[WIP] Current GemPy Patches

.github/workflows/pytest.yml

@@ -0,0 +1,117 @@
+name: GemPy CI Conda Requirements
+
+on:
+  push:
+    branches: [ dev_alexj, master, main, release, fixing_actions ]
+
+  pull_request:
+    branches: [ dev_alexj, master, main, release ]
+
+    # Allows you to run this workflow manually from the Actions tab
+    workflow_dispatch:
+
+jobs:
+  # A workflow run is made up of one or more jobs that can run sequentially or in parallel
+  testing_conda:
+    name: Conda install ${{ matrix.case.os }} py${{ matrix.case.python-version }} ${{ matrix.case.name }}
+    runs-on: ${{ matrix.case.os }}-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu, ]  # macos, windows]  # Only Linux currently.
+        case:
+          - python-version: 3.8
+            name: basic
+            os: ubuntu
+
+    env:
+      DISPLAY: ':99.0'
+      PYVISTA_OFF_SCREEN: 'True'
+      ALLOW_PLOTTING: true
+      SHELLOPTS: 'errexit:pipefail'
+      OS: ${{ matrix.case.os }}
+      PYTHON: ${{ matrix.case.python-version }}
+      GITHUBACTION: "true"
+
+    steps:
+      # Cancel any previous run of the test job; [pin v0.8.0 (2021-02-13)]
+      - name: Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@3d86a7cc43670094ac248017207be0295edbc31d
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v2
+      - name: Setup Headless Display
+        run: |
+            sudo apt-get update && sudo apt-get install libgl1-mesa-glx xvfb -y
+            sudo apt-get install -y xvfb
+            Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 &
+            sleep 3
+
+      - name: Install dependencies
+        run: |
+            conda list gempy
+            conda list gdal
+            conda list pyvista
+            conda list vtk
+            conda list pandas
+            conda list numpy
+            conda install gdal
+            python -m pip install --upgrade pip
+            pip install -r dev-requirements.txt
+
+      - name: Run tests with pytest
+        run: |
+          pytest
+
+  testing_pip:
+    name: Pip install ${{ matrix.case.os }} py${{ matrix.case.python-version }} ${{ matrix.case.name }}
+    runs-on: ${{ matrix.case.os }}-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu, ]  # macos, windows]  # Only Linux currently.
+        case:
+          - python-version: 3.8
+            name: basic
+            os: ubuntu
+
+    env:
+      DISPLAY: ':99.0'
+      PYVISTA_OFF_SCREEN: 'True'
+      ALLOW_PLOTTING: true
+      SHELLOPTS: 'errexit:pipefail'
+      OS: ${{ matrix.case.os }}
+      PYTHON: ${{ matrix.case.python-version }}
+      GITHUBACTION: "true"
+    steps:
+      # Cancel any previous run of the test job; [pin v0.8.0 (2021-02-13)]
+      - name: Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@3d86a7cc43670094ac248017207be0295edbc31d
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v2
+      - name: Setup Headless Display
+        run: |
+          sudo apt-get update && sudo apt-get install libgl1-mesa-glx xvfb -y
+          sudo apt-get install -y xvfb
+          Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 &
+          sleep 3
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r dev-requirements.txt
+
+      - name: Run tests with pytest
+        run: |
+          pytest

.travis.yml

@@ -43,7 +43,7 @@ install:
   - conda install theano
 
   # Installs from pip
-  - pip install welly pymc3 pooch
+  - pip install welly pymc3
 
   - pip install scikit-image>=0.17 sklearn
 
@@ -62,6 +62,8 @@ install:
 
   - python -c "import pyvista as pv;print(pv.Report())"
 
+  - pip install pooch
+
 stages:
   - test
 

CODE_OF_CONDUCT.md

@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at florian.wellmann@cgre.rwth-aachen.de. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

README.md

@@ -58,9 +58,9 @@ Follow these [guidelines](https://github.com/cgre-aachen/gempy/blob/WIP_readme-u
 
 ## Publications using GemPy
 
-* Güdük, N., de la Varga, M. Kaukolinna, J. and Wellmann, F. (in review). Model-Based Probabilistic Inversion Using Magnetic Data: A Case Study on the Kevitsa Deposit.
-* Schaaf, A., de la Varga, M., Wellmann, F., & Bond, C. E. (2020). [Constraining stochastic 3-D structural geological models with topology information using Approximate Bayesian Computation using GemPy 2.1](https://gmd.copernicus.org/preprints/gmd-2020-136/gmd-2020-136.pdf). Geoscientific Model Development Discussions, 1-24.
-* Stamm, F. A., de la Varga, M., and Wellmann, F. (2019). [Actors, actions, and uncertainties: optimizing decision-making based on 3-D structural geological models](https://se.copernicus.org/articles/10/2015/2019/se-10-2015-2019.html), Solid Earth, 10, 2015–2043.
+* Güdük, N.; de la Varga, M.; Kaukolinna, J.; Wellmann, F. (2021). [Model-Based Probabilistic Inversion Using Magnetic Data: A Case Study on the Kevitsa Deposit](https://doi.org/10.3390/geosciences11040150). Geosciences, 11, 150. https://doi.org/10.3390/geosciences11040150 (open access).
+* Schaaf, A., de la Varga, M., Wellmann, F., & Bond, C. E. (2020). [Constraining stochastic 3-D structural geological models with topology information using Approximate Bayesian Computation using GemPy 2.1](https://gmd.copernicus.org/preprints/gmd-2020-136/gmd-2020-136.pdf). Geoscientific Model Development Discussions, 1-24 (open access).
+* Stamm, F. A., de la Varga, M., and Wellmann, F. (2019). [Actors, actions, and uncertainties: optimizing decision-making based on 3-D structural geological models](https://se.copernicus.org/articles/10/2015/2019/se-10-2015-2019.html), Solid Earth, 10, 2015–2043 (open access).
 * 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.

dev-requirements.txt

@@ -1,7 +1,7 @@
 -r optional-requirements.txt
 
 # This are additional libraries necessary to run sphinx and all the test
-sphinx
+sphinx==3.5.4
 sphinx_gallery
 emg3d==0.11.0
 ipywidgets

docs/source/installation.rst

@@ -121,7 +121,7 @@ Here, we provide advice that should use in most cases (but certainly not all):
 
     ``$ conda install theano``
 
-    If the installation fails at some point try to re-install anaconda for a single user (no administrator priveleges)
+    If the installation fails at some point try to re-install anaconda for a single user (no administrator privileges)
     and with the Path Environment set.
     To use Theano with ``numpy version 1.16.0`` or following, it has to be updated to ``Theano 1.0.4`` using
 

environment_conda.yml

@@ -0,0 +1,7 @@
+name: gempy
+channels:
+  - conda-forge
+dependencies:
+  - subsurface
+  - geopandas
+  - gempy

environment_pip.yml

@@ -0,0 +1,10 @@
+name: gempy
+channels:
+  - conda-forge
+dependencies:
+  - subsurface
+  - geopandas
+  - pip
+  - pip:
+      - gempy
+      - pyqt5

examples/integrations/gempy_subsurface.py

@@ -10,9 +10,10 @@
 import subsurface as sb
 from subsurface.reader import read_netcdf
 
-data_url = "https://raw.githubusercontent.com/softwareunderground/subsurface/t21-main/examples/tutorials/wells_unstructured.nc"
+data_url = "https://raw.githubusercontent.com/softwareunderground/subsurface/main" \
+           "/examples/tutorials/wells_unstructured.nc"
 
-data_hash = '05198041f2bffcc03d138f7f2b1802657228725c4a895d819d4f5fbc0e9978ca'
+data_hash = "206290db4e563e379361725349ebf4a02628f4700d361599aedff37fab9cf5b9"
 borehole_unstructured_data_file = pooch.retrieve(url=data_url,
                                                  known_hash=data_hash)
 

examples/tutorials/ch1_fundamentals/ch1_1_basics.py

@@ -33,7 +33,7 @@
 #     -  Additional data
 #     -  Faults
 #
-# We will see each of this class in further detail in the future.
+# We will see each of these classes in further detail in the future.
 # 
 # Most of data can also be generated from raw data that comes in the form
 # of CSV-files (CSV = comma-separated values). Such files might be
@@ -42,13 +42,13 @@
 # Microsoft Excel or LibreOffice Calc.
 # 
 # In this tutorial, all input data is created by importing such CSV-files.
-# These exemplary files can be found in the ``input_data`` folder in the
+# These example files can be found in the ``input_data`` folder in the
 # root folder of GemPy. The data comprises :math:`x`-, :math:`y`- and
 # :math:`z`-positional values for all surface points and orientation
 # measurements. For the latter, poles, azimuth and polarity are
 # additionally included. Surface points are furthermore assigned a
 # formation. This might be a lithological unit such as "Sandstone" or a
-# structural feature such as "Main Fault". It is decisive to remember
+# structural feature such as "Main Fault". It is important to remember
 # that, in GemPy, interface position points mark the **bottom** of a
 # layer. If such points are needed to resemble a top of a formation (e.g.
 # when modeling an intrusion), this can be achieved by defining a
@@ -119,13 +119,13 @@
 # 
 # You can assign several surfaces to one series. The order of the units
 # within such as series is only relevant for the color code, thus we
-# recommend to be consistent. You can define this order via another
+# recommend being consistent. You can define this order via another
 # attribute "``order_formations``/ " or by using the specific command
 # ``set_order_formations``. (If the order of the pile differs from the
 # final result the color of the interfaces and input data will be
 # different.)
 # 
-# Every fault is treated as an independent series and have to be at set at
+# Every fault is treated as an independent series and has to be at set at
 # the **top of the pile**. The relative order between the distinct faults
 # defines the tectonic relation between them (first entry is the
 # youngest).
@@ -189,7 +189,7 @@
 # Our model input data, here named "*geo\_model*", contains all the
 # information that is essential for the construction of our model. You can
 # access different types of information by using ``gp.get_data`` or simply
-# by accessiong the atrribues.
+# by accessiong the atrributes.
 # 
 # We can, for example, return the coordinates of our modeling grid via:
 # 
@@ -283,15 +283,15 @@
 
 # %%
 # This function rescales the extent and coordinates of the original data
-# (and store it in the attribute ``geo_data_res`` which behaves as a usual
+# (and stores it in the attribute ``geo_data_res`` which behaves as a usual
 # ``InputData`` object) and adds mathematical parameters that are needed
 # for conducting the interpolation. The computation of this step may take
 # a while, as it also compiles a theano function which is required for the
 # model computation. However, should this not be needed, we can skip it by
 # declaring ``compile_theano = False`` in the function.
 # 
 # Furthermore, this preparation process includes an assignment of numbers
-# to each formation. Note that GemPy's always creates a default basement
+# to each formation. Note that GemPy always creates a default basement
 # formation as the last formation number. Afterwards, numbers are
 # allocated from youngest to oldest as defined by the sequence of series
 # and formations. On the property ``formations`` on our interpolation
@@ -315,7 +315,7 @@
 # ``compute_model``. By default, this will return two separate solutions
 # in the form of arrays. The first gives information on the lithological
 # formations, the second on the fault network in the model. These arrays
-# consist of two subarrays as entries each:
+# consist of two subarrays as entries described here:
 # 
 # 1. Lithology block model solution:
 # 

gempy/__init__.py

@@ -37,7 +37,7 @@
 from gempy.plot import _plot as _plot
 
 assert sys.version_info[0] >= 3, "GemPy requires Python 3.X"  # sys.version_info[1] for minor e.g. 6
-__version__ = '2.2.8'
+__version__ = '2.2.10'
 
 if __name__ == '__main__':
     pass