documentation edits

.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

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
 ------------

conda.recipe/bld.bat

@@ -0,0 +1 @@
+python setup.py install

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.

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']

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