Merge dev into master, release 0.6.0

.gitignore

@@ -52,8 +52,16 @@ __pycache__
 _pycache_
 augur/bin
 .pytest_cache
+.ipynb_checkpoints
 
 # Node #
 ########
 *node_modules/
 yarn.lock
+
+# Augur #
+#########
+runtime/
+*.repolist.txt
+*.config.*
+*.cfg.*

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "docs/metrics/upstream"]
+	path = docs/metrics/upstream
+	url = https://github.com/chaoss/metrics.git

.travis.yml

@@ -1,8 +1,7 @@
 language: python
 python:
-  - "2.7"
   - "3.6"
 # command to install dependencies
 install: "pip install ."
 # command to run tests
-script: "python -m pytest"
+script: "python -m pytest ./test"

CONTRIBUTING.md

@@ -6,26 +6,18 @@ Fork, then clone the repo:
 
     git clone [email protected]:your-username/augur.git
 
-Make your change and push to your fork. Then, [submit a pull request][pr].
+Make your change.
 
-[pr]: https://github.com/thoughtbot/factory_girl_rails/compare/
+When you are done making changes, run `make docs` to rebuild the documentation.
 
-At this point you're waiting on us. We like to at least comment on pull requests
-within three business days (and, typically, one business day).
+Push to your fork.
 
-Some things that will increase the chance that your pull request is accepted:
+Then, [submit a pull request](https://github.com/OSSHealth/augur/compare)
 
-* Inform the [mailing list][ml] of your pull request.
-* Use [Markdown][md] (we can fix this for you)
-
-[ml]: https://lists.linuxfoundation.org/pipermail/oss-health-metrics/
-[commit]: https://guides.github.com/features/mastering-markdown/#syntax
+At this point you're waiting on us. We like to at least comment on pull requests
+within three business days (and, typically, one business day).
 
 # Additional Resources
 
-* [CHAOSS Website][chaoss]
-* [CHAOSS Metrics Wiki][wiki]
-
-
-[chaoss]: https://chaoss.community/
-[wiki]: https://wiki.linuxfoundation.org/chaoss/metrics
+* [CHAOSS Website](https://chaoss.community/)
+* [CHAOSS Metrics Wiki](https://github.com/chaoss/metrics)

Dockerfile

@@ -4,7 +4,8 @@ FROM tiangolo/uwsgi-nginx-flask:python3.6
 
 ENV STATIC_INDEX 1
 
-COPY ./packaging/docker/uwsgi.ini /app/uwsgi.ini
+COPY ./util/packaging/docker/uwsgi.ini /app/uwsgi.ini
+COPY ./util/packaging/docker/prestart.sh /app/prestart.sh
 COPY ./frontend/public /app/static
 
 RUN mkdir /augur