Example command

[iimog]

As part of my JOSS review I ran the example command and I have some comments:

1. Installing spruceup through pip does not copy the examples directory to the users computer. So it would help to let the users know that in order to try the example they have to download the tar.gz or clone the repo (or at least download the files in examples from GitHub).
2. Running the example command exactly as stated in the README (from the spruceup directory not the examples directory) results in:
   Sorry, could not read input alignment file "test_aln_nt.fasta": No such file or directory
   Running the command from the examples directory works.
3. The example config does not work for single core machines. Running on a single core machine results in:
   You specified more (2) compute cores than are available (1). Exiting.
   I don't think this is a big problem as changing the setting to 1 is straightforward. However, 1 core is enough for this demo so you might as well change this setting to 1 by default in the demo to avoid this issue.

[marekborowiec]

These should now be resolved through 1. README instructions that specifically refer to example files when downloaded from source repo, 2. added explanation that the user must be running spruceup in the same directory as the alignment and config file or, alternatively, provide absolute paths in config and 3. default is now one core.