gempy-project · Leguark · Jul 27, 2020 · May 27, 2020 · May 28, 2020 · May 29, 2020
diff --git a/.travis.yml b/.travis.yml
@@ -1,47 +1,56 @@
 language: python
-
+os: linux
 dist: xenial
 
+branches:
+    only:
+        - master
+        - release
+
 python:
   - '3.7'
 
-env: TRAVIS=true
-
 before_install:
   # configure a headless display
   - git clone --depth 1 git://github.com/pyvista/gl-ci-helpers.git
   - source ./gl-ci-helpers/travis/setup_headless_display.sh
 
 install:
-  - wget https://repo.anaconda.com/pkgs/misc/conda-execs/conda-latest-linux-64.exe -O conda.exe
-  - chmod +x conda.exe
-  - export CONDA_ALWAYS_YES=1
-  # This is where you put any extra dependencies you may have.
-  - ./conda.exe create -p $HOME/miniconda python=$TRAVIS_PYTHON_VERSION conda conda-build pytest six pytest-cov pytest-mock
+  - sudo apt-get update
+  # We do this conditionally because it saves us some downloading if the
+  # version is the same.
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+  - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r
-  - pip install --upgrade setuptools pip
-  - pip install -r requirements.txt
-  - pip install sphinx-gallery
-  - pip install qgrid
-  - pip install nbval
-  - pip install pyevtk
-  - pip install arviz
-  - pip install recommonmark
-  - pip install dataclasses pyvista panel discretize # emg3d
-  - pip install welly
-  - conda install gdal
-  - conda install --yes -c conda-forge python-graphviz
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update --all
+  # Useful for debugging any issues with conda
+  - conda info -a
+
+  # Install and activate environment, install packages
+  - conda create -q -n tenv python=$TRAVIS_PYTHON_VERSION
+  - source activate tenv
+
+  # Installs from conda-forge
+  - conda install -c conda-forge python-graphviz emg3d
+    discretize==0.4.13 pip matplotlib ipython six pytest pytest-cov
+    pytest-mock gdal pandas seaborn>=0.9 qgrid sphinx-gallery
+    ipywidgets pyevtk arviz dataclasses scikit-image>=0.17
+    recommonmark networkx panel setuptools mkl-service
+
+  # Installs from anaconda
   - conda install -c anaconda libffi
-  - pip install pymc3
-  - pip install ipython
-    # Install untested, non-required code (linter fails without them)
-  - pip install ipython ipywidgets
-  - export PATH="./bin:$PATH"
 
-script:
-  - pytest -v notebooks/ --nbval-lax
-  - pytest
+  # Installs from pip
+  - pip install welly pymc3
+
+  # Install
+  - pip install -e .
+  # foo
+  - pip install pyvista==0.24.3 --force-reinstall
+
+  - python -c "import pyvista as pv;print(pv.Report())"
 
 stages:
   - test
@@ -51,13 +60,12 @@ jobs:
   include:
       - stage: test
         script:
-          - pytest
+          - pytest -v
       - stage: deploy
         name: Deploy to GitHub Pages
        # if: (NOT type IN (pull_request)) AND (branch = sphinx-gallery) # only deploy if merging on master
 
         before_script:
-         - pip install -e .
          - cd docs
         script: pipenv run make html
         deploy:
@@ -66,7 +74,7 @@ jobs:
           github_token: $travis_doc # defined via the Travis interface
           local_dir: docs/build/html
           on:
-            branch: sprint_2.2
+            branch: release
           target_branch: gh-pages
+          fqdn: docs.gempy.org
 cache: pip
-
diff --git a/DevelopersGuide.txt b/DevelopersGuide.txt
@@ -17,7 +17,6 @@ python3 setup.py sdist bdist_wheel
 twine upload dist/*
 
 
-
 ### Type of commits:
 
 ENH: Enhancement, new functionality

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1 +1,2 @@
-exclude notebooks/ *
+exclude notebooks/*
+include LICENSE
diff --git a/README.md b/README.md
@@ -5,9 +5,9 @@
 
 [![PyPI](https://img.shields.io/badge/python-3-blue.svg)](https://www.python.org/downloads/)
 [![PyPI](https://img.shields.io/badge/pypi-1.0-blue.svg)](https://pypi.org/project/gempy/)
-[![license: LGPL v3](https://img.shields.io/badge/license-LGPL%20v3-blue.svg)]()
+[![license: LGPL v3](https://img.shields.io/badge/license-LGPL%20v3-blue.svg)](https://github.com/cgre-aachen/gempy/blob/master/LICENSE)
 [![Documentation Status](https://assets.readthedocs.org/static/projects/badges/passing-flat.svg)](http://docs.gempy.org)
-[![Travis Build](https://travis-ci.org/cgre-aachen/gempy.svg?branch=master)]()
+[![Travis Build](https://travis-ci.org/cgre-aachen/gempy.svg?branch=master)](https://travis-ci.org/github/cgre-aachen/gempy/branches)
 [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/cgre-aachen/gempy/master)
 [![DOI](https://zenodo.org/badge/96211155.svg)](https://zenodo.org/badge/latestdoi/96211155)
 [![DOCKER](https://img.shields.io/docker/cloud/automated/leguark/gempy.svg)](https://cloud.docker.com/repository/docker/leguark/gempy)
@@ -67,7 +67,7 @@ gempy has been used for realistic models!  -->
 ### Interpolation approach
 
 The generation of complex structural settings is based on the powerful
-interpolation algorithm underlying `GemPy`, a unviersal cokriging method
+interpolation algorithm underlying `GemPy`, a universal cokriging method
 devoised by Lajaunie et al. (1997) and extended by Calcagno et al. (2008).
 This method is used to interpolate a 3D scalar field, such that geologically
 significant interfaces are isosurfces in this field.
@@ -197,4 +197,4 @@ providing detailed [tutorials](https://www.gempy.org/tutorials) on how to use it
 * Lajaunie, C., Courrioux, G., & Manuel, L. (1997). Foliation fields and 3D cartography in geology: principles of a method based on potential interpolation. Mathematical Geology, 29(4), 571-584.
 * Wellmann, F., Schaaf, A., de la Varga, M., & von Hagke, C. (2019). [From Google Earth to 3D Geology Problem 2: Seeing Below the Surface of the Digital Earth](
 https://www.sciencedirect.com/science/article/pii/B9780128140482000156).
-In Developments in Structural Geology and Tectonics (Vol. 5, pp. 189-204). Elsevier.
+In Developments in Structural Geology and Tectonics (Vol. 5, pp. 189-204). Elsevier.
diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -0,0 +1,8 @@
+# This are additional libraries necessary to run sphinx and all the test
+sphinx
+sphinx_gallery
+emg3d
+ipywidgets
+# This shold be installed with conda too: conda install -c conda-forge discretize==0.4.13
+welly
+requests
diff --git a/docs/Makefile b/docs/Makefile
@@ -18,3 +18,10 @@ help:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+html-noplot: export SPHX_GLR_THEME = $(theme)
+html-noplot:
+	$(SPHINXBUILD) -D plot_gallery=0 -b html $(ALLSPHINXOPTS) $(SOURCEDIR) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -36,6 +36,7 @@
 pyvista.rcParams['window_size'] = np.array([1024, 768]) * 2
 # Save figures in specified directory
 pyvista.FIGURE_PATH = os.path.join(os.path.abspath('./images/'), 'auto-generated/')
+pyvista.BUILDING_GALLERY = True
 if not os.path.exists(pyvista.FIGURE_PATH):
     os.makedirs(pyvista.FIGURE_PATH)
 
@@ -143,8 +144,6 @@
 
 
 # -- Sphinx Gallery Options
-from sphinx_gallery.sorting import FileNameSortKey
-
 sphinx_gallery_conf = {
     # path to your examples scripts
     "examples_dirs": [
@@ -204,7 +203,7 @@
     'logo_name': True,
     'travis_button': True,
     'page_width': '1200px',
-    'fixed_sidebar': True,
+    'fixed_sidebar': False,
     'show_related': True,
     'sidebar_collapse': True,
 }

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -3,31 +3,32 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-.. image:: ../logos/gempy1.png
+.. ../logos/gempy1.png
    :width: 30%
 
-about
+About
 =====
-Software for 3D structural geologic implicit modeling in Python.
+Open-source software for implicit 3D structural geological modeling in Python.
 ****************************************************************
 
 Overview
 --------
 
-``GemPy`` is a Python-based, **open-source geomodeling library**. It is
-capable of constructing complex **3D geological models** of folded
-structures, fault networks and unconformities, based on the underlying
-powerful **implicit representation** approach. ``GemPy`` was designed from the
-ground up to support easy embedding in probabilistic frameworks for the
-uncertainty analysis of subsurface structures.
+``GemPy`` is a Python-based, community-driven, **open-source geomodeling library**. It is
+capable of constructing complex **3D geological models** including various features such as
+fold structures, fault networks and unconformities, based on an underlying
+powerful **implicit** approach. From the ground up, ``GemPy`` was designed to be easily embedded in probabilistic frameworks for conducting
+uncertainty analysis regarding subsurface structures.
 
-Check out the documentation either in `gempy.org <https://www.gempy.org/>`_
+.. Check out the documentation either in `gempy.org <https://www.gempy.org/>`_
 (better option), or `read the docs <http://gempy.readthedocs.io/>`_.
 
 
+
+
 3D models created with GemPy may look like this:
 
-.. image:: ./images/model_example.png
+.. image:: ./images/perth_example.png
 
 Contents:
 
@@ -57,8 +58,8 @@ Contents:
 Features
 --------
 
-Geological objects
-^^^^^^^^^^^^^^^^^^
+Geological features
+^^^^^^^^^^^^^^^^^^^
 
 
 .. raw:: html
@@ -67,9 +68,7 @@ Geological objects
 
 
 
-``GemPy`` enables the modeling of complex 3D geological settings,
-on par with many commercial geomodeling packages, including:
-
+``GemPy`` is capable of modeling complex 3D geological scenarios, including:
 
 * Multiple conformal layers (e.g. sequences of sedimentary layers)
 * Several sequences of layers, with conformal continuation or unconformities
@@ -78,32 +77,32 @@ on par with many commercial geomodeling packages, including:
 * Full fault networks (faults affecting faults)
 * Folds (affecting single layers or entire layer stacks, including overturned and recumbent folds)
 
-The combination of these elements allows for the generation of realistic
-3-D geological models in most typical geological settings.
-
+Combining these elements in GemPy allows for the generation of realistic
+3D geological models, on a par with most commercial geomodeling software.
 
 .. raw:: html
 
    <!-- Note: we should inlcude here links to models and/or publications where
    gempy has been used for realistic models!  -->
 
 
+
 Interpolation approach
 ^^^^^^^^^^^^^^^^^^^^^^
 
 The generation of complex structural settings is based on the powerful
 interpolation algorithm underlying ``GemPy``\ , a unviersal cokriging method
-devoised by Lajaunie et al. (1997) and extended by Calcagno et al. (2008).
+devoised by `Lajaunie et al. (1997)` and extended by `Calcagno et al. (2008)`\ .
 This method is used to interpolate a 3D scalar field, such that geologically
 significant interfaces are isosurfces in this field.
 
 The algorithm allows for a direct integration of two of the most relevant
 geological input data types:
 
 
-* *Surface contact points*\ : 3D coordinates of points marking the boundaries
+* **Surface contact points**\ : 3D coordinates of points marking the boundaries
   between different features (e.g. layer interfaces, fault planes, unconformities).
-* *Orientation measurements*\ : Orientation of the poles perpendicular to
+* **Orientation measurements**\ : Orientation of the poles perpendicular to
   the dipping of surfaces at any point in the 3D space.
 
 ``GemPy`` also allows for the definition of topological elements such as
@@ -125,7 +124,7 @@ Models generated with ``GemPy`` can be visualized in several ways:
   representation of results;
 * interactive 3D visualization and model input manipulation using the
   Visualization Toolkit (VTK);
-* We also actively develop a link to the fantastic `
+* We also actively develop a link to the fantastic
   `pyvista <https://www.pyvista.org>`_ project
   for even better visualization and model interaction in 3D.
 
@@ -137,9 +136,9 @@ in a variety of ways:
   software such as ParaView;
 * Export of triangulated surface meshes (e.g. for further processing in
   meshing programs);
-* Export of images (e.g. geological maps) for
+* Export of images (e.g. geological maps).
 
-We are also currently working on a tighter integration wtih several
+We are also currently working on a tighter integration with several
 meshing libraries, notably `CGAL <https://www.cgal.org>`_ and `gmesh <https://gmsh.info>`_. In addition, we have
 established links to several other open-source libraries, including `pygiml <https://www.pygimli.org>`_
 for geophysical modeling and inversion. In the current state, however, these
@@ -155,7 +154,7 @@ feel free to contact us.
 Stochastic geological modeling
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-One of the most advanced features that sets ``gempy`` also apart from
+One of the most advanced features that sets ``GemPy`` also apart from
 available commercial packages is the full integration of stochastic
 geological modeling methods.
 ``GemPy`` was designed from the ground up to support stochastic geological
@@ -187,7 +186,7 @@ via PyMC will then result in different model realizations.
 
 Theano allows the automated computation of gradients, opening the door to
  the use of advanced gradient-based sampling methods
-coupling *GeMpy* and
+coupling ``GemPy`` and
 `PyMC3 <https://pymc-devs.github.io/pymc3/notebooks/getting_started.html>`_
 for advanced stochastic modeling. Also, the use of Theano allows making
 use of GPUs through cuda (see the Theano documentation for more information.
@@ -197,15 +196,15 @@ Making use of vtk interactivity and `Qgrid <https://github.com/quantopian/qgrid>
 
 For a more detailed elaboration of the theory behind ``GemPy``\ , we refer to the
 **open access scientific publication**\ :
-`\ *"GemPy 1.0: open-source stochastic geological modeling and inversion"*
-by de la Varga et al. (2018) <https://www.geosci-model-dev.net/12/1/2019/gmd-12-1-2019.pdf>`_.
+`\ "GemPy 1.0: open-source stochastic geological modeling and inversion"
+by de la Varga et al. (2019) <https://www.geosci-model-dev.net/12/1/2019/gmd-12-1-2019.pdf>`_.
 
 References
 ----------
 
-* de la Varga, M., Schaaf, A., & Wellmann, F. GemPy 1.0: open-source stochastic geological modeling and inversion.
-* Calcagno, P., Chilès, J. P., Courrioux, G., & Guillen, A. (2008). Geological modelling from field data and geological knowledge: Part I. Modelling method coupling 3D potential-field interpolation and geological rules. Physics of the Earth and Planetary Interiors, 171(1-4), 147-157.
-* Lajaunie, C., Courrioux, G., & Manuel, L. (1997). Foliation fields and 3D cartography in geology: principles of a method based on potential interpolation. Mathematical Geology, 29(4), 571-584.
+* de la Varga, M., Schaaf, A., and Wellmann, F.: GemPy 1.0: `open-source stochastic geological modeling and inversion,` Geosci. Model Dev., 12, 1–32, https://doi.org/10.5194/gmd-12-1-2019, 2019.
+* Calcagno, P., Chilès, J. P., Courrioux, G., & Guillen, A. (2008). `Geological modelling from field data and geological knowledge: Part I. Modelling method coupling 3D potential-field interpolation and geological rules.` Physics of the Earth and Planetary Interiors, 171(1-4), 147-157.
+* `Lajaunie, C., Courrioux, G., & Manuel, L. (1997). `Foliation fields and 3D cartography in geology: principles of a method based on potential interpolation.` Mathematical Geology, 29(4), 571-584.
 
 
 Indices and tables