update DECIMER to CDK 2.9 (or better)

[egonw]

• https://decimer.ai/

cc @Kohulan

[RvdPloeg]

The randepict code of decimer was upgraded to use cdk-2.9, see link.

[egonw]

@Kohulan, would it be that simple?

[Kohulan]

@egonw Yes. We are using the Jar directly. If there are no major changes to CDK then we don't have to change anything in the code.

[egonw]

@Kohulan, there should not be (m)any in 2.8 -> 2.9, but that is something we want to check and record. How can we best check this?

[Kohulan]

@egonw All tests have passed since our original implementation used CDK 2.8. The CDK functionalities we are currently using can be found at https://github.com/Steinbeck-Lab/RanDepict/blob/main/RanDepict/cdk_functionalities.py.

[egonw]

The CDK functionalities we are currently using can be found at https://github.com/Steinbeck-Lab/RanDepict/blob/main/RanDepict/cdk_functionalities.py.

Okay, scanned it and it looks like there have not been APi in the used code here.

@RvdPloeg, a simple test would be to just run the methods. If there are any major API change, that will cause an immediate error.