Last fall we announced the new Webmaster Tools API, which helps you to automate a number of important aspects using code. With the pending shutdown of ClientLogin, we're going to turn down the old Webmaster Tools API on April 20, 2015.
If you're still using the old API, getting started with the new one is fairly easy. The new API covers everything from the old version except for messages and keywords. We have examples in Python, Java, as well as OACurl (for command-line fans & quick testing). Additionally, there's the Site Verification API to add sites programmatically to your account. The Python search query data download will continue to be available for the moment, and replaced by an API in the upcoming quarters.
As always, should you have any questions, feel free to comment here, or post in our Webmaster Help Forum.