simplify conda setup, use current best practices; fixes #421

[sbenthall]

This simplifies the conda installation situation and brings it up to best practices:

• uses an environment.yml with some but not all pinned dependencies
• conda-setup.sh script now installs pip requirements from requirements.txt list directly, with appropriate update strategy for conda compatibility

This reduces the number of places where we need to update pip dependencies.

[nllz]

Hmmmm does this mean we completely drop setting up (and working in) a virtual environment? Asking this because creating an environment is now not a part of the installation anymore. Will this get us in trouble with software package versions down the road?

[nllz]

Not building for me, see this gist for error:

https://gist.github.com/nllz/28aad34154f109794fe06236b314ee24

Implies I should run this command as sudo, not sure we want that? Or else we need to put it into the instructions. @sbenthall

[sbenthall]

We still mention virtual environment setup in the pip instructions. For conda, the conda environment replaces the pip environment.

I'm not sure how that error is happening. Have you tried googling about it?

[nllz]

Yeah - the solution is running to 'sudo' so will add that to the instructions. Will first experiment with the notebooks to see all is working.

[sbenthall]

I'm a little concerned about this approach because a lot of people would find it very concerning to run a bash script, as opposed to an individual command, with sudo.

I could be wrong, but I believe this gets to the question of why one might want to use conda install instead of pip.

For packages with c binaries, I think sudo is necessary for a pip install.

I think it might not be for a conda install.

[nllz]

Seb - you were right! It was because of environment setting on my machine - on a Ubuntu liveCD with a clean install there were no issues whatsoever. So I removed sudo and made all pythons now python3 so everything runs cleanly.