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In Canada, if I hold copyright on a program's code but not a patent on what it does, and someone else patents "what it does", how would this affect my copyright? Lets assume this person did not learn "what it does" from my program's code.

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    Which came first? Assuming your code was published it might be evidence that the patent should not have been granted. Your copyright means someone (including the patent owner) can not copy your code. Someone's patents could mean you can't execture your code. Commented May 17, 2020 at 21:09
  • @GeorgeWhite Canada is a "first to file", not "first to invent" patent system, so conceivably the copyright could exist first without being "prior art" as copyright is granted on creation, not distribution. The OP could have created their code before the patent was filed and granted, but unless they distributed it then they could still be up a certain creek without a useful paddle.
    – user28517
    Commented May 17, 2020 at 21:23
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    @Moo - Almost everywhere is (now) on a first to file system. That is why I said "assuming it was published". I might have said assuming it was published before the patent appliation was filed. It is still the case that, regardless of the relative timing, the patent owner would need the OPs permission to copy the copyrighted code and the OP would need the patent owner's permission to execute the code. Commented May 17, 2020 at 23:55
  • @GeorgeWhite I was specifically commenting on "might be evidence that the patent should not have been granted" - in first to file, that probably wont be the case. The rest of your follow on comment is fine, I understand that.
    – user28517
    Commented May 18, 2020 at 0:13
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    The date of copyright registration is not important to the issue of patentablity, rather the date of public disclosure via publicly available publication. Commented May 18, 2020 at 4:38

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If the code reveals the invention, and the code is published, another person cannot later patent the invention disclosed in the code

A patent may be issued for any new, useful, and non-obvious process, machine, manufacture or composition of matter, or any new, useful, and non-obvious improvement in any art, process, machine, manufacture or composition of matter.

Novelty depends on the invention not having been disclosed to the world prior to the filing date of the patent application. (And if the person doing the disclosing and the person doing the patenting are the same person, they have a one-year grace period.)

Merely writing the code, and thereby gaining copyright to the code, is not enough to preclude a later patent to any invention emdodied by that code. Only if the code is shared, such that the invention is disclosed, would the code preclude a patent on novelty grounds.

A patent does not affect the copyrightability of code

Patent rights are independent of copyright. Patent protects the right to make, construct, use, or sell the invention. Copyright protects a bundle of rights associated with a particular original expression. Someone holding a patent to X does not gain the right to copy your code that implements X.

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