diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 00000000..ea458251 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,40 @@ +sudo: true +language: python +python: + - "2.7" + #- "3.3" +install: + - env | sort + - wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh + - bash miniconda.sh -b -p $HOME/miniconda + - export PATH="$HOME/miniconda/bin:$PATH" + - hash -r + - conda config --set always_yes yes --set changeps1 no + - conda config --add channels dsdale24 + - conda update -q conda + - conda info -a + - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION mock numpy pip + - source activate test-environment + - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then + conda install h5py + sudo apt-get update -qq; + sudo apt-get install -y python-gtk2 wget; + export SITE_PACKAGES="$HOME/miniconda/envs/test-environment/lib/python$TRAVIS_PYTHON_VERSION/site-packages/"; + ln -s /usr/lib/python2.7/dist-packages/glib/ $SITE_PACKAGES; + ln -s /usr/lib/python2.7/dist-packages/gobject/ $SITE_PACKAGES; + ln -s /usr/lib/python2.7/dist-packages/gtk-2.0* $SITE_PACKAGES; + ln -s /usr/lib/python2.7/dist-packages/pygtk.pth $SITE_PACKAGES; + ln -s /usr/lib/python2.7/dist-packages/cairo $SITE_PACKAGES; + fi + - pip install behave "colormath>=2.1.0" coverage coveralls nose-exclude + - wget http://johnvansickle.com/ffmpeg/releases/ffmpeg-release-64bit-static.tar.xz + - mkdir ffmpeg + - tar xf ffmpeg-release-64bit-static.tar.xz --strip-components 1 -C ffmpeg + - export PATH=$TRAVIS_BUILD_DIR/ffmpeg:$PATH +script: + - coverage run --source toyplot --omit toyplot/testing.py -m nose --exclude-dir toyplot + - coverage run --append --source toyplot --omit toyplot/testing.py -m behave + - coverage report + - python backend-report.py +after_script: + - coveralls \ No newline at end of file diff --git a/README.rst b/README.rst index 20c64186..df5305fb 100644 --- a/README.rst +++ b/README.rst @@ -6,10 +6,11 @@ Interactive assembly and analysis of RAD-seq data sets. Tutorials --------- -Documentation is in the works, for now there are working example tutorials_. +Documentation is in the works_, for now there are working example tutorials_. .. _tutorials: http://nbviewer.ipython.org/github/dereneaton/ipyrad/tree/master/tests/ +.. _works: http://ipyrad.readthedocs.org/en/latest/ Installation ------------ diff --git a/conda.recipe/bld.bat b/conda.recipe/bld.bat new file mode 100644 index 00000000..762d43b4 --- /dev/null +++ b/conda.recipe/bld.bat @@ -0,0 +1 @@ +python setup.py install diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml new file mode 100644 index 00000000..5f028018 --- /dev/null +++ b/conda.recipe/meta.yaml @@ -0,0 +1,27 @@ +package: + name: ipyrad + version: {{ environ['GIT_DESCRIBE_TAG'] }} + +source: + git_url: ../ + +build: + script: python setup.py install + number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }} + +requirements: + build: + - ipython + - ipyparallel + - cython + - scipy + - numpy >=1.7 + - h5py + run: + - numpy >=1.7 + + +about: + home: http://github.com/dereneaton/ipyrad + license: GPLv3 + summary: Interactive assembly and analysis of RAD-seq data sets. diff --git a/docs/conf.py b/docs/conf.py index 59587eda..9846a37c 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -64,7 +64,20 @@ def __getattr__(cls, name): # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. -extensions = [] +extensions = ["sphinx.ext.autodoc", + "sphinxcontrib.napolean"] + +# Napoleon settings +napoleon_google_docstring = True +napoleon_numpy_docstring = True +napoleon_include_private_with_doc = False +napoleon_include_special_with_doc = True +napoleon_use_admonition_for_examples = False +napoleon_use_admonition_for_notes = False +napoleon_use_admonition_for_references = False +napoleon_use_ivar = False +napoleon_use_param = True +napoleon_use_rtype = True # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] diff --git a/docs/test_rad.rst b/docs/test_rad.rst index cedf1082..e6e81937 100644 --- a/docs/test_rad.rst +++ b/docs/test_rad.rst @@ -156,7 +156,6 @@ sample that will be stored in the Assembly object. .. code:: python - %%time ## run step 1 to demultiplex the data data1.step1() @@ -166,7 +165,7 @@ sample that will be stored in the Assembly object. .. parsed-literal:: - state reads_raw reads_filtered clusters_total clusters_kept \ + state reads_raw reads_filtered clusters_total clusters_kept 1A_0 1 20099 NaN NaN NaN 1B_0 1 19977 NaN NaN NaN 1C_0 1 20114 NaN NaN NaN @@ -179,8 +178,6 @@ sample that will be stored in the Assembly object. 1C_0 NaN NaN NaN 1D_0 NaN NaN NaN 2E_0 NaN NaN NaN - CPU times: user 931 ms, sys: 66.6 ms, total: 998 ms - Wall time: 8.18 s Step 2: Filter reads