gempy-project
diff --git a/‎.github/workflows/main.yml‎
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diff --git a/‎.gitignore‎
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diff --git a/‎.travis.yml‎
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diff --git a/‎DevelopersGuide.txt‎
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diff --git a/‎Dockerfile‎
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@@ -1,8 +1,9 @@
 *-checkpoint.ipynb
 
+.vscode
 .idea
 .DS_Store
-
+.vs
 .cache/
 GeMpy/__pycache__/__init__.cpython-36.pyc
 GeMpy/__pycache__/geomodeller_xml_obj.cpython-36.pyc
@@ -137,8 +138,11 @@ notebooks/prototype notebooks/vtk_exp_smooth_trnasitions
 notebooks/prototype notebooks/plots
 
 docs/build
+docs/source
 test/figs
 
 Profiles
-notebooks/data/input_data/Claudius/Results_
+examples/data/input_data/Claudius/Results_
+
+/docs/source/gen_modules/
 
@@ -7,23 +7,66 @@ python:
 
 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
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
   - pip install --upgrade setuptools pip
-  - pip install cython
   - pip install -r requirements.txt
+  - pip install sphinx-gallery
   - 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
+  - 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 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/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 -v notebooks/ --nbval-lax
   - pytest
 
+stages:
+  - test
+  - deploy
+
+jobs:
+  include:
+      - stage: test
+        script:
+          - pytest
+      - 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:
+          provider: pages # deploy on github pages
+          skip_cleanup: true
+          github_token: $travis_doc # defined via the Travis interface
+          local_dir: docs/build/html
+          on:
+            branch: sprint_2.2
+          target_branch: gh-pages
 cache: pip
 
@@ -1,17 +1,10 @@
 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',
+[ ]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
@@ -35,3 +28,8 @@ BLD: Updates to the build process/scripts
 PERF: Performance improvement
 CLN: Code cleanup
 
+
+### Doc strings:
+
+- Use sphinx reference a lot
+- Use decorator for arguments
@@ -2,9 +2,8 @@
 # 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
+# This loads nvidia cuda image
+# FROM nvidia/cuda
 
 USER root
 
@@ -34,8 +33,8 @@ RUN apt-get update && apt-get install -yq --no-install-recommends \
     && apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-#RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
-#    locale-gen
+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 && \
@@ -49,59 +48,75 @@ 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
+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
+# Create 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
+# Setup 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
+# Install conda as
+ENV CONDA_VER latest
 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
+# Install Jupyter notebook
 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
-
+RUN conda install -c conda-forge pygpu
+RUN conda install theano gdal
 
 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
 
+# Clone gempy
 WORKDIR /home/$NB_USER/work
-RUN git clone https://github.com/cgre-aachen/gempy.git
+RUN git clone https://github.com/cgre-aachen/gempy.git --depth 1 --branch master
+
+WORKDIR /home/$NB_USER/work/gempy
+
+# Pull from release
+RUN echo '2014122501' >/dev/null && git pull
+# This is necessary to get rid off the scan.c file missing
+
+RUN pip install --upgrade --force-reinstall Theano>=1.0.4
+RUN pip install -e .
+RUN pip install -r optional-requirements.txt
+
+# Pyvista headless display
+RUN sudo apt-get -y update && \
+    sudo apt-get -y install xvfb & \
+    export DISPLAY=:99.0 && \
+    export PYVISTA_OFF_SCREEN=true && \
+    export PYVISTA_USE_PANEL=true && \
+    Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 & \
+    sleep 3
+
+RUN sudo apt update && sudo apt -y install python-qt4 libgl1-mesa-glx
 # ENTRYPOINT ["tini", "--"]
 
 ## Add local files as late as possible to avoid cache busting