Codable class does not conform to protocol Decodable

The compiler cannot synthesise the required init(from:) method due to the weak reference, so you need to write it yourself.

class Bookmark: Codable {
    weak var publication: Publication?
    var indexPath: [Int]
    var locationInText = 0

    private enum CodingKeys: String, CodingKey {
        case indexPath
        case locationInText
    }

    init(publication: Publication?, indexPath: [Int]) {
        self.publication = publication
        self.indexPath = indexPath
    }

    required init(from decoder:Decoder) throws {
        let values = try decoder.container(keyedBy: CodingKeys.self)
        indexPath = try values.decode([Int].self, forKey: .indexPath)
        locationInText = try values.decode(Int.self, forKey: .locationInText)
    }
}

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