Set up CI for report generation.

.gitignore

@@ -1,3 +1,5 @@
+
+
 #pickled files
 *.pkl
 
@@ -74,7 +76,11 @@ docs/_build/
 target/
 
 # Jupyter Notebook
-.ipynb_checkpoints
+**/*.ipynb_checkpoints/
+
+# LaTeX
+**/*.aux
+**/*.out
 
 # pyenv
 .python-version

.travis.yml

@@ -0,0 +1,39 @@
+language: python
+python:
+  # We don't actually use the Travis Python, but this keeps it organized.
+  - "3.6"
+install:
+  - 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
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  # Useful for debugging any issues with conda
+  - conda info -a
+
+  # Replace dep1 dep2 ... with your dependencies
+  - cd rosi_py
+  - conda env create -n test-environment -f environment.yml
+  - source activate test-environment
+
+  # Install TeXLive to be able to run pdflatex
+  - sudo apt-get install texlive-full
+
+script:
+  # Your test script goes here
+  - jupyter nbconvert --to latex rosi_py.ipynb
+  - patch < title_author.diff
+  - pdflatex rosi_py.tex
+  - source deactivate
+
+deploy:
+  provider: pages
+  skip-cleanup: true
+  github-token: $GITHUB_API_KEY  # Set in travis-ci.org dashboard.
+  keep-history: true
+  on:
+    branch: master

rosi_py/environment.yml

@@ -3,88 +3,25 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - appnope=0.1.0=py36_0
-  - backports=1.0=py36_1
-  - backports.functools_lru_cache=1.5=py36_0
   - blas=1.1=openblas
-  - bleach=2.1.3=py_0
-  - ca-certificates=2018.1.18=0
-  - certifi=2018.1.18=py36_0
-  - cycler=0.10.0=py36_0
-  - decorator=4.2.1=py36_0
-  - entrypoints=0.2.3=py36_1
-  - freetype=2.8.1=0
-  - html5lib=1.0.1=py_0
-  - icu=58.2=0
   - ipykernel=4.8.2=py36_0
   - ipython=6.2.1=py36_1
   - ipython_genutils=0.2.0=py36_0
-  - ipywidgets=7.1.2=py36_0
-  - jedi=0.11.1=py36_0
   - jinja2=2.10=py36_0
-  - jpeg=9b=2
-  - jsonschema=2.6.0=py36_1
   - jupyter=1.0.0=py36_0
   - jupyter_client=5.2.3=py36_0
   - jupyter_console=5.2.0=py36_0
   - jupyter_core=4.4.0=py_0
-  - kiwisolver=1.0.1=py36_1
-  - libgfortran=3.0.0=0
-  - libpng=1.6.34=0
-  - libsodium=1.0.15=1
-  - markupsafe=1.0=py36_0
   - matplotlib=2.2.0=py36_0
-  - mistune=0.8.3=py_0
   - nbconvert=5.3.1=py_1
   - nbformat=4.4.0=py36_0
-  - ncurses=5.9=10
   - notebook=5.4.0=py36_0
   - numpy=1.14.2=py36_blas_openblas_200
   - openblas=0.2.20=7
-  - openssl=1.0.2n=0
-  - pandas=0.22.0=py36_0
-  - pandoc=2.1.2=0
-  - pandocfilters=1.4.1=py36_0
-  - parso=0.1.1=py_0
-  - patsy=0.5.0=py36_0
-  - pexpect=4.4.0=py36_0
-  - pickleshare=0.7.4=py36_0
   - pip=9.0.1=py36_1
-  - prompt_toolkit=1.0.15=py36_0
-  - ptyprocess=0.5.2=py36_0
-  - pygments=2.2.0=py36_0
-  - pyparsing=2.2.0=py36_0
-  - pyqt=5.6.0=py36_4
   - python=3.6.4=0
-  - python-dateutil=2.6.1=py36_0
-  - pytz=2018.3=py_0
-  - pyzmq=17.0.0=py36_3
-  - qt=5.6.2=h9e3eb04_4
-  - qtconsole=4.3.1=py36_0
-  - readline=7.0=0
   - scipy=1.0.0=py36_blas_openblas_201
   - seaborn=0.8.1=py36_0
-  - send2trash=1.5.0=py_0
-  - setuptools=38.5.2=py36_0
-  - simplegeneric=0.8.1=py36_0
-  - sip=4.18=py36_1
-  - six=1.11.0=py36_1
-  - sqlite=3.20.1=2
-  - statsmodels=0.8.0=py36_0
-  - terminado=0.8.1=py36_0
-  - testpath=0.3.1=py36_0
-  - tk=8.6.7=0
-  - tornado=4.5.3=py36_0
-  - traitlets=4.3.2=py36_0
-  - wcwidth=0.1.7=py36_0
-  - webencodings=0.5=py36_0
-  - wheel=0.30.0=py36_2
-  - widgetsnbextension=3.1.4=py36_0
-  - xz=5.2.3=0
-  - zeromq=4.2.3=2
-  - zlib=1.2.11=0
   - pip:
     - cython==0.27.3
     - pystan==2.17.1.0
-prefix: /Users/itemgmt/anaconda2/envs/rosi_py
-

rosi_py/title_author.diff

@@ -0,0 +1,14 @@
+--- rosi_py.tex	2018-04-18 14:14:39.439388576 -0400
++++ rosi_py.tex	2018-04-18 14:15:29.883386466 -0400
+@@ -141,8 +141,9 @@
+     \def\gt{>}
+     \def\lt{<}
+     % Document parameters
+-    \title{rosi\_py}
+-    
++    \title{Assessing the Safety of Rosiglitazone\\
++    for the Treatment of Type 2 Diabetes}
++    \author{Konstantinos Vamvourellis}
+
+
+