santiago Soler <santiago.r.soler@gmail.com>
Date: Thu Jun 16 18:00:32 2022 -0300
Avoid checking floats in tesseroid doctests (fatiando#326)
Remove expected results for tesseroid calculations in docstring examples.
Printing floats in forward modelling examples isn't that meaningful and often
creates failures when running doctests: small differences between the expected
and the got value could occur under some dependency and OS combinations.
commit cc697af
Author: Matt Tankersley <81199856+mdtanker@users.noreply.github.com>
Date: Fri Jun 17 08:24:32 2022 +1200
Add progressbar to prism forward gravity calculations (fatiando#315)
Add optional `progressbar` flag to `prism_gravity` function and to the
`gravity` method of the prism layer accesor to print a progress bar using
`numba_progress`. Add `numba_progress` as optional dependency. Add test
functions for the new feature.
commit 5a1c895
Author: Santiago Soler <santiago.r.soler@gmail.com>
Date: Tue Jun 14 13:20:39 2022 -0300
Specify spherical latitude in point sources guide (fatiando#325)
Replaces latitude for spherical latitude in another place of the
`point.rst`. Fix typo on "Alternatively".
commit cb476b2
Author: Federico Esteban <federico.esteban@gmail.com>
Date: Tue Jun 14 11:33:22 2022 -0300
Note that spherical and geodetic latitudes are equal in spherical ellipsoids (fatiando#324)
Add sentence in the Coordinate Systems section of the User Guide noting that
if the reference ellipsoid were a sphere both the spherical latitude and the
geodetic latitude are equivalent.
commit 1256ff6
Author: Federico Esteban <federico.esteban@gmail.com>
Date: Mon Jun 13 11:35:02 2022 -0300
Add Federico Esteban to AUTHORS.md (fatiando#323)
Add his name, link to his GitHub account, affiliation and ORCID number.
commit 32de6e0
Author: Federico Esteban <federico.esteban@gmail.com>
Date: Thu Jun 9 15:44:48 2022 -0300
Specify "spherical latitude" when describing coordinates of point masses (fatiando#321)
Add "spherical" when describing the spherical latitude coordinate of point
masses in the user guide. This way we differentiate it from the "latitude"
geodetic coordinate.
commit 9667fab
Author: Santiago Soler <santiago.r.soler@gmail.com>
Date: Mon Jun 6 11:05:17 2022 -0300
Fix small format errors in the user guide (fatiando#319)
Fix link to EquivalentSources.predict method and fix superscripts in the docs.
commit 2f7fcb6
Author: Santiago Soler <santiago.r.soler@gmail.com>
Date: Fri Jun 3 11:17:51 2022 -0300
Update docs and create a proper user guide (fatiando#305)
Update Sphinx docs using sphinx-panels.
Add a proper User Guide that will ultimately replace the gallery examples.
Each page of the new User Guide is a .rst file that uses jupyter-sphinx to run example code blocks.
Added pages for: Coordinate systems, Forward Modelling, Gravity corrections and Equivalent Sources.
Added a new doc/versions.rst file with links to previous documentations.
commit cf4080c
Author: Santiago Soler <santiago.r.soler@gmail.com>
Date: Tue May 31 15:58:25 2022 -0300
Compute upward derivative of a grid in the frequency domain (fatiando#238)
Define a new derivative_upward function for computing the spatial upward
derivative of a 2D grid in the frequency domain. The function makes use of
xrft for handling Fourier transformations of xarray objects. Add a new
filters subpackage that includes FFT filters: functions that take grids in
frequency domain and return the desired filter also in frequency domain. Add
fft and ifft wrapper functions of the xrft.fft and xrft.ifft ones. Add
a new apply_filter function that takes a grid in the spatial domain, applies
fft, the filter and ifft and returns the filtered grid also in spatial domain.
Add tests for the new features and a gallery example for the upward derivative.
Add netcdf4 as requirement for testing.
commit 6a30797
Author: Santiago Soler <santiago.r.soler@gmail.com>
Date: Fri May 27 16:22:18 2022 -0300
Ditch soon-to-be deprecated args of equivalent sources grid method (fatiando#311)
The grid() method of Verde gridders now take a coordinates argument with
the coordinates of the target grid. The previous region, shape and
spacing arguments will be deprecated in Verde v2.0.0. This change makes it
easier for our equivalent sources classes: we don't need the extra upward
argument, users can create the coordinates of the target grid using
verde.grid_coordinates and pass them via coordinates argument. Ditch the
upward, shape, spacing and region arguments from the equivalent sources
gridders. Replace them for the new coordinates argument: users need to
provide the coordinates of the target grid instead of building it through the
grid method. Raise errors if any of those old arguments are being passed. Raise
warnings if any kwargs are passed: they are being ignored and not passed to the
BaseGridder.grid() method.
commit 51ceb7e
Author: Agustina <pesce.agustina@gmail.com>
Date: Mon May 23 11:03:54 2022 -0300
Remove deprecated point_mass_gravity function (fatiando#310)
Remove point_mass_gravity function from harmonica because it was deprecated on
PR fatiando#280. Remove related test functions.
commit f336aa8
Author: Santiago Soler <santiago.r.soler@gmail.com>
Date: Thu May 5 14:52:08 2022 -0300
Drop support for Python 3.6 (fatiando#309)
Remove the compatibility metadata, remove from the CI matrix, bump the
python_requires to 3.7+.
commit d132abb
Author: Santiago Soler <santiago.r.soler@gmail.com>
Date: Tue May 3 12:47:22 2022 -0300
Add computation of gravitational tensor components for point sources (fatiando#288)
Add new kernel functions to compute gravity tensor components generated by
point sources. Add test functions for the new feature: check that the diagonal
elements satisfy the Laplace equation, compare all components against finite
difference computations from the gravity acceleration. Add test class for
checking the symmetry of tensor components. Refactor old test functions for
point gravity: merge some functions into single ones through pytest
parametrizations. Avoid using "gradient" for specifying the gravity
acceleration vector: the "gravity gradient" is usually used to refer to the
tensor.
commit eb71d54
Author: Santiago Soler <santiago.r.soler@gmail.com>
Date: Fri Apr 22 17:23:00 2022 -0300
Add deprecations to datasets and synthetic modules (fatiando#304)
Add FutureWarnings to public functions of the synthetic and dataset
modules. Add tests for the new warnings. Both modules will be deprecated in
Harmonica v0.6.0. Instead of providing sample datasets, Harmonica will depend
on Ensaio for that. The synthetic surveys depend on some of the sample
datasets, but those functions are intended to be used in methodology articles,
so they should live somewhere else.
commit a4598ef
Author: Santiago Soler <santiago.r.soler@gmail.com>
Date: Fri Apr 22 17:06:43 2022 -0300
Add conversion of prisms or a prism layer to PyVista objects (fatiando#291)
Add a new visualization module that hosts prism_to_pyvista: a function to
convert a set of prisms into a pyvista.UnstructuredGrid. Include the new
module and this function in the API Reference. Add a new to_pyvista() method
to the PrismLayer accessor that converts a prism layer into a pyvista grid,
making it easier to plot it in 3D. The UnstructuredGrid has the information
about each prism as hexahedrons, along with their physical properties as cell
data. Add tests for the new features. Add pyvista and vtk as optional
dependencies to environment.yml and setup.cfg. Add a new example for
plotting a PrismLayer. Configure Sphinx to show pyvista plots in the gallery
and to use the pyvista-plot directive in docstrings.
commit 762d210
Author: Santiago Soler <santiago.r.soler@gmail.com>
Date: Mon Apr 4 14:09:45 2022 -0300
Update Black to its stable version (fatiando#301)
Black has released a stable version: 22.3.0. Now the style check tests use this
version. Fixes a bug on CI in which Black was trying to import a private module
of click that doesn't exist anymore. Rerun black: now Black hugs simple
power operators.
commit 10577fa
Author: Santiago Soler <santiago.r.soler@gmail.com>
Date: Mon Apr 4 14:00:42 2022 -0300
Update Sphinx version to 4.5.0 (fatiando#302)
Updates also sphinx gallery and sphinx book theme.
This fixes a issue between latest jinja2 and Sphinx 3.5.*.
commit f880065
Author: Leonardo Uieda <leouieda@gmail.com>
Date: Fri Mar 18 13:34:51 2022 +0000
Move configuration from setup.py to setup.cfg (fatiando#296)
Make the move away from setup.py following the recommendations from the
Python packaging guides. Moves the requirement listing to setup.cfg as
well and will use a script to extract this for conda installing on CI.
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Add a new
visualizationmodule that hostsprism_to_pyvista: a function toconvert a set of prisms into a
pyvista.UnstructuredGrid. Include the newmodule and this function in the API Reference. Add a new
to_pyvista()methodto the
PrismLayeraccessor that converts a prism layer into apyvistagrid,making it easier to plot it in 3D. The
UnstructuredGridhas the informationabout each prism as hexahedrons, along with their physical properties as cell
data. Add tests for the new features. Add
pyvistaandvtkas optionaldependencies to
environment.ymlandsetup.cfg. Add a new example forplotting a
PrismLayer. Configure Sphinx to show pyvista plots in the galleryand to use the
pyvista-plotdirective in docstrings.Reminders:
make formatandmake checkto make sure the code follows the style guide.doc/api/index.rstand the base__init__.pyfile for the package.AUTHORS.mdfile (if you haven't already) in case you'd like to be listed as an author on the Zenodo archive of the next release.