GemPy 2.2.3 #493
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GemPy 2.2.3 #493
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* Fix Travis for emg3d/pymc3. * Remove unused `script`-section
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.
Typo in universal.
Remove use of optional argument which was providing wrong index to fix #466
…ify the Color class
# Added new model for simple geometry examples
🌈 Fix 451: Adds random color generation for more than 66 surfaces
Have Travis only check master, release, and PR branches
Fix version of discretize installed by Travis
Fix typo in README.md
* 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 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>
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Description
Added rex writer