3. Installation

You should have Python and the required modules installed.

First, if you have Git installed, clone the Git repository:

$ git clone https://github.com/phyletica/SumTimes.git

If you do not have Git, you can download a snapshot of the repository as a tar or zip archive by clicking the respective folder icons at the top of this page. Either way, move into the downloaded directory:

$ cd SumTimes

Next, let’s make sure SumTimes is working as expected on your machine:

$ ./sumtimes.py --run-tests

This will run a suite of tests. All of SumTimes is self-contained within the sumtimes.py script, so to install, all you need to do is copy (or link) the sumtimes.py file to a location that is in your PATH. For example:

$ sudo cp sumtimes.py /usr/local/bin

Or:

$ cp sumtimes.py ~/bin

Alternatively, you can run sumtimes.py from your current directory by using the ./|st| like we did above when we ran the tests. However, the remainder of this documentation assumes the script is in your PATH, so if it is not, you will have to remember to add the “./” bit.

You should be able to call up the help menu of sumtimes.py:

$ ./sumtimes.py -h

You should see output that looks like:

usage: sumtimes.py [-h] [--np NP] [--seed SEED] YAML-CONFIG-PATH

sumtimes.py Version 0.1.0

positional arguments:
  YAML-CONFIG-PATH  Path to the YAML-formatted config file.

optional arguments:
  -h, --help        show this help message and exit
  --np NP           The maximum number of processes to run in parallel. The
                    default is the smaller of the number of tree files or the
                    number of CPUs available on the machine.
  --seed SEED       Random number seed to use for the analysis.