Young adult fantasy book about a girl with gray eyes and powers related to metal

Question

I read this book about 10 years ago in either late elementary/middle school. It was a light fantasy novel (perhaps YA) and I'll try to summarize all the main points I remember.

• The main character was a girl named Petra and she had gray eyes (which was important to the book) and powers related to metal/machinery. She has a pet metal spider who drinks oil.
• Her father left home a long time ago to help and never came back. Around the start of the story I believe she receives his eyes from palace messengers
• She meets a boy who is Romani and he teaches her to throw daggers, which she's uncannily good at
• This same boy is extremely talented at pickpocketing because he has a power that gives him "invisible fingers" and a small backstory is explained for this that goes thousands of years back (I think it had something to do with this man who had his fingers cut off, but I can't be sure)
• This girl goes to the palace to work for the prince in disguise as a maid (the aforementioned boy works there as a stableboy and so does his sister, but as a maid if I remember correctly)
• Petra gets tossed around a bunch and eventually ends up working for this woman named Iris(?) who works with dyes and almost no one likes her and I believe she's also very ugly. They come up with a new color for the arrogant prince in this story
• The last two vague details I remember are something with a clock tower and also a metal beating heart that hurts to touch

Answer 1

The Cabinet of Wonders (2008) by Marie Rutkoski, first book of the Kronos Chronicles.

From Goodreads:

Petra Kronos has a simple, happy life. But it's never been ordinary. She has a pet tin spider named Astrophil who likes to hide in her snarled hair and give her advice. Her best friend can trap lightning inside a glass sphere. Petra also has a father in faraway Prague who is able to move metal with his mind. He has been commissioned by the prince of Bohemia to build the world's finest astronomical clock.

Petra's life is forever changed when, one day, her father returns home – blind. The prince has stolen his eyes, enchanted them, and now wears them. But why? Petra doesn't know, but she knows this: she will go to Prague, sneak into Salamander Castle, and steal her father's eyes back.

Joining forces with Neel, whose fingers extend into invisible ghosts that pick locks and pockets, Petra finds that many people in the castle are not what they seem, and that her father's clock has powers capable of destroying their world.

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Found with the Google query fantasy novel petra gray eyes site:goodreads.com/book.