Yes, it was assumed that an alliance was being formed during the visit of the French fleet (23rd of July 1891) in Kronstadt.
Due to the 2 week celebrations in the last half of October 1893, where a Russian naval squadron made a return visit to the French fleet in Toulon, it was assumed that an military alliance had been completed.
The alliance was secret until 1897, when the French government realized that secrecy was defeating its deterrent value.
No source is given for this statement, but it is known that the French president Félix Faure visited St. Petersburg on a state visit in mid August 1897 and was widly publish as an Alliance.
As a follow-up question: do we know, in the context of international military treaties, how natural was Wilhelm II's (or anyone's) inference from this kind of Franco-Russian state ceremony to the existence of an alliance, in particular an alliance involving a provision like Article 1?
Since the initial contingency/deployment plans, that eventually lead to the Schlieffen Plan, was first developed in the spring of 1888, they already had a good idea of what such an alliance would entail.
This plan provided that in the event of a Russian invasion of the Balkans, the German armed forces should be evenly divided between the Eastern and Western fronts; in the west a purely defensive behavior would have been ordered, whereby a declaration of neutrality would have been demanded from France. In the east one would have tried to defeat the tsarist empire militarily.
This plan was eventually replaced by the Schlieffen Plan in April 1913.