Add requirement for R "ape" library >= 4.0-0.2

[hyanwong]

The most recent dev version of APE, 4.0-0.2 (http://ape-package.ird.fr/ape_installation.html#versions) contains some fixes which are required to run our metrics (see http://ape-package.ird.fr/NEWS: "read.nexus() has a new option, force.multi" and "A bug was fixed in multi2di.multiPhylo()"). It can be installed using the following command

install.packages("ape", repos = "http://ape-package.ird.fr/", type="source")

I'm not sure how to encode R package dependencies into rpy2 / Python.

[hyanwong]

At least we now do an assertion to that effect (line 7 of ARG_metrics.py). Not sure whether to leave this issue open (to add to requirements.txt) or not. @jeromekelleher does requirements.txt have a particular format that is read by python setup or whatever, or is it just a human-readable list, to which I can add extra lines for e.g. packages in R?

[jeromekelleher]

requirements.txt is used by pip (and other tools) to specify requirements. It can be used like pip install -r requirements.txt. This is a reason that it would have been nice to keep everything in Python as you can create a virtualenv or conda environment with all the required packages at exactly the right version in a single command. Since we're depending on R-libs then of course this isn't possible.

Is there an equivalent for R requirements? We could make a python3-requirements.txt and an r-requirements.txt or something?