Merge pull request #197 from bcgsc/develop

v2.2.6 scope review

.github/CONTRIBUTING.md

@@ -4,40 +4,70 @@
 If you are new to the project a good way to get started is by adding to the documentation, or adding unit tests where
 there is a lack of code coverage.
 
-### Installing for Development (new to python projects?)
+## Install (for Development)
 
 Clone the repository and switch to the development branch
 
-    git clone https://github.com/bcgsc/mavis.git
-    cd mavis
-    git checkout develop
+```bash
+git clone https://github.com/bcgsc/mavis.git
+cd mavis
+git checkout develop
+```
 
-Set up a python virtual environment. If you are developing in python setting up with a virtual environment can be 
+Set up a python virtual environment. If you are developing in python setting up with a virtual environment can be
 incredibly helpful as it allows for a clean install to test. Instructions for setting up the environment
 are below
 
-    pip install virtualenv
-    virtualenv venv
-    source venv/bin/activate
+```bash
+python3 -m venv venv
+source venv/bin/activate
+```
 
-Install the MAVIS python package. Running the setup in develop mode will ensure that your code changes are run when you 
+Install the MAVIS python package. Running the setup in develop mode will ensure that your code changes are run when you
 run MAVIS from within that virtual environment
 
-    python setup.py develop
+```bash
+pip install -e .[dev]
+```
 
-Run the unit tests and compute code coverage
+Run the tests and compute code coverage
 
-    python setup.py nosetests 
+```bash
+pytest tests
+```
 
-Make the user manual (optional)
+## Build the Sphinx Documentation
 
-    cd docs
-    make html
+```bash
+pip install .[docs]
+sphinx-build docs/source/ html
+```
 
 The contents of the user manual can then be viewed by opening the build/html/index.html in any available
 web browser (i.e. google-chrome, firefox, etc.)
 
 
+## Deploy to PyPi
+
+Install deployment dependencies
+
+```bash
+pip install .[deploy]
+```
+
+Build the distribution files
+
+```bash
+python setup.py install sdist bdist_wheel
+```
+
+Use twine to upload
+
+```bash
+twine upload -r pypi dist/*
+```
+
+
 ### Reporting a Bug
 
 Please make sure to search through the issues before reporting a bug to ensure there isn't already an open issue.
@@ -66,3 +96,15 @@ if you want to be more explicit with nested types, the following conventions are
 
 - all new code must have unit tests in the tests subdirectory
 - in general for assertEqual statements, the expected value is given first
+
+Tests can be run as follows
+
+```bash
+pytest tests
+```
+
+To run the tests with tox (multiple python installs tested). Note that you will need to have multiple python installs on your path
+
+```bash
+tox
+```

.gitignore

@@ -30,4 +30,7 @@ src
 analysis_scripts
 .vscode
 *.nfs*
-*eggs/
+*eggs/
+html
+.pytest*
+.tox

.readthedocs.yml

@@ -0,0 +1,26 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    -   method: pip
+        path: .
+        extra_requirements:
+            - docs

.travis.yml

@@ -1,4 +1,5 @@
 language: python
+dist: xenial
 os:
 - linux
 before_install:
@@ -8,6 +9,7 @@ before_install:
   wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat; chmod a+x blat; export PATH=$PATH:$(pwd);
 python:
 - 3.6
+- 3.7
 install: pip install -U tox-travis
 script: tox
 notifications:

README.md

@@ -41,7 +41,7 @@ a github issue to our [github page](https://github.com/bcgsc/mavis/issues) or co
 
 ## Install Instructions
 
-There are 3 major steps to setting up and installing [MAVIS](http://mavis.bcgsc.ca).
+There are 3 major steps to setting up and installing [MAVIS](http://mavis.bcgsc.ca). If you are a developer contributing to mavis, please see the [instructions for developers page](http://mavis.bcgsc.ca/docs/latest/development.html) instead
 
 ### 1. Install Aligner
 
@@ -121,40 +121,6 @@ Once the above 3 steps are complete [MAVIS](http://mavis.bcgsc.ca) is ready to b
 See the MAVIS [tutorial](http://mavis.bcgsc.ca/docs/latest/pipeline.html#mavis-mini-tutorial) to learn about running MAVIS.
 
 
-## Build the Sphinx Documentation
-
-```bash
-pip install .[docs]
-sphinx-build docs/source/ html
-```
-
-## Deploy to PyPi
-
-Install m2r to ensure the README is converted nicely
-
-```bash
-pip install m2r
-```
-
-Install to build the egg
-
-```bash
-python setup.py install
-```
-
-Build the other distribution files
-
-```bash
-python setup.py sdist
-```
-
-Use twine to upload
-
-```bash
-twine upload -r pypi dist/*
-```
-
-
 ## Citation
 
 If you use MAVIS as a part of your project please cite