I thought of programmatic but that doesn't seem right because it puts too much stress on the automation side and not on the actual development and logical side of it.
A place to collect your mathematical and [programming] thoughts.
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To fill in the blank in the specific phrase "[programming] thoughts," the most natural option to me is simply programming. (Examples of this type of phrasing being used: "Programming Thoughts" (Youtube Video), "Coding thoughts")
It's true that parallelism seems to call for an adjective in the construction "mathematical and [programming] thoughts," but there simply is no commonly used adjective with this meaning. Programmatic usually means
connected with, suggesting or following a plan
- programmatic reforms
(Oxford Advanced Learner's Dictionary)
and programmatical is very rarely used.
I'd advise rephrasing to something like "thoughts on mathematics and programming" or "thoughts about mathematics and programming."