transfer publication code on github

GP_old/.travis.yml

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+language: python
+
+dist: xenial
+
+python:
+  - '3.7'
+
+env: TRAVIS=true
+
+install:
+  - pip install --upgrade setuptools pip
+  - pip install cython
+  - pip install -r requirements.txt
+  - pip install qgrid
+  - pip install nbval
+  - pip install git+git://github.com/Leguark/scikit-image@master
+  - pip install vtk
+  - pip install pyevtk
+  - pip install dataclasses emg3d pyvista panel discretize
+
+script:
+
+  - pytest -v notebooks/integrations/ --nbval-lax --ignore-glob='*discret*'
+  - pytest -v notebooks/examples/ --nbval-lax --current-env --ignore-glob='*pography*' --ignore-glob='*lesmodel*' --ignore-glob='*Course*'
+  - pytest -v notebooks/tutorials/ --nbval-lax --current-env --ignore-glob='*ch1-6*' --ignore-glob='ch1-7*' --ignore-glob='*ch1-10*' --ignore-glob='*MaskedMarchinCube_Onlap_relations*'
+  - pytest
+
+cache: pip
+

GP_old/.vscode/launch.json

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+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Current File",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal"
+        }
+    ]
+}

GP_old/.vscode/settings.json

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+{
+    "python.pythonPath": "/Users/zhouji/anaconda3/envs/gempy/bin/python"
+}

GP_old/CONTRIBUTING.md

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+# Contributing
+
+We welcome and encoruage everyone to contribute to GemPy! 
+Contributions can be questions, bug reports, feature requests and new code. 
+Here is how to get started.
+
+## Issues 
+
+### Questions
+
+For questions about GemPy (e.g. its applications, functionality, and usage), 
+please [search the existing issues for related questions](https://github.com/cgre-aachen/gempy/issues).
+If your question has not already been asked, then [make a new issue](https://github.com/cgre-aachen/gempy/issues/new/choose).
+
+### Reporting Bugs
+
+Please report bugs on the [issue page using the bug report template](https://github.com/cgre-aachen/gempy/issues/new?assignees=&labels=&template=bug_report.md&title=) and label the issue as a bug.
+The template asks essential questions for you to answer so that we can to understand, reproduce, and fix the bug. 
+Be verbose!
+Whenever possible, provide tracebacks and/or error messages, screenshots, and sample code or other files.
+
+### Feature Requests
+
+We encourage users to submit ideas for improvements to the GemPy project. For
+this please create an issue on the
+ [issue page](https://github.com/cgre-aachen/gempy/issues) with the *Feature 
+ Request* template and label. Please make sure to use a descriptive title and to
+ provide ample background information to help us implement that functionality
+ in the future.
+
+## Contributing New Code
+
+Any code contributions are welcome, 
+whether fixing a typo or bug,
+adding new post-processing/plotting functionality,
+improve core functionality,
+or anything that you think should be in the repository. 
+
+Contributions should address an open issue (either a bug or a feature request).
+If you have found a new bug 
+or have an idea or a new feature, 
+then please [open the issue](https://github.com/cgre-aachen/gempy/issues/new/choose) 
+for discussion and link to that issue in your pull request.
+
+### Python code guidelines
+We aim to follow particular Python coding guidelines to improve the sustainability and positive impact of this community project:
+
+- Follow [The Zen of Python](https://www.python.org/dev/peps/pep-0020/), most importantly "readability counts" when writing Python code.
+- Adhere to the [Style Guide for Python Code (PEP8)](https://www.python.org/dev/peps/pep-0008/).
+- Write thorough and effective documentation: 
+Make a docstring for each module, function, class, and method, 
+all following [PEP 257](https://www.python.org/dev/peps/pep-0257/) for high-level guidelines
+and [Google Python Style Guidelines](http://google.github.io/styleguide/pyguide.html) for Syntax. 
+**Example function documentation:**
+```python
+def func(arg1: int, arg2: float) -> int:
+    """A concise one line summary of the function.
+    
+    Additional information and description of the function, if necessary. This
+    can be as long and verbose as you think is necessary for other users and 
+    developers to understand your functionality.
+    
+    Args:
+        arg1 (int): Description of the first argument.
+        arg2 (float): Description of the second argument. Please use hanging 
+            indentation for multi-line argument descriptions.
+    
+    Returns:
+        (int) Description of the return value(s)
+    """
+    return 42
+```
+- The code should explain the *what* and *how*. Add inline comments to explain the *why*.
+If an inline comment seems to be needed, consider first making the code more readable.
+For all comments, follow [PEP 8](https://www.python.org/dev/peps/pep-0008/).
+- Test every line of code. Untested code is dead code.
+
+### Licensing
+
+All contributed code will be licensed under 
+[a LGPL-3 license](https://github.com/cgre-aachen/gempy/blob/master/LICENSE).
+If you did not write the code yourself, 
+it is your responsibility to ensure that the existing license is compatible 
+and included in the contributed files. 
+In general we discourage contributing third party code.
+
+### Testing
+
+Our test suite uses [`pytest`](https://docs.pytest.org/). 
+You should be familiar with `pytest` before contributing.
+Please run all tests locally before creating a pull request. 
+You can do this by running `pytest` via your terminal in your GemPy folder:
+```bash
+cd ./path/to/gempy
+pytest
+```
+All tests are located in the `test` folder and its subfolders.  
+All contributed code must include test code in the pull request.
+
+### Pull Requests
+
+All contributions are made via pull requests (PR's) to the master branch. 
+You must complete the checklist in the [PR template](https://github.com/cgre-aachen/gempy/blob/master/.github/PULL_REQUEST_TEMPLATE.md) before we will review the PR and consider merging your contribution.

GP_old/DevelopersGuide.txt

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+Before a big commit.
+(we need to make the tests!!!)
+
+- Check all notebooks work fine
+- Check that requirements has all the necessary libraries. Otherwise readmydocs may not produce the code tab
+- run update_doc_elements.sh to update the Shpinx tutorial notebooks
+- if you add some math to the notebooks probably you have to go afterwards to the rst and change the latex enviroment
+  to ..math:
+- Then you can build or not the html to check offline if everything is in order
+- Push and check that readmydocs just worked fine
+
+# set version number in setup.py, both for version and in download_url, also in the config file of the documentation
+[ ]version='X.X',
+[] download_url='https://github.com/cgre-aachen/gempy/archive/X.X.tar.gz',
+[] in the config for sphinx
+
+# add new tag
+$ git tag X.X -m "Add X.X tag for PyPI"
+# push git tag
+$ git push --tags origin master
+# upload newest version to PyPi
+#  First create the dist
+python3 setup.py sdist bdist_wheel
+
+# Second upload the distributions
+twine upload dist/*
+
+
+
+### Type of commits:
+
+ENH: Enhancement, new functionality
+BUG: Bug fix
+DOC: Additions/updates to documentation
+TST: Additions/updates to tests
+BLD: Updates to the build process/scripts
+PERF: Performance improvement
+CLN: Code cleanup
+

GP_old/Dockerfile

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+# Heavily intspired by docker theano
+# Heavily Inspired from https://github.com/jupyter/docker-stacks/tree/master/minimal-notebook
+FROM nvidia/cuda:9.0-cudnn7-devel
+
+ENV THEANO_VERSION 1.0.3
+LABEL com.nvidia.theano.version="1.0.3"
+ENV PYGPU_VERSION 0.7.5
+
+USER root
+
+# Install all OS dependencies for fully functional notebook server
+ENV DEBIAN_FRONTEND noninteractive
+RUN apt-get update && apt-get install -yq --no-install-recommends \
+    git \
+    vim \
+    jed \
+    emacs \
+    wget \
+    build-essential \
+    python-dev \
+    ca-certificates \
+    bzip2 \
+    unzip \
+    libsm6 \
+    pandoc \
+    texlive-latex-base \
+    texlive-latex-extra \
+    texlive-fonts-extra \
+    texlive-fonts-recommended \
+    texlive-generic-recommended \
+    sudo \
+    locales \
+    libxrender1 \
+    && apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+#RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
+#    locale-gen
+
+# Install Tini
+RUN wget --quiet https://github.com/krallin/tini/releases/download/v0.9.0/tini && \
+    echo "faafbfb5b079303691a939a747d7f60591f2143164093727e870b289a44d9872 *tini" | sha256sum -c - && \
+    mv tini /usr/local/bin/tini && \
+    chmod +x /usr/local/bin/tini
+
+# Configure environment
+ENV CONDA_DIR /opt/conda
+ENV PATH $CONDA_DIR/bin:$PATH
+ENV SHELL /bin/bash
+ENV NB_USER gempy
+ENV NB_UID 1000
+#ENV LC_ALL en_US.UTF-8
+#ENV LANG en_US.UTF-8
+#ENV LANGUAGE en_US.UTF-8
+
+# Create jovyan user with UID=1000 and in the 'users' group
+RUN useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
+    mkdir -p /opt/conda && \
+    chown gempy /opt/conda
+
+USER gempy
+
+# Setup jovyan home directory
+RUN mkdir /home/$NB_USER/work && \
+    mkdir /home/$NB_USER/.jupyter && \
+    mkdir /home/$NB_USER/.local && \
+    echo "cacert=/etc/ssl/certs/ca-certificates.crt" > /home/$NB_USER/.curlrc
+
+# Install conda as jovyan
+ENV CONDA_VER 4.3.31
+ENV CONDA_MD5 7fe70b214bee1143e3e3f0467b71453c
+RUN cd /tmp && \
+    mkdir -p $CONDA_DIR && \
+    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${CONDA_VER}-Linux-x86_64.sh && \
+    echo "$CONDA_MD5 *Miniconda3-${CONDA_VER}-Linux-x86_64.sh" | md5sum -c - && \
+    /bin/bash Miniconda3-${CONDA_VER}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
+    rm Miniconda3-${CONDA_VER}-Linux-x86_64.sh && \
+    $CONDA_DIR/bin/conda install --quiet --yes conda==${CONDA_VER} && \
+    conda config --set auto_update_conda False && \
+    conda clean -tipsy
+
+# Install Jupyter notebook as jovyan
+RUN conda install --quiet --yes \
+    terminado \
+    mkl-service \
+    && conda clean -tipsy
+
+# Install Theano, pygpu
+RUN conda install -c mila-udem -y Theano=$THEANO_VERSION pygpu=$PYGPU_VERSION
+
+
+ENV MKL_THREADING_LAYER GNU
+
+USER root
+
+RUN pip install --upgrade --force-reinstall Theano>=1.0.4
+RUN pip install gempy pandas==0.24 cython pytest seaborn networkx ipywidgets scikit-image
+
+
+# Configure container startup as root
+EXPOSE 8888
+
+WORKDIR /home/$NB_USER/work
+RUN git clone https://github.com/cgre-aachen/gempy.git
+# ENTRYPOINT ["tini", "--"]
+
+## Add local files as late as possible to avoid cache busting
+## Start notebook server
+#COPY start-notebook.sh /usr/local/bin/
+#RUN chmod 755 /usr/local/bin/start-notebook.sh
+#COPY jupyter_notebook_config_secure.py /home/$NB_USER/.jupyter/jupyter_notebook_config.py
+#COPY notebook /home/$NB_USER/work/notebook
+
+## My own change
+#
+#RUN apt-get update && apt-get install -y \
+#        g++ \
+#    && \
+#    apt-get clean && \
+#    rm -rf /var/lib/apt/lists/*
+#
+#COPY theanorc /home/$NB_USER/.theanorc
+#
+## Make sure user jovyan owns files in HOME
+#RUN chown -R $NB_USER:users /home/$NB_USER
+#
+## Switch back to jovyan to avoid accidental container runs as root
+#USER jovyan
+#
+#RUN mkdir data && cd data && wget http://www.iro.umontreal.ca/~lisa/deep/data/mnist/mnist_py3k.pkl.gz -O mnist.pkl.gz
+#
+#CMD ["start-notebook.sh", "notebook"]