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[BUG] Computing a model only with sections mess up sorting surfaces with solutions #397

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Leguark opened this issue Apr 26, 2020 · 5 comments
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@Leguark
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Leguark commented Apr 26, 2020

Describe the bug
Computing a model only with sections mess up sorting surfaces with solutions

For some reason scalar fields at surface point are not in order

To Reproduce
Provide detailed steps to reproduce the behavior:

@pytest.fixture(scope='module')
def section_model(one_fault_model_topo_solution):
    geo_model = one_fault_model_topo_solution
    section_dict = {'section_SW-NE': ([250, 250], [1750, 1750], [100, 100]),
                    'section_NW-SE': ([250, 1750], [1750, 250], [100, 100])}
    geo_model.set_section_grid(section_dict)

    geo_model.set_active_grid('sections', reset=False)

    one_fault_model_topo_solution.update_additional_data()
    one_fault_model_topo_solution.update_to_interpolator()
    gp.compute_model(geo_model, sort_surfaces=True)
    return geo_model

Expected behavior
After one compute the color of the layers should converge

@Leguark Leguark added the bug label Apr 26, 2020
@Wh20-fly
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Hi, @Leguark .Now can GemPy obtain the 2D section in the NW-SE direction? A few days ago, an author said that GemPy cannot obtain the 2D section in this direction at present, as shown in the picture below. What does this BUG of yours show? Thank you very much.
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@Leguark
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Leguark commented Apr 27, 2020

No this bug is completely unrelated.
Can you make a pull request with a test showing that behavior? If you doing it like this, it is much easier for us to check what is the problem and submit a patch.

To do so:

  1. Pull a fresh branch from master
  2. Create in gempy/test//test_plotting/test_plot_section.py
  3. Add the function:
def test_plot_East-west():
     # Your code replicating the problem here
  1. git commit
  2. git push to your repo
  3. pull request

If you have any doubts on the way just contact one of us.

Leguark added a commit that referenced this issue Apr 27, 2020
[TEST]
- Added a test for JanN code
- Added a test for changing the order of the surfaces
- solved minor problems
@Wh20-fly
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Hi, @Leguark .In your comment,the third point "Add the function:",how can I do that,could you explain more detailedly.And the second point means what,how can I make it,and whether I finish the second one or the third one will solve my problem,thank you.

@Wh20-fly
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Hi, @Leguark .Can GemPy plot any direction's 2D section,for example NW-SE,I am in a hurry to get that function,thank you, and please see the upper comment of mine.

@AlexanderJuestel
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Hello,

please see ch1-7a-CrossSections for creating custom section.

I believe you actually worked with those before.

Leguark added a commit that referenced this issue May 20, 2020
* Update ch1-1_Basics.ipynb

* Revert "Update ch1-1_Basics.ipynb"

This reverts commit 1852684.

* play around with stochastics in exploratory notebook

* differentiate filename and path in moose export

* fix errors in moose notebook

* Delete main.yml

* [CLN] Refactored DataMutation and Model to ImplicitCoKriging and Project

* work on hierarchical modelling test notebook

* [DOC] finish notebook with example for hierarchical modeling

* [ENH] Giving up trying to edit current vista code

- Added 'hasData' column to surfaces

* [TEST] Ordering a bit the test

* [ENH] Init of the new vista class

* Added notebook with example of diamond square algorithm (and additional smoothing step)

* Some edits for PEP8 conformity

* [ENH] Added plot_surface_points

* Vectorized topography generation using DS algorithm - example notebook, first steps for single hierarchy

* Vectorized interpolation with padded checkerboard pattern to reduce number of possible cases

* Extension to point selection on multiple hierarchies

* Selection on multiple hierarchies, including padding and grid visualization; one problem with hierarchy calculation remaining, should be easy to fix.

* Hierarchical point selection now working - notebook contains example comparable to example on Wikipedia (https://en.wikipedia.org/wiki/Diamond-square_algorithm#/media/File:Diamond_Square.svg)

* Added hillshade example

* Generalized point selection in DS algorithm

* set up diamond-square module and test in gempy/utils

* Methods for grid size determination and set-up of class structure

* Updated module with grid selection plots and added (tutorial) notebook using the gempy.utils.diamond_square module

* Implemented full diamond-square interpolation algorithm

* Added tests for grid generation and point selection

* Full implementation vectorized and working! (Need to check parameter settings, next)

* Added possibility to initialize and interpolate on lower hierarchy levels

* Added type hints to function declarations

* Extended testing and fixed type hints

* [ENH] Added plot orientations, topography and structured grid

- [BUG] set_is_fault updates properly Surfaces

* [DOC] Added some docs and making test running

* Added several random functions to generate topography and extended description in tutorial notebook.

* Small changes in notebooks (stored to avoid problems in branch switch)

* [ENH] Capturing errors in gempy_to_rexfile.py

[CLN] Deleted old set_gravity_interpolator

* change interpolation function of topo along sections - still needs tests

* [CLN] Move API to the root folder of gempy

* add new topo section function for testing and comparing with old one

* [ENH] Added editing function
[CLN] Move gempy functions to modules and regions

* [CLN] Refactor all notebooks

* - minor

* [TEST] Minor refactor

* [ENH] First prototype of sphinx gallery running

* [ENH] Add first example

* [ENH] changed spline interpolation to interp2d cubic

* DataforPullRequest

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* clean up functions for interpolating topography along set sections

* move csv data of hierarchical modeling from notebooks to data

* remove my copy of metropolis notebook

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* Revert "[CLN] Move API to the root folder of gempy"

This reverts commit e908000

* Refactor notebooks/data to examples/data for tests

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* [DOC] Files converted in mac to avoid windows problems

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* ChangeGemPyAPI

* ChangeGemPyAPI

* ChangeGemPyAPI

* [DOC] Tidy up

* [DOC] Tutorials to %% format

* [DOC] Add subset of columns to render in the GeometricData

- Added verbosity arg to gp.get_data

* [BUG] Added default value to plot_2D

* [MERGE] Merging sphinx and api branches

* [MERGE] Merging pyvista polishing with api and sphinx

* add default for argument method in interpolate_zvals_at_xy

* [DOC] Tutorial one running
- plot_2d:
    - accepts block and values now
    - Different series
    - [BUG] If only one axes plots on the whole figure
- vista
   - [BUG] plot_data now works

- [ENH] compute_model check for an interpolator
- [Test] New test to try vista functionality api

* Updated and cleaned module and extended tests

* Fixed notebook and extended description; included comparison for different roughness values.

* [CLN] Added restricting wrapper to all data objects

* AddTypeHinting

* [CLN] Slit the data.py module and fixing the imports

* [CLN] Stack class encapsulates Series and faults

* [DOC] Some sphinx config

* [DOC] More shpinx config

* [ENH] Move new plotting api to the main frame

* [ENH] Lot of shpinx docs polishing

* [ENH] Fixed the autodocs deprecation!

* [CLN] Removed nptyping dependency

- Fixed lost of types in Stack/Series
- Lot of docstrings in ImplicitcoKriging

* [DOC] All the ImplicitKriging class docstrings updated

* [DOC] Plot 2D and 3D hyperlinks fixed

* [DOC] Docstring has links to examples

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [BUG] Fixed marching cubes bug

* [BUG] Fixed Colors topography pyvista

* [BUG] Fixing travis: Apparently pad does not have explicit mode anymore

* [TEST] Start porting the notebook test to a test file

* [BUG] Solved #397

[TEST]
- Added a test for JanN code
- Added a test for changing the order of the surfaces
- solved minor problems

* [MERGE] Florian's diamond random topo merged

* [ENH] First commit for topography.py rework

* [ENH] Merged hillshading

- Ported to the new plot2d code
- Added test

* [ENH] Topography fixed!!!

- Finally random and gdal are pointing to the same directions
- Test!!
[ENH] Vertical exaggeration in pyvista

* [ENH] Vertical exaggeration in 2d plot too

- More test for 2d plot

* [DOC] Added probability examples

- Topography is saved now
- Fixed latest arviz compatibility
- Moving some probability functionality to modules
- Minor plotting enhancements
- added test pymc

* [ENH] pyvista: scalar_bar

- mjnor stuff

* [ENH] Fixed masked marching cubes

- pyvista scalar_bar inverted

* [ENH] adapting code to scikit image 17.1

* [CLN] Minor cleaning

* [ENH] Size of figures grow with number of axis
- Better projection distance
[BUG] - Axis label were breaking
[TEST] - More 2D test

* [DOC] Moved half of the tutorials to sphinx gallery

* [ENH] Fixed mask returning from interpolator
- Fixed bug loading old models
- Fixed bug masking the faults
[TEST] Adding bunch of tests

* [ENH] Add gdal to travis?

* [ENH] Added a bunch of tutorials

* [DOC] All examples and integration added

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis - added more general documentation

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Adding installation and projects

* [CLN] Remove all notebooks!

* [CLN] small refactorings

* [TEST] added test to travis

* [ENH] All pyvista interactions running again!

* [DOC] Fixing interactive notebooks

* [DOC] Fixing travis to run test

* [TEST] Fixing last test

* [TEST] Fixing last test

Co-authored-by: Japhiolite <jan.niederau@rwth-aachen.de>
Co-authored-by: Florian Wellmann <flohorovicic@gmail.com>
Co-authored-by: alexander.juestel <alexander.juestel@rwth-aachen.de>
Co-authored-by: Alexander G. Zimmerman <alexander.zimmerman@rwth-aachen.de>
Leguark added a commit that referenced this issue May 29, 2020
* Update ch1-1_Basics.ipynb

* Revert "Update ch1-1_Basics.ipynb"

This reverts commit 1852684.

* play around with stochastics in exploratory notebook

* differentiate filename and path in moose export

* fix errors in moose notebook

* Delete main.yml

* [CLN] Refactored DataMutation and Model to ImplicitCoKriging and Project

* work on hierarchical modelling test notebook

* [DOC] finish notebook with example for hierarchical modeling

* Fix 335 (#336)

* [DOC] Updated version

* [BUGFIX] Fixes typing error

>>> import gempy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/namur/coding/gempy/gempy/__init__.py", line 10, in <module>
    import gempy.plot.plot_api as _plot
  File "/home/namur/coding/gempy/gempy/plot/plot_api.py", line 38, in <module>
    from .vista import _Vista as Vista
  File "/home/namur/coding/gempy/gempy/plot/vista.py", line 56, in <module>
    class Vista:
  File "/home/namur/coding/gempy/gempy/plot/vista.py", line 108, in Vista
    name='lith',
AttributeError: module 'gempy' has no attribute 'Solution'

Co-authored-by: varga <varga@aices.rwth-aachen.de>

* [BUG] Plot2D.extract_section_lines breaks

* [DOC] Updated requirements.txt and README.md for Win installation

* [ENH] Added the option in delete series to delete associated data

- Added a gpu_theano file to check the installation

* renamed file_path to table_source and added if/else for directly passing a dataframe instead of loading from csv

* renamed file_path to table_source

* added read_df function for directly reading from dataframe objects and added the corresponding kwargs to init_data function

* added integration test for loading by directly passing a dataframe

* adapted the case checking to incorporate dataframes as well

* fixed the test to actually cover the new behaviour properly

* [DOC] Added explanation to Data_Manipulation notebook, fixed broken link

* minor

* Fixture model (#340)

* [ENH] Added possible fixture model data and example notebook

* [ENH] Small fixes in naming conventions and scalar field plotting

* [META] Add .vs to gitignore

* [TEST] Added test for the old implementation of passing directly dfs

* [ENH] Added a better parser of columns when data is read

* [ENH] Refactored read_Df to set_geometric_data

* [ENH] Init data use the old way to pass frames

* [Test] Update test to the new code

* [DOC] Added export to gocad code to the implicit benchmark

* [DOC] Claudius low memory profile

- nugget effect small bug

* [TEST] Fixing travis

* [BUG] Fix broken Model().read_data when used old kwargs

* [ENH] Giving up trying to edit current vista code

- Added 'hasData' column to surfaces

* [TEST] Ordering a bit the test

* [ENH] Init of the new vista class

* [TEST] Tidying up test and creating only one interpolator
 fixture

* [TEST] Fixed gravity test

- Added gravity fixture
- Now it is possible to pass the centered grid after compilation
- update_additional data moved from api to Model

* [TEST] Fixed magnetics

- Added magnetics fixture
- added fw_magnetics to Solution

* [TEST] Fixed topology
- Added fabian and unconformity fixture

* [TEST] Fixed rest of the tests

* [Test] Added fixture model with folding/faulting/unconformity to conftest.py

* Added notebook with example of diamond square algorithm (and additional smoothing step)

* Some edits for PEP8 conformity

* [ENH] Added plot_surface_points

* [BUG] Small fixes

* Vectorized topography generation using DS algorithm - example notebook, first steps for single hierarchy

* Vectorized interpolation with padded checkerboard pattern to reduce number of possible cases

* Extension to point selection on multiple hierarchies

* Selection on multiple hierarchies, including padding and grid visualization; one problem with hierarchy calculation remaining, should be easy to fix.

* Hierarchical point selection now working - notebook contains example comparable to example on Wikipedia (https://en.wikipedia.org/wiki/Diamond-square_algorithm#/media/File:Diamond_Square.svg)

* Added hillshade example

* Generalized point selection in DS algorithm

* set up diamond-square module and test in gempy/utils

* Methods for grid size determination and set-up of class structure

* Updated module with grid selection plots and added (tutorial) notebook using the gempy.utils.diamond_square module

* Implemented full diamond-square interpolation algorithm

* Added tests for grid generation and point selection

* Full implementation vectorized and working! (Need to check parameter settings, next)

* Added possibility to initialize and interpolate on lower hierarchy levels

* Added type hints to function declarations

* Extended testing and fixed type hints

* [ENH] Added plot orientations, topography and structured grid

- [BUG] set_is_fault updates properly Surfaces

* [DOC] Added some docs and making test running

* Added several random functions to generate topography and extended description in tutorial notebook.

* Small changes in notebooks (stored to avoid problems in branch switch)

* [ENH] Capturing errors in gempy_to_rexfile.py

[CLN] Deleted old set_gravity_interpolator

* change interpolation function of topo along sections - still needs tests

* [CLN] Move API to the root folder of gempy

* add new topo section function for testing and comparing with old one

* [ENH] Added editing function
[CLN] Move gempy functions to modules and regions

* [CLN] Refactor all notebooks

* - minor

* [TEST] Minor refactor

* [ENH] First prototype of sphinx gallery running

* [ENH] Add first example

* [ENH] changed spline interpolation to interp2d cubic

* DataforPullRequest

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* clean up functions for interpolating topography along set sections

* move csv data of hierarchical modeling from notebooks to data

* remove my copy of metropolis notebook

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* Revert "[CLN] Move API to the root folder of gempy"

This reverts commit e908000

* Refactor notebooks/data to examples/data for tests

* [BUG] Fixed: colors for more than 67 surfaces.

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* [DOC] Files converted in mac to avoid windows problems

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* ChangeGemPyAPI

* ChangeGemPyAPI

* ChangeGemPyAPI

* [DOC] Tidy up

* [DOC] Tutorials to %% format

* [DOC] Add subset of columns to render in the GeometricData

- Added verbosity arg to gp.get_data

* [BUG] Added default value to plot_2D

* [MERGE] Merging sphinx and api branches

* [MERGE] Merging pyvista polishing with api and sphinx

* Generate colordict with own palette.

* add default for argument method in interpolate_zvals_at_xy

* [DOC] Tutorial one running
- plot_2d:
    - accepts block and values now
    - Different series
    - [BUG] If only one axes plots on the whole figure
- vista
   - [BUG] plot_data now works

- [ENH] compute_model check for an interpolator
- [Test] New test to try vista functionality api

* Updated and cleaned module and extended tests

* Fixed notebook and extended description; included comparison for different roughness values.

* [CLN] Added restricting wrapper to all data objects

* AddTypeHinting

* [CLN] Slit the data.py module and fixing the imports

* [CLN] Stack class encapsulates Series and faults

* [DOC] Some sphinx config

* [DOC] More shpinx config

* [ENH] Move new plotting api to the main frame

* [ENH] Lot of shpinx docs polishing

* [ENH] Fixed the autodocs deprecation!

* [CLN] Removed nptyping dependency

- Fixed lost of types in Stack/Series
- Lot of docstrings in ImplicitcoKriging

* [DOC] All the ImplicitKriging class docstrings updated

* [DOC] Plot 2D and 3D hyperlinks fixed

* [DOC] Docstring has links to examples

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [BUG] Fixed marching cubes bug

* [BUG] Fixed Colors topography pyvista

* [BUG] Fixing travis: Apparently pad does not have explicit mode anymore

* [TEST] Start porting the notebook test to a test file

* [BUG] Solved #397

[TEST]
- Added a test for JanN code
- Added a test for changing the order of the surfaces
- solved minor problems

* [MERGE] Florian's diamond random topo merged

* [ENH] First commit for topography.py rework

* [ENH] Merged hillshading

- Ported to the new plot2d code
- Added test

* [ENH] Topography fixed!!!

- Finally random and gdal are pointing to the same directions
- Test!!
[ENH] Vertical exaggeration in pyvista

* [ENH] Vertical exaggeration in 2d plot too

- More test for 2d plot

* [DOC] Added probability examples

- Topography is saved now
- Fixed latest arviz compatibility
- Moving some probability functionality to modules
- Minor plotting enhancements
- added test pymc

* [ENH] pyvista: scalar_bar

- mjnor stuff

* [ENH] Fixed masked marching cubes

- pyvista scalar_bar inverted

* [ENH] adapting code to scikit image 17.1

* [CLN] Minor cleaning

* [ENH] Size of figures grow with number of axis
- Better projection distance
[BUG] - Axis label were breaking
[TEST] - More 2D test

* [DOC] Moved half of the tutorials to sphinx gallery

* fixed get section polygons and updated tutorials notebook

* deleted plotting function

* [ENH] Fixed mask returning from interpolator
- Fixed bug loading old models
- Fixed bug masking the faults
[TEST] Adding bunch of tests

* [ENH] Add gdal to travis?

* [ENH] Added a bunch of tutorials

* [DOC] All examples and integration added

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis

* [DOC] Fixing travis

* Development flow update readme (#408)

* Restructured and edited introduction readme up to installation

* Updated readme, included now MacOSX 10.14 installation instructions.

* Updated table of contents

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis - added more general documentation

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Adding installation and projects

* [CLN] Remove all notebooks!

* [CLN] small refactorings

* [TEST] added test to travis

* [ENH] All pyvista interactions running again!

* [DOC] Fixing interactive notebooks

* [DOC] Fixing travis to run test

* [TEST] Fixing last test

* [TEST] Fixing last test

* [WIP] Sprint 2.2 - Merge of several open issues opened by me. (#396)

* Update ch1-1_Basics.ipynb

* Revert "Update ch1-1_Basics.ipynb"

This reverts commit 1852684.

* play around with stochastics in exploratory notebook

* differentiate filename and path in moose export

* fix errors in moose notebook

* Delete main.yml

* [CLN] Refactored DataMutation and Model to ImplicitCoKriging and Project

* work on hierarchical modelling test notebook

* [DOC] finish notebook with example for hierarchical modeling

* [ENH] Giving up trying to edit current vista code

- Added 'hasData' column to surfaces

* [TEST] Ordering a bit the test

* [ENH] Init of the new vista class

* Added notebook with example of diamond square algorithm (and additional smoothing step)

* Some edits for PEP8 conformity

* [ENH] Added plot_surface_points

* Vectorized topography generation using DS algorithm - example notebook, first steps for single hierarchy

* Vectorized interpolation with padded checkerboard pattern to reduce number of possible cases

* Extension to point selection on multiple hierarchies

* Selection on multiple hierarchies, including padding and grid visualization; one problem with hierarchy calculation remaining, should be easy to fix.

* Hierarchical point selection now working - notebook contains example comparable to example on Wikipedia (https://en.wikipedia.org/wiki/Diamond-square_algorithm#/media/File:Diamond_Square.svg)

* Added hillshade example

* Generalized point selection in DS algorithm

* set up diamond-square module and test in gempy/utils

* Methods for grid size determination and set-up of class structure

* Updated module with grid selection plots and added (tutorial) notebook using the gempy.utils.diamond_square module

* Implemented full diamond-square interpolation algorithm

* Added tests for grid generation and point selection

* Full implementation vectorized and working! (Need to check parameter settings, next)

* Added possibility to initialize and interpolate on lower hierarchy levels

* Added type hints to function declarations

* Extended testing and fixed type hints

* [ENH] Added plot orientations, topography and structured grid

- [BUG] set_is_fault updates properly Surfaces

* [DOC] Added some docs and making test running

* Added several random functions to generate topography and extended description in tutorial notebook.

* Small changes in notebooks (stored to avoid problems in branch switch)

* [ENH] Capturing errors in gempy_to_rexfile.py

[CLN] Deleted old set_gravity_interpolator

* change interpolation function of topo along sections - still needs tests

* [CLN] Move API to the root folder of gempy

* add new topo section function for testing and comparing with old one

* [ENH] Added editing function
[CLN] Move gempy functions to modules and regions

* [CLN] Refactor all notebooks

* - minor

* [TEST] Minor refactor

* [ENH] First prototype of sphinx gallery running

* [ENH] Add first example

* [ENH] changed spline interpolation to interp2d cubic

* DataforPullRequest

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* clean up functions for interpolating topography along set sections

* move csv data of hierarchical modeling from notebooks to data

* remove my copy of metropolis notebook

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* Revert "[CLN] Move API to the root folder of gempy"

This reverts commit e908000

* Refactor notebooks/data to examples/data for tests

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* [DOC] Files converted in mac to avoid windows problems

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* ChangeGemPyAPI

* ChangeGemPyAPI

* ChangeGemPyAPI

* [DOC] Tidy up

* [DOC] Tutorials to %% format

* [DOC] Add subset of columns to render in the GeometricData

- Added verbosity arg to gp.get_data

* [BUG] Added default value to plot_2D

* [MERGE] Merging sphinx and api branches

* [MERGE] Merging pyvista polishing with api and sphinx

* add default for argument method in interpolate_zvals_at_xy

* [DOC] Tutorial one running
- plot_2d:
    - accepts block and values now
    - Different series
    - [BUG] If only one axes plots on the whole figure
- vista
   - [BUG] plot_data now works

- [ENH] compute_model check for an interpolator
- [Test] New test to try vista functionality api

* Updated and cleaned module and extended tests

* Fixed notebook and extended description; included comparison for different roughness values.

* [CLN] Added restricting wrapper to all data objects

* AddTypeHinting

* [CLN] Slit the data.py module and fixing the imports

* [CLN] Stack class encapsulates Series and faults

* [DOC] Some sphinx config

* [DOC] More shpinx config

* [ENH] Move new plotting api to the main frame

* [ENH] Lot of shpinx docs polishing

* [ENH] Fixed the autodocs deprecation!

* [CLN] Removed nptyping dependency

- Fixed lost of types in Stack/Series
- Lot of docstrings in ImplicitcoKriging

* [DOC] All the ImplicitKriging class docstrings updated

* [DOC] Plot 2D and 3D hyperlinks fixed

* [DOC] Docstring has links to examples

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [BUG] Fixed marching cubes bug

* [BUG] Fixed Colors topography pyvista

* [BUG] Fixing travis: Apparently pad does not have explicit mode anymore

* [TEST] Start porting the notebook test to a test file

* [BUG] Solved #397

[TEST]
- Added a test for JanN code
- Added a test for changing the order of the surfaces
- solved minor problems

* [MERGE] Florian's diamond random topo merged

* [ENH] First commit for topography.py rework

* [ENH] Merged hillshading

- Ported to the new plot2d code
- Added test

* [ENH] Topography fixed!!!

- Finally random and gdal are pointing to the same directions
- Test!!
[ENH] Vertical exaggeration in pyvista

* [ENH] Vertical exaggeration in 2d plot too

- More test for 2d plot

* [DOC] Added probability examples

- Topography is saved now
- Fixed latest arviz compatibility
- Moving some probability functionality to modules
- Minor plotting enhancements
- added test pymc

* [ENH] pyvista: scalar_bar

- mjnor stuff

* [ENH] Fixed masked marching cubes

- pyvista scalar_bar inverted

* [ENH] adapting code to scikit image 17.1

* [CLN] Minor cleaning

* [ENH] Size of figures grow with number of axis
- Better projection distance
[BUG] - Axis label were breaking
[TEST] - More 2D test

* [DOC] Moved half of the tutorials to sphinx gallery

* [ENH] Fixed mask returning from interpolator
- Fixed bug loading old models
- Fixed bug masking the faults
[TEST] Adding bunch of tests

* [ENH] Add gdal to travis?

* [ENH] Added a bunch of tutorials

* [DOC] All examples and integration added

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis - added more general documentation

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Adding installation and projects

* [CLN] Remove all notebooks!

* [CLN] small refactorings

* [TEST] added test to travis

* [ENH] All pyvista interactions running again!

* [DOC] Fixing interactive notebooks

* [DOC] Fixing travis to run test

* [TEST] Fixing last test

* [TEST] Fixing last test

Co-authored-by: Japhiolite <jan.niederau@rwth-aachen.de>
Co-authored-by: Florian Wellmann <flohorovicic@gmail.com>
Co-authored-by: alexander.juestel <alexander.juestel@rwth-aachen.de>
Co-authored-by: Alexander G. Zimmerman <alexander.zimmerman@rwth-aachen.de>

* [DOC] Adding the notebooks!

* [DOC] Adding the notebooks!

* [DOC] Changes in Dockerfile

* [ENH] Updated Dockerfile for preparation of gempy-server

* [DOC] Some thoughts about Interpolator Epic

* [ENH] Improved the function that generate the default gempy colors. However the whole class
 needs a better explanation of the api

* [FIX] Added back the main 10 colors

* Moved Petrel integration to subsurface module (#357)

* [TEST] Refactor some test

* [DOC] More thoughts on next Epic

* [BUG] Fix elisas example

* [DOC] Latest changes before release

Co-authored-by: Japhiolite <jan.niederau@rwth-aachen.de>
Co-authored-by: Alexander Schaaf <a.schaaf@abdn.ac.uk>
Co-authored-by: Tobi Glaubach <tobias.glaubach@gmail.com>
Co-authored-by: Jan von Harten <38279459+javoha@users.noreply.github.com>
Co-authored-by: javoha <jan.von.harten@rwth-aachen.de>
Co-authored-by: Florian Wellmann <flohorovicic@gmail.com>
Co-authored-by: alexander.juestel <alexander.juestel@rwth-aachen.de>
Co-authored-by: Alexander G. Zimmerman <alexander.zimmerman@rwth-aachen.de>
Co-authored-by: Adam Kosík <adam.kosik@ost.ch>
Co-authored-by: elimh <elisa.heim@gmx.de>
Leguark added a commit that referenced this issue Jul 27, 2020
* GemPy 2.2.0 (#428)

* Update ch1-1_Basics.ipynb

* Revert "Update ch1-1_Basics.ipynb"

This reverts commit 1852684.

* play around with stochastics in exploratory notebook

* differentiate filename and path in moose export

* fix errors in moose notebook

* Delete main.yml

* [CLN] Refactored DataMutation and Model to ImplicitCoKriging and Project

* work on hierarchical modelling test notebook

* [DOC] finish notebook with example for hierarchical modeling

* Fix 335 (#336)

* [DOC] Updated version

* [BUGFIX] Fixes typing error

>>> import gempy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/namur/coding/gempy/gempy/__init__.py", line 10, in <module>
    import gempy.plot.plot_api as _plot
  File "/home/namur/coding/gempy/gempy/plot/plot_api.py", line 38, in <module>
    from .vista import _Vista as Vista
  File "/home/namur/coding/gempy/gempy/plot/vista.py", line 56, in <module>
    class Vista:
  File "/home/namur/coding/gempy/gempy/plot/vista.py", line 108, in Vista
    name='lith',
AttributeError: module 'gempy' has no attribute 'Solution'

Co-authored-by: varga <varga@aices.rwth-aachen.de>

* [BUG] Plot2D.extract_section_lines breaks

* [DOC] Updated requirements.txt and README.md for Win installation

* [ENH] Added the option in delete series to delete associated data

- Added a gpu_theano file to check the installation

* renamed file_path to table_source and added if/else for directly passing a dataframe instead of loading from csv

* renamed file_path to table_source

* added read_df function for directly reading from dataframe objects and added the corresponding kwargs to init_data function

* added integration test for loading by directly passing a dataframe

* adapted the case checking to incorporate dataframes as well

* fixed the test to actually cover the new behaviour properly

* [DOC] Added explanation to Data_Manipulation notebook, fixed broken link

* minor

* Fixture model (#340)

* [ENH] Added possible fixture model data and example notebook

* [ENH] Small fixes in naming conventions and scalar field plotting

* [META] Add .vs to gitignore

* [TEST] Added test for the old implementation of passing directly dfs

* [ENH] Added a better parser of columns when data is read

* [ENH] Refactored read_Df to set_geometric_data

* [ENH] Init data use the old way to pass frames

* [Test] Update test to the new code

* [DOC] Added export to gocad code to the implicit benchmark

* [DOC] Claudius low memory profile

- nugget effect small bug

* [TEST] Fixing travis

* [BUG] Fix broken Model().read_data when used old kwargs

* [ENH] Giving up trying to edit current vista code

- Added 'hasData' column to surfaces

* [TEST] Ordering a bit the test

* [ENH] Init of the new vista class

* [TEST] Tidying up test and creating only one interpolator
 fixture

* [TEST] Fixed gravity test

- Added gravity fixture
- Now it is possible to pass the centered grid after compilation
- update_additional data moved from api to Model

* [TEST] Fixed magnetics

- Added magnetics fixture
- added fw_magnetics to Solution

* [TEST] Fixed topology
- Added fabian and unconformity fixture

* [TEST] Fixed rest of the tests

* [Test] Added fixture model with folding/faulting/unconformity to conftest.py

* Added notebook with example of diamond square algorithm (and additional smoothing step)

* Some edits for PEP8 conformity

* [ENH] Added plot_surface_points

* [BUG] Small fixes

* Vectorized topography generation using DS algorithm - example notebook, first steps for single hierarchy

* Vectorized interpolation with padded checkerboard pattern to reduce number of possible cases

* Extension to point selection on multiple hierarchies

* Selection on multiple hierarchies, including padding and grid visualization; one problem with hierarchy calculation remaining, should be easy to fix.

* Hierarchical point selection now working - notebook contains example comparable to example on Wikipedia (https://en.wikipedia.org/wiki/Diamond-square_algorithm#/media/File:Diamond_Square.svg)

* Added hillshade example

* Generalized point selection in DS algorithm

* set up diamond-square module and test in gempy/utils

* Methods for grid size determination and set-up of class structure

* Updated module with grid selection plots and added (tutorial) notebook using the gempy.utils.diamond_square module

* Implemented full diamond-square interpolation algorithm

* Added tests for grid generation and point selection

* Full implementation vectorized and working! (Need to check parameter settings, next)

* Added possibility to initialize and interpolate on lower hierarchy levels

* Added type hints to function declarations

* Extended testing and fixed type hints

* [ENH] Added plot orientations, topography and structured grid

- [BUG] set_is_fault updates properly Surfaces

* [DOC] Added some docs and making test running

* Added several random functions to generate topography and extended description in tutorial notebook.

* Small changes in notebooks (stored to avoid problems in branch switch)

* [ENH] Capturing errors in gempy_to_rexfile.py

[CLN] Deleted old set_gravity_interpolator

* change interpolation function of topo along sections - still needs tests

* [CLN] Move API to the root folder of gempy

* add new topo section function for testing and comparing with old one

* [ENH] Added editing function
[CLN] Move gempy functions to modules and regions

* [CLN] Refactor all notebooks

* - minor

* [TEST] Minor refactor

* [ENH] First prototype of sphinx gallery running

* [ENH] Add first example

* [ENH] changed spline interpolation to interp2d cubic

* DataforPullRequest

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* clean up functions for interpolating topography along set sections

* move csv data of hierarchical modeling from notebooks to data

* remove my copy of metropolis notebook

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* Revert "[CLN] Move API to the root folder of gempy"

This reverts commit e908000

* Refactor notebooks/data to examples/data for tests

* [BUG] Fixed: colors for more than 67 surfaces.

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* [DOC] Files converted in mac to avoid windows problems

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* ChangeGemPyAPI

* ChangeGemPyAPI

* ChangeGemPyAPI

* [DOC] Tidy up

* [DOC] Tutorials to %% format

* [DOC] Add subset of columns to render in the GeometricData

- Added verbosity arg to gp.get_data

* [BUG] Added default value to plot_2D

* [MERGE] Merging sphinx and api branches

* [MERGE] Merging pyvista polishing with api and sphinx

* Generate colordict with own palette.

* add default for argument method in interpolate_zvals_at_xy

* [DOC] Tutorial one running
- plot_2d:
    - accepts block and values now
    - Different series
    - [BUG] If only one axes plots on the whole figure
- vista
   - [BUG] plot_data now works

- [ENH] compute_model check for an interpolator
- [Test] New test to try vista functionality api

* Updated and cleaned module and extended tests

* Fixed notebook and extended description; included comparison for different roughness values.

* [CLN] Added restricting wrapper to all data objects

* AddTypeHinting

* [CLN] Slit the data.py module and fixing the imports

* [CLN] Stack class encapsulates Series and faults

* [DOC] Some sphinx config

* [DOC] More shpinx config

* [ENH] Move new plotting api to the main frame

* [ENH] Lot of shpinx docs polishing

* [ENH] Fixed the autodocs deprecation!

* [CLN] Removed nptyping dependency

- Fixed lost of types in Stack/Series
- Lot of docstrings in ImplicitcoKriging

* [DOC] All the ImplicitKriging class docstrings updated

* [DOC] Plot 2D and 3D hyperlinks fixed

* [DOC] Docstring has links to examples

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [BUG] Fixed marching cubes bug

* [BUG] Fixed Colors topography pyvista

* [BUG] Fixing travis: Apparently pad does not have explicit mode anymore

* [TEST] Start porting the notebook test to a test file

* [BUG] Solved #397

[TEST]
- Added a test for JanN code
- Added a test for changing the order of the surfaces
- solved minor problems

* [MERGE] Florian's diamond random topo merged

* [ENH] First commit for topography.py rework

* [ENH] Merged hillshading

- Ported to the new plot2d code
- Added test

* [ENH] Topography fixed!!!

- Finally random and gdal are pointing to the same directions
- Test!!
[ENH] Vertical exaggeration in pyvista

* [ENH] Vertical exaggeration in 2d plot too

- More test for 2d plot

* [DOC] Added probability examples

- Topography is saved now
- Fixed latest arviz compatibility
- Moving some probability functionality to modules
- Minor plotting enhancements
- added test pymc

* [ENH] pyvista: scalar_bar

- mjnor stuff

* [ENH] Fixed masked marching cubes

- pyvista scalar_bar inverted

* [ENH] adapting code to scikit image 17.1

* [CLN] Minor cleaning

* [ENH] Size of figures grow with number of axis
- Better projection distance
[BUG] - Axis label were breaking
[TEST] - More 2D test

* [DOC] Moved half of the tutorials to sphinx gallery

* fixed get section polygons and updated tutorials notebook

* deleted plotting function

* [ENH] Fixed mask returning from interpolator
- Fixed bug loading old models
- Fixed bug masking the faults
[TEST] Adding bunch of tests

* [ENH] Add gdal to travis?

* [ENH] Added a bunch of tutorials

* [DOC] All examples and integration added

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis

* [DOC] Fixing travis

* Development flow update readme (#408)

* Restructured and edited introduction readme up to installation

* Updated readme, included now MacOSX 10.14 installation instructions.

* Updated table of contents

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis - added more general documentation

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Adding installation and projects

* [CLN] Remove all notebooks!

* [CLN] small refactorings

* [TEST] added test to travis

* [ENH] All pyvista interactions running again!

* [DOC] Fixing interactive notebooks

* [DOC] Fixing travis to run test

* [TEST] Fixing last test

* [TEST] Fixing last test

* [WIP] Sprint 2.2 - Merge of several open issues opened by me. (#396)

* Update ch1-1_Basics.ipynb

* Revert "Update ch1-1_Basics.ipynb"

This reverts commit 1852684.

* play around with stochastics in exploratory notebook

* differentiate filename and path in moose export

* fix errors in moose notebook

* Delete main.yml

* [CLN] Refactored DataMutation and Model to ImplicitCoKriging and Project

* work on hierarchical modelling test notebook

* [DOC] finish notebook with example for hierarchical modeling

* [ENH] Giving up trying to edit current vista code

- Added 'hasData' column to surfaces

* [TEST] Ordering a bit the test

* [ENH] Init of the new vista class

* Added notebook with example of diamond square algorithm (and additional smoothing step)

* Some edits for PEP8 conformity

* [ENH] Added plot_surface_points

* Vectorized topography generation using DS algorithm - example notebook, first steps for single hierarchy

* Vectorized interpolation with padded checkerboard pattern to reduce number of possible cases

* Extension to point selection on multiple hierarchies

* Selection on multiple hierarchies, including padding and grid visualization; one problem with hierarchy calculation remaining, should be easy to fix.

* Hierarchical point selection now working - notebook contains example comparable to example on Wikipedia (https://en.wikipedia.org/wiki/Diamond-square_algorithm#/media/File:Diamond_Square.svg)

* Added hillshade example

* Generalized point selection in DS algorithm

* set up diamond-square module and test in gempy/utils

* Methods for grid size determination and set-up of class structure

* Updated module with grid selection plots and added (tutorial) notebook using the gempy.utils.diamond_square module

* Implemented full diamond-square interpolation algorithm

* Added tests for grid generation and point selection

* Full implementation vectorized and working! (Need to check parameter settings, next)

* Added possibility to initialize and interpolate on lower hierarchy levels

* Added type hints to function declarations

* Extended testing and fixed type hints

* [ENH] Added plot orientations, topography and structured grid

- [BUG] set_is_fault updates properly Surfaces

* [DOC] Added some docs and making test running

* Added several random functions to generate topography and extended description in tutorial notebook.

* Small changes in notebooks (stored to avoid problems in branch switch)

* [ENH] Capturing errors in gempy_to_rexfile.py

[CLN] Deleted old set_gravity_interpolator

* change interpolation function of topo along sections - still needs tests

* [CLN] Move API to the root folder of gempy

* add new topo section function for testing and comparing with old one

* [ENH] Added editing function
[CLN] Move gempy functions to modules and regions

* [CLN] Refactor all notebooks

* - minor

* [TEST] Minor refactor

* [ENH] First prototype of sphinx gallery running

* [ENH] Add first example

* [ENH] changed spline interpolation to interp2d cubic

* DataforPullRequest

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* clean up functions for interpolating topography along set sections

* move csv data of hierarchical modeling from notebooks to data

* remove my copy of metropolis notebook

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* Revert "[CLN] Move API to the root folder of gempy"

This reverts commit e908000

* Refactor notebooks/data to examples/data for tests

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* [DOC] Files converted in mac to avoid windows problems

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* ChangeGemPyAPI

* ChangeGemPyAPI

* ChangeGemPyAPI

* [DOC] Tidy up

* [DOC] Tutorials to %% format

* [DOC] Add subset of columns to render in the GeometricData

- Added verbosity arg to gp.get_data

* [BUG] Added default value to plot_2D

* [MERGE] Merging sphinx and api branches

* [MERGE] Merging pyvista polishing with api and sphinx

* add default for argument method in interpolate_zvals_at_xy

* [DOC] Tutorial one running
- plot_2d:
    - accepts block and values now
    - Different series
    - [BUG] If only one axes plots on the whole figure
- vista
   - [BUG] plot_data now works

- [ENH] compute_model check for an interpolator
- [Test] New test to try vista functionality api

* Updated and cleaned module and extended tests

* Fixed notebook and extended description; included comparison for different roughness values.

* [CLN] Added restricting wrapper to all data objects

* AddTypeHinting

* [CLN] Slit the data.py module and fixing the imports

* [CLN] Stack class encapsulates Series and faults

* [DOC] Some sphinx config

* [DOC] More shpinx config

* [ENH] Move new plotting api to the main frame

* [ENH] Lot of shpinx docs polishing

* [ENH] Fixed the autodocs deprecation!

* [CLN] Removed nptyping dependency

- Fixed lost of types in Stack/Series
- Lot of docstrings in ImplicitcoKriging

* [DOC] All the ImplicitKriging class docstrings updated

* [DOC] Plot 2D and 3D hyperlinks fixed

* [DOC] Docstring has links to examples

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [BUG] Fixed marching cubes bug

* [BUG] Fixed Colors topography pyvista

* [BUG] Fixing travis: Apparently pad does not have explicit mode anymore

* [TEST] Start porting the notebook test to a test file

* [BUG] Solved #397

[TEST]
- Added a test for JanN code
- Added a test for changing the order of the surfaces
- solved minor problems

* [MERGE] Florian's diamond random topo merged

* [ENH] First commit for topography.py rework

* [ENH] Merged hillshading

- Ported to the new plot2d code
- Added test

* [ENH] Topography fixed!!!

- Finally random and gdal are pointing to the same directions
- Test!!
[ENH] Vertical exaggeration in pyvista

* [ENH] Vertical exaggeration in 2d plot too

- More test for 2d plot

* [DOC] Added probability examples

- Topography is saved now
- Fixed latest arviz compatibility
- Moving some probability functionality to modules
- Minor plotting enhancements
- added test pymc

* [ENH] pyvista: scalar_bar

- mjnor stuff

* [ENH] Fixed masked marching cubes

- pyvista scalar_bar inverted

* [ENH] adapting code to scikit image 17.1

* [CLN] Minor cleaning

* [ENH] Size of figures grow with number of axis
- Better projection distance
[BUG] - Axis label were breaking
[TEST] - More 2D test

* [DOC] Moved half of the tutorials to sphinx gallery

* [ENH] Fixed mask returning from interpolator
- Fixed bug loading old models
- Fixed bug masking the faults
[TEST] Adding bunch of tests

* [ENH] Add gdal to travis?

* [ENH] Added a bunch of tutorials

* [DOC] All examples and integration added

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis - added more general documentation

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Adding installation and projects

* [CLN] Remove all notebooks!

* [CLN] small refactorings

* [TEST] added test to travis

* [ENH] All pyvista interactions running again!

* [DOC] Fixing interactive notebooks

* [DOC] Fixing travis to run test

* [TEST] Fixing last test

* [TEST] Fixing last test

Co-authored-by: Japhiolite <jan.niederau@rwth-aachen.de>
Co-authored-by: Florian Wellmann <flohorovicic@gmail.com>
Co-authored-by: alexander.juestel <alexander.juestel@rwth-aachen.de>
Co-authored-by: Alexander G. Zimmerman <alexander.zimmerman@rwth-aachen.de>

* [DOC] Adding the notebooks!

* [DOC] Adding the notebooks!

* [DOC] Changes in Dockerfile

* [ENH] Updated Dockerfile for preparation of gempy-server

* [DOC] Some thoughts about Interpolator Epic

* [ENH] Improved the function that generate the default gempy colors. However the whole class
 needs a better explanation of the api

* [FIX] Added back the main 10 colors

* Moved Petrel integration to subsurface module (#357)

* [TEST] Refactor some test

* [DOC] More thoughts on next Epic

* [BUG] Fix elisas example

* [DOC] Latest changes before release

Co-authored-by: Japhiolite <jan.niederau@rwth-aachen.de>
Co-authored-by: Alexander Schaaf <a.schaaf@abdn.ac.uk>
Co-authored-by: Tobi Glaubach <tobias.glaubach@gmail.com>
Co-authored-by: Jan von Harten <38279459+javoha@users.noreply.github.com>
Co-authored-by: javoha <jan.von.harten@rwth-aachen.de>
Co-authored-by: Florian Wellmann <flohorovicic@gmail.com>
Co-authored-by: alexander.juestel <alexander.juestel@rwth-aachen.de>
Co-authored-by: Alexander G. Zimmerman <alexander.zimmerman@rwth-aachen.de>
Co-authored-by: Adam Kosík <adam.kosik@ost.ch>
Co-authored-by: elimh <elisa.heim@gmx.de>

* [BUG] Minor change

* - GemPy to Rex v2

* - GemPy to Rex v2

* - Fixed few bugs for editing operations

* - Fixed bug writing the rexfile

- Now rexfile has color

* - Minor changes

* - [TEST]
Fixed

Co-authored-by: Japhiolite <jan.niederau@rwth-aachen.de>
Co-authored-by: Alexander Schaaf <a.schaaf@abdn.ac.uk>
Co-authored-by: Tobi Glaubach <tobias.glaubach@gmail.com>
Co-authored-by: Jan von Harten <38279459+javoha@users.noreply.github.com>
Co-authored-by: javoha <jan.von.harten@rwth-aachen.de>
Co-authored-by: Florian Wellmann <flohorovicic@gmail.com>
Co-authored-by: alexander.juestel <alexander.juestel@rwth-aachen.de>
Co-authored-by: Alexander G. Zimmerman <alexander.zimmerman@rwth-aachen.de>
Co-authored-by: Adam Kosík <adam.kosik@ost.ch>
Co-authored-by: elimh <elisa.heim@gmx.de>
Co-authored-by: Miguel de la Varga <miguel@terranigma-solutions.com>
Leguark added a commit that referenced this issue Jul 27, 2020
* - init docs-devs branch
- fixbar

* [DOC] Fixing the bar

* fixed markup in installation.rst

* updated installation instructions for MacOS and minor edits

* [BUG] Minor bugs for strange order of calls

* [BUG] Travis sets the right domain for the documentation

* fixed typos and minor formatting

* minor formatting in index.rst

* [BUG] Second try fixing travis domain

* formatting and minor corrections in Ch1_1_basic

* minor corrections in installation.rst and unified heading style in ch1_1

* minor corrections and formatting in ch1_2a

* minor corrections and formatting in ch1_2b

* [DOC] Small changes to the installation.rst

* minor corrections and formatting in ch1_3a

* Small changes to Index

* Small changes to index

* - init docs-devs branch
- fixbar

* minor corrections and formatting in ch1_3c and merge with ch1_3d

* minor corrections in installation.rst

* [BUG] patching gempy to be compatible with pyvista 0.25

* [BUG] Allowing user to have pyvista .24 too

* [DOC] Added some links to the repo badges

* [BUG] Adding flag for pyvista sphinx

* [BUG] Fixing travis

* [BUG] Fixing travis

* [BUG] Fixing travis - Minor tweaks on to setup.py

* [BUG] Fixing travis - Minor tweaks on to setup.py

* Fix Travis for emg3d/pymc3. (#439)

* Fix Travis for emg3d/pymc3.

* Remove unused `script`-section

* Add the license to the manifest for inclusion in source code (#435)

distribution

* Update manifest.in to be explicit (#444)

I just realized my pr was not explicit about the include of the license, I don't think it would have broken anything but better to be safe.

* Update README.md

Typo in universal.

* Remove use of optional argument which was providing wrong index

* Have Travis only check master and release branches

* Randomly generate colors when deterministic colors run out. Also clarify the Color class

* # Added new model for simple geometry examples

* Fix version of discretize installed by Travis

* Fix4 (#490)

* Fix pyvistaqt deprecations

* [BUG] Adding verbosity to the testing in travis

* [BUG] adding mkl dependency and more verbosity

* [debug] print pyvista report on Travis

* - [BUG] Adapted code to matplotlib 3.3

* Added dev-requirements.txt

- Start fixing plot_posterior.py

* - arg image, also close the vtk window
travis still dies
- Trying something on travis

* - Fixing more broken code due to matplotlib release

* - Dealing with travis

* - Minor

* - Making GemPy compatible with pyvista 0.25 and 0.24

- Making travis to use 0.24

* - force reinstall in travis

* - Travis is picking the wrong commit?

Co-authored-by: banesullivan <banesulli@gmail.com>
Co-authored-by: Miguel de la Varga <miguel@terranigma-solutions.com>

* Gempy to rex (#485)

* GemPy 2.2.0 (#428)

* Update ch1-1_Basics.ipynb

* Revert "Update ch1-1_Basics.ipynb"

This reverts commit 1852684.

* play around with stochastics in exploratory notebook

* differentiate filename and path in moose export

* fix errors in moose notebook

* Delete main.yml

* [CLN] Refactored DataMutation and Model to ImplicitCoKriging and Project

* work on hierarchical modelling test notebook

* [DOC] finish notebook with example for hierarchical modeling

* Fix 335 (#336)

* [DOC] Updated version

* [BUGFIX] Fixes typing error

>>> import gempy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/namur/coding/gempy/gempy/__init__.py", line 10, in <module>
    import gempy.plot.plot_api as _plot
  File "/home/namur/coding/gempy/gempy/plot/plot_api.py", line 38, in <module>
    from .vista import _Vista as Vista
  File "/home/namur/coding/gempy/gempy/plot/vista.py", line 56, in <module>
    class Vista:
  File "/home/namur/coding/gempy/gempy/plot/vista.py", line 108, in Vista
    name='lith',
AttributeError: module 'gempy' has no attribute 'Solution'

Co-authored-by: varga <varga@aices.rwth-aachen.de>

* [BUG] Plot2D.extract_section_lines breaks

* [DOC] Updated requirements.txt and README.md for Win installation

* [ENH] Added the option in delete series to delete associated data

- Added a gpu_theano file to check the installation

* renamed file_path to table_source and added if/else for directly passing a dataframe instead of loading from csv

* renamed file_path to table_source

* added read_df function for directly reading from dataframe objects and added the corresponding kwargs to init_data function

* added integration test for loading by directly passing a dataframe

* adapted the case checking to incorporate dataframes as well

* fixed the test to actually cover the new behaviour properly

* [DOC] Added explanation to Data_Manipulation notebook, fixed broken link

* minor

* Fixture model (#340)

* [ENH] Added possible fixture model data and example notebook

* [ENH] Small fixes in naming conventions and scalar field plotting

* [META] Add .vs to gitignore

* [TEST] Added test for the old implementation of passing directly dfs

* [ENH] Added a better parser of columns when data is read

* [ENH] Refactored read_Df to set_geometric_data

* [ENH] Init data use the old way to pass frames

* [Test] Update test to the new code

* [DOC] Added export to gocad code to the implicit benchmark

* [DOC] Claudius low memory profile

- nugget effect small bug

* [TEST] Fixing travis

* [BUG] Fix broken Model().read_data when used old kwargs

* [ENH] Giving up trying to edit current vista code

- Added 'hasData' column to surfaces

* [TEST] Ordering a bit the test

* [ENH] Init of the new vista class

* [TEST] Tidying up test and creating only one interpolator
 fixture

* [TEST] Fixed gravity test

- Added gravity fixture
- Now it is possible to pass the centered grid after compilation
- update_additional data moved from api to Model

* [TEST] Fixed magnetics

- Added magnetics fixture
- added fw_magnetics to Solution

* [TEST] Fixed topology
- Added fabian and unconformity fixture

* [TEST] Fixed rest of the tests

* [Test] Added fixture model with folding/faulting/unconformity to conftest.py

* Added notebook with example of diamond square algorithm (and additional smoothing step)

* Some edits for PEP8 conformity

* [ENH] Added plot_surface_points

* [BUG] Small fixes

* Vectorized topography generation using DS algorithm - example notebook, first steps for single hierarchy

* Vectorized interpolation with padded checkerboard pattern to reduce number of possible cases

* Extension to point selection on multiple hierarchies

* Selection on multiple hierarchies, including padding and grid visualization; one problem with hierarchy calculation remaining, should be easy to fix.

* Hierarchical point selection now working - notebook contains example comparable to example on Wikipedia (https://en.wikipedia.org/wiki/Diamond-square_algorithm#/media/File:Diamond_Square.svg)

* Added hillshade example

* Generalized point selection in DS algorithm

* set up diamond-square module and test in gempy/utils

* Methods for grid size determination and set-up of class structure

* Updated module with grid selection plots and added (tutorial) notebook using the gempy.utils.diamond_square module

* Implemented full diamond-square interpolation algorithm

* Added tests for grid generation and point selection

* Full implementation vectorized and working! (Need to check parameter settings, next)

* Added possibility to initialize and interpolate on lower hierarchy levels

* Added type hints to function declarations

* Extended testing and fixed type hints

* [ENH] Added plot orientations, topography and structured grid

- [BUG] set_is_fault updates properly Surfaces

* [DOC] Added some docs and making test running

* Added several random functions to generate topography and extended description in tutorial notebook.

* Small changes in notebooks (stored to avoid problems in branch switch)

* [ENH] Capturing errors in gempy_to_rexfile.py

[CLN] Deleted old set_gravity_interpolator

* change interpolation function of topo along sections - still needs tests

* [CLN] Move API to the root folder of gempy

* add new topo section function for testing and comparing with old one

* [ENH] Added editing function
[CLN] Move gempy functions to modules and regions

* [CLN] Refactor all notebooks

* - minor

* [TEST] Minor refactor

* [ENH] First prototype of sphinx gallery running

* [ENH] Add first example

* [ENH] changed spline interpolation to interp2d cubic

* DataforPullRequest

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* clean up functions for interpolating topography along set sections

* move csv data of hierarchical modeling from notebooks to data

* remove my copy of metropolis notebook

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* Revert "[CLN] Move API to the root folder of gempy"

This reverts commit e908000

* Refactor notebooks/data to examples/data for tests

* [BUG] Fixed: colors for more than 67 surfaces.

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* [DOC] Files converted in mac to avoid windows problems

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* ChangeGemPyAPI

* ChangeGemPyAPI

* ChangeGemPyAPI

* [DOC] Tidy up

* [DOC] Tutorials to %% format

* [DOC] Add subset of columns to render in the GeometricData

- Added verbosity arg to gp.get_data

* [BUG] Added default value to plot_2D

* [MERGE] Merging sphinx and api branches

* [MERGE] Merging pyvista polishing with api and sphinx

* Generate colordict with own palette.

* add default for argument method in interpolate_zvals_at_xy

* [DOC] Tutorial one running
- plot_2d:
    - accepts block and values now
    - Different series
    - [BUG] If only one axes plots on the whole figure
- vista
   - [BUG] plot_data now works

- [ENH] compute_model check for an interpolator
- [Test] New test to try vista functionality api

* Updated and cleaned module and extended tests

* Fixed notebook and extended description; included comparison for different roughness values.

* [CLN] Added restricting wrapper to all data objects

* AddTypeHinting

* [CLN] Slit the data.py module and fixing the imports

* [CLN] Stack class encapsulates Series and faults

* [DOC] Some sphinx config

* [DOC] More shpinx config

* [ENH] Move new plotting api to the main frame

* [ENH] Lot of shpinx docs polishing

* [ENH] Fixed the autodocs deprecation!

* [CLN] Removed nptyping dependency

- Fixed lost of types in Stack/Series
- Lot of docstrings in ImplicitcoKriging

* [DOC] All the ImplicitKriging class docstrings updated

* [DOC] Plot 2D and 3D hyperlinks fixed

* [DOC] Docstring has links to examples

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [BUG] Fixed marching cubes bug

* [BUG] Fixed Colors topography pyvista

* [BUG] Fixing travis: Apparently pad does not have explicit mode anymore

* [TEST] Start porting the notebook test to a test file

* [BUG] Solved #397

[TEST]
- Added a test for JanN code
- Added a test for changing the order of the surfaces
- solved minor problems

* [MERGE] Florian's diamond random topo merged

* [ENH] First commit for topography.py rework

* [ENH] Merged hillshading

- Ported to the new plot2d code
- Added test

* [ENH] Topography fixed!!!

- Finally random and gdal are pointing to the same directions
- Test!!
[ENH] Vertical exaggeration in pyvista

* [ENH] Vertical exaggeration in 2d plot too

- More test for 2d plot

* [DOC] Added probability examples

- Topography is saved now
- Fixed latest arviz compatibility
- Moving some probability functionality to modules
- Minor plotting enhancements
- added test pymc

* [ENH] pyvista: scalar_bar

- mjnor stuff

* [ENH] Fixed masked marching cubes

- pyvista scalar_bar inverted

* [ENH] adapting code to scikit image 17.1

* [CLN] Minor cleaning

* [ENH] Size of figures grow with number of axis
- Better projection distance
[BUG] - Axis label were breaking
[TEST] - More 2D test

* [DOC] Moved half of the tutorials to sphinx gallery

* fixed get section polygons and updated tutorials notebook

* deleted plotting function

* [ENH] Fixed mask returning from interpolator
- Fixed bug loading old models
- Fixed bug masking the faults
[TEST] Adding bunch of tests

* [ENH] Add gdal to travis?

* [ENH] Added a bunch of tutorials

* [DOC] All examples and integration added

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis

* [DOC] Fixing travis

* Development flow update readme (#408)

* Restructured and edited introduction readme up to installation

* Updated readme, included now MacOSX 10.14 installation instructions.

* Updated table of contents

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis - added more general documentation

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Adding installation and projects

* [CLN] Remove all notebooks!

* [CLN] small refactorings

* [TEST] added test to travis

* [ENH] All pyvista interactions running again!

* [DOC] Fixing interactive notebooks

* [DOC] Fixing travis to run test

* [TEST] Fixing last test

* [TEST] Fixing last test

* [WIP] Sprint 2.2 - Merge of several open issues opened by me. (#396)

* Update ch1-1_Basics.ipynb

* Revert "Update ch1-1_Basics.ipynb"

This reverts commit 1852684.

* play around with stochastics in exploratory notebook

* differentiate filename and path in moose export

* fix errors in moose notebook

* Delete main.yml

* [CLN] Refactored DataMutation and Model to ImplicitCoKriging and Project

* work on hierarchical modelling test notebook

* [DOC] finish notebook with example for hierarchical modeling

* [ENH] Giving up trying to edit current vista code

- Added 'hasData' column to surfaces

* [TEST] Ordering a bit the test

* [ENH] Init of the new vista class

* Added notebook with example of diamond square algorithm (and additional smoothing step)

* Some edits for PEP8 conformity

* [ENH] Added plot_surface_points

* Vectorized topography generation using DS algorithm - example notebook, first steps for single hierarchy

* Vectorized interpolation with padded checkerboard pattern to reduce number of possible cases

* Extension to point selection on multiple hierarchies

* Selection on multiple hierarchies, including padding and grid visualization; one problem with hierarchy calculation remaining, should be easy to fix.

* Hierarchical point selection now working - notebook contains example comparable to example on Wikipedia (https://en.wikipedia.org/wiki/Diamond-square_algorithm#/media/File:Diamond_Square.svg)

* Added hillshade example

* Generalized point selection in DS algorithm

* set up diamond-square module and test in gempy/utils

* Methods for grid size determination and set-up of class structure

* Updated module with grid selection plots and added (tutorial) notebook using the gempy.utils.diamond_square module

* Implemented full diamond-square interpolation algorithm

* Added tests for grid generation and point selection

* Full implementation vectorized and working! (Need to check parameter settings, next)

* Added possibility to initialize and interpolate on lower hierarchy levels

* Added type hints to function declarations

* Extended testing and fixed type hints

* [ENH] Added plot orientations, topography and structured grid

- [BUG] set_is_fault updates properly Surfaces

* [DOC] Added some docs and making test running

* Added several random functions to generate topography and extended description in tutorial notebook.

* Small changes in notebooks (stored to avoid problems in branch switch)

* [ENH] Capturing errors in gempy_to_rexfile.py

[CLN] Deleted old set_gravity_interpolator

* change interpolation function of topo along sections - still needs tests

* [CLN] Move API to the root folder of gempy

* add new topo section function for testing and comparing with old one

* [ENH] Added editing function
[CLN] Move gempy functions to modules and regions

* [CLN] Refactor all notebooks

* - minor

* [TEST] Minor refactor

* [ENH] First prototype of sphinx gallery running

* [ENH] Add first example

* [ENH] changed spline interpolation to interp2d cubic

* DataforPullRequest

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* clean up functions for interpolating topography along set sections

* move csv data of hierarchical modeling from notebooks to data

* remove my copy of metropolis notebook

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* Revert "[CLN] Move API to the root folder of gempy"

This reverts commit e908000

* Refactor notebooks/data to examples/data for tests

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* [DOC] Files converted in mac to avoid windows problems

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* ChangeGemPyAPI

* ChangeGemPyAPI

* ChangeGemPyAPI

* [DOC] Tidy up

* [DOC] Tutorials to %% format

* [DOC] Add subset of columns to render in the GeometricData

- Added verbosity arg to gp.get_data

* [BUG] Added default value to plot_2D

* [MERGE] Merging sphinx and api branches

* [MERGE] Merging pyvista polishing with api and sphinx

* add default for argument method in interpolate_zvals_at_xy

* [DOC] Tutorial one running
- plot_2d:
    - accepts block and values now
    - Different series
    - [BUG] If only one axes plots on the whole figure
- vista
   - [BUG] plot_data now works

- [ENH] compute_model check for an interpolator
- [Test] New test to try vista functionality api

* Updated and cleaned module and extended tests

* Fixed notebook and extended description; included comparison for different roughness values.

* [CLN] Added restricting wrapper to all data objects

* AddTypeHinting

* [CLN] Slit the data.py module and fixing the imports

* [CLN] Stack class encapsulates Series and faults

* [DOC] Some sphinx config

* [DOC] More shpinx config

* [ENH] Move new plotting api to the main frame

* [ENH] Lot of shpinx docs polishing

* [ENH] Fixed the autodocs deprecation!

* [CLN] Removed nptyping dependency

- Fixed lost of types in Stack/Series
- Lot of docstrings in ImplicitcoKriging

* [DOC] All the ImplicitKriging class docstrings updated

* [DOC] Plot 2D and 3D hyperlinks fixed

* [DOC] Docstring has links to examples

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [BUG] Fixed marching cubes bug

* [BUG] Fixed Colors topography pyvista

* [BUG] Fixing travis: Apparently pad does not have explicit mode anymore

* [TEST] Start porting the notebook test to a test file

* [BUG] Solved #397

[TEST]
- Added a test for JanN code
- Added a test for changing the order of the surfaces
- solved minor problems

* [MERGE] Florian's diamond random topo merged

* [ENH] First commit for topography.py rework

* [ENH] Merged hillshading

- Ported to the new plot2d code
- Added test

* [ENH] Topography fixed!!!

- Finally random and gdal are pointing to the same directions
- Test!!
[ENH] Vertical exaggeration in pyvista

* [ENH] Vertical exaggeration in 2d plot too

- More test for 2d plot

* [DOC] Added probability examples

- Topography is saved now
- Fixed latest arviz compatibility
- Moving some probability functionality to modules
- Minor plotting enhancements
- added test pymc

* [ENH] pyvista: scalar_bar

- mjnor stuff

* [ENH] Fixed masked marching cubes

- pyvista scalar_bar inverted

* [ENH] adapting code to scikit image 17.1

* [CLN] Minor cleaning

* [ENH] Size of figures grow with number of axis
- Better projection distance
[BUG] - Axis label were breaking
[TEST] - More 2D test

* [DOC] Moved half of the tutorials to sphinx gallery

* [ENH] Fixed mask returning from interpolator
- Fixed bug loading old models
- Fixed bug masking the faults
[TEST] Adding bunch of tests

* [ENH] Add gdal to travis?

* [ENH] Added a bunch of tutorials

* [DOC] All examples and integration added

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis - added more general documentation

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Adding installation and projects

* [CLN] Remove all notebooks!

* [CLN] small refactorings

* [TEST] added test to travis

* [ENH] All pyvista interactions running again!

* [DOC] Fixing interactive notebooks

* [DOC] Fixing travis to run test

* [TEST] Fixing last test

* [TEST] Fixing last test

Co-authored-by: Japhiolite <jan.niederau@rwth-aachen.de>
Co-authored-by: Florian Wellmann <flohorovicic@gmail.com>
Co-authored-by: alexander.juestel <alexander.juestel@rwth-aachen.de>
Co-authored-by: Alexander G. Zimmerman <alexander.zimmerman@rwth-aachen.de>

* [DOC] Adding the notebooks!

* [DOC] Adding the notebooks!

* [DOC] Changes in Dockerfile

* [ENH] Updated Dockerfile for preparation of gempy-server

* [DOC] Some thoughts about Interpolator Epic

* [ENH] Improved the function that generate the default gempy colors. However the whole class
 needs a better explanation of the api

* [FIX] Added back the main 10 colors

* Moved Petrel integration to subsurface module (#357)

* [TEST] Refactor some test

* [DOC] More thoughts on next Epic

* [BUG] Fix elisas example

* [DOC] Latest changes before release

Co-authored-by: Japhiolite <jan.niederau@rwth-aachen.de>
Co-authored-by: Alexander Schaaf <a.schaaf@abdn.ac.uk>
Co-authored-by: Tobi Glaubach <tobias.glaubach@gmail.com>
Co-authored-by: Jan von Harten <38279459+javoha@users.noreply.github.com>
Co-authored-by: javoha <jan.von.harten@rwth-aachen.de>
Co-authored-by: Florian Wellmann <flohorovicic@gmail.com>
Co-authored-by: alexander.juestel <alexander.juestel@rwth-aachen.de>
Co-authored-by: Alexander G. Zimmerman <alexander.zimmerman@rwth-aachen.de>
Co-authored-by: Adam Kosík <adam.kosik@ost.ch>
Co-authored-by: elimh <elisa.heim@gmx.de>

* [BUG] Minor change

* - GemPy to Rex v2

* - GemPy to Rex v2

* - Fixed few bugs for editing operations

* - Fixed bug writing the rexfile

- Now rexfile has color

* - Minor changes

* - [TEST]
Fixed

Co-authored-by: Japhiolite <jan.niederau@rwth-aachen.de>
Co-authored-by: Alexander Schaaf <a.schaaf@abdn.ac.uk>
Co-authored-by: Tobi Glaubach <tobias.glaubach@gmail.com>
Co-authored-by: Jan von Harten <38279459+javoha@users.noreply.github.com>
Co-authored-by: javoha <jan.von.harten@rwth-aachen.de>
Co-authored-by: Florian Wellmann <flohorovicic@gmail.com>
Co-authored-by: alexander.juestel <alexander.juestel@rwth-aachen.de>
Co-authored-by: Alexander G. Zimmerman <alexander.zimmerman@rwth-aachen.de>
Co-authored-by: Adam Kosík <adam.kosik@ost.ch>
Co-authored-by: elimh <elisa.heim@gmx.de>
Co-authored-by: Miguel de la Varga <miguel@terranigma-solutions.com>

Co-authored-by: Miguel de la Varga <miguel@terranigma-solutions.com>
Co-authored-by: SimonVirgo <s.virgo@ged.rwth-aachen.de>
Co-authored-by: Fabian <f.a.stamm@gmail.com>
Co-authored-by: Dieter Werthmüller <prisae@users.noreply.github.com>
Co-authored-by: Andrew Annex <ama6fy@virginia.edu>
Co-authored-by: Blue Tyson <bluetyson@users.noreply.github.com>
Co-authored-by: Alexander G. Zimmerman <alexander.zimmerman@rwth-aachen.de>
Co-authored-by: Alexander Schaaf <a.schaaf@abdn.ac.uk>
Co-authored-by: javoha <jan.von.harten@rwth-aachen.de>
Co-authored-by: Alexander G. Zimmerman <alex.g.zimmerman@gmail.com>
Co-authored-by: banesullivan <banesulli@gmail.com>
Co-authored-by: Japhiolite <jan.niederau@rwth-aachen.de>
Co-authored-by: Tobi Glaubach <tobias.glaubach@gmail.com>
Co-authored-by: Jan von Harten <38279459+javoha@users.noreply.github.com>
Co-authored-by: Florian Wellmann <flohorovicic@gmail.com>
Co-authored-by: alexander.juestel <alexander.juestel@rwth-aachen.de>
Co-authored-by: Adam Kosík <adam.kosik@ost.ch>
Co-authored-by: elimh <elisa.heim@gmx.de>
Leguark added a commit that referenced this issue Aug 14, 2020
* - init docs-devs branch
- fixbar

* [DOC] Fixing the bar

* fixed markup in installation.rst

* updated installation instructions for MacOS and minor edits

* [BUG] Minor bugs for strange order of calls

* [BUG] Travis sets the right domain for the documentation

* fixed typos and minor formatting

* minor formatting in index.rst

* [BUG] Second try fixing travis domain

* formatting and minor corrections in Ch1_1_basic

* minor corrections in installation.rst and unified heading style in ch1_1

* minor corrections and formatting in ch1_2a

* minor corrections and formatting in ch1_2b

* [DOC] Small changes to the installation.rst

* minor corrections and formatting in ch1_3a

* Small changes to Index

* Small changes to index

* - init docs-devs branch
- fixbar

* minor corrections and formatting in ch1_3c and merge with ch1_3d

* minor corrections in installation.rst

* [BUG] patching gempy to be compatible with pyvista 0.25

* [BUG] Allowing user to have pyvista .24 too

* [DOC] Added some links to the repo badges

* [BUG] Adding flag for pyvista sphinx

* [BUG] Fixing travis

* [BUG] Fixing travis

* [BUG] Fixing travis - Minor tweaks on to setup.py

* [BUG] Fixing travis - Minor tweaks on to setup.py

* Fix Travis for emg3d/pymc3. (#439)

* Fix Travis for emg3d/pymc3.

* Remove unused `script`-section

* Add the license to the manifest for inclusion in source code (#435)

distribution

* Update manifest.in to be explicit (#444)

I just realized my pr was not explicit about the include of the license, I don't think it would have broken anything but better to be safe.

* Update README.md

Typo in universal.

* Remove use of optional argument which was providing wrong index

* Have Travis only check master and release branches

* Randomly generate colors when deterministic colors run out. Also clarify the Color class

* # Added new model for simple geometry examples

* Fix version of discretize installed by Travis

* Fix4 (#490)

* Fix pyvistaqt deprecations

* [BUG] Adding verbosity to the testing in travis

* [BUG] adding mkl dependency and more verbosity

* [debug] print pyvista report on Travis

* - [BUG] Adapted code to matplotlib 3.3

* Added dev-requirements.txt

- Start fixing plot_posterior.py

* - arg image, also close the vtk window
travis still dies
- Trying something on travis

* - Fixing more broken code due to matplotlib release

* - Dealing with travis

* - Minor

* - Making GemPy compatible with pyvista 0.25 and 0.24

- Making travis to use 0.24

* - force reinstall in travis

* - Travis is picking the wrong commit?

Co-authored-by: banesullivan <banesulli@gmail.com>
Co-authored-by: Miguel de la Varga <miguel@terranigma-solutions.com>

* Gempy to rex (#485)

* GemPy 2.2.0 (#428)

* Update ch1-1_Basics.ipynb

* Revert "Update ch1-1_Basics.ipynb"

This reverts commit 1852684.

* play around with stochastics in exploratory notebook

* differentiate filename and path in moose export

* fix errors in moose notebook

* Delete main.yml

* [CLN] Refactored DataMutation and Model to ImplicitCoKriging and Project

* work on hierarchical modelling test notebook

* [DOC] finish notebook with example for hierarchical modeling

* Fix 335 (#336)

* [DOC] Updated version

* [BUGFIX] Fixes typing error

>>> import gempy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/namur/coding/gempy/gempy/__init__.py", line 10, in <module>
    import gempy.plot.plot_api as _plot
  File "/home/namur/coding/gempy/gempy/plot/plot_api.py", line 38, in <module>
    from .vista import _Vista as Vista
  File "/home/namur/coding/gempy/gempy/plot/vista.py", line 56, in <module>
    class Vista:
  File "/home/namur/coding/gempy/gempy/plot/vista.py", line 108, in Vista
    name='lith',
AttributeError: module 'gempy' has no attribute 'Solution'

Co-authored-by: varga <varga@aices.rwth-aachen.de>

* [BUG] Plot2D.extract_section_lines breaks

* [DOC] Updated requirements.txt and README.md for Win installation

* [ENH] Added the option in delete series to delete associated data

- Added a gpu_theano file to check the installation

* renamed file_path to table_source and added if/else for directly passing a dataframe instead of loading from csv

* renamed file_path to table_source

* added read_df function for directly reading from dataframe objects and added the corresponding kwargs to init_data function

* added integration test for loading by directly passing a dataframe

* adapted the case checking to incorporate dataframes as well

* fixed the test to actually cover the new behaviour properly

* [DOC] Added explanation to Data_Manipulation notebook, fixed broken link

* minor

* Fixture model (#340)

* [ENH] Added possible fixture model data and example notebook

* [ENH] Small fixes in naming conventions and scalar field plotting

* [META] Add .vs to gitignore

* [TEST] Added test for the old implementation of passing directly dfs

* [ENH] Added a better parser of columns when data is read

* [ENH] Refactored read_Df to set_geometric_data

* [ENH] Init data use the old way to pass frames

* [Test] Update test to the new code

* [DOC] Added export to gocad code to the implicit benchmark

* [DOC] Claudius low memory profile

- nugget effect small bug

* [TEST] Fixing travis

* [BUG] Fix broken Model().read_data when used old kwargs

* [ENH] Giving up trying to edit current vista code

- Added 'hasData' column to surfaces

* [TEST] Ordering a bit the test

* [ENH] Init of the new vista class

* [TEST] Tidying up test and creating only one interpolator
 fixture

* [TEST] Fixed gravity test

- Added gravity fixture
- Now it is possible to pass the centered grid after compilation
- update_additional data moved from api to Model

* [TEST] Fixed magnetics

- Added magnetics fixture
- added fw_magnetics to Solution

* [TEST] Fixed topology
- Added fabian and unconformity fixture

* [TEST] Fixed rest of the tests

* [Test] Added fixture model with folding/faulting/unconformity to conftest.py

* Added notebook with example of diamond square algorithm (and additional smoothing step)

* Some edits for PEP8 conformity

* [ENH] Added plot_surface_points

* [BUG] Small fixes

* Vectorized topography generation using DS algorithm - example notebook, first steps for single hierarchy

* Vectorized interpolation with padded checkerboard pattern to reduce number of possible cases

* Extension to point selection on multiple hierarchies

* Selection on multiple hierarchies, including padding and grid visualization; one problem with hierarchy calculation remaining, should be easy to fix.

* Hierarchical point selection now working - notebook contains example comparable to example on Wikipedia (https://en.wikipedia.org/wiki/Diamond-square_algorithm#/media/File:Diamond_Square.svg)

* Added hillshade example

* Generalized point selection in DS algorithm

* set up diamond-square module and test in gempy/utils

* Methods for grid size determination and set-up of class structure

* Updated module with grid selection plots and added (tutorial) notebook using the gempy.utils.diamond_square module

* Implemented full diamond-square interpolation algorithm

* Added tests for grid generation and point selection

* Full implementation vectorized and working! (Need to check parameter settings, next)

* Added possibility to initialize and interpolate on lower hierarchy levels

* Added type hints to function declarations

* Extended testing and fixed type hints

* [ENH] Added plot orientations, topography and structured grid

- [BUG] set_is_fault updates properly Surfaces

* [DOC] Added some docs and making test running

* Added several random functions to generate topography and extended description in tutorial notebook.

* Small changes in notebooks (stored to avoid problems in branch switch)

* [ENH] Capturing errors in gempy_to_rexfile.py

[CLN] Deleted old set_gravity_interpolator

* change interpolation function of topo along sections - still needs tests

* [CLN] Move API to the root folder of gempy

* add new topo section function for testing and comparing with old one

* [ENH] Added editing function
[CLN] Move gempy functions to modules and regions

* [CLN] Refactor all notebooks

* - minor

* [TEST] Minor refactor

* [ENH] First prototype of sphinx gallery running

* [ENH] Add first example

* [ENH] changed spline interpolation to interp2d cubic

* DataforPullRequest

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* clean up functions for interpolating topography along set sections

* move csv data of hierarchical modeling from notebooks to data

* remove my copy of metropolis notebook

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* Revert "[CLN] Move API to the root folder of gempy"

This reverts commit e908000

* Refactor notebooks/data to examples/data for tests

* [BUG] Fixed: colors for more than 67 surfaces.

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* [DOC] Files converted in mac to avoid windows problems

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* ChangeGemPyAPI

* ChangeGemPyAPI

* ChangeGemPyAPI

* [DOC] Tidy up

* [DOC] Tutorials to %% format

* [DOC] Add subset of columns to render in the GeometricData

- Added verbosity arg to gp.get_data

* [BUG] Added default value to plot_2D

* [MERGE] Merging sphinx and api branches

* [MERGE] Merging pyvista polishing with api and sphinx

* Generate colordict with own palette.

* add default for argument method in interpolate_zvals_at_xy

* [DOC] Tutorial one running
- plot_2d:
    - accepts block and values now
    - Different series
    - [BUG] If only one axes plots on the whole figure
- vista
   - [BUG] plot_data now works

- [ENH] compute_model check for an interpolator
- [Test] New test to try vista functionality api

* Updated and cleaned module and extended tests

* Fixed notebook and extended description; included comparison for different roughness values.

* [CLN] Added restricting wrapper to all data objects

* AddTypeHinting

* [CLN] Slit the data.py module and fixing the imports

* [CLN] Stack class encapsulates Series and faults

* [DOC] Some sphinx config

* [DOC] More shpinx config

* [ENH] Move new plotting api to the main frame

* [ENH] Lot of shpinx docs polishing

* [ENH] Fixed the autodocs deprecation!

* [CLN] Removed nptyping dependency

- Fixed lost of types in Stack/Series
- Lot of docstrings in ImplicitcoKriging

* [DOC] All the ImplicitKriging class docstrings updated

* [DOC] Plot 2D and 3D hyperlinks fixed

* [DOC] Docstring has links to examples

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [BUG] Fixed marching cubes bug

* [BUG] Fixed Colors topography pyvista

* [BUG] Fixing travis: Apparently pad does not have explicit mode anymore

* [TEST] Start porting the notebook test to a test file

* [BUG] Solved #397

[TEST]
- Added a test for JanN code
- Added a test for changing the order of the surfaces
- solved minor problems

* [MERGE] Florian's diamond random topo merged

* [ENH] First commit for topography.py rework

* [ENH] Merged hillshading

- Ported to the new plot2d code
- Added test

* [ENH] Topography fixed!!!

- Finally random and gdal are pointing to the same directions
- Test!!
[ENH] Vertical exaggeration in pyvista

* [ENH] Vertical exaggeration in 2d plot too

- More test for 2d plot

* [DOC] Added probability examples

- Topography is saved now
- Fixed latest arviz compatibility
- Moving some probability functionality to modules
- Minor plotting enhancements
- added test pymc

* [ENH] pyvista: scalar_bar

- mjnor stuff

* [ENH] Fixed masked marching cubes

- pyvista scalar_bar inverted

* [ENH] adapting code to scikit image 17.1

* [CLN] Minor cleaning

* [ENH] Size of figures grow with number of axis
- Better projection distance
[BUG] - Axis label were breaking
[TEST] - More 2D test

* [DOC] Moved half of the tutorials to sphinx gallery

* fixed get section polygons and updated tutorials notebook

* deleted plotting function

* [ENH] Fixed mask returning from interpolator
- Fixed bug loading old models
- Fixed bug masking the faults
[TEST] Adding bunch of tests

* [ENH] Add gdal to travis?

* [ENH] Added a bunch of tutorials

* [DOC] All examples and integration added

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis

* [DOC] Fixing travis

* Development flow update readme (#408)

* Restructured and edited introduction readme up to installation

* Updated readme, included now MacOSX 10.14 installation instructions.

* Updated table of contents

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis - added more general documentation

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Adding installation and projects

* [CLN] Remove all notebooks!

* [CLN] small refactorings

* [TEST] added test to travis

* [ENH] All pyvista interactions running again!

* [DOC] Fixing interactive notebooks

* [DOC] Fixing travis to run test

* [TEST] Fixing last test

* [TEST] Fixing last test

* [WIP] Sprint 2.2 - Merge of several open issues opened by me. (#396)

* Update ch1-1_Basics.ipynb

* Revert "Update ch1-1_Basics.ipynb"

This reverts commit 1852684.

* play around with stochastics in exploratory notebook

* differentiate filename and path in moose export

* fix errors in moose notebook

* Delete main.yml

* [CLN] Refactored DataMutation and Model to ImplicitCoKriging and Project

* work on hierarchical modelling test notebook

* [DOC] finish notebook with example for hierarchical modeling

* [ENH] Giving up trying to edit current vista code

- Added 'hasData' column to surfaces

* [TEST] Ordering a bit the test

* [ENH] Init of the new vista class

* Added notebook with example of diamond square algorithm (and additional smoothing step)

* Some edits for PEP8 conformity

* [ENH] Added plot_surface_points

* Vectorized topography generation using DS algorithm - example notebook, first steps for single hierarchy

* Vectorized interpolation with padded checkerboard pattern to reduce number of possible cases

* Extension to point selection on multiple hierarchies

* Selection on multiple hierarchies, including padding and grid visualization; one problem with hierarchy calculation remaining, should be easy to fix.

* Hierarchical point selection now working - notebook contains example comparable to example on Wikipedia (https://en.wikipedia.org/wiki/Diamond-square_algorithm#/media/File:Diamond_Square.svg)

* Added hillshade example

* Generalized point selection in DS algorithm

* set up diamond-square module and test in gempy/utils

* Methods for grid size determination and set-up of class structure

* Updated module with grid selection plots and added (tutorial) notebook using the gempy.utils.diamond_square module

* Implemented full diamond-square interpolation algorithm

* Added tests for grid generation and point selection

* Full implementation vectorized and working! (Need to check parameter settings, next)

* Added possibility to initialize and interpolate on lower hierarchy levels

* Added type hints to function declarations

* Extended testing and fixed type hints

* [ENH] Added plot orientations, topography and structured grid

- [BUG] set_is_fault updates properly Surfaces

* [DOC] Added some docs and making test running

* Added several random functions to generate topography and extended description in tutorial notebook.

* Small changes in notebooks (stored to avoid problems in branch switch)

* [ENH] Capturing errors in gempy_to_rexfile.py

[CLN] Deleted old set_gravity_interpolator

* change interpolation function of topo along sections - still needs tests

* [CLN] Move API to the root folder of gempy

* add new topo section function for testing and comparing with old one

* [ENH] Added editing function
[CLN] Move gempy functions to modules and regions

* [CLN] Refactor all notebooks

* - minor

* [TEST] Minor refactor

* [ENH] First prototype of sphinx gallery running

* [ENH] Add first example

* [ENH] changed spline interpolation to interp2d cubic

* DataforPullRequest

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* [TRY] Using travis to build docs

* clean up functions for interpolating topography along set sections

* move csv data of hierarchical modeling from notebooks to data

* remove my copy of metropolis notebook

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* Revert "[CLN] Move API to the root folder of gempy"

This reverts commit e908000

* Refactor notebooks/data to examples/data for tests

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* [DOC] Files converted in mac to avoid windows problems

* [DOC] Converted all notebooks into .py files that can be rendered by sphinx-gallery

* ChangeGemPyAPI

* ChangeGemPyAPI

* ChangeGemPyAPI

* [DOC] Tidy up

* [DOC] Tutorials to %% format

* [DOC] Add subset of columns to render in the GeometricData

- Added verbosity arg to gp.get_data

* [BUG] Added default value to plot_2D

* [MERGE] Merging sphinx and api branches

* [MERGE] Merging pyvista polishing with api and sphinx

* add default for argument method in interpolate_zvals_at_xy

* [DOC] Tutorial one running
- plot_2d:
    - accepts block and values now
    - Different series
    - [BUG] If only one axes plots on the whole figure
- vista
   - [BUG] plot_data now works

- [ENH] compute_model check for an interpolator
- [Test] New test to try vista functionality api

* Updated and cleaned module and extended tests

* Fixed notebook and extended description; included comparison for different roughness values.

* [CLN] Added restricting wrapper to all data objects

* AddTypeHinting

* [CLN] Slit the data.py module and fixing the imports

* [CLN] Stack class encapsulates Series and faults

* [DOC] Some sphinx config

* [DOC] More shpinx config

* [ENH] Move new plotting api to the main frame

* [ENH] Lot of shpinx docs polishing

* [ENH] Fixed the autodocs deprecation!

* [CLN] Removed nptyping dependency

- Fixed lost of types in Stack/Series
- Lot of docstrings in ImplicitcoKriging

* [DOC] All the ImplicitKriging class docstrings updated

* [DOC] Plot 2D and 3D hyperlinks fixed

* [DOC] Docstring has links to examples

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [TEST] Travis doc generation

* [BUG] Fixed marching cubes bug

* [BUG] Fixed Colors topography pyvista

* [BUG] Fixing travis: Apparently pad does not have explicit mode anymore

* [TEST] Start porting the notebook test to a test file

* [BUG] Solved #397

[TEST]
- Added a test for JanN code
- Added a test for changing the order of the surfaces
- solved minor problems

* [MERGE] Florian's diamond random topo merged

* [ENH] First commit for topography.py rework

* [ENH] Merged hillshading

- Ported to the new plot2d code
- Added test

* [ENH] Topography fixed!!!

- Finally random and gdal are pointing to the same directions
- Test!!
[ENH] Vertical exaggeration in pyvista

* [ENH] Vertical exaggeration in 2d plot too

- More test for 2d plot

* [DOC] Added probability examples

- Topography is saved now
- Fixed latest arviz compatibility
- Moving some probability functionality to modules
- Minor plotting enhancements
- added test pymc

* [ENH] pyvista: scalar_bar

- mjnor stuff

* [ENH] Fixed masked marching cubes

- pyvista scalar_bar inverted

* [ENH] adapting code to scikit image 17.1

* [CLN] Minor cleaning

* [ENH] Size of figures grow with number of axis
- Better projection distance
[BUG] - Axis label were breaking
[TEST] - More 2D test

* [DOC] Moved half of the tutorials to sphinx gallery

* [ENH] Fixed mask returning from interpolator
- Fixed bug loading old models
- Fixed bug masking the faults
[TEST] Adding bunch of tests

* [ENH] Add gdal to travis?

* [ENH] Added a bunch of tutorials

* [DOC] All examples and integration added

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis and added getting started

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis - added more general documentation

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Fixing travis

* [DOC] Adding installation and projects

* [CLN] Remove all notebooks!

* [CLN] small refactorings

* [TEST] added test to travis

* [ENH] All pyvista interactions running again!

* [DOC] Fixing interactive notebooks

* [DOC] Fixing travis to run test

* [TEST] Fixing last test

* [TEST] Fixing last test

Co-authored-by: Japhiolite <jan.niederau@rwth-aachen.de>
Co-authored-by: Florian Wellmann <flohorovicic@gmail.com>
Co-authored-by: alexander.juestel <alexander.juestel@rwth-aachen.de>
Co-authored-by: Alexander G. Zimmerman <alexander.zimmerman@rwth-aachen.de>

* [DOC] Adding the notebooks!

* [DOC] Adding the notebooks!

* [DOC] Changes in Dockerfile

* [ENH] Updated Dockerfile for preparation of gempy-server

* [DOC] Some thoughts about Interpolator Epic

* [ENH] Improved the function that generate the default gempy colors. However the whole class
 needs a better explanation of the api

* [FIX] Added back the main 10 colors

* Moved Petrel integration to subsurface module (#357)

* [TEST] Refactor some test

* [DOC] More thoughts on next Epic

* [BUG] Fix elisas example

* [DOC] Latest changes before release

Co-authored-by: Japhiolite <jan.niederau@rwth-aachen.de>
Co-authored-by: Alexander Schaaf <a.schaaf@abdn.ac.uk>
Co-authored-by: Tobi Glaubach <tobias.glaubach@gmail.com>
Co-authored-by: Jan von Harten <38279459+javoha@users.noreply.github.com>
Co-authored-by: javoha <jan.von.harten@rwth-aachen.de>
Co-authored-by: Florian Wellmann <flohorovicic@gmail.com>
Co-authored-by: alexander.juestel <alexander.juestel@rwth-aachen.de>
Co-authored-by: Alexander G. Zimmerman <alexander.zimmerman@rwth-aachen.de>
Co-authored-by: Adam Kosík <adam.kosik@ost.ch>
Co-authored-by: elimh <elisa.heim@gmx.de>

* [BUG] Minor change

* - GemPy to Rex v2

* - GemPy to Rex v2

* - Fixed few bugs for editing operations

* - Fixed bug writing the rexfile

- Now rexfile has color

* - Minor changes

* - [TEST]
Fixed

Co-authored-by: Japhiolite <jan.niederau@rwth-aachen.de>
Co-authored-by: Alexander Schaaf <a.schaaf@abdn.ac.uk>
Co-authored-by: Tobi Glaubach <tobias.glaubach@gmail.com>
Co-authored-by: Jan von Harten <38279459+javoha@users.noreply.github.com>
Co-authored-by: javoha <jan.von.harten@rwth-aachen.de>
Co-authored-by: Florian Wellmann <flohorovicic@gmail.com>
Co-authored-by: alexander.juestel <alexander.juestel@rwth-aachen.de>
Co-authored-by: Alexander G. Zimmerman <alexander.zimmerman@rwth-aachen.de>
Co-authored-by: Adam Kosík <adam.kosik@ost.ch>
Co-authored-by: elimh <elisa.heim@gmx.de>
Co-authored-by: Miguel de la Varga <miguel@terranigma-solutions.com>

* Fix pandas version because of bug in 1.1.0 (#504)

* Remote Loading and tweaks in gempy_to_rex

* - [RELEASE] Change the version to 2.2.3

* - [ENH] Saving models into a zip

* - [ENH] Using pooch to grab remote models

* - [ENH] Adding topography and geological maps to the rex file

* - [TEST] Adapted test to new loading function

* - [ENH] Adding models to remote

* - [BUG] Better check if topography exist when we encode a rexfile

- [BUG] Onlap surfaces were not computed

* - [DOC] Improved error message when address is wrong

* - [BUG] Added pooch

* - [BUG] loading errors

* - [BUG] loading errors

* - [BUG] missing /

Co-authored-by: Miguel de la Varga <miguel@terranigma-solutions.com>

Co-authored-by: Miguel de la Varga <miguel@terranigma-solutions.com>
Co-authored-by: SimonVirgo <s.virgo@ged.rwth-aachen.de>
Co-authored-by: Fabian <f.a.stamm@gmail.com>
Co-authored-by: Dieter Werthmüller <prisae@users.noreply.github.com>
Co-authored-by: Andrew Annex <ama6fy@virginia.edu>
Co-authored-by: Blue Tyson <bluetyson@users.noreply.github.com>
Co-authored-by: Alexander G. Zimmerman <alexander.zimmerman@rwth-aachen.de>
Co-authored-by: Alexander Schaaf <a.schaaf@abdn.ac.uk>
Co-authored-by: javoha <jan.von.harten@rwth-aachen.de>
Co-authored-by: Alexander G. Zimmerman <alex.g.zimmerman@gmail.com>
Co-authored-by: banesullivan <banesulli@gmail.com>
Co-authored-by: Japhiolite <jan.niederau@rwth-aachen.de>
Co-authored-by: Tobi Glaubach <tobias.glaubach@gmail.com>
Co-authored-by: Jan von Harten <38279459+javoha@users.noreply.github.com>
Co-authored-by: Florian Wellmann <flohorovicic@gmail.com>
Co-authored-by: alexander.juestel <alexander.juestel@rwth-aachen.de>
Co-authored-by: Adam Kosík <adam.kosik@ost.ch>
Co-authored-by: elimh <elisa.heim@gmx.de>
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