AlignedCollectionViewFlowLayout

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Collection view header getting overlapped while setting let alignedFlowLayout = collectionView?.collectionViewLayout as? AlignedCollectionViewFlowLayout alignedFlowLayout?.horizontalAlignment = .left alignedFlowLayout?.verticalAlignment = .top

The issue is that verticalAlignmentAxisForLine is considering the supplementary views with the cells. Apply these changes below, and everything should work as expected.

private func verticalAlignmentAxisForLine(
        with layoutAttributes: [UICollectionViewLayoutAttributes]
    ) -> AlignmentAxis<VerticalAlignment>? {

        let cellAttributes = layoutAttributes.filter {

            return $0.representedElementCategory == .cell
        }

        guard let firstAttribute = cellAttributes.first
        else {

            return nil
        }

        let indexPath = firstAttribute.indexPath

        switch verticalAlignment {

        case .top:
            let minY = cellAttributes.reduce(CGFloat.greatestFiniteMagnitude) {
                min($0, $1.frame.minY)
            }

            return AlignmentAxis(
                alignment: .top,
                position: minY
            )

        case .bottom:
            let maxY = cellAttributes.reduce(0) {
                max($0, $1.frame.maxY)
            }

            return AlignmentAxis(
                alignment: .bottom,
                position: maxY
            )

        default:
            let centerY = firstAttribute.center.y

            return AlignmentAxis(
                alignment: .center,
                position: centerY
            )
        }
    }

fileprivate func isFrame(
        for firstItemAttributes: UICollectionViewLayoutAttributes,
        inSameLineAsFrameFor secondItemAttributes: UICollectionViewLayoutAttributes
    ) -> Bool {

        guard let lineWidth = contentWidth 
        else
        {
            return false
        }
        let firstItemFrame = firstItemAttributes.frame

        let lineFrame = CGRect(
            x: sectionInset.left,
            y: firstItemFrame.origin.y,
            width: lineWidth,
            height: firstItemFrame.size.height
        )

        return lineFrame.intersects(
            secondItemAttributes.frame
        )
    }

open override func layoutAttributesForSupplementaryView(
        ofKind elementKind: String,
        at indexPath: IndexPath
    ) -> UICollectionViewLayoutAttributes? {

        let attributes = super.layoutAttributesForSupplementaryView(
            ofKind: elementKind,
            at: indexPath
        )

        return attributes
    }

private func setFrame(
        forLayoutAttributes layoutAttributes: UICollectionViewLayoutAttributes
    ) {

        if layoutAttributes.representedElementCategory == .cell { // Do not modify header views etc.

            let indexPath = layoutAttributes.indexPath

            if let newFrame = layoutAttributesForItem(
                at: indexPath
            )?.frame {

                layoutAttributes.frame = newFrame
            }
        }

        if layoutAttributes.representedElementKind == UICollectionView.elementKindSectionHeader {

            let indexPath = layoutAttributes.indexPath

            if let newFrame = layoutAttributesForSupplementaryView(
                ofKind: UICollectionView.elementKindSectionHeader,
                at: indexPath
            )?.frame {

                layoutAttributes.frame = newFrame
            }
        }
    }