Merge pull request #181 from pepkit/dev

v0.12
pepkit · May 3, 2019 · c91559d · c91559d
2 parents 172f60a + 7a01cb0
commit c91559d
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diff --git a/.gitignore b/.gitignore
@@ -68,10 +68,12 @@ open_pipelines/
 # Reserved files for comparison
 *RESERVE*
 
+doc/
+build/
 dist/
 looper.egg-info/
 loopercli.egg-info/
 
 
 *ipynb_checkpoints*
-hello_looper-master*
+hello_looper-master*
diff --git a/.travis.yml b/.travis.yml
@@ -10,7 +10,7 @@ install:
   - pip install .
   - pip install -r requirements/requirements-dev.txt
   - pip install -r requirements/requirements-test.txt
-script: pytest
+script: pytest --cov=looper
 branches:
   only:
     - dev

diff --git a/README.md b/README.md
@@ -3,4 +3,4 @@
 [![Build Status](https://travis-ci.org/pepkit/looper.svg?branch=master)](https://travis-ci.org/pepkit/looper)
 [![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)
 
-`Looper` is a pipeline submission engine. The typical use case is to run a bioinformatics pipeline across many different input samples. Instructions are in the [documentation](http://code.databio.org/looper/).
+`Looper` is a pipeline submission engine. The typical use case is to run a bioinformatics pipeline across many different input samples. Instructions are in the [documentation](http://looper.databio.org/).
diff --git a/docs/README.md b/docs/README.md
@@ -24,13 +24,13 @@ Releases are posted as [GitHub releases](https://github.com/pepkit/looper/releas
 
 
 ```
-pip install --user https://github.com/pepkit/looper/zipball/master
+pip install --user loopercli
 ```
 
 Update with:
 
 ```
-pip install --user --upgrade https://github.com/pepkit/looper/zipball/master
+pip install --user --upgrade loopercli
 ```
 
 If the `looper` executable in not automatically in your `$PATH`, add the following line to your `.bashrc` or `.profile`:

diff --git a/docs/autodoc_build/.gitignore b/docs/autodoc_build/.gitignore
@@ -0,0 +1,2 @@
+*
+!.gitignore
diff --git a/docs/autodoc_build/api.md b/docs/autodoc_build/api.md