diff --git a/.gitignore b/.gitignore index 52632f3..d3bee33 100644 --- a/.gitignore +++ b/.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 diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..2200bfe --- /dev/null +++ b/.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 diff --git a/rosi_py/environment.yml b/rosi_py/environment.yml index 163aac9..7318edd 100644 --- a/rosi_py/environment.yml +++ b/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 - diff --git a/rosi_py/title_author.diff b/rosi_py/title_author.diff new file mode 100644 index 0000000..ae3f807 --- /dev/null +++ b/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} + + +