Add conda environment for dev

[willingc]

This PR adds an environment.yml file that installs a development environment (including conda and pip packages).

The environment channels used will be searched in the following order: conda-forge, r, bioconda. We tend to use conda-forge packages over Continuum's anaconda packages as they are more up to date where Continuum lags due to their release cycle. [Aside: you may wish to upload outrigger to conda-forge at some point.]

This includes dependencies for building docs (sphinx, theme, recommonmark - markdown support, nbsphinx - notebook support).

To use this environment:

conda env create -f environment.yml
source activate outrigger-env
pip install .

To check if installed: outrigger -h

[olgabot]

Great! That's really nice you can specify pip vs conda installers because it really drives me nuts to have the conda_requirements.txt and requirements.txt file be separate.

RE conda-forge - I'm working on adding this to bioconda which is a repository of bioinformatics packages: https://github.com/bioconda/bioconda-recipes/pull/2941 but the build failed because I didn't have pyflakes as a dependency even though it's a dependency of flake8. Sigh. So I'll probably just add pyflakes to the requirements.txt/environment.yml file

[willingc]

Added pyflakes by pip. Let's see if that helps.

[willingc]

Worst case: I think pinning pyflakes would help. pyflakes<1.1,>=0.8.1

[olgabot]

Yeah lint checking is getting too weird... because the pyflakes versions are going to change and it's not relevant to usage or installation. I'm making a separate environment for it in my travis: https://github.com/YeoLab/outrigger/pull/56

On Thu, Nov 17, 2016 at 8:50 AM Carol Willing notifications@github.com wrote:

Worst case: I think pinning pyflakes would help. pyflakes<1.1,>=0.8.1

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[willingc]

@olgabot Good plan 💯

[olgabot]

Awesome, I just added those changes. Can you rebase to master?

[olgabot]

Oh and remove flake8 and pyflakes from requirements... they're causing so much headache