perl had some history in bioinformatics but ruby and php never made any inroads into science or HPC to the level Python has. Python has almost entirely replaced perl in this context.

I chose Python over perl about 25 years ago and never would have considered ruby or php (both seemed squarely aimed at web developers not scientists). I believe Numeric Python was released around that time, and it was a revelation- especially to matlab users, who recognized the syntax and behavior.