To run the vote counting scripts, you need to perform several steps:

First, obtain copies of the ballot archive (referred to below as 2001-November.txt), the membership list (registered-voters.txt), and the two voting scripts, list-addresses.py and vote-counter.py

Then, extract the valid voting addresses from the membership list:

$ python list-addresses.py registered-voters.txt > addresses.txt

Next, run the vote counter script; it's probably best to save the results to a file (they are long):

$ python vote-counter.py 2001-November.txt 
gnome-foundation-secret-cXjoS6521 addresses.txt > results.txt

The results should be in results.txt. A list of errors will be generated at the top of the output, but note that many of those errors will represent problems which are fixed later in the archive (manifested by the voter having a counted ballot later in the results). The final tallies will be at the bottom.

To exactly replicate the posted results, you should apply this diff file, which represents the votetakers' changes to the voting archive to fix malformatted ballots to reflect the evident intent of the voters.