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I use Kate editor for scientific programming (Fortran, Python, matlab) and would like to leave spell check on, but have it automatically ignore words that have been run together to create a variable name, e.g., NewVariable or HugeMatrix. There is an option in the spelling menu, but the spell check still highlights these words. Any ideas?

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That is currently only possible by changing your highlighting xml files. Please read how to write a syntax highlighting file and look for the spellChecking attribute. A possible solution for you is to add a RegExpr rule that matches these RunTogether words (something along the lines [a-zA-Z_]+[A-Z]\w*) and set an itemData (attribute="...") where spellChecking="false".

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