Merge pull request #135 from databio/dev

Release 0.10
databio · Mar 26, 2019 · 6532168 · 6532168
2 parents c248527 + d9741a7
commit 6532168
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Showing 79 changed files with 2,301 additions and 1,762 deletions.
diff --git a/.gitignore b/.gitignore
@@ -12,6 +12,11 @@ tests/test/*
 
 # ignore built docs
 doc/build/*
+docs_jupyter/build/*
+docs/autodoc_build/*
+
+# ignore test results
+example_pipelines/hello_pypiper_results/*
 
 # generic ignore list:
 *.lst
@@ -77,3 +82,7 @@ build/
 dist/
 pypiper.egg-info/
 piper.egg-info/
+
+
+*ipynb_checkpoints*
+*.egg-info*
diff --git a/.travis.yml b/.travis.yml
@@ -11,7 +11,9 @@ install:
   - pip install .
   - pip install -r requirements/reqs-ngstk.txt
   - pip install -r requirements/reqs-test.txt
-script: pytest
+script: pytest -v --cov=pypiper
+after_success:
+  - coveralls
 branches:
   only:
     - dev

diff --git a/README.md b/README.md
@@ -1,8 +1,8 @@
-<img src="logo_pypiper.svg" alt="Pypiper logo" height="70" align="left"/>
+<img src="https://raw.githubusercontent.com/databio/pypiper/master/logo_pypiper.svg?sanitize=true" alt="Pypiper logo" height="70" align="left"/>
 
 # Pypiper
 
 [![Documentation Status](https://readthedocs.org/projects/pypiper/badge/?version=latest)](http://pypiper.readthedocs.org/en/latest/?badge=latest)
 [![Build Status](https://travis-ci.org/databio/pypiper.svg?branch=master)](https://travis-ci.org/databio/pypiper)
 
-A lightweight python toolkit for gluing together restartable, robust command line pipelines. The best place to learn more is at the [documentation hosted at Read the Docs](http://pypiper.readthedocs.org/).
+A lightweight python toolkit for gluing together restartable, robust command line pipelines. The best place to learn more is at the [documentation](http://code.databio.org/pypiper/).
diff --git a/doc/Makefile b/doc/Makefile
diff --git a/doc/source/advanced.rst b/doc/source/advanced.rst
diff --git a/doc/source/api.rst b/doc/source/api.rst
diff --git a/doc/source/best-practices.rst b/doc/source/best-practices.rst
diff --git a/doc/source/contributing.rst b/doc/source/contributing.rst
diff --git a/doc/source/develop-arguments.rst b/doc/source/develop-arguments.rst